Implementing Journaling in a Linux Shared Disk File System

NASA Technical Reports Server (NTRS)

Preslan, Kenneth W.; Barry, Andrew; Brassow, Jonathan; Cattelan, Russell; Manthei, Adam; Nygaard, Erling; VanOort, Seth; Teigland, David; Tilstra, Mike; O'Keefe, Matthew;

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

PubMed

Abreu, Rui Mv; Froufe, Hugo Jc; Queiroz, Maria João Rp; Ferreira, Isabel Cfr

2010-10-28

Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.

minimega v. 3.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crussell, Jonathan; Erickson, Jeremy; Fritz, David

minimega is an emulytics platform for creating testbeds of networked devices. The platoform consists of easily deployable tools to facilitate bringing up large networks of virtual machines including Windows, Linux, and Android. minimega allows experiments to be brought up quickly with almost no configuration. minimega also includes tools for simple cluster, management, as well as tools for creating Linux-based virtual machines. This release of minimega includes new emulated sensors for Android devices to improve the fidelity of testbeds that include mobile devices. Emulated sensors include GPS and

Using Mosix for Wide-Area Compuational Resources

USGS Publications Warehouse

Maddox, Brian G.

2004-01-01

One of the problems with using traditional Beowulf-type distributed processing clusters is that they require an investment in dedicated computer resources. These resources are usually needed in addition to pre-existing ones such as desktop computers and file servers. Mosix is a series of modifications to the Linux kernel that creates a virtual computer, featuring automatic load balancing by migrating processes from heavily loaded nodes to less used ones. An extension of the Beowulf concept is to run a Mosixenabled Linux kernel on a large number of computer resources in an organization. This configuration would provide a very large amount of computational resources based on pre-existing equipment. The advantage of this method is that it provides much more processing power than a traditional Beowulf cluster without the added costs of dedicating resources.

a Linux PC Cluster for Lattice QCD with Exact Chiral Symmetry

NASA Astrophysics Data System (ADS)

Chiu, Ting-Wai; Hsieh, Tung-Han; Huang, Chao-Hsi; Huang, Tsung-Ren

A computational system for lattice QCD with overlap Dirac quarks is described. The platform is a home-made Linux PC cluster, built with off-the-shelf components. At present the system constitutes of 64 nodes, with each node consisting of one Pentium 4 processor (1.6/2.0/2.5 GHz), one Gbyte of PC800/1066 RDRAM, one 40/80/120 Gbyte hard disk, and a network card. The computationally intensive parts of our program are written in SSE2 codes. The speed of our system is estimated to be 70 Gflops, and its price/performance ratio is better than $1.0/Mflops for 64-bit (double precision) computations in quenched QCD. We discuss how to optimize its hardware and software for computing propagators of overlap Dirac quarks.

Improving Memory Error Handling Using Linux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlton, Michael Andrew; Blanchard, Sean P.; Debardeleben, Nathan A.

As supercomputers continue to get faster and more powerful in the future, they will also have more nodes. If nothing is done, then the amount of memory in supercomputer clusters will soon grow large enough that memory failures will be unmanageable to deal with by manually replacing memory DIMMs. "Improving Memory Error Handling Using Linux" is a process oriented method to solve this problem by using the Linux kernel to disable (offline) faulty memory pages containing bad addresses, preventing them from being used again by a process. The process of offlining memory pages simplifies error handling and results in reducingmore » both hardware and manpower costs required to run Los Alamos National Laboratory (LANL) clusters. This process will be necessary for the future of supercomputing to allow the development of exascale computers. It will not be feasible without memory error handling to manually replace the number of DIMMs that will fail daily on a machine consisting of 32-128 petabytes of memory. Testing reveals the process of offlining memory pages works and is relatively simple to use. As more and more testing is conducted, the entire process will be automated within the high-performance computing (HPC) monitoring software, Zenoss, at LANL.« less

KNBD: A Remote Kernel Block Server for Linux

NASA Technical Reports Server (NTRS)

Becker, Jeff

1999-01-01

I am developing a prototype of a Linux remote disk block server whose purpose is to serve as a lower level component of a parallel file system. Parallel file systems are an important component of high performance supercomputers and clusters. Although supercomputer vendors such as SGI and IBM have their own custom solutions, there has been a void and hence a demand for such a system on Beowulf-type PC Clusters. Recently, the Parallel Virtual File System (PVFS) project at Clemson University has begun to address this need (1). Although their system provides much of the functionality of (and indeed was inspired by) the equivalent file systems in the commercial supercomputer market, their system is all in user-space. Migrating their 10 services to the kernel could provide a performance boost, by obviating the need for expensive system calls. Thanks to Pavel Machek, the Linux kernel has provided the network block device (2) with kernels 2.1.101 and later. You can configure this block device to redirect reads and writes to a remote machine's disk. This can be used as a building block for constructing a striped file system across several nodes.

SU-E-T-314: The Application of Cloud Computing in Pencil Beam Scanning Proton Therapy Monte Carlo Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Z; Gao, M

Purpose: Monte Carlo simulation plays an important role for proton Pencil Beam Scanning (PBS) technique. However, MC simulation demands high computing power and is limited to few large proton centers that can afford a computer cluster. We study the feasibility of utilizing cloud computing in the MC simulation of PBS beams. Methods: A GATE/GEANT4 based MC simulation software was installed on a commercial cloud computing virtual machine (Linux 64-bits, Amazon EC2). Single spot Integral Depth Dose (IDD) curves and in-air transverse profiles were used to tune the source parameters to simulate an IBA machine. With the use of StarCluster softwaremore » developed at MIT, a Linux cluster with 2–100 nodes can be conveniently launched in the cloud. A proton PBS plan was then exported to the cloud where the MC simulation was run. Results: The simulated PBS plan has a field size of 10×10cm{sup 2}, 20cm range, 10cm modulation, and contains over 10,000 beam spots. EC2 instance type m1.medium was selected considering the CPU/memory requirement and 40 instances were used to form a Linux cluster. To minimize cost, master node was created with on-demand instance and worker nodes were created with spot-instance. The hourly cost for the 40-node cluster was $0.63 and the projected cost for a 100-node cluster was $1.41. Ten million events were simulated to plot PDD and profile, with each job containing 500k events. The simulation completed within 1 hour and an overall statistical uncertainty of < 2% was achieved. Good agreement between MC simulation and measurement was observed. Conclusion: Cloud computing is a cost-effective and easy to maintain platform to run proton PBS MC simulation. When proton MC packages such as GATE and TOPAS are combined with cloud computing, it will greatly facilitate the pursuing of PBS MC studies, especially for newly established proton centers or individual researchers.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayan Ghosh, Jeff Hammond

OpenSHMEM is a community effort to unifyt and standardize the SHMEM programming model. MPI (Message Passing Interface) is a well-known community standard for parallel programming using distributed memory. The most recen t release of MPI, version 3.0, was designed in part to support programming models like SHMEM.OSHMPI is an implementation of the OpenSHMEM standard using MPI-3 for the Linux operating system. It is the first implementation of SHMEM over MPI one-sided communication and has the potential to be widely adopted due to the portability and widely availability of Linux and MPI-3. OSHMPI has been tested on a variety of systemsmore » and implementations of MPI-3, includingInfiniBand clusters using MVAPICH2 and SGI shared-memory supercomputers using MPICH. Current support is limited to Linux but may be extended to Apple OSX if there is sufficient interest. The code is opensource via https://github.com/jeffhammond/oshmpi« less

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

NUMERICAL NOISE PM SIMULATION IN CMAQ

EPA Science Inventory

We have found that numerical noise in the latest release of CMAQ using the yamo advection scheme when compiled on Linux cluster with pgf90 (5.0 or 6.0). We recommend to use -C option to eliminate the numerical noise.

Birds of a Feather: Supporting Secure Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Braswell III, H V

2006-04-24

Over the past few years Lawrence Livermore National Laboratory has begun the process of moving to a diskless environment in the Secure Computer Support realm. This movement has included many moving targets and increasing support complexity. We would like to set up a forum for Security and Support professionals to get together from across the Complex and discuss current deployments, lessons learned, and next steps. This would include what hardware, software, and hard copy based solutions are being used to manage Secure Computing. The topics to be discussed include but are not limited to: Diskless computing, port locking and management,more » PC, Mac, and Linux/UNIX support and setup, system imaging, security setup documentation and templates, security documentation and management, customer tracking, ticket tracking, software download and management, log management, backup/disaster recovery, and mixed media environments.« less

Simple Linux Utility for Resource Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jette, M.

2009-09-09

SLURM is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small computer clusters. As a cluster resource manager, SLURM has three key functions. First, it allocates exclusive and/or non exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allciated nodes. Finally, it arbitrates conflicting requests for resouces by managing a queue of pending work.

Performance Analysis of the ARL Linux Networx Cluster

DTIC Science & Technology

2004-06-01

OVERFLOW, used processors selected by SGE. All benchmarks on the GAMESS, COBALT, LSDYNA and FLUENT. Each code Origin 3800 were executed using IRIX cpusets...scheduler. for these benchmarks defines a missile with grid fins consisting of seventeen million cells [31. 4. Application Performance Results and

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

Tri-Laboratory Linux Capacity Cluster 2007 SOW

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seager, M

2007-03-22

The Advanced Simulation and Computing (ASC) Program (formerly know as Accelerated Strategic Computing Initiative, ASCI) has led the world in capability computing for the last ten years. Capability computing is defined as a world-class platform (in the Top10 of the Top500.org list) with scientific simulations running at scale on the platform. Example systems are ASCI Red, Blue-Pacific, Blue-Mountain, White, Q, RedStorm, and Purple. ASC applications have scaled to multiple thousands of CPUs and accomplished a long list of mission milestones on these ASC capability platforms. However, the computing demands of the ASC and Stockpile Stewardship programs also include a vastmore » number of smaller scale runs for day-to-day simulations. Indeed, every 'hero' capability run requires many hundreds to thousands of much smaller runs in preparation and post processing activities. In addition, there are many aspects of the Stockpile Stewardship Program (SSP) that can be directly accomplished with these so-called 'capacity' calculations. The need for capacity is now so great within the program that it is increasingly difficult to allocate the computer resources required by the larger capability runs. To rectify the current 'capacity' computing resource shortfall, the ASC program has allocated a large portion of the overall ASC platforms budget to 'capacity' systems. In addition, within the next five to ten years the Life Extension Programs (LEPs) for major nuclear weapons systems must be accomplished. These LEPs and other SSP programmatic elements will further drive the need for capacity calculations and hence 'capacity' systems as well as future ASC capability calculations on 'capability' systems. To respond to this new workload analysis, the ASC program will be making a large sustained strategic investment in these capacity systems over the next ten years, starting with the United States Government Fiscal Year 2007 (GFY07). However, given the growing need for 'capability' systems as well, the budget demands are extreme and new, more cost effective ways of fielding these systems must be developed. This Tri-Laboratory Linux Capacity Cluster (TLCC) procurement represents the ASC first investment vehicle in these capacity systems. It also represents a new strategy for quickly building, fielding and integrating many Linux clusters of various sizes into classified and unclassified production service through a concept of Scalable Units (SU). The programmatic objective is to dramatically reduce the overall Total Cost of Ownership (TCO) of these 'capacity' systems relative to the best practices in Linux Cluster deployments today. This objective only makes sense in the context of these systems quickly becoming very robust and useful production clusters under the crushing load that will be inflicted on them by the ASC and SSP scientific simulation capacity workload.« less

Historical habitat barriers prevent ring-like genetic continuity throughout the distribution of threatened Alameda Striped Racers (Coluber lateralis euryxanthus)

USGS Publications Warehouse

Richmond, Jonathan Q.; Wood, Dustin A.; Swaim, Karen; Fisher, Robert N.; Vandergast, Amy

2016-01-01

We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We used cluster assignments to characterize population genetic structuring with respect to land management units and approximate Bayesian analysis to rank the ability of five alternative evolutionary hypotheses to explain the inferred structure. Then, we estimated rates of contemporary and historical migration among the major clusters and measured the fit of different historical migration models to better understand the formation of the current population structure. Our results reveal a ring-like pattern of historical connectivity around the Tri-Valley area of the East Bay (i.e., San Ramon, Amador, and Livermore valleys), with clusters largely corresponding to different management units. We found no evidence of continuous gene flow throughout the ring, however, and that the main gap in continuity is centered across the Livermore Valley. Historical migration models support higher rates of gene flow away from the terminal ends of the ring on the north and south sides of the Valley, compared with rates into those areas from western sites that border the interior San Francisco Bay. We attribute the break in ring-like connectivity to the presence of unsuitable habitat within the Livermore Valley that has been reinforced by 20th century urbanization, and the asymmetry in gene flow rates to spatial constraints on movement and east–west environmental gradients influenced by the proximity of the San Francisco Bay.

Galaxy CloudMan: delivering cloud compute clusters.

PubMed

Afgan, Enis; Baker, Dannon; Coraor, Nate; Chapman, Brad; Nekrutenko, Anton; Taylor, James

2010-12-21

Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is "cloud computing", which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate "as is" use by experimental biologists. We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon's EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.

Galaxy CloudMan: delivering cloud compute clusters

PubMed Central

2010-01-01

Background Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists. Results We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. Conclusions The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge. PMID:21210983

U. S. Atlantic Fleet, Eighth Amphibious Force. Operation Plan Number 2-44

DTIC Science & Technology

1944-01-01

distributed with this Operation Order. (c) Panoramic Bench Sketches No. P-l for Boach 259 and No. P~3 for Loach 26l (South) givo viator level...To indicate tank or ID targets. (g) Green Cluster, White Cluster - Lift Artillery fire. Page 32 of 33. ANNEX KENS . GTMFIRS SUPPORT PLAN. TABLE VI...AURORA . SFCP 5 AUX GROUND SPOT - LIVERMORS SFCP 6 AUX GROUND SPOT - LA GLOIRE SFCP 7 AUX GROUND -SPOT ~ TERM- ERIC SFCP 8 AUX GROUND SPOT - ORION-KEAR

GREEN SUPERCOMPUTING IN A DESKTOP BOX

DOE Office of Scientific and Technical Information (OSTI.GOV)

HSU, CHUNG-HSING; FENG, WU-CHUN; CHING, AVERY

2007-01-17

The computer workstation, introduced by Sun Microsystems in 1982, was the tool of choice for scientists and engineers as an interactive computing environment for the development of scientific codes. However, by the mid-1990s, the performance of workstations began to lag behind high-end commodity PCs. This, coupled with the disappearance of BSD-based operating systems in workstations and the emergence of Linux as an open-source operating system for PCs, arguably led to the demise of the workstation as we knew it. Around the same time, computational scientists started to leverage PCs running Linux to create a commodity-based (Beowulf) cluster that provided dedicatedmore » computer cycles, i.e., supercomputing for the rest of us, as a cost-effective alternative to large supercomputers, i.e., supercomputing for the few. However, as the cluster movement has matured, with respect to cluster hardware and open-source software, these clusters have become much more like their large-scale supercomputing brethren - a shared (and power-hungry) datacenter resource that must reside in a machine-cooled room in order to operate properly. Consequently, the above observations, when coupled with the ever-increasing performance gap between the PC and cluster supercomputer, provide the motivation for a 'green' desktop supercomputer - a turnkey solution that provides an interactive and parallel computing environment with the approximate form factor of a Sun SPARCstation 1 'pizza box' workstation. In this paper, they present the hardware and software architecture of such a solution as well as its prowess as a developmental platform for parallel codes. In short, imagine a 12-node personal desktop supercomputer that achieves 14 Gflops on Linpack but sips only 185 watts of power at load, resulting in a performance-power ratio that is over 300% better than their reference SMP platform.« less

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

Optimizing ion channel models using a parallel genetic algorithm on graphical processors.

PubMed

Ben-Shalom, Roy; Aviv, Amit; Razon, Benjamin; Korngreen, Alon

2012-01-01

We have recently shown that we can semi-automatically constrain models of voltage-gated ion channels by combining a stochastic search algorithm with ionic currents measured using multiple voltage-clamp protocols. Although numerically successful, this approach is highly demanding computationally, with optimization on a high performance Linux cluster typically lasting several days. To solve this computational bottleneck we converted our optimization algorithm for work on a graphical processing unit (GPU) using NVIDIA's CUDA. Parallelizing the process on a Fermi graphic computing engine from NVIDIA increased the speed ∼180 times over an application running on an 80 node Linux cluster, considerably reducing simulation times. This application allows users to optimize models for ion channel kinetics on a single, inexpensive, desktop "super computer," greatly reducing the time and cost of building models relevant to neuronal physiology. We also demonstrate that the point of algorithm parallelization is crucial to its performance. We substantially reduced computing time by solving the ODEs (Ordinary Differential Equations) so as to massively reduce memory transfers to and from the GPU. This approach may be applied to speed up other data intensive applications requiring iterative solutions of ODEs. Copyright © 2012 Elsevier B.V. All rights reserved.

MCR Container Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

PubMed Central

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H.A.; Hlavacek, William S.; Posner, Richard G.

2016-01-01

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary information: Supplementary data are available at Bioinformatics online. Contact: bionetgen.help@gmail.com PMID:26556387

fluff: exploratory analysis and visualization of high-throughput sequencing data

PubMed Central

Georgiou, Georgios

2016-01-01

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. PMID:27547532

Establishing Linux Clusters for High-Performance Computing (HPC) at NPS

DTIC Science & Technology

2004-09-01

52 e. Intel Roll..................................................................................53 f. Area51 Roll...results of generating md5summ for Area51 roll. All the file information is available. This number can be used to be checked against the number that the...vendor provides fro the particular piece of software. ......51 Figure 22 The given md5summ for Area51 roll form the download site. This number can

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

PubMed

Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

2012-03-19

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

PubMed Central

2012-01-01

Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them. PMID:22429538

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

PubMed

Thomas, Brandon R; Chylek, Lily A; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H A; Hlavacek, William S; Posner, Richard G

2016-03-01

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary data are available at Bioinformatics online. bionetgen.help@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

STAR Data Reconstruction at NERSC/Cori, an adaptable Docker container approach for HPC

NASA Astrophysics Data System (ADS)

Mustafa, Mustafa; Balewski, Jan; Lauret, Jérôme; Porter, Jefferson; Canon, Shane; Gerhardt, Lisa; Hajdu, Levente; Lukascsyk, Mark

2017-10-01

As HPC facilities grow their resources, adaptation of classic HEP/NP workflows becomes a need. Linux containers may very well offer a way to lower the bar to exploiting such resources and at the time, help collaboration to reach vast elastic resources on such facilities and address their massive current and future data processing challenges. In this proceeding, we showcase STAR data reconstruction workflow at Cori HPC system at NERSC. STAR software is packaged in a Docker image and runs at Cori in Shifter containers. We highlight two of the typical end-to-end optimization challenges for such pipelines: 1) data transfer rate which was carried over ESnet after optimizing end points and 2) scalable deployment of conditions database in an HPC environment. Our tests demonstrate equally efficient data processing workflows on Cori/HPC, comparable to standard Linux clusters.

A Business Case Study of Open Source Software

DTIC Science & Technology

2001-07-01

LinuxPPC LinuxPPC www.linuxppc.com MandrakeSoft Linux -Mandrake www.linux-mandrake.com/ en / CLE Project CLE cle.linux.org.tw/CLE/e_index.shtml Red Hat... en Coyote Linux www2.vortech.net/coyte/coyte.htm MNIS www.mnis.fr Data-Portal www.data-portal.com Mr O’s Linux Emporium www.ouin.com DLX Linux www.wu...1998 1999 Year S h ip m en ts ( in m ill io n s) Source: IDC, 2000. Figure 11. Worldwide New Linux Shipments (Client and Server) 3.2.2 Market

MOLAR: Modular Linux and Adaptive Runtime Support for HEC OS/R Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frank Mueller

2009-02-05

MOLAR is a multi-institution research effort that concentrates on adaptive, reliable,and efficient operating and runtime system solutions for ultra-scale high-end scientific computing on the next generation of supercomputers. This research addresses the challenges outlined by the FAST-OS - forum to address scalable technology for runtime and operating systems --- and HECRTF --- high-end computing revitalization task force --- activities by providing a modular Linux and adaptable runtime support for high-end computing operating and runtime systems. The MOLAR research has the following goals to address these issues. (1) Create a modular and configurable Linux system that allows customized changes based onmore » the requirements of the applications, runtime systems, and cluster management software. (2) Build runtime systems that leverage the OS modularity and configurability to improve efficiency, reliability, scalability, ease-of-use, and provide support to legacy and promising programming models. (3) Advance computer reliability, availability and serviceability (RAS) management systems to work cooperatively with the OS/R to identify and preemptively resolve system issues. (4) Explore the use of advanced monitoring and adaptation to improve application performance and predictability of system interruptions. The overall goal of the research conducted at NCSU is to develop scalable algorithms for high-availability without single points of failure and without single points of control.« less

JESPP: Joint Experimentation on Scalable Parallel Processors Supercomputers

DTIC Science & Technology

2010-03-01

were for the relatively small market of scientific and engineering applications. Contrast this with GPUs that are designed to improve the end- user...experience in mass- market arenas such as gaming. In order to get meaningful speed-up using the GPU, it was determined that the data transfer and...Included) Conference Year Effectively using a Large GPGPU-Enhanced Linux Cluster HPCMP UGC 2009 FLOPS per Watt: Heterogeneous-Computing’s Approach

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

PubMed Central

2010-01-01

Background Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. Description An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Conclusions Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms. PMID:21210976

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

PubMed

Taylor, Ronald C

2010-12-21

Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.

A computational system for lattice QCD with overlap Dirac quarks

NASA Astrophysics Data System (ADS)

Chiu, Ting-Wai; Hsieh, Tung-Han; Huang, Chao-Hsi; Huang, Tsung-Ren

2003-05-01

We outline the essential features of a Linux PC cluster which is now being developed at National Taiwan University, and discuss how to optimize its hardware and software for lattice QCD with overlap Dirac quarks. At present, the cluster constitutes of 30 nodes, with each node consisting of one Pentium 4 processor (1.6/2.0 GHz), one Gbyte of PC800 RDRAM, one 40/80 Gbyte hard disk, and a network card. The speed of this system is estimated to be 30 Gflops, and its price/performance ratio is better than $1.0/Mflops for 64-bit (double precision) computations in quenched lattice QCD with overlap Dirac quarks.

Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.

PubMed

Roguev, Assen; Ryan, Colm J; Xu, Jiewei; Colson, Isabelle; Hartsuiker, Edgar; Krogan, Nevan

2018-02-01

This protocol describes computational analysis of genetic interaction screens, ranging from data capture (plate imaging) to downstream analyses. Plate imaging approaches using both digital camera and office flatbed scanners are included, along with a protocol for the extraction of colony size measurements from the resulting images. A commonly used genetic interaction scoring method, calculation of the S-score, is discussed. These methods require minimal computer skills, but some familiarity with MATLAB and Linux/Unix is a plus. Finally, an outline for using clustering and visualization software for analysis of resulting data sets is provided. © 2018 Cold Spring Harbor Laboratory Press.

FLY MPI-2: a parallel tree code for LSS

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Antonuccio-Delogu, V.

2006-04-01

New version program summaryProgram title: FLY 3.1 Catalogue identifier: ADSC_v2_0 Licensing provisions: yes Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSC_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 158 172 No. of bytes in distributed program, including test data, etc.: 4 719 953 Distribution format: tar.gz Programming language: Fortran 90, C Computer: Beowulf cluster, PC, MPP systems Operating system: Linux, Aix RAM: 100M words Catalogue identifier of previous version: ADSC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 155 (2003) 159 Does the new version supersede the previous version?: yes Nature of problem: FLY is a parallel collisionless N-body code for the calculation of the gravitational force Solution method: FLY is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986) Reasons for the new version: The new version of FLY is implemented by using the MPI-2 standard: the distributed version 3.1 was developed by using the MPICH2 library on a PC Linux cluster. Today the FLY performance allows us to consider the FLY code among the most powerful parallel codes for tree N-body simulations. Another important new feature regards the availability of an interface with hydrodynamical Paramesh based codes. Simulations must follow a box large enough to accurately represent the power spectrum of fluctuations on very large scales so that we may hope to compare them meaningfully with real data. The number of particles then sets the mass resolution of the simulation, which we would like to make as fine as possible. The idea to build an interface between two codes, that have different and complementary cosmological tasks, allows us to execute complex cosmological simulations with FLY, specialized for DM evolution, and a code specialized for hydrodynamical components that uses a Paramesh block structure. Summary of revisions: The parallel communication schema was totally changed. The new version adopts the MPICH2 library. Now FLY can be executed on all Unix systems having an MPI-2 standard library. The main data structure, is declared in a module procedure of FLY (fly_h.F90 routine). FLY creates the MPI Window object for one-sided communication for all the shared arrays, with a call like the following: CALL MPI_WIN_CREATE(POS, SIZE, REAL8, MPI_INFO_NULL, MPI_COMM_WORLD, WIN_POS, IERR) the following main window objects are created: win_pos, win_vel, win_acc: particles positions velocities and accelerations, win_pos_cell, win_mass_cell, win_quad, win_subp, win_grouping: cells positions, masses, quadrupole momenta, tree structure and grouping cells. Other windows are created for dynamic load balance and global counters. Restrictions: The program uses the leapfrog integrator schema, but could be changed by the user. Unusual features: FLY uses the MPI-2 standard: the MPICH2 library on Linux systems was adopted. To run this version of FLY the working directory must be shared among all the processors that execute FLY. Additional comments: Full documentation for the program is included in the distribution in the form of a README file, a User Guide and a Reference manuscript. Running time: IBM Linux Cluster 1350, 512 nodes with 2 processors for each node and 2 GB RAM for each processor, at Cineca, was adopted to make performance tests. Processor type: Intel Xeon Pentium IV 3.0 GHz and 512 KB cache (128 nodes have Nocona processors). Internal Network: Myricom LAN Card "C" Version and "D" Version. Operating System: Linux SuSE SLES 8. The code was compiled using the mpif90 compiler version 8.1 and with basic optimization options in order to have performances that could be useful compared with other generic clusters Processors

Scalable Unix commands for parallel processors : a high-performance implementation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

Development of EnergyPlus Utility to Batch Simulate Building Energy Performance on a National Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valencia, Jayson F.; Dirks, James A.

2008-08-29

EnergyPlus is a simulation program that requires a large number of details to fully define and model a building. Hundreds or even thousands of lines in a text file are needed to run the EnergyPlus simulation depending on the size of the building. To manually create these files is a time consuming process that would not be practical when trying to create input files for thousands of buildings needed to simulate national building energy performance. To streamline the process needed to create the input files for EnergyPlus, two methods were created to work in conjunction with the National Renewable Energymore » Laboratory (NREL) Preprocessor; this reduced the hundreds of inputs needed to define a building in EnergyPlus to a small set of high-level parameters. The first method uses Java routines to perform all of the preprocessing on a Windows machine while the second method carries out all of the preprocessing on the Linux cluster by using an in-house built utility called Generalized Parametrics (GPARM). A comma delimited (CSV) input file is created to define the high-level parameters for any number of buildings. Each method then takes this CSV file and uses the data entered for each parameter to populate an extensible markup language (XML) file used by the NREL Preprocessor to automatically prepare EnergyPlus input data files (idf) using automatic building routines and macro templates. Using a Linux utility called “make”, the idf files can then be automatically run through the Linux cluster and the desired data from each building can be aggregated into one table to be analyzed. Creating a large number of EnergyPlus input files results in the ability to batch simulate building energy performance and scale the result to national energy consumption estimates.« less

Zachary D. Barker: Final DHS HS-STEM Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barker, Z D

Working at Lawrence Livermore National Laboratory (LLNL) this summer has provided a very unique and special experience for me. I feel that the research opportunities given to me have allowed me to significantly benefit my research group, the laboratory, the Department of Homeland Security, and the Department of Energy. The researchers in the Single Particle Aerosol Mass Spectrometry (SPAMS) group were very welcoming and clearly wanted me to get the most out of my time in Livermore. I feel that my research partner, Veena Venkatachalam of MIT, and I have been extremely productive in meeting our research goals throughout thismore » summer, and have learned much about working in research at a national laboratory such as Lawrence Livermore. I have learned much about the technical aspects of research while working at LLNL, however I have also gained important experience and insight into how research groups at national laboratories function. I believe that this internship has given me valuable knowledge and experience which will certainly help my transition to graduate study and a career in engineering. My work with Veena Venkatachalam in the SPAMS group this summer has focused on two major projects. Initially, we were tasked with an analysis of data collected by the group this past spring in a large public environment. The SPAMS instrument was deployed for over two months, collecting information on many of the ambient air particles circulating through the area. Our analysis of the particle data collected during this deployment concerned several aspects, including finding groups, or clusters, of particles that seemed to appear more during certain times of day, analyzing the mass spectral data of clusters and comparing them with mass spectral data of known substances, and comparing the real-time detection capability of the SPAMS instrument with that of a commercially available biological detection instrument. This analysis was performed in support of a group report to the Department of Homeland Security on the results of the deployment. The analysis of the deployment data revealed some interesting applications of the SPAMS instrument to homeland security situations. Using software developed in-house by SPAMS group member Dr. Paul Steele, Veena and I were able to cluster a subset of data over a certain timeframe (ranging from a single hour to an entire week). The software used makes clusters based on the mass spectral characteristics of the each particle in the data set, as well as other parameters. By looking more closely at the characteristics of individual clusters, including the mass spectra, conclusions could be made about what these particles are. This was achieved partially through examination and discussion of the mass spectral data with the members of the SPAMS group, as well as through comparison with known mass spectra collected from substances tested in the laboratory. In many cases, broad conclusions could be drawn about the identity of a cluster of particles.« less

Introduction to LINUX OS for new LINUX users - Basic Information Before Using The Kurucz Codes Under LINUX-.

NASA Astrophysics Data System (ADS)

Çay, M. Taşkin

Recently the ATLAS suite (Kurucz) was ported to LINUX OS (Sbordone et al.). Those users of the suite unfamiliar with LINUX need to know some basic information to use these versions. This paper is a quick overview and introduction to LINUX OS. The reader is highly encouraged to own a book on LINUX OS for comprehensive use. Although the subjects and examples in this paper are for general use, they to help with the installation and running the ATLAS suite.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

NASA Astrophysics Data System (ADS)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

AIRE-Linux

NASA Astrophysics Data System (ADS)

Zhou, Jianfeng; Xu, Benda; Peng, Chuan; Yang, Yang; Huo, Zhuoxi

2015-08-01

AIRE-Linux is a dedicated Linux system for astronomers. Modern astronomy faces two big challenges: massive observed raw data which covers the whole electromagnetic spectrum, and overmuch professional data processing skill which exceeds personal or even a small team's abilities. AIRE-Linux, which is a specially designed Linux and will be distributed to users by Virtual Machine (VM) images in Open Virtualization Format (OVF), is to help astronomers confront the challenges. Most astronomical software packages, such as IRAF, MIDAS, CASA, Heasoft etc., will be integrated into AIRE-Linux. It is easy for astronomers to configure and customize the system and use what they just need. When incorporated into cloud computing platforms, AIRE-Linux will be able to handle data intensive and computing consuming tasks for astronomers. Currently, a Beta version of AIRE-Linux is ready for download and testing.

Data Intensive Computing on Amazon Web Services

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magana-Zook, S. A.

The Geophysical Monitoring Program (GMP) has spent the past few years building up the capability to perform data intensive computing using what have been referred to as “big data” tools. These big data tools would be used against massive archives of seismic signals (>300 TB) to conduct research not previously possible. Examples of such tools include Hadoop (HDFS, MapReduce), HBase, Hive, Storm, Spark, Solr, and many more by the day. These tools are useful for performing data analytics on datasets that exceed the resources of traditional analytic approaches. To this end, a research big data cluster (“Cluster A”) was setmore » up as a collaboration between GMP and Livermore Computing (LC).« less

Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

NASA Technical Reports Server (NTRS)

Tilton, James C.

2003-01-01

A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic region growing.

Computation Directorate 2008 Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, D L

2009-03-25

Whether a computer is simulating the aging and performance of a nuclear weapon, the folding of a protein, or the probability of rainfall over a particular mountain range, the necessary calculations can be enormous. Our computers help researchers answer these and other complex problems, and each new generation of system hardware and software widens the realm of possibilities. Building on Livermore's historical excellence and leadership in high-performance computing, Computation added more than 331 trillion floating-point operations per second (teraFLOPS) of power to LLNL's computer room floors in 2008. In addition, Livermore's next big supercomputer, Sequoia, advanced ever closer to itsmore » 2011-2012 delivery date, as architecture plans and the procurement contract were finalized. Hyperion, an advanced technology cluster test bed that teams Livermore with 10 industry leaders, made a big splash when it was announced during Michael Dell's keynote speech at the 2008 Supercomputing Conference. The Wall Street Journal touted Hyperion as a 'bright spot amid turmoil' in the computer industry. Computation continues to measure and improve the costs of operating LLNL's high-performance computing systems by moving hardware support in-house, by measuring causes of outages to apply resources asymmetrically, and by automating most of the account and access authorization and management processes. These improvements enable more dollars to go toward fielding the best supercomputers for science, while operating them at less cost and greater responsiveness to the customers.« less

The writer independent online handwriting recognition system frog on hand and cluster generative statistical dynamic time warping.

PubMed

Bahlmann, Claus; Burkhardt, Hans

2004-03-01

In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.

Grid Computing Environment using a Beowulf Cluster

NASA Astrophysics Data System (ADS)

Alanis, Fransisco; Mahmood, Akhtar

2003-10-01

Custom-made Beowulf clusters using PCs are currently replacing expensive supercomputers to carry out complex scientific computations. At the University of Texas - Pan American, we built a 8 Gflops Beowulf Cluster for doing HEP research using RedHat Linux 7.3 and the LAM-MPI middleware. We will describe how we built and configured our Cluster, which we have named the Sphinx Beowulf Cluster. We will describe the results of our cluster benchmark studies and the run-time plots of several parallel application codes that were compiled in C on the cluster using the LAM-XMPI graphics user environment. We will demonstrate a "simple" prototype grid environment, where we will submit and run parallel jobs remotely across multiple cluster nodes over the internet from the presentation room at Texas Tech. University. The Sphinx Beowulf Cluster will be used for monte-carlo grid test-bed studies for the LHC-ATLAS high energy physics experiment. Grid is a new IT concept for the next generation of the "Super Internet" for high-performance computing. The Grid will allow scientist worldwide to view and analyze huge amounts of data flowing from the large-scale experiments in High Energy Physics. The Grid is expected to bring together geographically and organizationally dispersed computational resources, such as CPUs, storage systems, communication systems, and data sources.

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

Parallel FEM Simulation of Electromechanics in the Heart

NASA Astrophysics Data System (ADS)

Xia, Henian; Wong, Kwai; Zhao, Xiaopeng

2011-11-01

Cardiovascular disease is the leading cause of death in America. Computer simulation of complicated dynamics of the heart could provide valuable quantitative guidance for diagnosis and treatment of heart problems. In this paper, we present an integrated numerical model which encompasses the interaction of cardiac electrophysiology, electromechanics, and mechanoelectrical feedback. The model is solved by finite element method on a Linux cluster and the Cray XT5 supercomputer, kraken. Dynamical influences between the effects of electromechanics coupling and mechanic-electric feedback are shown.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

Development of Automatic Live Linux Rebuilding System with Flexibility in Science and Engineering Education and Applying to Information Processing Education

NASA Astrophysics Data System (ADS)

Sonoda, Jun; Yamaki, Kota

We develop an automatic Live Linux rebuilding system for science and engineering education, such as information processing education, numerical analysis and so on. Our system is enable to easily and automatically rebuild a customized Live Linux from a ISO image of Ubuntu, which is one of the Linux distribution. Also, it is easily possible to install/uninstall packages and to enable/disable init daemons. When we rebuild a Live Linux CD using our system, we show number of the operations is 8, and the rebuilding time is about 33 minutes on CD version and about 50 minutes on DVD version. Moreover, we have applied the rebuilded Live Linux CD in a class of information processing education in our college. As the results of a questionnaires survey from our 43 students who used the Live Linux CD, we obtain that the our Live Linux is useful for about 80 percents of students. From these results, we conclude that our system is able to easily and automatically rebuild a useful Live Linux in short time.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

TICK: Transparent Incremental Checkpointing at Kernel Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrini, Fabrizio; Gioiosa, Roberto

2004-10-25

TICK is a software package implemented in Linux 2.6 that allows the save and restore of user processes, without any change to the user code or binary. With TICK a process can be suspended by the Linux kernel upon receiving an interrupt and saved in a file. This file can be later thawed in another computer running Linux (potentially the same computer). TICK is implemented as a Linux kernel module, in the Linux version 2.6.5

Potential performance bottleneck in Linux TCP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system tomore » its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.« less

Experimental Studies of Very-High Mach Number Hydrodynamics

DTIC Science & Technology

1994-02-14

BUCKINGHAM Lawrence Livermore National Laboratory Livermore, California IRA KOHLBERG Kohlberg Associates, Inc. Alexandria, Virginia 9 / 1 321 February 14...34** Lawrence Livermore National Laboratory, Livermore, CA tKohlberg Associates, Inc., Alexandria, VA 12a. DISTRIBUTION/AVAILABlUTY STATEMENT 12b...Kohlberg 3 IPlasma Physics Division, Naval Research Laboratory, Washington DC 20375, USA 2 Lawrence Livermore National Laboratory, Liveraore, Ca. USA 3

Manipulation of volumetric patient data in a distributed virtual reality environment.

PubMed

Dech, F; Ai, Z; Silverstein, J C

2001-01-01

Due to increases in network speed and bandwidth, distributed exploration of medical data in immersive Virtual Reality (VR) environments is becoming increasingly feasible. The volumetric display of radiological data in such environments presents a unique set of challenges. The shear size and complexity of the datasets involved not only make them difficult to transmit to remote sites, but these datasets also require extensive user interaction in order to make them understandable to the investigator and manageable to the rendering hardware. A sophisticated VR user interface is required in order for the clinician to focus on the aspects of the data that will provide educational and/or diagnostic insight. We will describe a software system of data acquisition, data display, Tele-Immersion, and data manipulation that supports interactive, collaborative investigation of large radiological datasets. The hardware required in this strategy is still at the high-end of the graphics workstation market. Future software ports to Linux and NT, along with the rapid development of PC graphics cards, open the possibility for later work with Linux or NT PCs and PC clusters.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

76 FR 28305 - Amendment of Class D and Class E Airspace; Livermore, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... E airspace at Livermore, CA, to accommodate aircraft using new Instrument Landing System (ILS... surface of the earth. * * * * * AWP CA E5 Livermore, CA [Amended] Livermore Municipal Airport, CA (Lat. 37...

The Linux operating system: An introduction

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Linux is a Unix-like operating system for Intel 386/486/Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyrighted by the author, may be freely distributed. A world-wide group has collaborated in developing Linux on the Internet. Linux can run the powerful set of compilers and programming tools of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TeX, LaTeX, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs, etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, it provides an essentially cost-free path away from DOS into the world of Unix and X Windows.

Testing SLURM open source batch system for a Tierl/Tier2 HEP computing facility

NASA Astrophysics Data System (ADS)

Donvito, Giacinto; Salomoni, Davide; Italiano, Alessandro

2014-06-01

In this work the testing activities that were carried on to verify if the SLURM batch system could be used as the production batch system of a typical Tier1/Tier2 HEP computing center are shown. SLURM (Simple Linux Utility for Resource Management) is an Open Source batch system developed mainly by the Lawrence Livermore National Laboratory, SchedMD, Linux NetworX, Hewlett-Packard, and Groupe Bull. Testing was focused both on verifying the functionalities of the batch system and the performance that SLURM is able to offer. We first describe our initial set of requirements. Functionally, we started configuring SLURM so that it replicates all the scheduling policies already used in production in the computing centers involved in the test, i.e. INFN-Bari and the INFN-Tier1 at CNAF, Bologna. Currently, the INFN-Tier1 is using IBM LSF (Load Sharing Facility), while INFN-Bari, an LHC Tier2 for both CMS and Alice, is using Torque as resource manager and MAUI as scheduler. We show how we configured SLURM in order to enable several scheduling functionalities such as Hierarchical FairShare, Quality of Service, user-based and group-based priority, limits on the number of jobs per user/group/queue, job age scheduling, job size scheduling, and scheduling of consumable resources. We then show how different job typologies, like serial, MPI, multi-thread, whole-node and interactive jobs can be managed. Tests on the use of ACLs on queues or in general other resources are then described. A peculiar SLURM feature we also verified is triggers on event, useful to configure specific actions on each possible event in the batch system. We also tested highly available configurations for the master node. This feature is of paramount importance since a mandatory requirement in our scenarios is to have a working farm cluster even in case of hardware failure of the server(s) hosting the batch system. Among our requirements there is also the possibility to deal with pre-execution and post-execution scripts, and controlled handling of the failure of such scripts. This feature is heavily used, for example, at the INFN-Tier1 in order to check the health status of a worker node before execution of each job. Pre- and post-execution scripts are also important to let WNoDeS, the IaaS Cloud solution developed at INFN, use SLURM as its resource manager. WNoDeS has already been supporting the LSF and Torque batch systems for some time; in this work we show the work done so that WNoDeS supports SLURM as well. Finally, we show several performance tests that we carried on to verify SLURM scalability and reliability, detailing scalability tests both in terms of managed nodes and of queued jobs.

REX3DV1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holm, Elizabeth A.

2002-03-28

This code is a FORTRAN code for three-dimensional Monte Carol Potts Model (MCPM) Recrystallization and grain growth. A continuum grain structure is mapped onto a three-dimensional lattice. The mapping procedure is analogous to color bitmapping the grain structure; grains are clusters of pixels (sites) of the same color (spin). The total system energy is given by the Pott Hamiltonian and the kinetics of grain growth are determined through a Monte Carlo technique with a nonconserved order parameter (Glauber dynamics). The code can be compiled and run on UNIX/Linux platforms.

The Roots of Beowulf

NASA Technical Reports Server (NTRS)

Fischer, James R.

2014-01-01

The first Beowulf Linux commodity cluster was constructed at NASA's Goddard Space Flight Center in 1994 and its origins are a part of the folklore of high-end computing. In fact, the conditions within Goddard that brought the idea into being were shaped by rich historical roots, strategic pressures brought on by the ramp up of the Federal High-Performance Computing and Communications Program, growth of the open software movement, microprocessor performance trends, and the vision of key technologists. This multifaceted story is told here for the first time from the point of view of NASA project management.

Abstract of talk for Silicon Valley Linux Users Group

NASA Technical Reports Server (NTRS)

Clanton, Sam

2003-01-01

The use of Linux for research at NASA Ames is discussed.Topics include:work with the Atmospheric Physics branch on software for a spectrometer to be used in the CRYSTAL-FACE mission this summer; work on in the Neuroengineering Lab with code IC including an introduction to the extension of the human senses project,advantages with using linux for real-time biological data processing,algorithms utilized on a linux system, goals of the project,slides of people with Neuroscan caps on, and progress that has been made and how linux has helped.

Livermore Site Spill Prevention, Control, and Countermeasures Plan, May 2017

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffin, D.; Mertesdorf, E.

This Spill Prevention, Control, and Countermeasure (SPCC) Plan describes the measures that are taken at Lawrence Livermore National Laboratory’s (LLNL) Livermore Site in Livermore, California, to prevent, control, and handle potential spills from aboveground containers that can contain 55 gallons or more of oil.

Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust.

PubMed

Cun, Yupeng; Yang, Tsun-Po; Achter, Viktor; Lang, Ulrich; Peifer, Martin

2018-06-01

The genomes of cancer cells constantly change during pathogenesis. This evolutionary process can lead to the emergence of drug-resistant mutations in subclonal populations, which can hinder therapeutic intervention in patients. Data derived from massively parallel sequencing can be used to infer these subclonal populations using tumor-specific point mutations. The accurate determination of copy-number changes and tumor impurity is necessary to reliably infer subclonal populations by mutational clustering. This protocol describes how to use Sclust, a copy-number analysis method with a recently developed mutational clustering approach. In a series of simulations and comparisons with alternative methods, we have previously shown that Sclust accurately determines copy-number states and subclonal populations. Performance tests show that the method is computationally efficient, with copy-number analysis and mutational clustering taking <10 min. Sclust is designed such that even non-experts in computational biology or bioinformatics with basic knowledge of the Linux/Unix command-line syntax should be able to carry out analyses of subclonal populations.

Development of an Autonomous Navigation Technology Test Vehicle

DTIC Science & Technology

2004-08-01

as an independent thread on processors using the Linux operating system. The computer hardware selected for the nodes that host the MRS threads...communications system design. Linux was chosen as the operating system for all of the single board computers used on the Mule. Linux was specifically...used for system analysis and development. The simple realization of multi-thread processing and inter-process communications in Linux made it a

Parallel implementation of D-Phylo algorithm for maximum likelihood clusters.

PubMed

Malik, Shamita; Sharma, Dolly; Khatri, Sunil Kumar

2017-03-01

This study explains a newly developed parallel algorithm for phylogenetic analysis of DNA sequences. The newly designed D-Phylo is a more advanced algorithm for phylogenetic analysis using maximum likelihood approach. The D-Phylo while misusing the seeking capacity of k -means keeps away from its real constraint of getting stuck at privately conserved motifs. The authors have tested the behaviour of D-Phylo on Amazon Linux Amazon Machine Image(Hardware Virtual Machine)i2.4xlarge, six central processing unit, 122 GiB memory, 8  ×  800 Solid-state drive Elastic Block Store volume, high network performance up to 15 processors for several real-life datasets. Distributing the clusters evenly on all the processors provides us the capacity to accomplish a near direct speed if there should arise an occurrence of huge number of processors.

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.

PubMed

Chew, Teong Han; Joyce-Tan, Kwee Hong; Akma, Farizuwana; Shamsir, Mohd Shahir

2011-05-01

birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware. The birgHPC Live CD and relevant user guide are available for free at http://birg1.fbb.utm.my/birghpc.

Development of small scale cluster computer for numerical analysis

NASA Astrophysics Data System (ADS)

Zulkifli, N. H. N.; Sapit, A.; Mohammed, A. N.

2017-09-01

In this study, two units of personal computer were successfully networked together to form a small scale cluster. Each of the processor involved are multicore processor which has four cores in it, thus made this cluster to have eight processors. Here, the cluster incorporate Ubuntu 14.04 LINUX environment with MPI implementation (MPICH2). Two main tests were conducted in order to test the cluster, which is communication test and performance test. The communication test was done to make sure that the computers are able to pass the required information without any problem and were done by using simple MPI Hello Program where the program written in C language. Additional, performance test was also done to prove that this cluster calculation performance is much better than single CPU computer. In this performance test, four tests were done by running the same code by using single node, 2 processors, 4 processors, and 8 processors. The result shows that with additional processors, the time required to solve the problem decrease. Time required for the calculation shorten to half when we double the processors. To conclude, we successfully develop a small scale cluster computer using common hardware which capable of higher computing power when compare to single CPU processor, and this can be beneficial for research that require high computing power especially numerical analysis such as finite element analysis, computational fluid dynamics, and computational physics analysis.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Simplified Virtualization in a HEP/NP Environment with Condor

NASA Astrophysics Data System (ADS)

Strecker-Kellogg, W.; Caramarcu, C.; Hollowell, C.; Wong, T.

2012-12-01

In this work we will address the development of a simple prototype virtualized worker node cluster, using Scientific Linux 6.x as a base OS, KVM and the libvirt API for virtualization, and the Condor batch software to manage virtual machines. The discussion in this paper provides details on our experience with building, configuring, and deploying the various components from bare metal, including the base OS, creation and distribution of the virtualized OS images and the integration of batch services with the virtual machines. Our focus was on simplicity and interoperability with our existing architecture.

Benchmark Comparison of Dual- and Quad-Core Processor Linux Clusters with Two Global Climate Modeling Workloads

NASA Technical Reports Server (NTRS)

McGalliard, James

2008-01-01

This viewgraph presentation details the science and systems environments that NASA High End computing program serves. Included is a discussion of the workload that is involved in the processing for the Global Climate Modeling. The Goddard Earth Observing System Model, Version 5 (GEOS-5) is a system of models integrated using the Earth System Modeling Framework (ESMF). The GEOS-5 system was used for the Benchmark tests, and the results of the tests are shown and discussed. Tests were also run for the Cubed Sphere system, results for these test are also shown.

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

PubMed

Thakur, Shalabh; Guttman, David S

2016-06-30

Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .

A program for the Bayesian Neural Network in the ROOT framework

NASA Astrophysics Data System (ADS)

Zhong, Jiahang; Huang, Run-Sheng; Lee, Shih-Chang

2011-12-01

We present a Bayesian Neural Network algorithm implemented in the TMVA package (Hoecker et al., 2007 [1]), within the ROOT framework (Brun and Rademakers, 1997 [2]). Comparing to the conventional utilization of Neural Network as discriminator, this new implementation has more advantages as a non-parametric regression tool, particularly for fitting probabilities. It provides functionalities including cost function selection, complexity control and uncertainty estimation. An example of such application in High Energy Physics is shown. The algorithm is available with ROOT release later than 5.29. Program summaryProgram title: TMVA-BNN Catalogue identifier: AEJX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: BSD license No. of lines in distributed program, including test data, etc.: 5094 No. of bytes in distributed program, including test data, etc.: 1,320,987 Distribution format: tar.gz Programming language: C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system Operating system: Most UNIX/Linux systems. The application programs were thoroughly tested under Fedora and Scientific Linux CERN. Classification: 11.9 External routines: ROOT package version 5.29 or higher ( http://root.cern.ch) Nature of problem: Non-parametric fitting of multivariate distributions Solution method: An implementation of Neural Network following the Bayesian statistical interpretation. Uses Laplace approximation for the Bayesian marginalizations. Provides the functionalities of automatic complexity control and uncertainty estimation. Running time: Time consumption for the training depends substantially on the size of input sample, the NN topology, the number of training iterations, etc. For the example in this manuscript, about 7 min was used on a PC/Linux with 2.0 GHz processors.

Tuning Linux to meet real time requirements

NASA Astrophysics Data System (ADS)

Herbel, Richard S.; Le, Dang N.

2007-04-01

There is a desire to use Linux in military systems. Customers are requesting contractors to use open source to the maximal possible extent in contracts. Linux is probably the best operating system of choice to meet this need. It is widely used. It is free. It is royalty free, and, best of all, it is completely open source. However, there is a problem. Linux was not originally built to be a real time operating system. There are many places where interrupts can and will be blocked for an indeterminate amount of time. There have been several attempts to bridge this gap. One of them is from RTLinux, which attempts to build a microkernel underneath Linux. The microkernel will handle all interrupts and then pass it up to the Linux operating system. This does insure good interrupt latency; however, it is not free [1]. Another is RTAI, which provides a similar typed interface; however, the PowerPC platform, which is used widely in real time embedded community, was stated as "recovering" [2]. Thus this is not suited for military usage. This paper provides a method for tuning a standard Linux kernel so it can meet the real time requirement of an embedded system.

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

Development of a Computing Cluster At the University of Richmond

NASA Astrophysics Data System (ADS)

Carbonneau, J.; Gilfoyle, G. P.; Bunn, E. F.

2010-11-01

The University of Richmond has developed a computing cluster to support the massive simulation and data analysis requirements for programs in intermediate-energy nuclear physics, and cosmology. It is a 20-node, 240-core system running Red Hat Enterprise Linux 5. We have built and installed the physics software packages (Geant4, gemc, MADmap...) and developed shell and Perl scripts for running those programs on the remote nodes. The system has a theoretical processing peak of about 2500 GFLOPS. Testing with the High Performance Linpack (HPL) benchmarking program (one of the standard benchmarks used by the TOP500 list of fastest supercomputers) resulted in speeds of over 900 GFLOPS. The difference between the maximum and measured speeds is due to limitations in the communication speed among the nodes; creating a bottleneck for large memory problems. As HPL sends data between nodes, the gigabit Ethernet connection cannot keep up with the processing power. We will show how both the theoretical and actual performance of the cluster compares with other current and past clusters, as well as the cost per GFLOP. We will also examine the scaling of the performance when distributed to increasing numbers of nodes.

Linux thin-client conversion in a large cardiology practice: initial experience.

PubMed

Echt, Martin P; Rosen, Jordan

2004-01-01

Capital Cardiology Associates (CCA) is a single-specialty cardiology practice with offices in New York and Massachusetts. In 2003, CCA converted its IT system from a Microsoft-based network to a Linux network employing Linux thin-client technology with overall positive outcomes.

Perl Extension to the Bproc Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grunau, Daryl W.

2004-06-07

The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less

Optimizing CMS build infrastructure via Apache Mesos

NASA Astrophysics Data System (ADS)

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter; Eulisse, Giulio; Mendez, David; Muzaffar, Shahzad

2015-12-01

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux. Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora, and other applications on a dynamically shared pool of nodes. We present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.

Efficiency of parallel direct optimization

NASA Technical Reports Server (NTRS)

Janies, D. A.; Wheeler, W. C.

2001-01-01

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

Development and Testing of a High-Speed Real-Time Kinematic Precise DGPS Positioning System Between Two Aircraft

DTIC Science & Technology

2006-09-01

work-horse for this thesis. He spent hours writing some of the more tedious code, and as much time helping me learn C++ and Linux . He was always there...compared with C++, and the need to use Linux as the operating system, the filter was coded using C++ and KDevelop [28] in SUSE LINUX Professional 9.2 [42...The driving factor for using Linux was the operating system’s ability to access the serial ports in a reliable fashion. Under the original MATLAB® and

Open discovery: An integrated live Linux platform of Bioinformatics tools.

PubMed

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

75 FR 4822 - Decision To Evaluate a Petition To Designate a Class of Employees for the Lawrence Livermore...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

...: Lawrence Livermore National Laboratory. Location: Livermore, California. Job Titles and/or Job Duties: All... L. Hinnefeld, Interim Director, Office of Compensation Analysis and Support, National Institute for...

Scientific Cluster Deployment and Recovery - Using puppet to simplify cluster management

NASA Astrophysics Data System (ADS)

Hendrix, Val; Benjamin, Doug; Yao, Yushu

2012-12-01

Deployment, maintenance and recovery of a scientific cluster, which has complex, specialized services, can be a time consuming task requiring the assistance of Linux system administrators, network engineers as well as domain experts. Universities and small institutions that have a part-time FTE with limited time for and knowledge of the administration of such clusters can be strained by such maintenance tasks. This current work is the result of an effort to maintain a data analysis cluster (DAC) with minimal effort by a local system administrator. The realized benefit is the scientist, who is the local system administrator, is able to focus on the data analysis instead of the intricacies of managing a cluster. Our work provides a cluster deployment and recovery process (CDRP) based on the puppet configuration engine allowing a part-time FTE to easily deploy and recover entire clusters with minimal effort. Puppet is a configuration management system (CMS) used widely in computing centers for the automatic management of resources. Domain experts use Puppet's declarative language to define reusable modules for service configuration and deployment. Our CDRP has three actors: domain experts, a cluster designer and a cluster manager. The domain experts first write the puppet modules for the cluster services. A cluster designer would then define a cluster. This includes the creation of cluster roles, mapping the services to those roles and determining the relationships between the services. Finally, a cluster manager would acquire the resources (machines, networking), enter the cluster input parameters (hostnames, IP addresses) and automatically generate deployment scripts used by puppet to configure it to act as a designated role. In the event of a machine failure, the originally generated deployment scripts along with puppet can be used to easily reconfigure a new machine. The cluster definition produced in our CDRP is an integral part of automating cluster deployment in a cloud environment. Our future cloud efforts will further build on this work.

77 FR 5864 - BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano Superlattice Technology, Inc.; Order of Suspension of... current and accurate information concerning the securities of BluePoint Linux Software Corp. because it...

Kernel-based Linux emulation for Plan 9.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minnich, Ronald G.

2010-09-01

CNKemu is a kernel-based system for the 9k variant of the Plan 9 kernel. It is designed to provide transparent binary support for programs compiled for IBM's Compute Node Kernel (CNK) on the Blue Gene series of supercomputers. This support allows users to build applications with the standard Blue Gene toolchain, including C++ and Fortran compilers. While the CNK is not Linux, IBM designed the CNK so that the user interface has much in common with the Linux 2.0 system call interface. The Plan 9 CNK emulator hence provides the foundation of kernel-based Linux system call support on Plan 9.more » In this paper we discuss cnkemu's implementation and some of its more interesting features, such as the ability to easily intermix Plan 9 and Linux system calls.« less

Open discovery: An integrated live Linux platform of Bioinformatics tools

PubMed Central

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery ‐ a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. Availability The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in PMID:19238235

Massive Signal Analysis with Hadoop (Invited)

NASA Astrophysics Data System (ADS)

Addair, T.

2013-12-01

The Geophysical Monitoring Program (GMP) at Lawrence Livermore National Laboratory is in the process of transitioning from a primarily human-driven analysis pipeline to a more automated and exploratory system. Waveform correlation represents a significant part of this effort, and the results that come out of this processing could lead to the development of more sophisticated event detection and analysis systems that require less human interaction, and address fundamental shortcomings in existing systems. Furthermore, use of distributed IO systems fundamentally addresses a scalability concern for the GMP as our data holdings continue to grow rapidly. As the data volume increases, it becomes less reasonable to rely upon human analysts to sift through all the information. Not only is more automation essential to keeping up with the ingestion rate, but so too do we require faster and more sophisticated tools for visualizing and interacting with the data. These issues of scalability are not unique to GMP or the seismic domain. All across the lab, and throughout industry, we hear about the promise of 'big data' to address the need of quickly analyzing vast amounts of data in fundamentally new ways. Our waveform correlation system finds and correlates nearby seismic events across the entire Earth. In our original implementation of the system, we processed some 50 TB of data on an in-house traditional HPC cluster (44 cores, 1 filesystem) over the span of 42 days. Having determined the primary bottleneck in the performance to be reading waveforms off a single BlueArc file server, we began investigating distributed IO solutions like Hadoop. As a test case, we took a 1 TB subset of our data and ported it to Livermore Computing's development Hadoop cluster. Through a pilot project sponsored by Livermore Computing (LC), the GMP successfully implemented the waveform correlation system in the Hadoop distributed MapReduce computing framework. Hadoop is an open source implementation of the MapReduce distributed programming framework. We used the Hadoop scripting framework known as Pig for putting together the multi-job MapReduce pipeline used to extract as much parallelism as possible from the algorithms. We also made use the Sqoop data ingestion tool to pull metadata tables from our Oracle database into HDFS (the Hadoop Distributed Filesystem). Running on our in-house HPC cluster, processing this test dataset took 58 hours to complete. In contrast, running our Hadoop implementation on LC's 10 node (160 core) cluster, we were able to cross-correlate the 1 TB of nearby seismic events in just under 3 hours, over a factor of 19 improvement from our existing implementation. This project is one of the first major data mining and analysis tasks performed at the lab or anywhere else correlating the entire Earth's seismicity. Through the success of this project, we believe we've shown that a MapReduce solution can be appropriate for many large-scale Earth science data analysis and exploration problems. Given Hadoop's position as the dominant data analytics solution in industry, we believe Hadoop can be applied to many previously intractable Earth science problems.

The Research on Linux Memory Forensics

NASA Astrophysics Data System (ADS)

Zhang, Jun; Che, ShengBing

2018-03-01

Memory forensics is a branch of computer forensics. It does not depend on the operating system API, and analyzes operating system information from binary memory data. Based on the 64-bit Linux operating system, it analyzes system process and thread information from physical memory data. Using ELF file debugging information and propose a method for locating kernel structure member variable, it can be applied to different versions of the Linux operating system. The experimental results show that the method can successfully obtain the sytem process information from physical memory data, and can be compatible with multiple versions of the Linux kernel.

Real-time data collection in Linux: a case study.

PubMed

Finney, S A

2001-05-01

Multiuser UNIX-like operating systems such as Linux are often considered unsuitable for real-time data collection because of the potential for indeterminate timing latencies resulting from preemptive scheduling. In this paper, Linux is shown to be fully adequate for precisely controlled programming with millisecond resolution or better. The Linux system calls that subserve such timing control are described and tested and then utilized in a MIDI-based program for tapping and music performance experiments. The timing of this program, including data input and output, is shown to be accurate at the millisecond level. This demonstrates that Linux, with proper programming, is suitable for real-time experiment software. In addition, the detailed description and test of both the operating system facilities and the application program itself may serve as a model for publicly documenting programming methods and software performance on other operating systems.

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

27 CFR 9.46 - Livermore Valley.

Code of Federal Regulations, 2011 CFR

2011-04-01

....” (b) Approved maps. The appropriate maps for determining the boundary of the Livermore Valley... 1980); (12) Hayward, CA (1993); and (13) Las Trampas Ridge, CA (1995). (c) Boundary. The Livermore... miles, passing through the Dublin map near Walpert Ridge, onto the Hayward map to the point where the...

27 CFR 9.46 - Livermore Valley.

Code of Federal Regulations, 2010 CFR

2010-04-01

....” (b) Approved maps. The appropriate maps for determining the boundary of the Livermore Valley... 1980); (12) Hayward, CA (1993); and (13) Las Trampas Ridge, CA (1995). (c) Boundary. The Livermore... miles, passing through the Dublin map near Walpert Ridge, onto the Hayward map to the point where the...

03-NIF Dedication: Norm Pattiz

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norm Pattiz

2009-07-02

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Norm Pattiz, the chairman of Lawrence Livermore National Security, which manages Lawrence Livermore National Laboratory for the U.S. Department of Energy.

03-NIF Dedication: Norm Pattiz

ScienceCinema

Norm Pattiz

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Norm Pattiz, the chairman of Lawrence Livermore National Security, which manages Lawrence Livermore National Laboratory for the U.S. Department of Energy.

Evolution of Linux operating system network

NASA Astrophysics Data System (ADS)

Xiao, Guanping; Zheng, Zheng; Wang, Haoqin

2017-01-01

Linux operating system (LOS) is a sophisticated man-made system and one of the most ubiquitous operating systems. However, there is little research on the structure and functionality evolution of LOS from the prospective of networks. In this paper, we investigate the evolution of the LOS network. 62 major releases of LOS ranging from versions 1.0 to 4.1 are modeled as directed networks in which functions are denoted by nodes and function calls are denoted by edges. It is found that the size of the LOS network grows almost linearly, while clustering coefficient monotonically decays. The degree distributions are almost the same: the out-degree follows an exponential distribution while both in-degree and undirected degree follow power-law distributions. We further explore the functionality evolution of the LOS network. It is observed that the evolution of functional modules is shown as a sequence of seven events (changes) succeeding each other, including continuing, growth, contraction, birth, splitting, death and merging events. By means of a statistical analysis of these events in the top 4 largest components (i.e., arch, drivers, fs and net), it is shown that continuing, growth and contraction events occupy more than 95% events. Our work exemplifies a better understanding and describing of the dynamics of LOS evolution.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Science & Technology Review November 2002

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budil, K

This months issue of Science and Technology Review has the following articles: (1) High-Tech Help for Fighting Wildfires--Commentary by Leland W. Younker; (2) This Model Can Take the Heat--A physics-based simulation program to combat wildfires combines the capabilities and resources of Lawrence Livermore and Los Alamos national laboratories. (3) The Best and the Brightest Come to Livermore--The Lawrence Fellowship Program attracts the most sought-after postdoctoral researchers to the Laboratory. (4) A view to Kill--Livermore sensors are aimed at the ''kill'' vehicle when it intercepts an incoming ballistic missile. (5) 50th Anniversary Highlight--Biological Research Evolves at Livermore--Livermore's biological research program keepsmore » pace with emerging national issues, from studying the effects of ionizing radiation to detecting agents of biological warfare.« less

M31 Globular Clusters and Galaxy Formation

NASA Astrophysics Data System (ADS)

Gregg, M. D.; Karick, A. M.

2005-12-01

The brightest globular cluster in the halo of M31, cluster G1, has properties which suggest that it is not an ordinary globular but an ultra-compact dwarf galaxy: its velocity dispersion, M/L, and ellipticity are all atypically large, and its color-magnitude diagram suggests an abundance spread. Using the Keck Laser Guide Star Adaptive Optics system with NIRC2, we have begun an imaging campaign of globular clusters in M31 to measure their core sizes. Combining these data with high dispersion spectroscopy will produce masses and M/L ratios to determine if there are additional UCDs masquerading as M31 globulars. UCDs are thought to be the remnant nuclei from tidally stripped dwarf ellipticals or small spirals; finding additional examples in the cluster system of M31 has implications for galaxy formation processes. The K-band image quality during our first LGS run was very stable over many hours, with Strehl ratios of 0.35 or better, producing point sources with FWHM of 0\\farcs05. The core sizes of the clusters, which range from 0\\farcs2 to 0\\farcs8 can be easily measured from these data. The observing conditions were nearly as good in the J-band, and we obtained both colors for a number of clusters. We discuss our efforts to produce photometrically-calibrated color-magnitude diagrams of the clusters. This work is supported by National Science Foundation Grant No. 0407445 and was done at the Institute of Geophysics and Planetary Physics, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi.

PubMed

Sapes, Jordi; Solsona, Francesc

2016-02-06

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux.

Science& Technology Review June 2003

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, D

This month's issue has the following articles: (1) Livermore's Three-Pronged Strategy for High-Performance Computing, Commentary by Dona Crawford; (2) Riding the Waves of Supercomputing Technology--Livermore's Computation Directorate is exploiting multiple technologies to ensure high-performance, cost-effective computing; (3) Chromosome 19 and Lawrence Livermore Form a Long-Lasting Bond--Lawrence Livermore biomedical scientists have played an important role in the Human Genome Project through their long-term research on chromosome 19; (4) A New Way to Measure the Mass of Stars--For the first time, scientists have determined the mass of a star in isolation from other celestial bodies; and (5) Flexibly Fueled Storage Tank Bringsmore » Hydrogen-Powered Cars Closer to Reality--Livermore's cryogenic hydrogen fuel storage tank for passenger cars of the future can accommodate three forms of hydrogen fuel separately or in combination.« less

Lawrence Livermore National Laboratory Environmental Report 2014

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, H. E.; Bertoldo, N. A.; Blake, R. G.

The purposes of the Lawrence Livermore National Laboratory Environmental Report 2014 are to record Lawrence Livermore National Laboratory’s (LLNL’s) compliance with environmental standards and requirements, describe LLNL’s environmental protection and remediation programs, and present the results of environmental monitoring at the two LLNL sites—the Livermore Site and Site 300. The report is prepared for the U.S. Department of Energy (DOE) by LLNL’s Environmental Functional Area. Submittal of the report satisfies requirements under DOE Order 231.1B, “Environment, Safety and Health Reporting,” and DOE Order 458.1, “Radiation Protection of the Public and Environment.”

Lawrence Livermore National Laboratory Environmental Report 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosene, C. A.; Jones, H. E.

The purposes of the Lawrence Livermore National Laboratory Environmental Report 2015 are to record Lawrence Livermore National Laboratory’s (LLNL’s) compliance with environmental standards and requirements, describe LLNL’s environmental protection and remediation programs, and present the results of environmental monitoring at the two LLNL sites—the Livermore Site and Site 300. The report is prepared for the U.S. Department of Energy (DOE) by LLNL’s Environmental Functional Area. Submittal of the report satisfies requirements under DOE Order 231.1B, “Environment, Safety and Health Reporting,” and DOE Order 458.1, “Radiation Protection of the Public and Environment.”

The Stellar Populations of Ultra-Compact Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Karick, Arna; Gregg, M. D.

2006-12-01

We have discovered an intracluster population of ultra-luminous compact stellar systems in the Fornax cluster. Originally coined "ultra-compact dwarf galaxies" (UCDs), these objects were thought to be remnant nuclei of tidally stripped dE,Ns. Subsequent searches in Fornax (2dF+VLT) have revealed many fainter UCDs; making them the most numerous galaxy type in the cluster and fueling controversy over their origin. UCDs may be the bright tail of the globular cluster (GCs) population associated with NGC1399. Alternatively they may be real intracluster GCs, resulting from hierarchical cluster formation and merging in intracluster space. Determining the stellar populations of these enigmatic objects is challenging. UCDs are unresolved from the ground but our HST/STIS+ACS imaging reveals faint halos around the brightest UCDs. Here we present deep u'g'r'i'z' images of the cluster core using the CTIO 4m Mosaic. Combined with GALEX/UV imaging and using SSP isochrones, UCDs appear to be old, red and unlike cluster dEs. In contrast, our recent IMACS and Keck/LRIS+ESI spectroscopy shows that UCDs are unlike GCs and have intermediate stellar populations with significant variations in their Mg and Hβ line strength indices. This work is supported by National Science Foundation Grant No. 0407445 and was done at the Institute of Geophysics and Planetary Physics, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi

PubMed Central

Sapes, Jordi; Solsona, Francesc

2016-01-01

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux. PMID:26861340

Analytical capabilities and services of Lawrence Livermore Laboratory's General Chemistry Division. [Methods available at Lawrence Livermore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gutmacher, R.; Crawford, R.

This comprehensive guide to the analytical capabilities of Lawrence Livermore Laboratory's General Chemistry Division describes each analytical method in terms of its principle, field of application, and qualitative and quantitative uses. Also described are the state and quantity of sample required for analysis, processing time, available instrumentation, and responsible personnel.

Improving Block-level Efficiency with scsi-mq

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldwell, Blake A

2015-01-01

Current generation solid-state storage devices are exposing a new bottlenecks in the SCSI and block layers of the Linux kernel, where IO throughput is limited by lock contention, inefficient interrupt handling, and poor memory locality. To address these limitations, the Linux kernel block layer underwent a major rewrite with the blk-mq project to move from a single request queue to a multi-queue model. The Linux SCSI subsystem rework to make use of this new model, known as scsi-mq, has been merged into the Linux kernel and work is underway for dm-multipath support in the upcoming Linux 4.0 kernel. These piecesmore » were necessary to make use of the multi-queue block layer in a Lustre parallel filesystem with high availability requirements. We undertook adding support of the 3.18 kernel to Lustre with scsi-mq and dm-multipath patches to evaluate the potential of these efficiency improvements. In this paper we evaluate the block-level performance of scsi-mq with backing storage hardware representative of a HPC-targerted Lustre filesystem. Our findings show that SCSI write request latency is reduced by as much as 13.6%. Additionally, when profiling the CPU usage of our prototype Lustre filesystem, we found that CPU idle time increased by a factor of 7 with Linux 3.18 and blk-mq as compared to a standard 2.6.32 Linux kernel. Our findings demonstrate increased efficiency of the multi-queue block layer even with disk-based caching storage arrays used in existing parallel filesystems.« less

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

A Fault-Oblivious Extreme-Scale Execution Environment (FOX)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Hensbergen, Eric; Speight, William; Xenidis, Jimi

IBM Research’s contribution to the Fault Oblivious Extreme-scale Execution Environment (FOX) revolved around three core research deliverables: • collaboration with Boston University around the Kittyhawk cloud infrastructure which both enabled a development and deployment platform for the project team and provided a fault-injection testbed to evaluate prototypes • operating systems research focused on exploring role-based operating system technologies through collaboration with Sandia National Labs on the NIX research operating system and collaboration with the broader IBM Research community around a hybrid operating system model which became known as FusedOS • IBM Research also participated in an advisory capacity with themore » Boston University SESA project, the core of which was derived from the K42 operating system research project funded in part by DARPA’s HPCS program. Both of these contributions were built on a foundation of previous operating systems research funding by the Department of Energy’s FastOS Program. Through the course of the X-stack funding we were able to develop prototypes, deploy them on production clusters at scale, and make them available to other researchers. As newer hardware, in the form of BlueGene/Q, came online, we were able to port the prototypes to the new hardware and release the source code for the resulting prototypes as open source to the community. In addition to the open source coded for the Kittyhawk and NIX prototypes, we were able to bring the BlueGene/Q Linux patches up to a more recent kernel and contribute them for inclusion by the broader Linux community. The lasting impact of the IBM Research work on FOX can be seen in its effect on the shift of IBM’s approach to HPC operating systems from Linux and Compute Node Kernels to role-based approaches as prototyped by the NIX and FusedOS work. This impact can be seen beyond IBM in follow-on ideas being incorporated into the proposals for the Exasacale Operating Systems/Runtime program.« less

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

High Performance Geostatistical Modeling of Biospheric Resources

NASA Astrophysics Data System (ADS)

Pedelty, J. A.; Morisette, J. T.; Smith, J. A.; Schnase, J. L.; Crosier, C. S.; Stohlgren, T. J.

2004-12-01

We are using parallel geostatistical codes to study spatial relationships among biospheric resources in several study areas. For example, spatial statistical models based on large- and small-scale variability have been used to predict species richness of both native and exotic plants (hot spots of diversity) and patterns of exotic plant invasion. However, broader use of geostastics in natural resource modeling, especially at regional and national scales, has been limited due to the large computing requirements of these applications. To address this problem, we implemented parallel versions of the kriging spatial interpolation algorithm. The first uses the Message Passing Interface (MPI) in a master/slave paradigm on an open source Linux Beowulf cluster, while the second is implemented with the new proprietary Xgrid distributed processing system on an Xserve G5 cluster from Apple Computer, Inc. These techniques are proving effective and provide the basis for a national decision support capability for invasive species management that is being jointly developed by NASA and the US Geological Survey.

Optimizing CMS build infrastructure via Apache Mesos

DOE PAGES

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter; ...

2015-12-23

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux.Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora,more » and other applications on a dynamically shared pool of nodes. Lastly, we present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.« less

GPU computing with Kaczmarz’s and other iterative algorithms for linear systems

PubMed Central

Elble, Joseph M.; Sahinidis, Nikolaos V.; Vouzis, Panagiotis

2009-01-01

The graphics processing unit (GPU) is used to solve large linear systems derived from partial differential equations. The differential equations studied are strongly convection-dominated, of various sizes, and common to many fields, including computational fluid dynamics, heat transfer, and structural mechanics. The paper presents comparisons between GPU and CPU implementations of several well-known iterative methods, including Kaczmarz’s, Cimmino’s, component averaging, conjugate gradient normal residual (CGNR), symmetric successive overrelaxation-preconditioned conjugate gradient, and conjugate-gradient-accelerated component-averaged row projections (CARP-CG). Computations are preformed with dense as well as general banded systems. The results demonstrate that our GPU implementation outperforms CPU implementations of these algorithms, as well as previously studied parallel implementations on Linux clusters and shared memory systems. While the CGNR method had begun to fall out of favor for solving such problems, for the problems studied in this paper, the CGNR method implemented on the GPU performed better than the other methods, including a cluster implementation of the CARP-CG method. PMID:20526446

Optimizing CMS build infrastructure via Apache Mesos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdurachmanov, David; Degano, Alessandro; Elmer, Peter

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux.Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora,more » and other applications on a dynamically shared pool of nodes. Lastly, we present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.« less

Comparison of Monte Carlo simulated and measured performance parameters of miniPET scanner

NASA Astrophysics Data System (ADS)

Kis, S. A.; Emri, M.; Opposits, G.; Bükki, T.; Valastyán, I.; Hegyesi, Gy.; Imrek, J.; Kalinka, G.; Molnár, J.; Novák, D.; Végh, J.; Kerek, A.; Trón, L.; Balkay, L.

2007-02-01

In vivo imaging of small laboratory animals is a valuable tool in the development of new drugs. For this purpose, miniPET, an easy to scale modular small animal PET camera has been developed at our institutes. The system has four modules, which makes it possible to rotate the whole detector system around the axis of the field of view. Data collection and image reconstruction are performed using a data acquisition (DAQ) module with Ethernet communication facility and a computer cluster of commercial PCs. Performance tests were carried out to determine system parameters, such as energy resolution, sensitivity and noise equivalent count rate. A modified GEANT4-based GATE Monte Carlo software package was used to simulate PET data analogous to those of the performance measurements. GATE was run on a Linux cluster of 10 processors (64 bit, Xeon with 3.0 GHz) and controlled by a SUN grid engine. The application of this special computer cluster reduced the time necessary for the simulations by an order of magnitude. The simulated energy spectra, maximum rate of true coincidences and sensitivity of the camera were in good agreement with the measured parameters.

The Current and Historical Distribution of Special Status Amphibians at the Livermore Site and Site 300

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hattem, M V; Paterson, L; Woollett, J

2008-08-20

65 surveys were completed in 2002 to assess the current distribution of special status amphibians at the Lawrence Livermore National Laboratory's (LLNL) Livermore Site and Site 300. Combined with historical information from previous years, the information presented herein illustrates the dynamic and probable risk that amphibian populations face at both sites. The Livermore Site is developed and in stark contrast to the mostly undeveloped Site 300. Yet both sites have significant issues threatening the long-term sustainability of their respective amphibian populations. Livermore Site amphibians are presented with a suite of challenges inherent of urban interfaces, most predictably the bullfrog (Ranamore » catesbeiana), while Site 300's erosion issues and periodic feral pig (Sus scrofa) infestations reduce and threaten populations. The long-term sustainability of LLNL's special status amphibians will require active management and resource commitment to maintain and restore amphibian habitat at both sites.« less

Linux Kernel Co-Scheduling and Bulk Synchronous Parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2012-01-01

This paper describes a kernel scheduling algorithm that is based on coscheduling principles and that is intended for parallel applications running on 1000 cores or more. Experimental results for a Linux implementation on a Cray XT5 machine are presented. The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

The Pyramid Liner Concept

DTIC Science & Technology

2003-06-01

Albuquerque, NM, 1992. Dobratz, B. M. LLNL Explosives Handbook; UCRL -5299; Lawrence Livermore Laboratory: Livermore, CA, 1981 Geiger, W.; Honcia, G...L.; Hornig, H. C.; Kury, J. W. Adiabatic Expansion of High Explosive Detonation Products; UCRL -50422; Lawrence Livermore National Laboratory...ARMAMENT LAB AFATL DLJR J FOSTER D LAMBERT EGLIN AFB FL 32542-6810 2 DARPA W SNOWDEN S WAX 3701 N FAIRFAX DR ARLINGTON VA

77 FR 21762 - ReEnergy Livermore Falls LLC; Supplemental Notice That Revised Market-Based Rate Tariff Filing...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-11

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. ER12-1432-000] ReEnergy Livermore Falls LLC; Supplemental Notice That Revised Market-Based Rate Tariff Filing Includes Request for Blanket Section 204 Authorization This is a supplemental notice in the above-referenced proceeding of ReEnergy Livermore Falls LLC's tariff...

Collaboration rules.

PubMed

Evans, Philip; Wolf, Bob

2005-01-01

Corporate leaders seeking to boost growth, learning, and innovation may find the answer in a surprising place: the Linux open-source software community. Linux is developed by an essentially volunteer, self-organizing community of thousands of programmers. Most leaders would sell their grandmothers for workforces that collaborate as efficiently, frictionlessly, and creatively as the self-styled Linux hackers. But Linux is software, and software is hardly a model for mainstream business. The authors have, nonetheless, found surprising parallels between the anarchistic, caffeinated, hirsute world of Linux hackers and the disciplined, tea-sipping, clean-cut world of Toyota engineering. Specifically, Toyota and Linux operate by rules that blend the self-organizing advantages of markets with the low transaction costs of hierarchies. In place of markets' cash and contracts and hierarchies' authority are rules about how individuals and groups work together (with rigorous discipline); how they communicate (widely and with granularity); and how leaders guide them toward a common goal (through example). Those rules, augmented by simple communication technologies and a lack of legal barriers to sharing information, create rich common knowledge, the ability to organize teams modularly, extraordinary motivation, and high levels of trust, which radically lowers transaction costs. Low transaction costs, in turn, make it profitable for organizations to perform more and smaller transactions--and so increase the pace and flexibility typical of high-performance organizations. Once the system achieves critical mass, it feeds on itself. The larger the system, the more broadly shared the knowledge, language, and work style. The greater individuals' reputational capital, the louder the applause and the stronger the motivation. The success of Linux is evidence of the power of that virtuous circle. Toyota's success is evidence that it is also powerful in conventional companies.

Elan4/SPARC V9 Cross Loader and Dynamic Linker

DOE Office of Scientific and Technical Information (OSTI.GOV)

anf Fabien Lebaillif-Delamare, Fabrizio Petrini

2004-10-25

The Elan4/Sparc V9 Croos Loader and Liner is a part of the Linux system software that allows the dynamic loading and linking of user code in the network interface Quadrics QsNETII, also called as Elan4 Quadrics. Elan44 uses a thread processor that is based on the assembly instruction set of the Sparc V9. All this software is integrated as a Linux kernel module in the Linux 2.6.5 release.

Memory Analysis of the KBeast Linux Rootkit: Investigating Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-06-01

examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills , can successfully...memory images and malware, this new series of reports will be directed at those who must analyse Linux malware-infected memory images. The skills ...disable 1287 1000 1000 /usr/lib/policykit-1-gnome/polkit-gnome-authentication- agent-1 1310 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1350

The Power of Partnership

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazi, A

2005-09-20

Institutions Lawrence Livermore National Laboratory conduct similar or complementary research often excel through collaboration. Indeed, much of Lawrence Livermore's research involves collaboration with other institutions, including universities, other national laboratories, government agencies, and private industry. In particular, Livermore's strategic collaborations with other University of California (UC) campuses have proven exceptionally successful in combining basic science and applied multidisciplinary research. In joint projects, the collaborating institutions benefit from sharing expertise and resources as they work toward their distinctive missions in education, research, and public service. As Laboratory scientists and engineers identify resources needed to conduct their work, they often turn tomore » university researchers with complementary expertise. Successful projects can expand in scope to include additional scientists and engineers both from the Laboratory and from UC, and these projects may become an important element of the research portfolios of the cognizant Livermore directorate and the university department. Additional funding may be provided to broaden or deepen a research project or perhaps develop it for transfer to the private sector for commercial release. Occasionally, joint projects evolve into a strategic collaboration at the institutional level, attracting the attention of the Laboratory director and the UC chancellor. Government agencies or private industries may contribute funding in recognition of the potential payoff of the joint research, and a center may be established at one of the UC campuses. Livermore scientists and engineers and UC faculty are recruited to these centers to focus on a particular area and achieve goals through interdisciplinary research. Some of these researchers hold multilocation appointments, allowing them to work at Livermore and another UC campus. Such centers also attract postdoctoral researchers and graduate students pursuing careers in the centers specialized areas of science. foster university collaboration is through the Laboratory's institutes, which have been established to focus university outreach efforts in fields of scientific importance to Livermore's programs and missions. Some of these joint projects may grow to the level of a strategic collaboration. Others may assist in Livermore's national security mission; provide a recruiting pipeline from universities to the Laboratory; or enhance university interactions and the vitality of Livermore's science and technology environment through seminars, workshops, and visitor programs.« less

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

PubMed

De Oliveira, T; Miller, R; Tarin, M; Cassol, S

2003-01-01

Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

A Framework for Adaptable Operating and Runtime Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sterling, Thomas

The emergence of new classes of HPC systems where performance improvement is enabled by Moore’s Law for technology is manifest through multi-core-based architectures including specialized GPU structures. Operating systems were originally designed for control of uniprocessor systems. By the 1980s multiprogramming, virtual memory, and network interconnection were integral services incorporated as part of most modern computers. HPC operating systems were primarily derivatives of the Unix model with Linux dominating the Top-500 list. The use of Linux for commodity clusters was first pioneered by the NASA Beowulf Project. However, the rapid increase in number of cores to achieve performance gain throughmore » technology advances has exposed the limitations of POSIX general-purpose operating systems in scaling and efficiency. This project was undertaken through the leadership of Sandia National Laboratories and in partnership of the University of New Mexico to investigate the alternative of composable lightweight kernels on scalable HPC architectures to achieve superior performance for a wide range of applications. The use of composable operating systems is intended to provide a minimalist set of services specifically required by a given application to preclude overheads and operational uncertainties (“OS noise”) that have been demonstrated to degrade efficiency and operational consistency. This project was undertaken as an exploration to investigate possible strategies and methods for composable lightweight kernel operating systems towards support for extreme scale systems.« less

Testing the Archivas Cluster (Arc) for Ozone Monitoring Instrument (OMI) Scientific Data Storage

NASA Technical Reports Server (NTRS)

Tilmes, Curt

2005-01-01

The Ozone Monitoring Instrument (OMI) launched on NASA's Aura Spacecraft, the third of the major platforms of the EOS program on July 15,2004. In addition to the long term archive and distribution of the data from OM1 through the Goddard Earth Science Distributed Active Archive Center (GESDAAC), we are evaluating other archive mechanisms that can archive the data in a more immediately available method where it can be used for futher data production and analysis. In 2004, Archivas, Inc. was selected by NASA s Small Business Innovative Research (SBIR) program for the development of their Archivas Cluster (ArC) product. Arc is an online disk based system utilizing self-management and automation on a Linux cluster. Its goal is to produce a low cost solution coupled with the ease of management. The OM1 project is an application partner of the SBIR program, and has deployed a small cluster (5TB) based on the beta Archwas software. We performed extensive testing of the unit using production OM1 data since launch. In 2005, Archivas, Inc. was funded in SBIR Phase II for further development, which will include testing scalability with the deployment of a larger (35TB) cluster at Goddard. We plan to include Arc in the OM1 Team Leader Computing Facility (TLCF) hosting OM1 data for direct access and analysis by the OMI Science Team. This presentation will include a brief technical description of the Archivas Cluster, a summary of the SBIR Phase I beta testing results, and an overview of the OMI ground data processing architecture including its interaction with the Phase II Archivas Cluster and hosting of OMI data for the scientists.

Hybrid cloud and cluster computing paradigms for life science applications

PubMed Central

2010-01-01

Background Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Results Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. Conclusions The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. Methods We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments. PMID:21210982

Hybrid cloud and cluster computing paradigms for life science applications.

PubMed

Qiu, Judy; Ekanayake, Jaliya; Gunarathne, Thilina; Choi, Jong Youl; Bae, Seung-Hee; Li, Hui; Zhang, Bingjing; Wu, Tak-Lon; Ruan, Yang; Ekanayake, Saliya; Hughes, Adam; Fox, Geoffrey

2010-12-21

Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.

Linux Kernel Co-Scheduling For Bulk Synchronous Parallel Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R

2011-01-01

This paper describes a kernel scheduling algorithm that is based on co-scheduling principles and that is intended for parallel applications running on 1000 cores or more where inter-node scalability is key. Experimental results for a Linux implementation on a Cray XT5 machine are presented.1 The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Develop, Build, and Test a Virtual Lab to Support a Vulnerability Training System

DTIC Science & Technology

2004-09-01

docs.us.dell.com/support/edocs/systems/pe1650/ en /it/index.htm> (20 August 2004) “HOWTO: Installing Web Services with Linux /Tomcat/Apache/Struts...configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web server was configured as the external interface to...1650, dual processor, blade servers were configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web

Monte Carlo investigation of the increased radiation deposition due to gold nanoparticles using kilovoltage and megavoltage photons in a 3D randomized cell model.

PubMed

Douglass, Michael; Bezak, Eva; Penfold, Scott

2013-07-01

Investigation of increased radiation dose deposition due to gold nanoparticles (GNPs) using a 3D computational cell model during x-ray radiotherapy. Two GNP simulation scenarios were set up in Geant4; a single 400 nm diameter gold cluster randomly positioned in the cytoplasm and a 300 nm gold layer around the nucleus of the cell. Using an 80 kVp photon beam, the effect of GNP on the dose deposition in five modeled regions of the cell including cytoplasm, membrane, and nucleus was simulated. Two Geant4 physics lists were tested: the default Livermore and custom built Livermore/DNA hybrid physics list. 10(6) particles were simulated at 840 cells in the simulation. Each cell was randomly placed with random orientation and a diameter varying between 9 and 13 μm. A mathematical algorithm was used to ensure that none of the 840 cells overlapped. The energy dependence of the GNP physical dose enhancement effect was calculated by simulating the dose deposition in the cells with two energy spectra of 80 kVp and 6 MV. The contribution from Auger electrons was investigated by comparing the two GNP simulation scenarios while activating and deactivating atomic de-excitation processes in Geant4. The physical dose enhancement ratio (DER) of GNP was calculated using the Monte Carlo model. The model has demonstrated that the DER depends on the amount of gold and the position of the gold cluster within the cell. Individual cell regions experienced statistically significant (p < 0.05) change in absorbed dose (DER between 1 and 10) depending on the type of gold geometry used. The DER resulting from gold clusters attached to the cell nucleus had the more significant effect of the two cases (DER ≈ 55). The DER value calculated at 6 MV was shown to be at least an order of magnitude smaller than the DER values calculated for the 80 kVp spectrum. Based on simulations, when 80 kVp photons are used, Auger electrons have a statistically insignificant (p < 0.05) effect on the overall dose increase in the cell. The low energy of the Auger electrons produced prevents them from propagating more than 250-500 nm from the gold cluster and, therefore, has a negligible effect on the overall dose increase due to GNP. The results presented in the current work show that the primary dose enhancement is due to the production of additional photoelectrons.

HEP Computing

Science.gov Websites

Computing Visitors who do not need a HEP linux account Visitors with laptops can use wireless network HEP linux account Step 1: Click Here for New Account Application After submitting the application, you

Approval of Las Positas College in Livermore: A Report to the Governor and Legislature on the Development of Las Positas College (Formerly the Livermore Education Center of Chabot College).

ERIC Educational Resources Information Center

California State Postsecondary Education Commission, Sacramento.

The Livermore Education Center (LEC), an off-campus center of Chabot College, was established in 1975. In 1986, the South County Community College District designated the LEC a full-service community college campus eligible for state funding of facilities, and in 1988, the Board of Governors of the California Community Colleges approved Las…

Experiences with Transitioning Science Data Production from a Symmetric Multiprocessor Platform to a Linux Cluster Environment

NASA Astrophysics Data System (ADS)

Walter, R. J.; Protack, S. P.; Harris, C. J.; Caruthers, C.; Kusterer, J. M.

2008-12-01

NASA's Atmospheric Science Data Center at the NASA Langley Research Center performs all of the science data processing for the Multi-angle Imaging SpectroRadiometer (MISR) instrument. MISR is one of the five remote sensing instruments flying aboard NASA's Terra spacecraft. From the time of Terra launch in December 1999 until February 2008, all MISR science data processing was performed on a Silicon Graphics, Inc. (SGI) platform. However, dramatic improvements in commodity computing technology coupled with steadily declining project budgets during that period eventually made transitioning MISR processing to a commodity computing environment both feasible and necessary. The Atmospheric Science Data Center has successfully ported the MISR science data processing environment from the SGI platform to a Linux cluster environment. There were a multitude of technical challenges associated with this transition. Even though the core architecture of the production system did not change, the manner in which it interacted with underlying hardware was fundamentally different. In addition, there are more potential throughput bottlenecks in a cluster environment than there are in a symmetric multiprocessor environment like the SGI platform and each of these had to be addressed. Once all the technical issues associated with the transition were resolved, the Atmospheric Science Data Center had a MISR science data processing system with significantly higher throughput than the SGI platform at a fraction of the cost. In addition to the commodity hardware, free and open source software such as S4PM, Sun Grid Engine, PostgreSQL and Ganglia play a significant role in the new system. Details of the technical challenges and resolutions, software systems, performance improvements, and cost savings associated with the transition will be discussed. The Atmospheric Science Data Center in Langley's Science Directorate leads NASA's program for the processing, archival and distribution of Earth science data in the areas of radiation budget, clouds, aerosols, and tropospheric chemistry. The Data Center was established in 1991 to support NASA's Earth Observing System and the U.S. Global Change Research Program. It is unique among NASA data centers in the size of its archive, cutting edge computing technology, and full range of data services. For more information regarding ASDC data holdings, documentation, tools and services, visit http://eosweb.larc.nasa.gov

Survey of MapReduce frame operation in bioinformatics.

PubMed

Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

2014-07-01

Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

An MPI-based MoSST core dynamics model

NASA Astrophysics Data System (ADS)

Jiang, Weiyuan; Kuang, Weijia

2008-09-01

Distributed systems are among the main cost-effective and expandable platforms for high-end scientific computing. Therefore scalable numerical models are important for effective use of such systems. In this paper, we present an MPI-based numerical core dynamics model for simulation of geodynamo and planetary dynamos, and for simulation of core-mantle interactions. The model is developed based on MPI libraries. Two algorithms are used for node-node communication: a "master-slave" architecture and a "divide-and-conquer" architecture. The former is easy to implement but not scalable in communication. The latter is scalable in both computation and communication. The model scalability is tested on Linux PC clusters with up to 128 nodes. This model is also benchmarked with a published numerical dynamo model solution.

RELAP5-3D developmental assessment: Comparison of version 4.2.1i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul D.

2014-06-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.2i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

RELAP5-3D Developmental Assessment. Comparison of Version 4.3.4i on Linux and Windows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayless, Paul David

2015-10-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.3i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

Livermore Site Spill Prevention, Control, and Countermeasures (SPCC) Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bellah, W.; Griffin, D.; Mertesdorf, E.

This Spill Prevention, Control, and Countermeasure (SPCC) Plan describes the measures that are taken at Lawrence Livermore National Laboratory’s (LLNL) Livermore Site in Livermore, California, to prevent, control, and handle potential spills from aboveground containers that can contain 55 gallons or more of oil. This SPCC Plan complies with the Oil Pollution Prevention regulation in Title 40 of the Code of Federal Regulations (40 CFR), Part 112 (40 CFR 112) and with 40 CFR 761.65(b) and (c), which regulates the temporary storage of polychlorinated biphenyls (PCBs). This Plan has also been prepared in accordance with Division 20, Chapter 6.67 ofmore » the California Health and Safety Code (HSC 6.67) requirements for oil pollution prevention (referred to as the Aboveground Petroleum Storage Act [APSA]), and the United States Department of Energy (DOE) Order No. 436.1. This SPCC Plan establishes procedures, methods, equipment, and other requirements to prevent the discharge of oil into or upon the navigable waters of the United States or adjoining shorelines for aboveground oil storage and use at the Livermore Site.« less

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

A Collection of Articles Reprinted from Science & Technology Review on University Relations Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radousky, H; Rennie, G; Henke, A

2006-08-23

This month's issue has the following articles: (1) The Power of Partnership--Livermore researchers forge strategic collaborations with colleagues from other University of California campuses to further science and better protect the nation; (2) Collaborative Research Prepares Our Next-Generation Scientists and Engineers--Commentary by Laura R. Gilliom; (3) Next-Generation Scientists and Engineers Tap Lab's Resources--University of California Ph.D. candidates work with Livermore scientists and engineers to conduct fundamental research as part of their theses; (4) The Best and the Brightest Come to Livermore--The Lawrence Fellowship Program attracts the most sought-after postdoctoral researchers to the Laboratory; and (5) Faculty on Sabbatical Find amore » Good Home at Livermore--Faculty members from around the world come to the Laboratory as sabbatical scholars.« less

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

PubMed

Fidaner, Işık Barış; Cankorur-Cetinkaya, Ayca; Dikicioglu, Duygu; Kirdar, Betul; Cemgil, Ali Taylan; Oliver, Stephen G

2016-02-01

Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets. We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. This algorithm involves two components of operation. Component 1 constructs a Bayesian non-parametric model (Infinite Mixture of Piecewise Linear Sequences) and Component 2, which applies a novel clustering methodology (Two-Stage Clustering). The software can also assign biological meaning to the identified clusters using an appropriate ontology. It applies multiple hypothesis testing to report the significance of these enrichments. The algorithm has a four-phase pipeline. The application can be executed using either command-line tools or a user-friendly Graphical User Interface. The latter has been developed to address the needs of both specialist and non-specialist users. We use three diverse test cases to demonstrate the flexibility of the proposed strategy. In all cases, CLUSTERnGO not only outperformed existing algorithms in assigning unique GO term enrichments to the identified clusters, but also revealed novel insights regarding the biological systems examined, which were not uncovered in the original publications. The C++ and QT source codes, the GUI applications for Windows, OS X and Linux operating systems and user manual are freely available for download under the GNU GPL v3 license at http://www.cmpe.boun.edu.tr/content/CnG. sgo24@cam.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Performance comparison analysis library communication cluster system using merge sort

NASA Astrophysics Data System (ADS)

Wulandari, D. A. R.; Ramadhan, M. E.

2018-04-01

Begins by using a single processor, to increase the speed of computing time, the use of multi-processor was introduced. The second paradigm is known as parallel computing, example cluster. The cluster must have the communication potocol for processing, one of it is message passing Interface (MPI). MPI have many library, both of them OPENMPI and MPICH2. Performance of the cluster machine depend on suitable between performance characters of library communication and characters of the problem so this study aims to analyze the comparative performances libraries in handling parallel computing process. The case study in this research are MPICH2 and OpenMPI. This case research execute sorting’s problem to know the performance of cluster system. The sorting problem use mergesort method. The research method is by implementing OpenMPI and MPICH2 on a Linux-based cluster by using five computer virtual then analyze the performance of the system by different scenario tests and three parameters for to know the performance of MPICH2 and OpenMPI. These performances are execution time, speedup and efficiency. The results of this study showed that the addition of each data size makes OpenMPI and MPICH2 have an average speed-up and efficiency tend to increase but at a large data size decreases. increased data size doesn’t necessarily increased speed up and efficiency but only execution time example in 100000 data size. OpenMPI has a execution time greater than MPICH2 example in 1000 data size average execution time with MPICH2 is 0,009721 and OpenMPI is 0,003895 OpenMPI can customize communication needs.

Enabling Diverse Software Stacks on Supercomputers using High Performance Virtual Clusters.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Younge, Andrew J.; Pedretti, Kevin; Grant, Ryan

While large-scale simulations have been the hallmark of the High Performance Computing (HPC) community for decades, Large Scale Data Analytics (LSDA) workloads are gaining attention within the scientific community not only as a processing component to large HPC simulations, but also as standalone scientific tools for knowledge discovery. With the path towards Exascale, new HPC runtime systems are also emerging in a way that differs from classical distributed com- puting models. However, system software for such capabilities on the latest extreme-scale DOE supercomputing needs to be enhanced to more appropriately support these types of emerging soft- ware ecosystems. In thismore » paper, we propose the use of Virtual Clusters on advanced supercomputing resources to enable systems to support not only HPC workloads, but also emerging big data stacks. Specifi- cally, we have deployed the KVM hypervisor within Cray's Compute Node Linux on a XC-series supercomputer testbed. We also use libvirt and QEMU to manage and provision VMs directly on compute nodes, leveraging Ethernet-over-Aries network emulation. To our knowledge, this is the first known use of KVM on a true MPP supercomputer. We investigate the overhead our solution using HPC benchmarks, both evaluating single-node performance as well as weak scaling of a 32-node virtual cluster. Overall, we find single node performance of our solution using KVM on a Cray is very efficient with near-native performance. However overhead increases by up to 20% as virtual cluster size increases, due to limitations of the Ethernet-over-Aries bridged network. Furthermore, we deploy Apache Spark with large data analysis workloads in a Virtual Cluster, ef- fectively demonstrating how diverse software ecosystems can be supported by High Performance Virtual Clusters.« less

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

PubMed

Medema, Marnix H; Paalvast, Yared; Nguyen, Don D; Melnik, Alexey; Dorrestein, Pieter C; Takano, Eriko; Breitling, Rainer

2014-09-01

Nonribosomally and ribosomally synthesized bioactive peptides constitute a source of molecules of great biomedical importance, including antibiotics such as penicillin, immunosuppressants such as cyclosporine, and cytostatics such as bleomycin. Recently, an innovative mass-spectrometry-based strategy, peptidogenomics, has been pioneered to effectively mine microbial strains for novel peptidic metabolites. Even though mass-spectrometric peptide detection can be performed quite fast, true high-throughput natural product discovery approaches have still been limited by the inability to rapidly match the identified tandem mass spectra to the gene clusters responsible for the biosynthesis of the corresponding compounds. With Pep2Path, we introduce a software package to fully automate the peptidogenomics approach through the rapid Bayesian probabilistic matching of mass spectra to their corresponding biosynthetic gene clusters. Detailed benchmarking of the method shows that the approach is powerful enough to correctly identify gene clusters even in data sets that consist of hundreds of genomes, which also makes it possible to match compounds from unsequenced organisms to closely related biosynthetic gene clusters in other genomes. Applying Pep2Path to a data set of compounds without known biosynthesis routes, we were able to identify candidate gene clusters for the biosynthesis of five important compounds. Notably, one of these clusters was detected in a genome from a different subphylum of Proteobacteria than that in which the molecule had first been identified. All in all, our approach paves the way towards high-throughput discovery of novel peptidic natural products. Pep2Path is freely available from http://pep2path.sourceforge.net/, implemented in Python, licensed under the GNU General Public License v3 and supported on MS Windows, Linux and Mac OS X.

[Study for lung sound acquisition module based on ARM and Linux].

PubMed

Lu, Qiang; Li, Wenfeng; Zhang, Xixue; Li, Junmin; Liu, Longqing

2011-07-01

A acquisition module with ARM and Linux as a core was developed. This paper presents the hardware configuration and the software design. It is shown that the module can extract human lung sound reliably and effectively.

Environmental Report 1994

DOT National Transportation Integrated Search

1995-09-01

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

Environmental Report 1995

DOT National Transportation Integrated Search

1996-09-03

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

Environmental Report 1993

DOT National Transportation Integrated Search

1994-09-01

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

BioMake: a GNU make-compatible utility for declarative workflow management.

PubMed

Holmes, Ian H; Mungall, Christopher J

2017-11-01

The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog. BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/. ihholmes + biomake@gmail.com or cmungall + biomake@gmail.com. Feature table comparing BioMake to similar tools. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

Environmental Report 1996 Volume 2

DOT National Transportation Integrated Search

1997-09-01

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

Environmental Report 1996 Volume 1

DOT National Transportation Integrated Search

1997-09-01

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

76 FR 72002 - National Register of Historic Places; Notification of Pending Nominations and Related Actions

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-21

.../National Historic Landmarks Program. CALIFORNIA Alameda County Livermore Carnegie Library and Park, (California Carnegie Libraries MPS) 2155 3rd St., Livermore, 11000876 COLORADO Routt County Steamboat...

Environmental Report 1995, Volume 2

DOT National Transportation Integrated Search

1996-09-03

This report, prepared by Lawrence Livermore National Laboratory (LLNL) for the U.S. Department of Energy, Oakland Operations Office (DOE/OAK), provides a comprehensive summary of the environmental program activities at Lawrence Livermore National Lab...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blackwell, Matt; Rodger, Arthur; Kennedy, Tom

When the California Academy of Sciences created the "Earthquake: Evidence of a Restless Planet" exhibit, they called on Lawrence Livermore to help combine seismic research with the latest data-driven visualization techniques. The outcome is a series of striking visualizations of earthquakes, tsunamis and tectonic plate evolution. Seismic-wave research is a core competency at Livermore. While most often associated with earthquakes, the research has many other applications of national interest, such as nuclear explosion monitoring, explosion forensics, energy exploration, and seismic acoustics. For the Academy effort, Livermore researchers simulated the San Andreas and Hayward fault events at high resolutions. Such calculationsmore » require significant computational resources. To simulate the 1906 earthquake, for instance, visualizing 125 seconds of ground motion required over 1 billion grid points, 10,000 time steps, and 7.5 hours of processor time on 2,048 cores of Livermore's Sierra machine.« less

Supercomputing meets seismology in earthquake exhibit

ScienceCinema

Blackwell, Matt; Rodger, Arthur; Kennedy, Tom

2018-02-14

When the California Academy of Sciences created the "Earthquake: Evidence of a Restless Planet" exhibit, they called on Lawrence Livermore to help combine seismic research with the latest data-driven visualization techniques. The outcome is a series of striking visualizations of earthquakes, tsunamis and tectonic plate evolution. Seismic-wave research is a core competency at Livermore. While most often associated with earthquakes, the research has many other applications of national interest, such as nuclear explosion monitoring, explosion forensics, energy exploration, and seismic acoustics. For the Academy effort, Livermore researchers simulated the San Andreas and Hayward fault events at high resolutions. Such calculations require significant computational resources. To simulate the 1906 earthquake, for instance, visualizing 125 seconds of ground motion required over 1 billion grid points, 10,000 time steps, and 7.5 hours of processor time on 2,048 cores of Livermore's Sierra machine.

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

PubMed

Nepusz, Tamás; Sasidharan, Rajkumar; Paccanaro, Alberto

2010-03-09

An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community. SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences) and the complete genome of the yeast Saccharomyces cerevisiae (6,690 sequences). Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with external tools such as BLAST and Cytoscape, and it can produce publication-quality graphical representations of the clusters obtained, thus constituting a comprehensive and effective tool for practical research in computational biology. Source code and precompiled executables for Windows, Linux and Mac OS X are freely available at http://www.paccanarolab.org/software/scps.

Launching large computing applications on a disk-less cluster

NASA Astrophysics Data System (ADS)

Schwemmer, Rainer; Caicedo Carvajal, Juan Manuel; Neufeld, Niko

2011-12-01

The LHCb Event Filter Farm system is based on a cluster of the order of 1.500 disk-less Linux nodes. Each node runs one instance of the filtering application per core. The amount of cores in our current production environment is 8 per machine for the old cluster and 12 per machine on extension of the cluster. Each instance has to load about 1.000 shared libraries, weighting 200 MB from several directory locations from a central repository. The repository is currently hosted on a SAN and exported via NFS. The libraries are all available in the local file system cache on every node. Loading a library still causes a huge number of requests to the server though, because the loader will try to probe every available path. Measurements show there are between 100.000-200.000 calls per application instance start up. Multiplied by the numbers of cores in the farm, this translates into a veritable DDoS attack on the servers, which lasts several minutes. Since the application is being restarted frequently, a better solution had to be found.scp Rolling out the software to the nodes is out of the question, because they have no disks and the software in it's entirety is too large to put into a ram disk. To solve this problem we developed a FUSE based file systems which acts as a permanent, controllable cache that keeps the essential files that are necessary in stock.

Science & Technology Review October 2005

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aufderheide III, M B

This month's issue has the following articles: (1) Important Missions, Great Science, and Innovative Technology--Commentary by Cherry A. Murray; (2) NanoFoil{reg_sign} Solders with Less Heat--Soldering and brazing to join an array of materials are now Soldering and brazing to join an array of materials are now possible without furnaces, torches, or lead; (3) Detecting Radiation on the Move--An award-winning technology can detect even small amounts An award-winning technology can detect even small amounts of radioactive material in transit; (4) Identifying Airborne Pathogens in Time to Respond--A mass spectrometer identifies airborne spores in less than A mass spectrometer identifies airborne sporesmore » in less than a minute with no false positives; (5) Picture Perfect with VisIt--The Livermore-developed software tool VisIt helps scientists The Livermore-developed software tool VisIt helps scientists visualize and analyze large data sets; (6) Revealing the Mysteries of Water--Scientists are using Livermore's Thunder supercomputer and new algorithms to understand the phases of water; and (7) Lightweight Target Generates Bright, Energetic X Rays--Livermore scientists are producing aerogel targets for use in inertial Livermore scientists are producing aerogel targets for use in inertial confinement fusion experiments and radiation-effects testing.« less

Volunteer Computing Experience with ATLAS@Home

NASA Astrophysics Data System (ADS)

Adam-Bourdarios, C.; Bianchi, R.; Cameron, D.; Filipčič, A.; Isacchini, G.; Lançon, E.; Wu, W.; ATLAS Collaboration

2017-10-01

ATLAS@Home is a volunteer computing project which allows the public to contribute to computing for the ATLAS experiment through their home or office computers. The project has grown continuously since its creation in mid-2014 and now counts almost 100,000 volunteers. The combined volunteers’ resources make up a sizeable fraction of overall resources for ATLAS simulation. This paper takes stock of the experience gained so far and describes the next steps in the evolution of the project. These improvements include running natively on Linux to ease the deployment on for example university clusters, using multiple cores inside one task to reduce the memory requirements and running different types of workload such as event generation. In addition to technical details the success of ATLAS@Home as an outreach tool is evaluated.

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

PubMed

Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

2018-05-22

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

Real Time Linux - The RTOS for Astronomy?

NASA Astrophysics Data System (ADS)

Daly, P. N.

The BoF was attended by about 30 participants and a free CD of real time Linux-based upon RedHat 5.2-was available. There was a detailed presentation on the nature of real time Linux and the variants for hard real time: New Mexico Tech's RTL and DIAPM's RTAI. Comparison tables between standard Linux and real time Linux responses to time interval generation and interrupt response latency were presented (see elsewhere in these proceedings). The present recommendations are to use RTL for UP machines running the 2.0.x kernels and RTAI for SMP machines running the 2.2.x kernel. Support, both academically and commercially, is available. Some known limitations were presented and the solutions reported e.g., debugging and hardware support. The features of RTAI (scheduler, fifos, shared memory, semaphores, message queues and RPCs) were described. Typical performance statistics were presented: Pentium-based oneshot tasks running > 30kHz, 486-based oneshot tasks running at ~ 10 kHz, periodic timer tasks running in excess of 90 kHz with average zero jitter peaking to ~ 13 mus (UP) and ~ 30 mus (SMP). Some detail on kernel module programming, including coding examples, were presented showing a typical data acquisition system generating simulated (random) data writing to a shared memory buffer and a fifo buffer to communicate between real time Linux and user space. All coding examples were complete and tested under RTAI v0.6 and the 2.2.12 kernel. Finally, arguments were raised in support of real time Linux: it's open source, free under GPL, enables rapid prototyping, has good support and the ability to have a fully functioning workstation capable of co-existing hard real time performance. The counter weight-the negatives-of lack of platforms (x86 and PowerPC only at present), lack of board support, promiscuous root access and the danger of ignorance of real time programming issues were also discussed. See ftp://orion.tuc.noao.edu/pub/pnd/rtlbof.tgz for the StarOffice overheads for this presentation.

10-NIF Dedication: Ellen Tauscher

DOE Office of Scientific and Technical Information (OSTI.GOV)

Congresswoman Ellen Tauscher

2009-07-02

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Congresswoman Ellen Tauscher, of California's 10th district, which includes Livermore.

10-NIF Dedication: Ellen Tauscher

ScienceCinema

Congresswoman Ellen Tauscher

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Congresswoman Ellen Tauscher, of California's 10th district, which includes Livermore.

Science& Technology Review September 2003

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, D

2003-09-01

This September 2003 issue of ''Science and Technology Review'' covers the following articles: (1) ''The National Ignition Facility Is Born''; (2) ''The National Ignition Facility Comes to Life'' Over the last 15 years, thousands of Livermore engineers, scientists, and technicians as well as hundreds of industrial partners have worked to bring the National Ignition Facility into being. (3) ''Tracking the Activity of Bacteria Underground'' Using real-time polymerase chain reaction and liquid chromatography/tandem mass spectrometry, researchers at Livermore are gaining knowledge on how bacteria work underground to break down compounds of environmental concern. (4) ''When Every Second Counts--Pathogen Identification in Lessmore » Than a Minute'' Livermore has developed a system that can quickly identify airborne pathogens such as anthrax. (5) ''Portable Radiation Detector Provides Laboratory-Scale Precision in the Field'' A team of Livermore physicists and engineers has developed a handheld, mechanically cooled germanium detector designed to identify radioisotopes.« less

Space Communications Emulation Facility

NASA Technical Reports Server (NTRS)

Hill, Chante A.

2004-01-01

Establishing space communication between ground facilities and other satellites is a painstaking task that requires many precise calculations dealing with relay time, atmospheric conditions, and satellite positions, to name a few. The Space Communications Emulation Facility (SCEF) team here at NASA is developing a facility that will approximately emulate the conditions in space that impact space communication. The emulation facility is comprised of a 32 node distributed cluster of computers; each node representing a satellite or ground station. The objective of the satellites is to observe the topography of the Earth (water, vegetation, land, and ice) and relay this information back to the ground stations. Software originally designed by the University of Kansas, labeled the Emulation Manager, controls the interaction of the satellites and ground stations, as well as handling the recording of data. The Emulation Manager is installed on a Linux Operating System, employing both Java and C++ programming codes. The emulation scenarios are written in extensible Markup Language, XML. XML documents are designed to store, carry, and exchange data. With XML documents data can be exchanged between incompatible systems, which makes it ideal for this project because Linux, MAC and Windows Operating Systems are all used. Unfortunately, XML documents cannot display data like HTML documents. Therefore, the SCEF team uses XML Schema Definition (XSD) or just schema to describe the structure of an XML document. Schemas are very important because they have the capability to validate the correctness of data, define restrictions on data, define data formats, and convert data between different data types, among other things. At this time, in order for the Emulation Manager to open and run an XML emulation scenario file, the user must first establish a link between the schema file and the directory under which the XML scenario files are saved. This procedure takes place on the command line on the Linux Operating System. Once this link has been established the Emulation manager validates all the XML files in that directory against the schema file, before the actual scenario is run. Using some very sophisticated commercial software called the Satellite Tool Kit (STK) installed on the Linux box, the Emulation Manager is able to display the data and graphics generated by the execution of a XML emulation scenario file. The Emulation Manager software is written in JAVA programming code. Since the SCEF project is in the developmental stage, the source code for this type of software is being modified to better fit the requirements of the SCEF project. Some parameters for the emulation are hard coded, set at fixed values. Members of the SCEF team are altering the code to allow the user to choose the values of these hard coded parameters by inserting a toolbar onto the preexisting GUI.

Supplement analysis for continued operation of Lawrence Livermore National Laboratory and Sandia National Laboratories, Livermore. Volume 2: Comment response document

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1999-03-01

The US Department of Energy (DOE), prepared a draft Supplement Analysis (SA) for Continued Operation of Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories, Livermore (SNL-L), in accordance with DOE`s requirements for implementation of the National Environmental Policy Act of 1969 (NEPA) (10 Code of Federal Regulations [CFR] Part 1021.314). It considers whether the Final Environmental Impact Statement and Environmental Impact Report for Continued Operation of Lawrence Livermore National Laboratory and Sandia National Laboratories, Livermore (1992 EIS/EIR) should be supplement3ed, whether a new environmental impact statement (EIS) should be prepared, or no further NEPA documentation is required. The SAmore » examines the current project and program plans and proposals for LLNL and SNL-L, operations to identify new or modified projects or operations or new information for the period from 1998 to 2002 that was not considered in the 1992 EIS/EIR. When such changes, modifications, and information are identified, they are examined to determine whether they could be considered substantial or significant in reference to the 1992 proposed action and the 1993 Record of Decision (ROD). DOE released the draft SA to the public to obtain stakeholder comments and to consider those comments in the preparation of the final SA. DOE distributed copies of the draft SA to those who were known to have an interest in LLNL or SNL-L activities in addition to those who requested a copy. In response to comments received, DOE prepared this Comment Response Document.« less

Modeling of Near-Field Blast Performance

DTIC Science & Technology

2013-11-01

The freeze-out temperature is chosen by comparison of calorimetry experiments (2, 3) and thermoequilibrium calculations using CHEETAH (4). The near...P.; Vitello, P. CHEETAH Users Manual; Lawrence Livermore National Laboratory: Livermore, CA, 2012. 5. Walter, P. Introduction to Air Blast

07-NIF Dedication: Jerry McNerney

DOE Office of Scientific and Technical Information (OSTI.GOV)

Congressman Jerry McNerney

2009-07-02

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Congressman Jerry McNerney, of California's 11th district, which adjoins Livermore.

07-NIF Dedication: Jerry McNerney

ScienceCinema

Congressman Jerry McNerney

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Congressman Jerry McNerney, of California's 11th district, which adjoins Livermore.

Linux Incident Response Volatile Data Analysis Framework

ERIC Educational Resources Information Center

McFadden, Matthew

2013-01-01

Cyber incident response is an emphasized subject area in cybersecurity in information technology with increased need for the protection of data. Due to ongoing threats, cybersecurity imposes many challenges and requires new investigative response techniques. In this study a Linux Incident Response Framework is designed for collecting volatile data…

Onboard Flow Sensing For Downwash Detection and Avoidance On Small Quadrotor Helicopters

DTIC Science & Technology

2015-01-01

onboard computers, one for flight stabilization and a Linux computer for sensor integration and control calculations . The Linux computer runs Robot...Hirokawa, D. Kubo , S. Suzuki, J. Meguro, and T. Suzuki. Small uav for immediate hazard map generation. In AIAA Infotech@Aerospace Conf, May 2007. 8F

Cross platform development using Delphi and Kylix

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, J.L.; Nishimura, H.; Timossi, C.

2002-10-08

A cross platform component for EPICS Simple Channel Access (SCA) has been developed for the use with Delphi on Windows and Kylix on Linux. An EPICS controls GUI application developed on Windows runs on Linux by simply rebuilding it, and vice versa. This paper describes the technical details of the component.

Design of the SLAC RCE Platform: A General Purpose ATCA Based Data Acquisition System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herbst, R.; Claus, R.; Freytag, M.

2015-01-23

The SLAC RCE platform is a general purpose clustered data acquisition system implemented on a custom ATCA compliant blade, called the Cluster On Board (COB). The core of the system is the Reconfigurable Cluster Element (RCE), which is a system-on-chip design based upon the Xilinx Zynq family of FPGAs, mounted on custom COB daughter-boards. The Zynq architecture couples a dual core ARM Cortex A9 based processor with a high performance 28nm FPGA. The RCE has 12 external general purpose bi-directional high speed links, each supporting serial rates of up to 12Gbps. 8 RCE nodes are included on a COB, eachmore » with a 10Gbps connection to an on-board 24-port Ethernet switch integrated circuit. The COB is designed to be used with a standard full-mesh ATCA backplane allowing multiple RCE nodes to be tightly interconnected with minimal interconnect latency. Multiple shelves can be clustered using the front panel 10-gbps connections. The COB also supports local and inter-blade timing and trigger distribution. An experiment specific Rear Transition Module adapts the 96 high speed serial links to specific experiments and allows an experiment-specific timing and busy feedback connection. This coupling of processors with a high performance FPGA fabric in a low latency, multiple node cluster allows high speed data processing that can be easily adapted to any physics experiment. RTEMS and Linux are both ported to the module. The RCE has been used or is the baseline for several current and proposed experiments (LCLS, HPS, LSST, ATLAS-CSC, LBNE, DarkSide, ILC-SiD, etc).« less

Fast structure similarity searches among protein models: efficient clustering of protein fragments

PubMed Central

2012-01-01

Background For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD) comparison is performed. Most of the time is typically spent on comparison of non-similar structures. For sets with more than, say, 10,000 models this procedure is very time-consuming and alternative faster algorithms, restricting comparisons only to most similar structures would be useful. Results We exploit the inverse triangle inequality on the RMSD between two structures given the RMSDs with a third structure. The lower bound on RMSD may be used, when restricting the search of similarity to a reasonably low RMSD threshold value, to speed up similarity searches significantly. Tests are performed on large sets of decoys which are widely used as test cases for predictive methods, with a speed-up of up to 100 times with respect to all-vs-all comparison depending on the set and parameters used. Sample applications are shown. Conclusions The algorithm presented here allows fast comparison of large data sets of structures with limited memory requirements. As an example of application we present clustering of more than 100000 fragments of length 5 from the top500H dataset into few hundred representative fragments. A more realistic scenario is provided by the search of similarity within the very large decoy sets used for the tests. Other applications regard filtering nearly-indentical conformation in selected CASP9 datasets and clustering molecular dynamics snapshots. Availability A linux executable and a Perl script with examples are given in the supplementary material (Additional file 1). The source code is available upon request from the authors. PMID:22642815

Precision and manufacturing at the Lawrence Livermore National Laboratory

NASA Technical Reports Server (NTRS)

Saito, Theodore T.; Wasley, Richard J.; Stowers, Irving F.; Donaldson, Robert R.; Thompson, Daniel C.

1994-01-01

Precision Engineering is one of the Lawrence Livermore National Laboratory's core strengths. This paper discusses the past and present current technology transfer efforts of LLNL's Precision Engineering program and the Livermore Center for Advanced Manufacturing and Productivity (LCAMP). More than a year ago the Precision Machine Commercialization project embodied several successful methods of transferring high technology from the National Laboratories to industry. Currently, LCAMP has already demonstrated successful technology transfer and is involved in a broad spectrum of current programs. In addition, this paper discusses other technologies ripe for future transition including the Large Optics Diamond Turning Machine.

Precision and manufacturing at the Lawrence Livermore National Laboratory

NASA Astrophysics Data System (ADS)

Saito, Theodore T.; Wasley, Richard J.; Stowers, Irving F.; Donaldson, Robert R.; Thompson, Daniel C.

1994-02-01

Precision Engineering is one of the Lawrence Livermore National Laboratory's core strengths. This paper discusses the past and present current technology transfer efforts of LLNL's Precision Engineering program and the Livermore Center for Advanced Manufacturing and Productivity (LCAMP). More than a year ago the Precision Machine Commercialization project embodied several successful methods of transferring high technology from the National Laboratories to industry. Currently, LCAMP has already demonstrated successful technology transfer and is involved in a broad spectrum of current programs. In addition, this paper discusses other technologies ripe for future transition including the Large Optics Diamond Turning Machine.

Oak Ridge Institutional Cluster Autotune Test Drive Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jibonananda, Sanyal; New, Joshua Ryan

2014-02-01

The Oak Ridge Institutional Cluster (OIC) provides general purpose computational resources for the ORNL staff to run computation heavy jobs that are larger than desktop applications but do not quite require the scale and power of the Oak Ridge Leadership Computing Facility (OLCF). This report details the efforts made and conclusions derived in performing a short test drive of the cluster resources on Phase 5 of the OIC. EnergyPlus was used in the analysis as a candidate user program and the overall software environment was evaluated against anticipated challenges experienced with resources such as the shared memory-Nautilus (JICS) and Titanmore » (OLCF). The OIC performed within reason and was found to be acceptable in the context of running EnergyPlus simulations. The number of cores per node and the availability of scratch space per node allow non-traditional desktop focused applications to leverage parallel ensemble execution. Although only individual runs of EnergyPlus were executed, the software environment on the OIC appeared suitable to run ensemble simulations with some modifications to the Autotune workflow. From a standpoint of general usability, the system supports common Linux libraries, compilers, standard job scheduling software (Torque/Moab), and the OpenMPI library (the only MPI library) for MPI communications. The file system is a Panasas file system which literature indicates to be an efficient file system.« less

Implementation of image transmission server system using embedded Linux

NASA Astrophysics Data System (ADS)

Park, Jong-Hyun; Jung, Yeon Sung; Nam, Boo Hee

2005-12-01

In this paper, we performed the implementation of image transmission server system using embedded system that is for the specified object and easy to install and move. Since the embedded system has lower capability than the PC, we have to reduce the quantity of calculation of the baseline JPEG image compression and transmission. We used the Redhat Linux 9.0 OS at the host PC and the target board based on embedded Linux. The image sequences are obtained from the camera attached to the FPGA (Field Programmable Gate Array) board with ALTERA cooperation chip. For effectiveness and avoiding some constraints from the vendor's own, we made the device driver using kernel module.

Composite Flywheel Development for Energy Storage

DTIC Science & Technology

2005-01-01

Fiber-Composite Flywheel Program: Quarterly Progress Report; UCRL -50033-76-4; Lawrence Livermore National Laboratory: Livermore, CA, 1976. 2...BEACH DAHLGREN VA 22448 1 WATERWAYS EXPERIMENT D SCOTT 3909 HALLS FERRY RD SC C VICKSBURG MS 39180 1 DARPA B WILCOX 3701 N FAIRFAX DR

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

PubMed

Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

2012-01-01

Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene ontology (GO) annotation, promoter identification, gene expression (co-expression), and evolutionary analysis. This database not only provides a way to define lineage-specific and species-specific gene clusters but also facilitates future studies on gene co-regulation, epigenetic control of gene expression (DNA methylation and histone marks), and chromosomal structures in a context of gene clusters and species evolution. LCGbase is freely available at http://lcgbase.big.ac.cn/LCGbase.

Tiger Team Assessment of the Sandia National Laboratories, Livermore, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1990-08-01

This report provides the results of the Tiger Team Assessment of the Sandia National Laboratories (SNL) in Livermore, California, conducted from April 30 to May 18, 1990. The purpose of the assessment was to provide the Secretary of Energy with the status of environment, safety and health (ES H) activities at SNL, Livermore. The assessment was conducted by a team consisting of three subteams of federal and private sector technical specialists in the disciplines of environment, safety and health, and management. On-site activities for the assessment included document reviews, observation of site operations, and discussions and interviews with DOE personnel,more » site contractor personnel, and regulators. Using these sources of information and data, the Tiger Team identified a significant number of findings and concerns having to do with the environment, safety and health, and management, as well as concerns regarding noncompliance with Occupational Safety and Health Administration (OSHA) standards. Although the Tiger Team concluded that none of the findings or concerns necessitated immediate cessation of any operations at SNL, Livermore, it does believe that a sizable number of them require prompt management attention. A special area of concern identified for the near-term health and safety of on-site personnel pertained to the on-site Trudell Auto Repair Shop site. Several significant OSHA concerns and environmental findings relating to this site prompted the Tiger Team Leader to immediately advise SNL, Livermore and AL management of the situation. A case study was prepared by the Team, because the root causes of the problems associated with this site were believed to reflect the overall root causes for the areas of ES H noncompliance at SNL, Livermore. 4 figs., 3 tabs.« less

Linux Adventures on a Laptop. Computers in Small Libraries

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

Drowning in PC Management: Could a Linux Solution Save Us?

ERIC Educational Resources Information Center

Peters, Kathleen A.

2004-01-01

Short on funding and IT staff, a Western Canada library struggled to provide adequate public computing resources. Staff turned to a Linux-based solution that supports up to 10 users from a single computer, and blends Web browsing and productivity applications with session management, Internet filtering, and user authentication. In this article,…

78 FR 57648 - Notice of Issuance of Final Determination Concerning Video Teleconferencing Server

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... the Chinese- origin Video Board and the Filter Board, impart the essential character to the video... includes the codec; a network filter electronic circuit board (``Filter Board''); a housing case; a power... (``Linux software''). The Linux software allows the Filter Board to inspect each Ethernet packet of...

Impact of the Shodan Computer Search Engine on Internet-facing Industrial Control System Devices

DTIC Science & Technology

2014-03-27

bridge implementation. The transparent bridge is designed using a Raspberry Pi configured with Linux IPtables and bridge-utils to bridge the on board...Ethernet card and a second USB Ethernet adapter. A Raspberry Pi is a credit-card-sized single-board computer running a version of Debian Linux. There

Chicks in Charge: Andrea Baker & Amy Daniels--Airport High School Media Center, Columbia, SC

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

This article briefly discusses two librarians exploration of Linux. Andrea Baker and Amy Daniels were tired of telling their students that new technology items were not in the budget. They explored Linux, which is a program that recycles older computers, installs free operating systems and free software.

Diversifying the Department of Defense Network Enterprise with Linux

DTIC Science & Technology

2010-03-01

Cyberspace, Cyberwar, Legacy, Inventory, Acquisition, Competitive Advantage, Coalition Communications, Ubiquitous, Strategic, Centricity, Kaizen , ISO... Kaizen , ISO, Outsource CLASSIFICATION: Unclassified Historically, the United States and its closest allies have grown increasingly reliant...control through the use of continuous improvement processes ( Kaizen )34. In choosing the Linux client operating system, the move encourages open standards

Development of a portable Linux-based ECG measurement and monitoring system.

PubMed

Tan, Tan-Hsu; Chang, Ching-Su; Huang, Yung-Fa; Chen, Yung-Fu; Lee, Cheng

2011-08-01

This work presents a portable Linux-based electrocardiogram (ECG) signals measurement and monitoring system. The proposed system consists of an ECG front end and an embedded Linux platform (ELP). The ECG front end digitizes 12-lead ECG signals acquired from electrodes and then delivers them to the ELP via a universal serial bus (USB) interface for storage, signal processing, and graphic display. The proposed system can be installed anywhere (e.g., offices, homes, healthcare centers and ambulances) to allow people to self-monitor their health conditions at any time. The proposed system also enables remote diagnosis via Internet. Additionally, the system has a 7-in. interactive TFT-LCD touch screen that enables users to execute various functions, such as scaling a single-lead or multiple-lead ECG waveforms. The effectiveness of the proposed system was verified by using a commercial 12-lead ECG signal simulator and in vivo experiments. In addition to its portability, the proposed system is license-free as Linux, an open-source code, is utilized during software development. The cost-effectiveness of the system significantly enhances its practical application for personal healthcare.

Managing a Real-Time Embedded Linux Platform with Buildroot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

Numerical Simulations of 3D Seismic Data Final Report CRADA No. TC02095.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedmann, S. J.; Kostov, C.

This was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of Califomia)/Lawrence-Livermore National Laboratory (LLNL) and Schlumberger Cambridge Research (SCR), to develop synthetic seismic data sets and supporting codes.

Recent Livermore Excitation and Dielectronic Recombination Measurements for Laboratory and Astrophysical Spectral Modeling

NASA Technical Reports Server (NTRS)

Beiersdorfer, P.; Brown, G. V.; Gu, M.-F.; Harris, C. L.; Kahn, S. M.; Kim, S.-H.; Neill, P. A.; Savin, D. W.; Smith, A. J.; Utter, S. B.

2000-01-01

Using the EBIT facility in Livermore we produce definitive atomic data for input into spectral synthesis codes. Recent measurements of line excitation and dielectronic recombination of highly charged K-shell and L-shell ions are presented to illustrate this point.

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

Level 1 Processing of MODIS Direct Broadcast Data at the GSFC DAAC

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Kempler, Steven J. (Technical Monitor)

2001-01-01

The GSFC DAAC is working to test and package the MODIS Level 1 Processing software for Aqua Direct Broadcast data. This entails the same code base, but different lookup tables for Aqua and Terra. However, the most significant change is the use of ancillary attitude and ephemeris files instead of orbit/attitude information within the science data stream (as with Terra). In addition, we are working on Linux: ports of the algorithms, which could eventually enable processing on PC clusters. Finally, the GSFC DAAC is also working with the GSFC Direct Readout laboratory to ingest Level 0 data from the GSFC DB antenna into the main DAAC, enabling level 1 production in near real time in support of applications users, such as the Synergy project. The mechanism developed for this could conceivably be extended to other participating stations.

On the predictability of protein database search complexity and its relevance to optimization of distributed searches.

PubMed

Deciu, Cosmin; Sun, Jun; Wall, Mark A

2007-09-01

We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.

Realization of Vilnius UPXYZVS photometric system for AltaU42 CCD camera at the MAO NAS of Ukraine

NASA Astrophysics Data System (ADS)

Vid'Machenko, A. P.; Andruk, V. M.; Samoylov, V. S.; Delets, O. S.; Nevodovsky, P. V.; Ivashchenko, Yu. M.; Kovalchuk, G. U.

2005-06-01

The description of two-inch glass filters of the Vilnius UPXYZVS photometric system, which are made at the Main Astronomical Observatory of NAS of Ukraine for AltaU42 CCD camera with format of 2048×2048 pixels, is presented in the paper. Reaction curves of instrumental system are shown. Estimations of minimal star's magnitudes for each filter's band in comparison with the visual V one are obtained. New software for automation of CCD frames processing is developed in program shell of LINUX/MIDAS/ROMAFOT. It is planned to carry out observations with the purpose to create the catalogue of primary UPXYZVS CCD standards in selected field of the sky for some radio-sources, globular and open clusters, etc. Numerical estimations of astrometric and photometric accuracy are obtained.

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Ronald C.

Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBasemore » project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.« less

Science & Technology Review November 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radousky, H

This months issue has the following articles: (1) Expanded Supercomputing Maximizes Scientific Discovery--Commentary by Dona Crawford; (2) Thunder's Power Delivers Breakthrough Science--Livermore's Thunder supercomputer allows researchers to model systems at scales never before possible. (3) Extracting Key Content from Images--A new system called the Image Content Engine is helping analysts find significant but hard-to-recognize details in overhead images. (4) Got Oxygen?--Oxygen, especially oxygen metabolism, was key to evolution, and a Livermore project helps find out why. (5) A Shocking New Form of Laserlike Light--According to research at Livermore, smashing a crystal with a shock wave can result in coherent light.

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

PubMed

González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

2016-12-15

MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Implementation of Grid Tier 2 and Tier 3 facilities on a Distributed OpenStack Cloud

NASA Astrophysics Data System (ADS)

Limosani, Antonio; Boland, Lucien; Coddington, Paul; Crosby, Sean; Huang, Joanna; Sevior, Martin; Wilson, Ross; Zhang, Shunde

2014-06-01

The Australian Government is making a AUD 100 million investment in Compute and Storage for the academic community. The Compute facilities are provided in the form of 30,000 CPU cores located at 8 nodes around Australia in a distributed virtualized Infrastructure as a Service facility based on OpenStack. The storage will eventually consist of over 100 petabytes located at 6 nodes. All will be linked via a 100 Gb/s network. This proceeding describes the development of a fully connected WLCG Tier-2 grid site as well as a general purpose Tier-3 computing cluster based on this architecture. The facility employs an extension to Torque to enable dynamic allocations of virtual machine instances. A base Scientific Linux virtual machine (VM) image is deployed in the OpenStack cloud and automatically configured as required using Puppet. Custom scripts are used to launch multiple VMs, integrate them into the dynamic Torque cluster and to mount remote file systems. We report on our experience in developing this nation-wide ATLAS and Belle II Tier 2 and Tier 3 computing infrastructure using the national Research Cloud and storage facilities.

Shape component analysis: structure-preserving dimension reduction on biological shape spaces.

PubMed

Lee, Hao-Chih; Liao, Tao; Zhang, Yongjie Jessica; Yang, Ge

2016-03-01

Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques. We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins. Source code and data for reproducing results of this article are freely available at https://github.com/ccdlcmu/shape_component_analysis_Matlab The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS. geyang@andrew.cmu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Malware Memory Analysis of the Jynx2 Linux Rootkit (Part 1): Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2014-10-01

indication that not a single scanner was able to detect the rootkit as malicious or infected. SHA256 ...clear indication that not a single scanner was able detect it as malicious, infected or associated to the Jynx2 rootkit. SHA256

Teaching Hands-On Linux Host Computer Security

ERIC Educational Resources Information Center

Shumba, Rose

2006-01-01

In the summer of 2003, a project to augment and improve the teaching of information assurance courses was started at IUP. Thus far, ten hands-on exercises have been developed. The exercises described in this article, and presented in the appendix, are based on actions required to secure a Linux host. Publicly available resources were used to…

A PC parallel port button box provides millisecond response time accuracy under Linux.

PubMed

Stewart, Neil

2006-02-01

For psychologists, it is sometimes necessary to measure people's reaction times to the nearest millisecond. This article describes how to use the PC parallel port to receive signals from a button box to achieve millisecond response time accuracy. The workings of the parallel port, the corresponding port addresses, and a simple Linux program for controlling the port are described. A test of the speed and reliability of button box signal detection is reported. If the reader is moderately familiar with Linux, this article should provide sufficient instruction for him or her to build and test his or her own parallel port button box. This article also describes how the parallel port could be used to control an external apparatus.

Will Your Next Supercomputer Come from Costco?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farber, Rob

2007-04-15

A fun topic for April, one that is not an April fool’s joke, is that you can purchase a commodity 200+ Gflop (single-precision) Linux supercomputer for around $600 from your favorite electronic vendor. Yes, it’s true. Just walk in and ask for a Sony Playstation 3 (PS3), take it home and install Linux on it. IBM has provided an excellent tutorial for installing Linux and building applications at http://www-128.ibm.com/developerworks/power/library/pa-linuxps3-1. If you want to raise some eyebrows at work, then submit a purchase request for a Sony PS3 game console and watch the reactions as your paperwork wends its way throughmore » the procurement process.« less

Final Report on Contract N00014-92-C-0173 (Office of Naval Research)

DTIC Science & Technology

2001-01-10

PHILPOTTI* t Lawrence Livermore National Laboratory, University of California, Livermore, CA 94550, USA SIBM Research Division, Almaden Research Center...defines the ITP on one electrode and adsorbed hydrated lithium ion defines the OlIP on the second electrode. Ions have been classified according to

High-Resolution Regional Phase Attenuation Models of the Iranian Plateau and Zagros (Postprint)

DTIC Science & Technology

2012-05-12

15 September 2011, Tucson, AZ, Volume I, pp 153-160. Government Purpose Rights. Johann Wolfgang Goethe -Universität 1, and Lawrence Livermore...University of Missouri1, Johann Wolfgang Goethe -Universität 2, and Lawrence Livermore National Laboratory3 Sponsored by the Air Force

360 Video Tour of 3D Printing Labs at LLNL

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

Additive manufacturing is changing the way the world thinks about manufacturing and design. And here at Lawrence Livermore National Laboratory, it’s changing the way our scientists approach research and development. Today we’ll look around three of the additive manufacturing research labs on the Lawrence Livermore campus.

Analysis of Proton Transport Experiments.

DTIC Science & Technology

1980-09-05

which can inhibit transport, may grow . The abrupt loss of transport at higher currents in the small channel suggests this possibility. Future experiments... Unicorn Park Drive Woburn, MA 01801 Attn: H. Linnerud 1 copy Lawrence Livermore Laboratory P. 0. Box 808 Livermore, CA 94550 Attn: R. J. Briggs 1 copy R

Sandia National Laboratories: Livermore Valley Open Campus (LVOC)

Science.gov Websites

Visiting the LVOC Locations Livermore Valley Open Campus (LVOC) Open engagement Expanding opportunities for open engagement of the broader scientific community. Building on success Sandia's Combustion Research Facility pioneered open collaboration over 30 years ago. Access to DOE-funded capabilities Expanding access

A package of Linux scripts for the parallelization of Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Badal, Andreu; Sempau, Josep

2006-09-01

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1Title of program:clonEasy Catalogue identifier:ADYD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYD_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a Unix style shell (bash), support for the Secure Shell protocol and a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1) Compilers:GNU FORTRAN g77 (Linux); g95 (Linux); Intel Fortran Compiler 7.1 (Linux) Programming language used:Linux shell (bash) script, FORTRAN 77 No. of bits in a word:32 No. of lines in distributed program, including test data, etc.:1916 No. of bytes in distributed program, including test data, etc.:18 202 Distribution format:tar.gz Nature of the physical problem:There are many situations where a Monte Carlo simulation involves a huge amount of CPU time. The parallelization of such calculations is a simple way of obtaining a relatively low statistical uncertainty using a reasonable amount of time. Method of solution:The presented collection of Linux scripts and auxiliary FORTRAN programs implement Secure Shell-based communication between a "master" computer and a set of "clones". The aim of this communication is to execute a code that performs a Monte Carlo simulation on all the clones simultaneously. The code is unique, but each clone is fed with a different set of random seeds. Hence, clonEasy effectively permits the parallelization of the calculation. Restrictions on the complexity of the program:clonEasy can only be used with programs that produce statistically independent results using the same code, but with a different sequence of random numbers. Users must choose the initialization values for the random number generator on each computer and combine the output from the different executions. A FORTRAN program to combine the final results is also provided. Typical running time:The execution time of each script largely depends on the number of computers that are used, the actions that are to be performed and, to a lesser extent, on the network connexion bandwidth. Unusual features of the program:Any computer on the Internet with a Secure Shell client/server program installed can be used as a node of a virtual computer cluster for parallel calculations with the sequential source code. The simplicity of the parallelization scheme makes the use of this package a straightforward task, which does not require installing any additional libraries. Program summary 2Title of program:seedsMLCG Catalogue identifier:ADYE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYE_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1), MS Windows (2000, XP) Compilers:GNU FORTRAN g77 (Linux and Windows); g95 (Linux); Intel Fortran Compiler 7.1 (Linux); Compaq Visual Fortran 6.1 (Windows) Programming language used:FORTRAN 77 No. of bits in a word:32 Memory required to execute with typical data:500 kilobytes No. of lines in distributed program, including test data, etc.:492 No. of bytes in distributed program, including test data, etc.:5582 Distribution format:tar.gz Nature of the physical problem:Statistically independent results from different runs of a Monte Carlo code can be obtained using uncorrelated sequences of random numbers on each execution. Multiplicative linear congruential generators (MLCG), or other generators that are based on them such as RANECU, can be adapted to produce these sequences. Method of solution:For a given MLCG, the presented program calculates initialization values that produce disjoint, consecutive sequences of pseudo-random numbers. The calculated values initiate the generator in distant positions of the random number cycle and can be used, for instance, on a parallel simulation. The values are found using the formula S=(aS)MODm, which gives the random value that will be generated after J iterations of the MLCG. Restrictions on the complexity of the program:The 32-bit length restriction for the integer variables in standard FORTRAN 77 limits the produced seeds to be separated a distance smaller than 2 31, when the distance J is expressed as an integer value. The program allows the user to input the distance as a power of 10 for the purpose of efficiently splitting the sequence of generators with a very long period. Typical running time:The execution time depends on the parameters of the used MLCG and the distance between the generated seeds. The generation of 10 6 seeds separated 10 12 units in the sequential cycle, for one of the MLCGs found in the RANECU generator, takes 3 s on a 2.4 GHz Intel Pentium 4 using the g77 compiler.

Science and Technology Review December 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radousky, H B

2006-10-30

This month's issue has the following articles: (1) Livermore's Biosecurity Research Directly Benefits Public Health--Commentary by Raymond J. Juzaitis; (2) Diagnosing Flu Fast--Livermore's FluIDx device can diagnose flu and four other respiratory viruses in just two hours; (3) An Action Plan to Reopen a Contaminated Airport--New planning tools and faster sample analysis methods will hasten restoration of a major airport to full use following a bioterrorist attack; (4) Early Detection of Bone Disease--A Livermore technique detects small changes in skeletal calcium balance that may signal bone disease; and (5) Taking a Gander with Gamma Rays--Gamma rays may be the nextmore » source for looking deep inside the atom.« less

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Linux OS Jitter Measurements at Large Node Counts using a BlueGene/L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Terry R; Tauferner, Mr. Andrew; Inglett, Mr. Todd

2010-01-01

We present experimental results for a coordinated scheduling implementation of the Linux operating system. Results were collected on an IBM Blue Gene/L machine at scales up to 16K nodes. Our results indicate coordinated scheduling was able to provide a dramatic improvement in scaling performance for two applications characterized as bulk synchronous parallel programs.

Computer-Aided Design of Drugs on Emerging Hybrid High Performance Computers

DTIC Science & Technology

2013-09-01

solutions to virtualization include lightweight, user-level implementations on Linux operating systems , but these solutions are often dependent on a...virtualization include lightweight, user-level implementations on Linux operating systems , but these solutions are often dependent on a specific version of...Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA, 22202-4302

Interactivity vs. fairness in networked linux systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wenji; Crawford, Matt; /Fermilab

In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Thoughmore » each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.« less

High explosive corner turning performance and the LANL Mushroom test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, L.G.; Seitz, W.L.; Forest, C.A.

1997-09-01

The Mushroom test is designed to characterize the corner turning performance of a new generation of less insensitive booster explosives. The test is described in detail, and three corner turning figures-of-merit are examined using pure TATB (both Livermore`s Ultrafine and a Los Alamos research blend) and PBX9504 as examples.

HCCI Combustion Engines Final Report CRADA No. TC02032.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aceves, S.; Lyford-Pike, E.

This was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of California)/Lawrence Livermore National Laboratory (LLNL) and Cummins Engine Company (Cwnmins), to advance the state of the art on HomogeneousCharge Compression-Ignition (HCCI) engines, resulting in a clean, high-efficiency alternative to diesel engines.

2015 Cross-Domain Deterrence Seminar Summary Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juarez, A.

2016-01-11

Lawrence Livermore National Laboratory (LLNL) hosted the 2nd Annual Cross-Domain Deterrence Seminar on November 17th, 2015 in Livermore, CA. The seminar was sponsored by LLNL’s Center for Global Security Research (CGSR), National Security Office (NSO), and Global Security program. This summary covers the seminar’s panels and subsequent discussions.

Bringing Theory into Practice: A Study of Effective Leadership at Lawrence Livermore National Laboratory

ERIC Educational Resources Information Center

Khoury, Anne

2006-01-01

Leadership development, a component of HRD, is becoming an area of increasingly important practice for all organizations. When companies such as Lawrence Livermore National Laboratory rely on knowledge workers for success, leadership becomes even more important. This research paper tests the hypothesis that leadership credibility and the courage…

Rapid Assessment of Individual Soldier Operational Readiness Final Report CRADA No. TC02104.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turteltaub, K.; Mapes, J.

This was a collaborative effort between Lawrence Livermore National Security (LLNS) (formerly The Regents of the University of California), Lawrence Livermore National Laboratory (LLNL) and Rules Based Medicine, Inc. {RBM), to identify markers in blood that would be candidates for determining the combat readiness of troops.

High Peak Power Ka-Band Gyrotron Oscillator Experiments with Slotted and Unslotted Cavities.

DTIC Science & Technology

1987-11-10

cylindrical graphite cathode by explosive plasma formation. (In order to optimize the compression ratio for these experiments, a graphite cathode was employed...48106 Attn: S.B. Segall I copy Lawrence Livermore National Laboratory P.O. Box 808 Livermore, California 94550 Attn: Dr. D. Prosnitz 1 copy Dr. T.J

Megavolt, Multi-Kiloamp Ka-Band Gyrotron Oscillator Experiment

DTIC Science & Technology

1989-03-15

pulseline accelerator with 20 K2 output impedance and 55 nsec voltage pulse was used to generate a multi-kiloamp annular electron beam by explosive plasma...Lawrence Livermore National Laboratory P.O. Box 808 Livermore, California 94550 Attn: Dr. D. Prosnitz 1 copy Dr. T.J. Orzechowski 1 copy Dr. J. Chase 1

LINCS: Livermore's network architecture. [Octopus computing network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fletcher, J.G.

1982-01-01

Octopus, a local computing network that has been evolving at the Lawrence Livermore National Laboratory for over fifteen years, is currently undergoing a major revision. The primary purpose of the revision is to consolidate and redefine the variety of conventions and formats, which have grown up over the years, into a single standard family of protocols, the Livermore Interactive Network Communication Standard (LINCS). This standard treats the entire network as a single distributed operating system such that access to a computing resource is obtained in a single way, whether that resource is local (on the same computer as the accessingmore » process) or remote (on another computer). LINCS encompasses not only communication but also such issues as the relationship of customer to server processes and the structure, naming, and protection of resources. The discussion includes: an overview of the Livermore user community and computing hardware, the functions and structure of each of the seven layers of LINCS protocol, the reasons why we have designed our own protocols and why we are dissatisfied by the directions that current protocol standards are taking.« less

X-LUNA: Extending Free/Open Source Real Time Executive for On-Board Space Applications

NASA Astrophysics Data System (ADS)

Braga, P.; Henriques, L.; Zulianello, M.

2008-08-01

In this paper we present xLuna, a system based on the RTEMS [1] Real-Time Operating System that is able to run on demand a GNU/Linux Operating System [2] as RTEMS' lowest priority task. Linux runs in user-mode and in a different memory partition. This allows running Hard Real-Time tasks and Linux applications on the same system sharing the Hardware resources while keeping a safe isolation and the Real-Time characteristics of RTEMS. Communication between both Systems is possible through a loose coupled mechanism based on message queues. Currently only SPARC LEON2 processor with Memory Management Unit (MMU) is supported. The advantage in having two isolated systems is that non critical components are quickly developed or simply ported reducing time-to-market and budget.

A Parallel Processing Algorithm for Remote Sensing Classification

NASA Technical Reports Server (NTRS)

Gualtieri, J. Anthony

2005-01-01

A current thread in parallel computation is the use of cluster computers created by networking a few to thousands of commodity general-purpose workstation-level commuters using the Linux operating system. For example on the Medusa cluster at NASA/GSFC, this provides for super computing performance, 130 G(sub flops) (Linpack Benchmark) at moderate cost, $370K. However, to be useful for scientific computing in the area of Earth science, issues of ease of programming, access to existing scientific libraries, and portability of existing code need to be considered. In this paper, I address these issues in the context of tools for rendering earth science remote sensing data into useful products. In particular, I focus on a problem that can be decomposed into a set of independent tasks, which on a serial computer would be performed sequentially, but with a cluster computer can be performed in parallel, giving an obvious speedup. To make the ideas concrete, I consider the problem of classifying hyperspectral imagery where some ground truth is available to train the classifier. In particular I will use the Support Vector Machine (SVM) approach as applied to hyperspectral imagery. The approach will be to introduce notions about parallel computation and then to restrict the development to the SVM problem. Pseudocode (an outline of the computation) will be described and then details specific to the implementation will be given. Then timing results will be reported to show what speedups are possible using parallel computation. The paper will close with a discussion of the results.

Linux containers for fun and profit in HPC

DOE PAGES

Priedhorsky, Reid; Randles, Timothy C.

2017-10-01

This article outlines options for user-defined software stacks from an HPC perspective. Here, we argue that a lightweight approach based on Linux containers is most suitable for HPC centers because it provides the best balance between maximizing service of user needs and minimizing risks. We also discuss how containers work and several implementations, including Charliecloud, our own open-source solution developed at Los Alamos.

Linux containers for fun and profit in HPC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priedhorsky, Reid; Randles, Timothy C.

This article outlines options for user-defined software stacks from an HPC perspective. Here, we argue that a lightweight approach based on Linux containers is most suitable for HPC centers because it provides the best balance between maximizing service of user needs and minimizing risks. We also discuss how containers work and several implementations, including Charliecloud, our own open-source solution developed at Los Alamos.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

Conversion of the Livermore Education Center to College Status.

ERIC Educational Resources Information Center

Freitas, Joseph M.; And Others

In March 1988, the South County Community College District (SCCCD) requested the approval of the Board of Governors of the California Community Colleges to change the status of the Livermore Education Center from an "educational center" to a "college." An analysis by the Chancellor's Office of the request indicated that the District met Title 5…

360 Video Tour of 3D Printing Labs at LLNL

ScienceCinema

None

2018-01-16

Additive manufacturing is changing the way the world thinks about manufacturing and design. And here at Lawrence Livermore National Laboratory, it’s changing the way our scientists approach research and development. Today we’ll look around three of the additive manufacturing research labs on the Lawrence Livermore campus.

A Uniaxial Nonlinear Thermoviscoelastic Constitutive Model with Damage for M30 Gun Propellant

DTIC Science & Technology

1994-06-01

Gun Propellants at High Pressure." Lawrence Livermore National Laboratory, UCRL -88521, 1983. n g Design - k _ ao tics of Gum-’ AMCP 706-150, U.S. Army...07806-5000 Bethesda, MD 20054-5000 2 Commander 5 Director DARPA Lawrence Livermore National ATTN: J. Kelly Laboratory B. Wilcox ATTN: R. Christensen 3701

Voiced Excitations

DTIC Science & Technology

2004-12-01

3701 North Fairfax Drive Arlington, VA 22203-1714 NA NA NA Radar & EM Speech, Voiced Speech Excitations 61 ULUNCLASSIFIED UNCLASSIFIED UNCLASSIFIED...New Ideas for Speech Recognition and Related Technologies”, Lawrence Livermore National Laboratory Report, UCRL -UR-120310 , 1995 . Available from...Livermore Laboratory report UCRL -JC-134775M Holzrichter 2003, Holzrichter J.F., Kobler, J. B., Rosowski, J.J., Burke, G.J., (2003) “EM wave

LLNL: Science in the National Interest

ScienceCinema

George Miller

2017-12-09

This is Lawrence Livermore National Laboratory. located in the Livermore Valley about 50 miles east of San Francisco, the Lab is where the nations topmost science, engineering and technology come together. National security, counter-terrorism, medical technologies, energy, climate change our researchers are working to develop solutions to these challenges. For more than 50 years, we have been keeping America strong.

LIP: The Livermore Interpolation Package, Version 1.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fritsch, F. N.

2016-01-04

This report describes LIP, the Livermore Interpolation Package. LIP was totally rewritten from the package described in [1]. In particular, the independent variables are now referred to as x and y, since it is a general-purpose package that need not be restricted to equation of state data, which uses variables ρ (density) and T (temperature).

Science and Technology Review June 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radousky, H

2006-04-20

This month's issue has the following articles: (1) Maintaining Excellence through Intellectual Vitality--Commentary by Cherry A. Murray; (2) Next-Generation Scientists and Engineers Tap Lab's Resources--University of California Ph.D. candidates work with Livermore scientists and engineers to conduct fundamental research as part of their theses; (3) Adaptive Optics Provide a Clearer View--The Center for Adaptive Optics is sharpening the view of celestial objects and retinal cells; (4) Wired on the Nanoscale--A Lawrence Fellow at Livermore is using genetically engineered viruses to create nanostructures such as tiny gold wires; and (5) Too Hot to Handle--Livermore scientists couple carbon-cycle and climate models tomore » predict the global effects of depleting Earth's fossil-fuel supply.« less

NASA's Climate in a Box: Desktop Supercomputing for Open Scientific Model Development

NASA Astrophysics Data System (ADS)

Wojcik, G. S.; Seablom, M. S.; Lee, T. J.; McConaughy, G. R.; Syed, R.; Oloso, A.; Kemp, E. M.; Greenseid, J.; Smith, R.

2009-12-01

NASA's High Performance Computing Portfolio in cooperation with its Modeling, Analysis, and Prediction program intends to make its climate and earth science models more accessible to a larger community. A key goal of this effort is to open the model development and validation process to the scientific community at large such that a natural selection process is enabled and results in a more efficient scientific process. One obstacle to others using NASA models is the complexity of the models and the difficulty in learning how to use them. This situation applies not only to scientists who regularly use these models but also non-typical users who may want to use the models such as scientists from different domains, policy makers, and teachers. Another obstacle to the use of these models is that access to high performance computing (HPC) accounts, from which the models are implemented, can be restrictive with long wait times in job queues and delays caused by an arduous process of obtaining an account, especially for foreign nationals. This project explores the utility of using desktop supercomputers in providing a complete ready-to-use toolkit of climate research products to investigators and on demand access to an HPC system. One objective of this work is to pre-package NASA and NOAA models so that new users will not have to spend significant time porting the models. In addition, the prepackaged toolkit will include tools, such as workflow, visualization, social networking web sites, and analysis tools, to assist users in running the models and analyzing the data. The system architecture to be developed will allow for automatic code updates for each user and an effective means with which to deal with data that are generated. We plan to investigate several desktop systems, but our work to date has focused on a Cray CX1. Currently, we are investigating the potential capabilities of several non-traditional development environments. While most NASA and NOAA models are designed for Linux operating systems (OS), the arrival of the WindowsHPC 2008 OS provides the opportunity to evaluate the use of a new platform on which to develop and port climate and earth science models. In particular, we are evaluating Microsoft's Visual Studio Integrated Developer Environment to determine its appropriateness for the climate modeling community. In the initial phases of this project, we have ported GEOS-5, WRF, GISS ModelE, and GFS to Linux on a CX1 and are in the process of porting WRF and ModelE to WindowsHPC 2008. Initial tests on the CX1 Linux OS indicate favorable comparisons in terms of performance and consistency of scientific results when compared with experiments executed on NASA high end systems. As in the past, NASA's large clusters will continue to be an important part of our objectives. We envision a seamless environment in which an investigator performs model development and testing on a desktop system and can seamlessly transfer execution to supercomputer clusters for production.

VizieR Online Data Catalog: RefleX : X-ray-tracing code (Paltani+, 2017)

NASA Astrophysics Data System (ADS)

Paltani, S.; Ricci, C.

2017-11-01

We provide here the RefleX executable, for both Linux and MacOSX, together with the User Manual and example script file and output file Running (for instance): reflex_linux will produce the file reflex.out Note that the results may differ slightly depending on the OS, because of slight differences in some implementations numerical computations. The difference are scientifically meaningless. (5 data files).

Adaptive Multilevel Middleware for Object Systems

DTIC Science & Technology

2006-12-01

the system at the system-call level or using the CORBA-standard Extensible Transport Framework ( ETF ). Transparent insertion is highly desirable from an...often as it needs to. This is remedied by using the real-time scheduling class in a stock Linux kernel. We used schedsetscheduler system call (with...real-time scheduling class (SCHEDFIFO) for all the ML-NFD programs, later experiments with CPU load indicate that a stock Linux kernel is not

Algorithms and Architectures for Elastic-Wave Inversion Final Report CRADA No. TC02144.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, S.; Lindtjorn, O.

2017-08-15

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Schlumberger Technology Corporation (STC), to perform a computational feasibility study that investigates hardware platforms and software algorithms applicable to STC for Reverse Time Migration (RTM) / Reverse Time Inversion (RTI) of 3-D seismic data.

Rarefaction Shock Wave Cutter for Offshore Oil-Gas Platform Removal Final Report CRADA No. TC02009.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glenn, L. A.; Barker, J.

This was a collaborative effort between Lawrence Livermore National Security, LLC/Lawrence Livermore National Laboratory (LLNL) (formerly the University of California) and Jet Research Center, a wholly owned division of Halliburton Energy Services, Inc. to design and prototype an improved explosive cutter for cutting the support legs of offshore oil and gas platforms.

Special-Status Plant Species Surveys and Vegetation Mapping at Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, R E

This report presents the results of Jones & Stokes special-status plant surveys and vegetation mapping for the University of California, Lawrence Livermore National Laboratory (LLNL). Special-status plant surveys were conducted at Site 300 in April to May 1997 and in March to April 2002. Eight special-status plants were identified at Site 300: large-flowered fiddleneck, big tarplant, diamond-petaled poppy, round-leaved filaree, gypsum-loving larkspur, California androsace, stinkbells, and hogwallow starfish. Maps identifying the locations of these species, a discussion of the occurrence of these species at Site 300, and a checklist of the flora of Site 300 are presented. A reconnaissance surveymore » of the LLNL Livermore Site was conducted in June 2002. This survey concluded that no special-status plants occur at the Livermore Site. Vegetation mapping was conducted in 2001 at Site 300 to update a previous vegetation study done in 1986. The purpose of the vegetation mapping was to update and to delineate more precisely the boundaries between vegetation types and to map vegetation types that previously were not mapped. The vegetation map is presented with a discussion of the vegetation classification used.« less

Science & Technology Review October/November 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogt, R. L.; Meissner, C. N.; Kotta, P. R.

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world. The Laboratory is operated by Lawrence Livermore National Security, LLC (LLNS), for the Department of Energy’smore » National Nuclear Security Administration. LLNS is a partnership involving Bechtel National, University of California, Babcock & Wilcox, Washington Division of URS Corporation, and Battelle in affiliation with Texas A&M University. More information about LLNS is available online at www.llnsllc.com. Please address any correspondence (including name and address changes) to S&TR, Mail Stop L-664, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94551, or telephone (925) 423-3893. Our e-mail address is str-mail@llnl.gov. S&TR is available on the Web at str.llnl.gov.« less

Serving the Nation for Fifty Years: 1952 - 2002 Lawrence Livermore National Laboratory [LLNL], Fifty Years of Accomplishments

DOE R&D Accomplishments Database

2002-01-01

For 50 years, Lawrence Livermore National Laboratory has been making history and making a difference. The outstanding efforts by a dedicated work force have led to many remarkable accomplishments. Creative individuals and interdisciplinary teams at the Laboratory have sought breakthrough advances to strengthen national security and to help meet other enduring national needs. The Laboratory's rich history includes many interwoven stories -- from the first nuclear test failure to accomplishments meeting today's challenges. Many stories are tied to Livermore's national security mission, which has evolved to include ensuring the safety, security, and reliability of the nation's nuclear weapons without conducting nuclear tests and preventing the proliferation and use of weapons of mass destruction. Throughout its history and in its wide range of research activities, Livermore has achieved breakthroughs in applied and basic science, remarkable feats of engineering, and extraordinary advances in experimental and computational capabilities. From the many stories to tell, one has been selected for each year of the Laboratory's history. Together, these stories give a sense of the Laboratory -- its lasting focus on important missions, dedication to scientific and technical excellence, and drive to made the world more secure and a better place to live.

Seismic site characterization of an urban dedimentary basin, Livermore Valley, California: Site tesponse, basin-edge-induced surface waves, and 3D simulations

USGS Publications Warehouse

Hartzell, Stephen; Leeds, Alena L.; Ramirez-Guzman, Leonardo; Allen, James P.; Schmitt, Robert G.

2016-01-01

Thirty‐two accelerometers were deployed in the Livermore Valley, California, for approximately one year to study sedimentary basin effects. Many local and near‐regional earthquakes were recorded, including the 24 August 2014 Mw 6.0 Napa, California, earthquake. The resulting ground‐motion data set is used to quantify the seismic response of the Livermore basin, a major structural depression in the California Coast Range Province bounded by active faults. Site response is calculated by two methods: the reference‐site spectral ratio method and a source‐site spectral inversion method. Longer‐period (≥1  s) amplification factors follow the same general pattern as Bouguer gravity anomaly contours. Site response spectra are inverted for shallow shear‐wave velocity profiles, which are consistent with independent information. Frequency–wavenumber analysis is used to analyze plane‐wave propagation across the Livermore Valley and to identify basin‐edge‐induced surface waves with back azimuths different from the source back azimuth. Finite‐element simulations in a 3D velocity model of the region illustrate the generation of basin‐edge‐induced surface waves and point out strips of elevated ground velocities along the margins of the basin.

Nuclear winter from gulf war discounted

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marshall, E.

Would a major conflagration in Kuwait's oil fields trigger a climate catastrophe akin to the 'nuclear winter' that got so much attention in the 1980s This question prompted a variety of opinions. The British Meteorological Office and researchers at Lawrence Livermore National Laboratory concluded that the effect of smoke from major oil fires in Kuwait on global temperatures is likely to be small; however, the obscuration of sunlight might significantly reduce surface temperatures locally. Michael MacCracken, leader of the researchers at Livermore, predicts that the worst plausible oil fires in the Gulf would produce a cloud of pollution about asmore » severe as that found on a bad day at the Los Angeles airport. The results of some mathematical modeling by the Livermore research group are reported.« less

Science & Technology Review November 2007

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chinn, D J

2007-10-16

This month's issue has the following articles: (1) Simulating the Electromagnetic World--Commentary by Steven R. Patterson; (2) A Code to Model Electromagnetic Phenomena--EMSolve, a Livermore supercomputer code that simulates electromagnetic fields, is helping advance a wide range of research efforts; (3) Characterizing Virulent Pathogens--Livermore researchers are developing multiplexed assays for rapid detection of pathogens; (4) Imaging at the Atomic Level--A powerful new electron microscope at the Laboratory is resolving materials at the atomic level for the first time; (5) Scientists without Borders--Livermore scientists lend their expertise on peaceful nuclear applications to their counterparts in other countries; and (6) Probing Deepmore » into the Nucleus--Edward Teller's contributions to the fast-growing fields of nuclear and particle physics were part of a physics golden age.« less

Coulomb clusters in RETRAP

NASA Astrophysics Data System (ADS)

Steiger, J.; Beck, B. R.; Gruber, L.; Church, D. A.; Holder, J. P.; Schneider, D.

1999-01-01

Storage rings and Penning traps are being used to study ions in their highest charge states. Both devices must have the capability for ion cooling in order to perform high precision measurements such as mass spectrometry and laser spectroscopy. This is accomplished in storage rings in a merged beam arrangement where a cold electron beam moves at the speed of the ions. In RETRAP, a Penning trap located at Lawrence Livermore National Laboratory, a sympathetic laser/ion cooling scheme has been implemented. In a first step, singly charged beryllium ions are cooled electronically by a tuned circuit and optically by a laser. Then hot, highly charged ions are merged into the cold Be plasma. By collisions, their kinetic energy is reduced to the temperature of the Be plasma. First experiments indicate that the highly charged ions form a strongly coupled plasma with a Coulomb coupling parameter exceeding 1000.

Plancton: an opportunistic distributed computing project based on Docker containers

NASA Astrophysics Data System (ADS)

Concas, Matteo; Berzano, Dario; Bagnasco, Stefano; Lusso, Stefano; Masera, Massimo; Puccio, Maximiliano; Vallero, Sara

2017-10-01

The computing power of most modern commodity computers is far from being fully exploited by standard usage patterns. In this work we describe the development and setup of a virtual computing cluster based on Docker containers used as worker nodes. The facility is based on Plancton: a lightweight fire-and-forget background service. Plancton spawns and controls a local pool of Docker containers on a host with free resources, by constantly monitoring its CPU utilisation. It is designed to release the resources allocated opportunistically, whenever another demanding task is run by the host user, according to configurable policies. This is attained by killing a number of running containers. One of the advantages of a thin virtualization layer such as Linux containers is that they can be started almost instantly upon request. We will show how fast the start-up and disposal of containers eventually enables us to implement an opportunistic cluster based on Plancton daemons without a central control node, where the spawned Docker containers behave as job pilots. Finally, we will show how Plancton was configured to run up to 10 000 concurrent opportunistic jobs on the ALICE High-Level Trigger facility, by giving a considerable advantage in terms of management compared to virtual machines.

Performance of an MPI-only semiconductor device simulator on a quad socket/quad core InfiniBand platform.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shadid, John Nicolas; Lin, Paul Tinphone

2009-01-01

This preliminary study considers the scaling and performance of a finite element (FE) semiconductor device simulator on a capacity cluster with 272 compute nodes based on a homogeneous multicore node architecture utilizing 16 cores. The inter-node communication backbone for this Tri-Lab Linux Capacity Cluster (TLCC) machine is comprised of an InfiniBand interconnect. The nonuniform memory access (NUMA) nodes consist of 2.2 GHz quad socket/quad core AMD Opteron processors. The performance results for this study are obtained with a FE semiconductor device simulation code (Charon) that is based on a fully-coupled Newton-Krylov solver with domain decomposition and multilevel preconditioners. Scaling andmore » multicore performance results are presented for large-scale problems of 100+ million unknowns on up to 4096 cores. A parallel scaling comparison is also presented with the Cray XT3/4 Red Storm capability platform. The results indicate that an MPI-only programming model for utilizing the multicore nodes is reasonably efficient on all 16 cores per compute node. However, the results also indicated that the multilevel preconditioner, which is critical for large-scale capability type simulations, scales better on the Red Storm machine than the TLCC machine.« less

MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

2012-08-01

We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885-10907.

Source Code Analysis Laboratory (SCALe) for Energy Delivery Systems

DTIC Science & Technology

2010-12-01

the software for reevaluation. Once the ree- valuation process is completed, CERT provides the client a report detailing the software’s con - formance...Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8% Wine...inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with energy system software will help

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Covert Android Rootkit Detection: Evaluating Linux Kernel Level Rootkits on the Android Operating System

DTIC Science & Technology

2012-06-14

the attacker . Thus, this race condition causes a privilege escalation . 2.2.5 Summary This section reviewed software exploitation of a Linux kernel...has led to increased targeting by malware writers. Android attacks have naturally sparked interest in researching protections for Android . This...release, Android 4.0 Ice Cream Sandwich. These rootkits focused on covert techniques to hide the presence of data used by an attacker to infect a

The Ubuntu Chat Corpus for Multiparticipant Chat Analysis

DTIC Science & Technology

2013-03-01

Intelligence (www.aaai.org). All rights reserved. the # LINUX corpus (Elsner and Charniak 2010), and the #IPHONE/#PHYSICS/#PYTHON corpus (Adams 2008). For many...made publicly available, making it difficult to comparatively evaluate dif- ferent techniques. Corpus Description Ubuntu, a Linux -based operating...Kubuntu (Ubuntu with KDE ) support #ubuntu-devel 2 112 074 12 140 53.7 2004-10-01 Developmental team coordination #ubuntu+1 1 621 680 26 805 52.6 2007-04-04

MVC for Content Management on the Cloud

DTIC Science & Technology

2011-09-01

Windows, Linux , MacOS, PalmOS and other customized ones (Qiu). Figure 20 illustrates implementation of MVC architecture. Qiu examines a “universal...Listing of Unzipped Text Document (From O’Reilly & Associates, Inc, 2005) Figure 37 shows the results of unzipping this file in Linux . The contents of the...ODF Adoption TC, and the ODF Alliance include members from Adobe, BBC, Bristol City Council, Bull, Corel, EDS, EMC, GNOME, IBM, Intel, KDE , MySQL

[Making a low cost IPSec router on Linux and the assessment for practical use].

PubMed

Amiki, M; Horio, M

2001-09-01

We installed Linux and FreeS/WAN on a PC/AT compatible machine to make an IPSec router. We measured the time of ping/ftp, only in the university, between the university and the external network. Between the university and the external network (the Internet), there were no differences. Therefore, we concluded that CPU load was not remarkable at low speed networks, because packets exchanged via the Internet are small, or compressions of VPN are more effective than encoding and decoding. On the other hand, in the university, the IPSec router performed down about 20-30% compared with normal IP communication, but this is not a serious problem for practical use. Recently, VPN machines are becoming cheaper, but they do not function sufficiently to create a fundamental VPN environment. Therefore, if one wants a fundamental VPN environment at a low cost, we believe you should select a VPN router on Linux.

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

LXtoo: an integrated live Linux distribution for the bioinformatics community.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

2012-07-19

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

Timing characterization and analysis of the Linux-based, closed loop control computer for the Subaru Telescope laser guide star adaptive optics system

NASA Astrophysics Data System (ADS)

Dinkins, Matthew; Colley, Stephen

2008-07-01

Hardware and software specialized for real time control reduce the timing jitter of executables when compared to off-the-shelf hardware and software. However, these specialized environments are costly in both money and development time. While conventional systems have a cost advantage, the jitter in these systems is much larger and potentially problematic. This study analyzes the timing characterstics of a standard Dell server running a fully featured Linux operating system to determine if such a system would be capable of meeting the timing requirements for closed loop operations. Investigations are preformed on the effectiveness of tools designed to make off-the-shelf system performance closer to specialized real time systems. The Gnu Compiler Collection (gcc) is compared to the Intel C Compiler (icc), compiler optimizations are investigated, and real-time extensions to Linux are evaluated.

Fixatives Application for Risk Mitigation Following Contamination with a Biological Agent

DTIC Science & Technology

2011-11-02

PRES-  Gruinard Island 5% formaldehyde  Sverdlosk Release UNKNOWN: but washing, chloramines , soil disposal believed to have been used...507816 Lawrence Livermore National Laboratory LLNL-PRES- 4 Disinfectant >6 Log Reduction on Materials (EPA, 2010a,b; Wood et al., 2011...LL L-PRES-507816 Lawrence Livermore National Laboratory LLNL-PRES-  High disinfectant concentrations increase operational costs and risk

Material Modeling for Terminal Ballistic Simulation

DTIC Science & Technology

1992-09-01

DYNA-3D-a nonlinear, explicit, three-dimensional finite element code for solid and structural mechanics- user manual. Technical Report UCRL -MA...Rep. UCRL -50108, Rev. 1, Lawrence Livermore Laboratory, 1977. [34] S. P. Marsh. LASL Shock Hugoniot Data. University of California Press, Berkeley, CA...Steinberg. Equation of state and strength properties of selected ma- teriaJs. Tech. Rep. UCRL -MA-106439, Lawrence Livermore National Labo- ratory, 1991. [371

Characterization of Jets From Exploding Bridge Wire Detonators

DTIC Science & Technology

2005-05-01

Laboratories: Albuquerque, NM, 1992. 8. Lee, E. L; Hornig, H. C.; Kury, J. W. Adiabatic Expansion of High Explosive Detonation Products; UCRL ...Dobratz, B. M. LLNL Explosives Handbook; UCRL -5299; Lawrence Livermore Laboratory, University of California: Livermore, CA 1981. 22...ATTN AFATL DLJR D LAMBERT EGLIN AFB FL 32542-6810 2 DARPA ATTN W SNOWDEN S WAX 3701 N FAIRFAX DR ARLINGTON VA 22203-1714 2 LOS

78 FR 56706 - Decision to Evaluate a Petition to Designate a Class of Employees from the Sandia National...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

...NIOSH gives notice as required by Department of Health and Human Services regulations of a decision to evaluate a petition to designate a class of employees from the Sandia National Laboratory- Livermore in Livermore, California to be included in the Special Exposure Cohort under the Energy Employees Occupational Illness Compensation Program Act of 2000.

Astronomy Applications of Adaptive Optics at Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bauman, B J; Gavel, D T

2003-04-23

Astronomical applications of adaptive optics at Lawrence Livermore National Laboratory (LLNL) has a history that extends from 1984. The program started with the Lick Observatory Adaptive Optics system and has progressed through the years to lever-larger telescopes: Keck, and now the proposed CELT (California Extremely Large Telescope) 30m telescope. LLNL AO continues to be at the forefront of AO development and science.

Livermore Accelerator Source for Radionuclide Science (LASRS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Scott; Bleuel, Darren; Johnson, Micah

The Livermore Accelerator Source for Radionuclide Science (LASRS) will generate intense photon and neutron beams to address important gaps in the study of radionuclide science that directly impact Stockpile Stewardship, Nuclear Forensics, and Nuclear Material Detection. The co-location of MeV-scale neutral and photon sources with radiochemical analytics provides a unique facility to meet current and future challenges in nuclear security and nuclear science.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikolic, R J

This month's issue has the following articles: (1) Honoring a Legacy of Service to the Nation - The nation pays tribute to George Miller, who retired in December 2011 as the Laboratory's tenth director; (2) Life-Extension Programs Encompass All Our Expertise - Commentary by Bruce T. Goodwin; (3) Extending the Life of an Aging Weapon - Stockpile stewards have begun work on a multiyear effort to extend the service life of the aging W78 warhead by 30 years; (4) Materials by Design - Material microstructures go three-dimensional with improved additive manufacturing techniques developed at Livermore; (5) Friendly Microbes Power Energy-Producingmore » Devices - Livermore researchers are demonstrating how electrogenic bacteria and microbial fuel cell technologies can produce clean, renewable energy and purify water; and (6) Chemical Sensor Is All Wires, No Batteries - Livermore's 'batteryless' nanowire sensor could benefit applications in diverse fields such as homeland security and medicine.« less

CDC 7600 LTSS programming stratagens: preparing your first production code for the Livermore Timesharing System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fong, K. W.

1977-08-15

This report deals with some techniques in applied programming using the Livermore Timesharing System (LTSS) on the CDC 7600 computers at the National Magnetic Fusion Energy Computer Center (NMFECC) and the Lawrence Livermore Laboratory Computer Center (LLLCC or Octopus network). This report is based on a document originally written specifically about the system as it is implemented at NMFECC but has been revised to accommodate differences between LLLCC and NMFECC implementations. Topics include: maintaining programs, debugging, recovering from system crashes, and using the central processing unit, memory, and input/output devices efficiently and economically. Routines that aid in these procedures aremore » mentioned. The companion report, UCID-17556, An LTSS Compendium, discusses the hardware and operating system and should be read before reading this report.« less

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

System Data Model (SDM) Source Code

DTIC Science & Technology

2012-08-23

CROSS_COMPILE=/opt/gumstix/build_arm_nofpu/staging_dir/bin/arm-linux-uclibcgnueabi- 8 : CC=$(CROSS_COMPILE)gcc 9: CXX=$(CROSS_COMPILE)g++ 10 : AR...and flags to pass to it 6: LEX=flex 7: LEXFLAGS=-B 8 : 9: ## The parser generator to invoke and flags to pass to it 10 : YACC=bison 11: YACCFLAGS...5: # Point to default PetaLinux root directory 6: ifndef ROOTDIR 7: ROOTDIR=$(PETALINUX)/software/petalinux-dist 8 : endif 9: 10 : PATH:=$(PATH

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

Navigation/Prop Software Suite

NASA Technical Reports Server (NTRS)

Bruchmiller, Tomas; Tran, Sanh; Lee, Mathew; Bucker, Scott; Bupane, Catherine; Bennett, Charles; Cantu, Sergio; Kwong, Ping; Propst, Carolyn

2012-01-01

Navigation (Nav)/Prop software is used to support shuttle mission analysis, production, and some operations tasks. The Nav/Prop suite containing configuration items (CIs) resides on IPS/Linux workstations. It features lifecycle documents, and data files used for shuttle navigation and propellant analysis for all flight segments. This suite also includes trajectory server, archive server, and RAT software residing on MCC/Linux workstations. Navigation/Prop represents tool versions established during or after IPS Equipment Rehost-3 or after the MCC Rehost.

Malware Memory Analysis of the IVYL Linux Rootkit: Investigating a Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-04-01

report is to examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills ...The skills amassed by incident handlers and investigators alike while using Volatility to examine Windows memory images will be of some help...bin/pulseaudio --start --log-target=syslog 1362 1000 1000 nautilus 1366 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1370 1000 1000 nm-applet

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

Porting and refurbishment of the WSS TNG control software

NASA Astrophysics Data System (ADS)

Caproni, Alessandro; Zacchei, Andrea; Vuerli, Claudio; Pucillo, Mauro

2004-09-01

The Workstation Software Sytem (WSS) is the high level control software of the Italian Galileo Galilei Telescope settled in La Palma Canary Island developed at the beginning of '90 for HP-UX workstations. WSS may be seen as a middle layer software system that manages the communications between the real time systems (VME), different workstations and high level applications providing a uniform distributed environment. The project to port the control software from the HP workstation to Linux environment started at the end of 2001. It is aimed to refurbish the control software introducing some of the new software technologies and languages, available for free in the Linux operating system. The project was realized by gradually substituting each HP workstation with a Linux PC with the goal to avoid main changes in the original software running under HP-UX. Three main phases characterized the project: creation of a simulated control room with several Linux PCs running WSS (to check all the functionality); insertion in the simulated control room of some HPs (to check the mixed environment); substitution of HP workstation in the real control room. From a software point of view, the project introduces some new technologies, like multi-threading, and the possibility to develop high level WSS applications with almost every programming language that implements the Berkley sockets. A library to develop java applications has also been created and tested.

Positron Annihilation Spectroscopy Characterization of Nanostructural Features in Reactor Steels

NASA Astrophysics Data System (ADS)

Glade, Stephen; Wirth, Brian; Asoka-Kumar, Palakkal; Sterne, Philip; Alinger, Matthew; Odette, George

2004-03-01

Irradiation embrittlement in nuclear reactor pressure vessel steels results from the formation of a high number density of nanometer sized copper rich precipitates and sub-nanometer defect-solute clusters. We present results of study to characterize the size and compositions of simple binary and ternary Fe-Cu-Mn model alloys and more representative Fe-Cu-Mn-Ni-Si-Mo-C reactor pressure vessel steels using positron annihilation spectroscopy (PAS). Using a recently developed spin-polarized PAS technique, we have also measured the magnetic properties of the nanometer-sized copper rich precipitates. Mn retards the precipitation kinetics and inhibits large vacancy cluster formation, suggesting a strong Mn-vacancy interaction which reduces radiation enhanced diffusion. The spin-polarized PAS measurements reveal the non-magnetic nature of the copper precipitates, discounting the notion that the precipitates contain significant quantities of Fe and providing an upper limit of at most a few percent Fe in the precipitates. PAS results on oxide dispersion-strengthened steel for use in fusion reactors will also be presented. Part of this work was performed under the auspices of the US Department of Energy by the University of California, Lawrence Livermore National Laboratory, under contract No. W-7405-ENG-48 with partial support provided from Basic Energy Sciences, Division of Materials Science.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, C. V.; Mendez, A. J.

This was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of California)/Lawrence Livermore National Laboratory (LLNL) and Mendez R & D Associates (MRDA) to develop and demonstrate a reconfigurable and cost effective design for optical code division multiplexing (O-CDM) with high spectral efficiency and throughput, as applied to the field of distributed computing, including multiple accessing (sharing of communication resources) and bidirectional data distribution in fiber-to-the-premise (FTTx) networks.

Feasibility of Wide-Area Decontamination of Bacillus anthracis Spores Using a Germination-Lysis Approach

DTIC Science & Technology

2011-11-16

Security, LLC 2011 CBD S& T Conference November 16, 2011 LLNL-PRES-508394 Lawrence Livermore National Laboratory LLNL-PRES-  Background...PRES-  Gruinard Island 5% formaldehyde  Sverdlosk Release UNKNOWN: but washing, chloramines , soil disposal believed to have been used...508394 Lawrence Livermore National Laboratory LLNL-PRES- 4 Disinfectant >6 Log Reduction on Materials (EPA, 2010a,b; Wood et al., 2011

Numerical Modeling of Buried Mine Explosions

DTIC Science & Technology

2001-03-01

Lawrence Livermore Laboratory Report, UCRL -50108, Rev. 1, June 1977. 12. Dobratz, B. M., and P. C. Crawford. “LLNL Explosives Handbook.” Lawrence...Livermore National Laboratory Report, UCRL -52997, January 1985. 13. Kerley, G. I. “Multiphase Equation of State for Iron.” Sandia National Laboratories...BOX 202797 AUSTIN TX 78720-2797 1 DARPA B KASPAR 3701 N FAIRFAX DR ARLINGTON VA 22203-1714 1 US MILITARY ACADEMY MATH SCI

Studies in Seismic Verification

DTIC Science & Technology

1992-05-01

NTS and Shagan River nuclear explosions, Rep. UCRL -102276, Lawrence Livermore Natl. Lab., Livermore, Calif., 1990. Taylor, S. R., and P. D. Marshall...western U.S. earthquakes and implications for the tectonic stress field, Report UCRL -JC-105880, 36 pp., 1990. Randall, M. J., The spectral theory of...Alewine, III Dr. Stephen Bratt DARPA/NMRO Center for Seismic Studies 3701 North Fairfax Drive 1300 North 17th Street Arlington, VA 22203-1714 Suite 1450

Final Report Bald and Golden Eagle Territory Surveys for the Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fratanduono, M. L.

2014-11-25

Garcia and Associates (GANDA) was contracted by the Lawrence Livermore National Laboratory (LLNL) to conduct surveys for bald eagles (Haliaeetus leucocephalus) and golden eagles (Aquila chrysaetos) at Site 300 and in the surrounding area out to 10-miles. The survey effort was intended to document the boundaries of eagle territories by careful observation of eagle behavior from selected viewing locations throughout the study area.

Sending an Instrument to Psyche, the Largest Metal Asteroid in the Solar System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burks, Morgan

In a few years, an instrument designed and built by Lawrence Livermore National Laboratory researchers will be flying hundreds of millions of miles through space to explore a rare, largely metal asteroid. The Livermore gamma ray spectrometer will be built in collaboration with researchers from the Johns Hopkins Applied Physics Laboratory for the first-ever visit to Psyche, the largest metal asteroid in the solar system.

The effect of Livermore OPAL opacities on the evolutionary masses of RR Lyrae stars

NASA Technical Reports Server (NTRS)

Yi, Sukyoung; Lee, Young-Wook; Demarque, Pierre

1993-01-01

We have investigated the effect of the new Livermore OPAL opacities on the evolution of horizontal-branch (HB) stars. This work was motivated by the recent stellar pulsation calculations using the new Livermore opacities, which suggest that the masses of double-mode RR Lyrae stars are 0.1-0.2 solar mass larger than those based on earlier opacities. Unlike the pulsation calculations, we find that the effect of opacity change on the evolution of HB stars is not significant. In particular, the effect of the mean masses of RR Lyrae stars is very small, showing a decrease of only 0.01-0.02 solar mass compared to the models based on old Cox-Stewart opacities. Consequently, with the new Livermore OPAL opacities, both the stellar pulsation and evolution models now predict approximately the same masses for the RR Lyrae stars. Our evolutionary models suggest that the mean masses of the RR Lyrae stars are about 0.76 and about 0.71 solar mass for M15 (Oosterhoff group II) and M3 (group I), respectively. If (alpha/Fe) = 0.4, these values are decreased by about 0.03 solar mass. Variations of the mean masses of RR Lyrae stars with HB morphology and metallicity are also presented.

genepop'007: a complete re-implementation of the genepop software for Windows and Linux.

PubMed

Rousset, François

2008-01-01

This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls. © 2007 The Author.

Empirical tests of Zipf's law mechanism in open source Linux distribution.

PubMed

Maillart, T; Sornette, D; Spaeth, S; von Krogh, G

2008-11-21

Zipf's power law is a ubiquitous empirical regularity found in many systems, thought to result from proportional growth. Here, we establish empirically the usually assumed ingredients of stochastic growth models that have been previously conjectured to be at the origin of Zipf's law. We use exceptionally detailed data on the evolution of open source software projects in Linux distributions, which offer a remarkable example of a growing complex self-organizing adaptive system, exhibiting Zipf's law over four full decades.

A Framework for Automated Digital Forensic Reporting

DTIC Science & Technology

2009-03-01

provide a simple way to extract local accounts from a full system image. Unix, Linux and the BSD variants store user accounts in the /etc/ passwd file...with hashes of the user passwords in the /etc/shadow file for linux or /etc/master.passwd for BSD. /etc/ passwd also contains mappings from usernames to... passwd file may not map directly to real-world names, it can be a crucial link in this eventual mapping. Following are two examples where it could prove

Development of a Low-Latency, High Data Rate, Differential GPS Relative Positioning System for UAV Formation Flight Control

DTIC Science & Technology

2006-09-01

spiral development cycle involved transporting the software processes from a Windows XP / MATLAB environment to a Linux / C++ environment. This...tested on. Additionally, in the case of the GUMSTIX PC boards, the LINUX operating system is burned into the read-only memory. Lastly, both PC-104 and...both the real-time environment and the post-processed en - vironment. When the system operates in real-time mode, an output file is generated which

MONO FOR CROSS-PLATFORM CONTROL SYSTEM ENVIRONMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Hiroshi; Timossi, Chris

2006-10-19

Mono is an independent implementation of the .NET Frameworkby Novell that runs on multiple operating systems (including Windows,Linux and Macintosh) and allows any .NET compatible application to rununmodified. For instance Mono can run programs with graphical userinterfaces (GUI) developed with the C# language on Windows with VisualStudio (a full port of WinForm for Mono is in progress). We present theresults of tests we performed to evaluate the portability of our controlssystem .NET applications from MS Windows to Linux.

Progress Toward a Multidimensional Representation of the 5.56-mm Interior Ballistics

DTIC Science & Technology

2009-08-01

were performed as a check of all the major species formed at one atmosphere pressure. Cheetah (17) thermodynamics calculations were performed under...in impermeable boundaries that only yield to gas-dynamic flow after a prescribed pressure load is reached act as rigid bodies within the chamber... Cheetah Code, version 4.0; Lawrence Livermore National Laboratory: Livermore, CA, 2005. 18. Williams, A. W.; Brant, A. L.; Kaste, P. J.; Colburn, J. W

Development of a Laser for Landmine Destruction Final Report CRADA No. TC02126.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamamoto, R.; Sheppard, C.

2017-08-31

This was one of two CRADAs between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and First Alliance Technologies, LLC (First Alliance), to conduct research and development activity toward an integrated system for the detecting, locating, and destroying of landmines and unexploded ordinance using a laser to destroy landmines and unexploded ordinance and First Alliance’s Land Mine Locator (LML) system.

Trends in Anti-Nuclear Protests in the United States, 1984-1987

DTIC Science & Technology

1989-01-01

Obispo, CA. 2 days of peaceful protests at Diablo Canyon nuclear powerplant against licensing of plant. Date: January 12 and 13, 1984 Group: Abalone ...Members of the Abalone Alliance and the Livermore Action Group blocked entrance to Bohemian Grove club, a conservative all-male club to which Reagan...belongs, to protest the club members’ connections to the nuclear weapons industry. Date: July 22, 1984 Group: Abalone and Livermore Action Group

Recent Methodological Developments in Magnitude Determination and Yield Estimation with Applications to Semipalatinsk Explosions

DTIC Science & Technology

1991-07-16

UCRL -51414-REV1, Lawrence Livermore Laboratory, University of California, CA. - 47 - North, R. G. (1977). Station magnitude bias --- its determination...1976 at and near the nuclear testing ground in eastern Kazakhstan, UCRL -52856, Lawrence Livermore Laboratory, University of California, CA. Ryall, A...VA 24061 Dr. Ralph Alewine, I Dr. Stephen Bratt DARPA/NMRO Center for Seismic Studies 3701 North Fairfax Drive 1300 North 17th Street Arlington, VA

Manufacturing Steps for Commercial Production of Nano-Structure Capacitors Final Report CRADA No. TC02159.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barbee, T. W.; Schena, D.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and TroyCap LLC, to develop manufacturing steps for commercial production of nano-structure capacitors. The technical objective of this project was to demonstrate high deposition rates of selected dielectric materials which are 2 to 5 times larger than typical using current technology.

LLNL NESHAPs 2015 Annual Report - June 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, K. R.; Gallegos, G. M.; MacQueen, D. H.

2016-06-01

Lawrence Livermore National Security, LLC operates facilities at Lawrence Livermore National Laboratory (LLNL) in which radionuclides are handled and stored. These facilities are subject to the U.S. Environmental Protection Agency (EPA) National Emission Standards for Hazardous Air Pollutants (NESHAPs) in Code of Federal Regulations (CFR) Title 40, Part 61, Subpart H, which regulates radionuclide emissions to air from Department of Energy (DOE) facilities. Specifically, NESHAPs limits the emission of radionuclides to the ambient air to levels resulting in an annual effective dose equivalent of 10 mrem (100 μSv) to any member of the public. Using measured and calculated emissions, andmore » building-specific and common parameters, LLNL personnel applied the EPA-approved computer code, CAP88-PC, Version 4.0.1.17, to calculate the dose to the maximally exposed individual member of the public for the Livermore Site and Site 300.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

East, D. R.; Sexton, J.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and IBM TJ Watson Research Center to research, assess feasibility and develop an implementation plan for a High Performance Computing Innovation Center (HPCIC) in the Livermore Valley Open Campus (LVOC). The ultimate goal of this work was to help advance the State of California and U.S. commercial competitiveness in the arena of High Performance Computing (HPC) by accelerating the adoption of computational science solutions, consistent with recent DOE strategy directives. The desired result of this CRADA was a well-researched,more » carefully analyzed market evaluation that would identify those firms in core sectors of the US economy seeking to adopt or expand their use of HPC to become more competitive globally, and to define how those firms could be helped by the HPCIC with IBM as an integral partner.« less

Emergency Response Capability Baseline Needs Assessment - Compliance Assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharry, John A.

This document was prepared by John A. Sharry, LLNL Fire Marshal and Division Leader for Fire Protection and was reviewed by LLNL Emergency Management Department Head, James Colson. This document is the second of a two-part analysis on Emergency Response Capabilities of Lawrence Livermore National Laboratory. The first part, 2016 Baseline Needs Assessment Requirements Document established the minimum performance criteria necessary to meet mandatory requirements. This second part analyses the performance of Lawrence Livermore Laboratory Emergency Management Department to the contents of the Requirements Document. The document was prepared based on an extensive review of information contained in the 2016more » BNA, a review of Emergency Planning Hazards Assessments, a review of building construction, occupancy, fire protection features, dispatch records, LLNL alarm system records, fire department training records, and fire department policies and procedures. The 2013 BNA was approved by NNSA’s Livermore Field Office on January 22, 2014.« less

Science& Technology Review March 2004

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, D H

2004-01-23

This month's issue has the following articles: (1) ''Rethinking Atoms for Peace and the Future of Nuclear Technology'' a commentary by Ronald F. Lehman II; (2) ''Rich Legacy from Atoms for Peace'' In 1953, President Eisenhower encouraged world leaders to pursue peaceful uses of nuclear technology. Many of Livermore's contributions in the spirit of this initiative continue to benefit society today. (3) ''Tropopause Height Becomes Another Climate-Change Fingerprint'' Simulations and observational data show that human activities are largely responsible for the steady elevation of the tropopause, the boundary between the troposphere and the stratosphere. (4) ''A Better Method for Certifyingmore » the Nuclear Stockpile'' Livermore and Los Alamos are developing a common framework for evaluating the reliability and safety of nuclear weapons. (5) ''Observing How Proteins Loop the Loop'' A new experimental method developed at Livermore allows scientists to monitor the folding processes of proteins, one molecule at a time.« less

LTSS compendium: an introduction to the CDC 7600 and the Livermore Timesharing System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fong, K. W.

1977-08-15

This report is an introduction to the CDC 7600 computer and to the Livermore Timesharing System (LTSS) used by the National Magnetic Fusion Energy Computer Center (NMFECC) and the Lawrence Livermore Laboratory Computer Center (LLLCC or Octopus network) on their 7600's. This report is based on a document originally written specifically about the system as it is implemented at NMFECC but has been broadened to point out differences in implementation at LLLCC. It also contains information about LLLCC not relevant to NMFECC. This report is written for computational physicists who want to prepare large production codes to run under LTSSmore » on the 7600's. The generalized discussion of the operating system focuses on creating and executing controllees. This document and its companion, UCID-17557, CDC 7600 LTSS Programming Stratagems, provide a basis for understanding more specialized documents about individual parts of the system.« less

Unsteady, Cooled Turbine Simulation Using a PC-Linux Analysis System

NASA Technical Reports Server (NTRS)

List, Michael G.; Turner, Mark G.; Chen, Jen-Pimg; Remotigue, Michael G.; Veres, Joseph P.

2004-01-01

The fist stage of the high-pressure turbine (HPT) of the GE90 engine was simulated with a three-dimensional unsteady Navier-Sokes solver, MSU Turbo, which uses source terms to simulate the cooling flows. In addition to the solver, its pre-processor, GUMBO, and a post-processing and visualization tool, Turbomachinery Visual3 (TV3) were run in a Linux environment to carry out the simulation and analysis. The solver was run both with and without cooling. The introduction of cooling flow on the blade surfaces, case, and hub and its effects on both rotor-vane interaction as well the effects on the blades themselves were the principle motivations for this study. The studies of the cooling flow show the large amount of unsteadiness in the turbine and the corresponding hot streak migration phenomenon. This research on the GE90 turbomachinery has also led to a procedure for running unsteady, cooled turbine analysis on commodity PC's running the Linux operating system.

BigWig and BigBed: enabling browsing of large distributed datasets.

PubMed

Kent, W J; Zweig, A S; Barber, G; Hinrichs, A S; Karolchik, D

2010-09-01

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

Development of EPA Protocol Information Enquiry Service System Based on Embedded ARM Linux

NASA Astrophysics Data System (ADS)

Peng, Daogang; Zhang, Hao; Weng, Jiannian; Li, Hui; Xia, Fei

Industrial Ethernet is a new technology for industrial network communications developed in recent years. In the field of industrial automation in China, EPA is the first standard accepted and published by ISO, and has been included in the fourth edition IEC61158 Fieldbus of NO.14 type. According to EPA standard, Field devices such as industrial field controller, actuator and other instruments are all able to realize communication based on the Ethernet standard. The Atmel AT91RM9200 embedded development board and open source embedded Linux are used to develop an information inquiry service system of EPA protocol based on embedded ARM Linux in this paper. The system is capable of designing an EPA Server program for EPA data acquisition procedures, the EPA information inquiry service is available for programs in local or remote host through Socket interface. The EPA client can access data and information of other EPA equipments on the EPA network when it establishes connection with the monitoring port of the server.

Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system

NASA Astrophysics Data System (ADS)

Meier, Konrad; Fleig, Georg; Hauth, Thomas; Janczyk, Michael; Quast, Günter; von Suchodoletz, Dirk; Wiebelt, Bernd

2016-10-01

Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications. To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare policies of the cluster. The developed thin integration layer between OpenStack and Moab can be adapted to other batch servers and virtualization systems, making the concept also applicable for other cluster operators. This contribution will report on the concept and implementation of an OpenStack-virtualized cluster used for HEP workflows. While the full cluster will be installed in spring 2016, a test-bed setup with 800 cores has been used to study the overall system performance and dedicated HEP jobs were run in a virtualized environment over many weeks. Furthermore, the dynamic integration of the virtualized worker nodes, depending on the workload at the institute's computing system, will be described.

A Damage Mechanics Source Model for Underground Nuclear Explosions.

DTIC Science & Technology

1991-08-01

California Institute of Technology Reston, VA 22091 Pasadena, CA 91125 Mr. William J. Best Prof. F. A. Dahlen 907 Westwood Drive Geological and Geophysical...ENSCO, Inc. Department of Geological Sciences 445 Pineda Court . , -7’- 9 Meibcurr..e, F 3940 6 William Kikendall Prof. Amos Nur Teledyne Geotech...Teledyne Geotech Lawrence Livermore National Laboratory 3a¢,l Shiloh Road L-205 Garland, TX 75041 P. 0. Box 808 Livermore, CA 94550 Dr. Matthew Sibol

Computations for Truck Sliding with TRUCK 3.1 Code

DTIC Science & Technology

1989-08-01

16 REFERENCES 1. L u. \\Villiam N.. Hobbs. Norman P. and Atkinson, Michael. TRUCK 3.1-An Improrcd Digital (’oiputtr Program for Calculating the Response...for Operations and Plans ATIN: Technical Libary Director of Chemical & Nuear Operations Dpartnt of the AIW Waskbington, DC 20310 1 Cocaeder US Ay...Lawrenoe Livermore Lab. ATIN: Code 2124, Tedhnical ATTN: Tech Info Dept L-3 Reports Libary P.O. Be 808 Monterey, CA 93940 Livermore, CA 94550 AFSC

Fiber Based Optical Amplifier for High Energy Laser Pulses Final Report CRADA No. TC02100.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Messerly, M.; Cunningham, P.

This was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of California)/Lawrence Livermore National Laboratory (LLNL), and The Boeing Company to develop an optical fiber-based laser amplifier capable of producing and sustaining very high-energy, nanosecond-scale optical pulses. The overall technical objective of this CRADA was to research, design, and develop an optical fiber-based amplifier that would meet specific metrics.

Demonstration of Regional Discrimination of Eurasian Seismic Events Using Observations at Soviet IRIS and CDSN Stations

DTIC Science & Technology

1992-03-01

Propagation of Lg Waves Across Eastern Europe and Asia, Lawrence Livermore National Laboratory Report, LLNL Report No. UCRL -52494. Press, F., and M. Ewing...the Nuclear Testing Ground in Eastern Kazakhstan, Lawrence Livermore National Laboratory Report, LLNL Report No. UCRL -52856. Ruzaikin, A., I. Nersesov...Derring Hall University Park, PA 16802 Blacksburg, VA 24061 Dr. Ralph Alewine, III Dr. Stephen Bratt DARPAftMRO Center for Seismic Studies 3701 North Fairax

Computational Studies of X-ray Framing Cameras for the National Ignition Facility

DTIC Science & Technology

2013-06-01

Livermore National Laboratory 7000 East Avenue Livermore, CA 94550 USA Abstract The NIF is the world’s most powerful laser facility and is...a phosphor screen where the output is recorded. The x-ray framing cameras have provided excellent information. As the yields at NIF have increased...experiments on the NIF . The basic operation of these cameras is shown in Fig. 1. Incident photons generate photoelectrons both in the pores of the MCP and

The Future Role and Need for Nuclear Weapons in the 21st Century

DTIC Science & Technology

2007-01-01

program, the Manhattan Project : Einstein‘s letter to Roosevelt in 1939 regarding the use of the energy from uranium for bombs, ―the imaginary German...succeed, nuclear weapons were introduced by the US into our world in 1945. The Manhattan Project efforts produced four bombs within its first three...Proceedings‖ (Livermore, CA: Lawrence Livermore National Laboratory, 1991), 14. 6 Ibid. , 12. 7 ― Manhattan Project ,‖ MSN Encarta, 2, http://encarta

2003 Lawrence Livermore National Laboratory Annual Illness and Injury Surveillance Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

U.S. Department of Energy, Office of Health, Safety and Security, Office of Illness and Injury Prevention Programs

2007-05-23

Annual Illness and Injury Surveillance Program report for 2003 for Lawrence Livermore National Lab. The U.S. Department of Energy’s (DOE) commitment to assuring the health and safety of its workers includes the conduct of epidemiologic surveillance activities that provide an early warning system for health problems among workers. The IISP monitors illnesses and health conditions that result in an absence of workdays, occupational injuries and illnesses, and disabilities and deaths among current workers.

Calculating the Vulnerability of Synthetic Polymers to Autoignition during Nuclear Flash.

DTIC Science & Technology

1985-03-01

Lawrence Livermore National Laboratory P.O. Box 808 2561C Livermore, California 94550 II. CONTROLLING OFFICE NAME AND ADDRESS 12. REPORT DATE~March...34Low Emissivity and Solar Control Coatings on Architectural Glass," Proc. SPIE 37, 324 (1982). 10. R. C. Weast, Ed., Handbook of Chemistry and Physics...Attn: Michael Frankel Chief of Engineers Washington, D.C. 20305 Department of the Army Attn: DAEN-RDZ-A Command and Control Technical Center Washington

IGA-ADS: Isogeometric analysis FEM using ADS solver

NASA Astrophysics Data System (ADS)

Łoś, Marcin M.; Woźniak, Maciej; Paszyński, Maciej; Lenharth, Andrew; Hassaan, Muhamm Amber; Pingali, Keshav

2017-08-01

In this paper we present a fast explicit solver for solution of non-stationary problems using L2 projections with isogeometric finite element method. The solver has been implemented within GALOIS framework. It enables parallel multi-core simulations of different time-dependent problems, in 1D, 2D, or 3D. We have prepared the solver framework in a way that enables direct implementation of the selected PDE and corresponding boundary conditions. In this paper we describe the installation, implementation of exemplary three PDEs, and execution of the simulations on multi-core Linux cluster nodes. We consider three case studies, including heat transfer, linear elasticity, as well as non-linear flow in heterogeneous media. The presented package generates output suitable for interfacing with Gnuplot and ParaView visualization software. The exemplary simulations show near perfect scalability on Gilbert shared-memory node with four Intel® Xeon® CPU E7-4860 processors, each possessing 10 physical cores (for a total of 40 cores).

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

Real-time monitoring and massive inversion of source parameters of very long period seismic signals: An application to Stromboli Volcano, Italy

USGS Publications Warehouse

Auger, E.; D'Auria, L.; Martini, M.; Chouet, B.; Dawson, P.

2006-01-01

We present a comprehensive processing tool for the real-time analysis of the source mechanism of very long period (VLP) seismic data based on waveform inversions performed in the frequency domain for a point source. A search for the source providing the best-fitting solution is conducted over a three-dimensional grid of assumed source locations, in which the Green's functions associated with each point source are calculated by finite differences using the reciprocal relation between source and receiver. Tests performed on 62 nodes of a Linux cluster indicate that the waveform inversion and search for the best-fitting signal over 100,000 point sources require roughly 30 s of processing time for a 2-min-long record. The procedure is applied to post-processing of a data archive and to continuous automatic inversion of real-time data at Stromboli, providing insights into different modes of degassing at this volcano. Copyright 2006 by the American Geophysical Union.

NBodyLab Simulation Experiments with GRAPE-6a AND MD-GRAPE2 Acceleration

NASA Astrophysics Data System (ADS)

Johnson, V.; Ates, A.

2005-12-01

NbodyLab is an astrophysical N-body simulation testbed for student research. It is accessible via a web interface and runs as a backend framework under Linux. NbodyLab can generate data models or perform star catalog lookups, transform input data sets, perform direct summation gravitational force calculations using a variety of integration schemes, and produce analysis and visualization output products. NEMO (Teuben 1994), a popular stellar dynamics toolbox, is used for some functions. NbodyLab integrators can optionally utilize two types of low-cost desktop supercomputer accelerators, the newly available GRAPE-6a (125 Gflops peak) and the MD-GRAPE2 (64-128 Gflops peak). The initial version of NBodyLab was presented at ADASS 2002. This paper summarizes software enhancements developed subsequently, focusing on GRAPE-6a related enhancements, and gives examples of computational experiments and astrophysical research, including star cluster and solar system studies, that can be conducted with the new testbed functionality.

Integrating Multibody Simulation and CFD: toward Complex Multidisciplinary Design Optimization

NASA Astrophysics Data System (ADS)

Pieri, Stefano; Poloni, Carlo; Mühlmeier, Martin

This paper describes the use of integrated multidisciplinary analysis and optimization of a race car model on a predefined circuit. The objective is the definition of the most efficient geometric configuration that can guarantee the lowest lap time. In order to carry out this study it has been necessary to interface the design optimization software modeFRONTIER with the following softwares: CATIA v5, a three dimensional CAD software, used for the definition of the parametric geometry; A.D.A.M.S./Motorsport, a multi-body dynamic simulation software; IcemCFD, a mesh generator, for the automatic generation of the CFD grid; CFX, a Navier-Stokes code, for the fluid-dynamic forces prediction. The process integration gives the possibility to compute, for each geometrical configuration, a set of aerodynamic coefficients that are then used in the multiboby simulation for the computation of the lap time. Finally an automatic optimization procedure is started and the lap-time minimized. The whole process is executed on a Linux cluster running CFD simulations in parallel.

Low latency network and distributed storage for next generation HPC systems: the ExaNeSt project

NASA Astrophysics Data System (ADS)

Ammendola, R.; Biagioni, A.; Cretaro, P.; Frezza, O.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Paolucci, P. S.; Pastorelli, E.; Pisani, F.; Simula, F.; Vicini, P.; Navaridas, J.; Chaix, F.; Chrysos, N.; Katevenis, M.; Papaeustathiou, V.

2017-10-01

With processor architecture evolution, the HPC market has undergone a paradigm shift. The adoption of low-cost, Linux-based clusters extended the reach of HPC from its roots in modelling and simulation of complex physical systems to a broader range of industries, from biotechnology, cloud computing, computer analytics and big data challenges to manufacturing sectors. In this perspective, the near future HPC systems can be envisioned as composed of millions of low-power computing cores, densely packed — meaning cooling by appropriate technology — with a tightly interconnected, low latency and high performance network and equipped with a distributed storage architecture. Each of these features — dense packing, distributed storage and high performance interconnect — represents a challenge, made all the harder by the need to solve them at the same time. These challenges lie as stumbling blocks along the road towards Exascale-class systems; the ExaNeSt project acknowledges them and tasks itself with investigating ways around them.

A hybrid neurogenetic approach for stock forecasting.

PubMed

Kwon, Yung-Keun; Moon, Byung-Ro

2007-05-01

In this paper, we propose a hybrid neurogenetic system for stock trading. A recurrent neural network (NN) having one hidden layer is used for the prediction model. The input features are generated from a number of technical indicators being used by financial experts. The genetic algorithm (GA) optimizes the NN's weights under a 2-D encoding and crossover. We devised a context-based ensemble method of NNs which dynamically changes on the basis of the test day's context. To reduce the time in processing mass data, we parallelized the GA on a Linux cluster system using message passing interface. We tested the proposed method with 36 companies in NYSE and NASDAQ for 13 years from 1992 to 2004. The neurogenetic hybrid showed notable improvement on the average over the buy-and-hold strategy and the context-based ensemble further improved the results. We also observed that some companies were more predictable than others, which implies that the proposed neurogenetic hybrid can be used for financial portfolio construction.

Mean PB To Failure - Initial results from a long-term study of disk storage patterns at the RACF

NASA Astrophysics Data System (ADS)

Caramarcu, C.; Hollowell, C.; Rao, T.; Strecker-Kellogg, W.; Wong, A.; Zaytsev, S. A.

2015-12-01

The RACF (RHIC-ATLAS Computing Facility) has operated a large, multi-purpose dedicated computing facility since the mid-1990’s, serving a worldwide, geographically diverse scientific community that is a major contributor to various HEPN projects. A central component of the RACF is the Linux-based worker node cluster that is used for both computing and data storage purposes. It currently has nearly 50,000 computing cores and over 23 PB of storage capacity distributed over 12,000+ (non-SSD) disk drives. The majority of the 12,000+ disk drives provide a cost-effective solution for dCache/XRootD-managed storage, and a key concern is the reliability of this solution over the lifetime of the hardware, particularly as the number of disk drives and the storage capacity of individual drives grow. We report initial results of a long-term study to measure lifetime PB read/written to disk drives in the worker node cluster. We discuss the historical disk drive mortality rate, disk drive manufacturers' published MPTF (Mean PB to Failure) data and how they are correlated to our results. The results help the RACF understand the productivity and reliability of its storage solutions and have implications for other highly-available storage systems (NFS, GPFS, CVMFS, etc) with large I/O requirements.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

Fast Image Subtraction Using Multi-cores and GPUs

NASA Astrophysics Data System (ADS)

Hartung, Steven; Shukla, H.

2013-01-01

Many important image processing techniques in astronomy require a massive number of computations per pixel. Among them is an image differencing technique known as Optimal Image Subtraction (OIS), which is very useful for detecting and characterizing transient phenomena. Like many image processing routines, OIS computations increase proportionally with the number of pixels being processed, and the number of pixels in need of processing is increasing rapidly. Utilizing many-core graphical processing unit (GPU) technology in a hybrid conjunction with multi-core CPU and computer clustering technologies, this work presents a new astronomy image processing pipeline architecture. The chosen OIS implementation focuses on the 2nd order spatially-varying kernel with the Dirac delta function basis, a powerful image differencing method that has seen limited deployment in part because of the heavy computational burden. This tool can process standard image calibration and OIS differencing in a fashion that is scalable with the increasing data volume. It employs several parallel processing technologies in a hierarchical fashion in order to best utilize each of their strengths. The Linux/Unix based application can operate on a single computer, or on an MPI configured cluster, with or without GPU hardware. With GPU hardware available, even low-cost commercial video cards, the OIS convolution and subtraction times for large images can be accelerated by up to three orders of magnitude.

Physics and Advanced Technologies 2003 Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazi, A; Sketchley, J

2005-01-20

The Physics and Advanced Technologies (PAT) Directorate overcame significant challenges in 2003 to deliver a wealth of scientific and programmatic milestones, and move toward closer alignment with programs at Lawrence Livermore National Laboratory. We acted aggressively in enabling the PAT Directorate to contribute to future, growing Lawrence Livermore missions in homeland security and at the National Ignition Facility (NIF). We made heavy investments to bring new capabilities to the Laboratory, to initiate collaborations with major Laboratory programs, and to align with future Laboratory directions. Consistent with our mission, we sought to ensure that Livermore programs have access to the bestmore » science and technology, today and tomorrow. For example, in a move aimed at revitalizing the Laboratory's expertise in nuclear and radiation detection, we brought the talented Measurement Sciences Group to Livermore from Lawrence Berkeley National Laboratory, after its mission there had diminished. The transfer to our I Division entailed significant investment by PAT in equipment and infrastructure required by the group. In addition, the move occurred at a time when homeland security funding was expected, but not yet available. By the end of the year, though, the group was making crucial contributions to the radiation detection program at Livermore, and nearly every member was fully engaged in programmatic activities. Our V Division made a move of a different sort, relocating en masse from Building 121 to the NIF complex. This move was designed to enhance interaction and collaboration among high-energy-density experimental scientists at the Laboratory, a goal that is essential to the effective use of NIF in the future. Since then, V Division has become increasingly integrated with NIF activities. Division scientists are heavily involved in diagnostic development and fielding and are poised to perform equation-of-state and high-temperature hohlraum experiments in 2004 as part of the NIF Early Light program.« less

[Design of an embedded stroke rehabilitation apparatus system based on Linux computer engineering].

PubMed

Zhuang, Pengfei; Tian, XueLong; Zhu, Lin

2014-04-01

A realizaton project of electrical stimulator aimed at motor dysfunction of stroke is proposed in this paper. Based on neurophysiological biofeedback, this system, using an ARM9 S3C2440 as the core processor, integrates collection and display of surface electromyography (sEMG) signal, as well as neuromuscular electrical stimulation (NMES) into one system. By embedding Linux system, the project is able to use Qt/Embedded as a graphical interface design tool to accomplish the design of stroke rehabilitation apparatus. Experiments showed that this system worked well.

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds

PubMed Central

2012-01-01

Background The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. In Bioinformatics, MapReduce has already been adopted to various case scenarios such as mapping next generation sequencing data to a reference genome, finding SNPs from short read data or matching strings in genotype files. Nevertheless, tasks like installing and maintaining MapReduce on a cluster system, importing data into its distributed file system or executing MapReduce programs require advanced knowledge in computer science and could thus prevent scientists from usage of currently available and useful software solutions. Results Here we present Cloudgene, a freely available platform to improve the usability of MapReduce programs in Bioinformatics by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house (private clouds) and rented clusters (public clouds). The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface. Since Cloudgene can be executed on private clusters, sensitive datasets can be kept in house at all time and data transfer times are therefore minimized. Conclusions Our results show that MapReduce programs can be integrated into Cloudgene with little effort and without adding any computational overhead to existing programs. This platform gives developers the opportunity to focus on the actual implementation task and provides scientists a platform with the aim to hide the complexity of MapReduce. In addition to MapReduce programs, Cloudgene can also be used to launch predefined systems (e.g. Cloud BioLinux, RStudio) in public clouds. Currently, five different bioinformatic programs using MapReduce and two systems are integrated and have been successfully deployed. Cloudgene is freely available at http://cloudgene.uibk.ac.at. PMID:22888776

Accelerator-Detector Complex for Photonuclear Detection of Hidden Explosives Final Report CRADA No. TC2065.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowdermilk, W. H.; Brothers, L. J.

This was a collaborative effort by Lawrence Livermore National Security (formerly the University of California)/Lawrence Livermore National Laboratory (LLNL), Valley Forge Composite Technologies, Inc., and the following Russian Institutes: P. N. Lebedev Physical Institute (LPI), Innovative Technologies Center.(AUO CIT), Central Design Bureau-Almas (CDB Almaz), Moscow Instrument Automation Research Institute, and Institute for High Energy Physics (IBEP) to develop equipment and procedures for detecting explosive materials concealed in airline checked baggage and cargo.

Manufacturing and Characterization of Ultra Pure Ferrous Alloys Final Report CRADA No. TC02069.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesuer, D.; McGreevy, T. E.

This CRADA was a.collaborative effort between the Lawrence Livermore National Security LLC (formerly University of California)/Lawrence Livermore National Laboratory (LLNL),and Caterpillar Inc. (CaterpiHar), to further advance levitation casting techniques (developed at the Central Research Institute for Material (CRIM) in St. Petersburg, Russia) for use in manufacturing high purity metal alloys. This DOE Global Initiatives for Proliferation Prevention Program (IPP) project was to develop and demonstrate the levitation casting technology for producing ultra-pure alloys.

Studies of Near-Source and Near-Receiver Scattering and Low-Frequency Lg from East Kazakh and NTS Explosions

DTIC Science & Technology

1991-12-04

ADDRESS(ES) 10. SPONSORING/MONITORING DARPA/NMRO Phillips Laboratory AGENCY REPORT NUMBER (Attn: Dr. A. Ryall) Hanscom AFB, MA 01731-5000 3701 North...areas and media at the USERDA Nevada Test Site, UCRL -51948, Lawrence Livermore La- boratory, Livermore, California. Stead, R. J. and D. V. HeImberger...University Park, PA 16802 Blacksburg, VA 24061 Dr. Ralph Alewine, III Dr. Stephen Bratt DARPA/NMRO Center for Seismic Studies 3701 North Fairfax Drive 1300

Proceedings of the Annual PL/DARPA Seismic Research Symposium (14th) Held in Tucson, AZ on 16-18 September 1992

DTIC Science & Technology

1992-08-17

01731-5000 UP, No. 1106 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSORING/ MONITORING AGENCY REPORT NUMBER DARPA/NMRO 3701 North...the peaceful uses of nuclear explosives, UCRL -5414, Lawrence Livermore National Laboratory, 1973. Nordyke, M.D., A review of Soviet data on the peaceful...Lawrence Livermore national Laboratory, UCRL -JC-107941, preprint. Haskell, N. A. (1964). Radiation pattern of surface waves from point sources in a

Lawrence Livermore National Laboratory Experimental Test Site, Site 300, Biological Review, January 1, 2009 through December 31, 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paterson, Lisa E.; Woollett, Jim S.

2014-01-01

The Lawrence Livermore National Laboratory’s (LLNL’s) Environmental Restoration Department (ERD) is required to conduct an ecological review at least every five years to ensure that biological and contaminant conditions in areas undergoing remediation have not changed such that existing conditions pose an ecological hazard (Dibley et al. 2009a). This biological review is being prepared by the Natural Resources Team within LLNL’s Environmental Functional Area (EFA) to support the 2013 five-year ecological review.

PHYSICS: Will Livermore Laser Ever Burn Brightly?

PubMed

Seife, C; Malakoff, D

2000-08-18

The National Ignition Facility (NIF), a superlaser being built here at Lawrence Livermore National Laboratory in an effort to use lasers rather than nuclear explosions to create a fusion reaction, is supposed to allow weapons makers to preserve the nuclear arsenal--and do nifty fusion science, too. But a new report that examines its troubled past also casts doubt on its future. Even some of NIF's scientific and political allies are beginning to talk openly of a scaled-down version of the original 192-laser design.

The Use of Carbon Aerogel Electrodes for Deionizing Water and Treating Aqueous Process Wastes

DTIC Science & Technology

1996-01-01

Wastes Joseph C. Farmer, Gregory V. Mack and David V. Fix Lawrence Livermore National Laboratory Livermore, California 94550 Abstract A wide variety of...United States Department of Interior, 190 pages, May (1966). 9. A. M. Johnson, A. W. Venolia, J. Newman, R. G. Wilbourne , C. M. Wong, , W. S. Gillam...Dept. Interior Pub. 200 056, 31 pages, March (1970). 10. A. M. Johnson, A. W. Venolia, R. G Wilbourne , J. Newman, "The Electrosorb Process for

Lawrence Livermore National Laboratory safeguards and security quarterly progress report to the US Department of Energy quarter ending September 30, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, G.; Mansur, D.L.; Ruhter, W.D.

1994-10-01

This report presents the details of the Lawrence Livermore National Laboratory safeguards and securities program. This program is focused on developing new technology, such as x- and gamma-ray spectrometry, for measurement of special nuclear materials. This program supports the Office of Safeguards and Securities in the following five areas; safeguards technology, safeguards and decision support, computer security, automated physical security, and automated visitor access control systems.

Radioprotective Drugs: A Synopsis of Current Research and a Proposed Research Plan for the Federal Emergency Management Agency.

DTIC Science & Technology

1985-04-01

Lawrence Livermore National Laboratory *P.O. Box 808 2431D Livermore, CA 94550 ______ 11. CONTROLLING OFFICE NAME AND ADDRESS 12. REPORT DATE April 1985...administration of drugs is preferred, to give the highest degree of control possible. Specific tumors are to be made more sensitive to radiation, while the...PJlanification c/Evaristo San Miguel, 8 Madrid-8 SPAIN Ministero dell Interno * ~Direzione Generale della -’- - Protezione Civile 00100 Rome ITALY

A case-control study of malignant melanoma among Lawrence Livermore National Laboratory employees: A critical evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kupper, L.L.; Setzer, R.W.; Schwartzbaum, J.

1987-07-01

This document reports on a reevaluation of data obtained in a previous report on occupational factors associated with the development of malignant melanomas at Lawrence Livermore National Laboratory. The current report reduces the number of these factors from five to three based on a rigorous statistical analysis of the original data. Recommendations include restructuring the original questionnaire and trying to contact more individuals that worked with volatile photographic chemicals. 17 refs., 7 figs., 22 tabs. (TEM)

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

Results of Surveys for Special Status Reptiles at the Site 300 Facilities of Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woollett, J J

2008-09-18

The purpose of this report is to present the results of a live-trapping and visual surveys for special status reptiles at the Site 300 Facilities of Lawrence Livermore National Laboratory (LLNL). The survey was conducted under the authority of the Federal recovery permit of Swaim Biological Consulting (PRT-815537) and a Memorandum of Understanding issued from the California Department of Fish and Game. Site 300 is located between Livermore and Tracy just north of Tesla road (Alameda County) and Corral Hollow Road (San Joaquin County) and straddles the Alameda and San Joaquin County line (Figures 1 and 2). It encompasses portionsmore » of the USGS 7.5 minute Midway and Tracy quadrangles (Figure 2). Focused surveys were conducted for four special status reptiles including the Alameda whipsnake (Masticophis lateralis euryxanthus), the San Joaquin Whipsnake (Masticophis Hagellum ruddock), the silvery legless lizard (Anniella pulchra pulchra), and the California horned lizard (Phrynosoma coronanum frontale).« less

Multi-pulse power injection and spheromak sustainment in SSPX

NASA Astrophysics Data System (ADS)

Stallard, B. W.; Hill, D. N.; Hooper, E. B.; Bulmer, R. H.; McLean, H. S.; Wood, R. D.; Woodruff, S.; Sspx Team

2000-10-01

Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. Spheromak formation (gun injection phase) and sustainment experiments are now routine in SSPX using a multi-bank power system. Gun voltage, impedance, and power coupling show a clear current threshold dependence on gun flux (I_th~=λ_0φ_gun/μ_0), increasing with current above the threshold, and are compared with CTX results. The characteristic gun inductance, L_gun~=0.6 μH, derived from the gun voltage dependence on di/dt, is larger than expected from Corsica modeling of the spheromak equilibrium. It’s value is consistent with the n=1 ‘doughook’ mode structure reported in SPHEX and believed important for helicity injection and toroidal current drive. Results of helicity and power balance calculations of spheromak poloidal field buildup are compared with experiment and used to project sustainment with a future longer pulse power supply. This work was performed under the auspices of US DOE by the University of California Lawrence Livermore National Laboratory under Contract No. W-7405-ENG-48.

Lawrence Livermore National Laboratory environmental report for 1990

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sims, J.M.; Surano, K.A.; Lamson, K.C.

1990-01-01

This report documents the results of the Environmental Monitoring Program at the Lawrence Livermore National Laboratory (LLNL) and presents summary information about environmental compliance for 1990. To evaluate the effect of LLNL operations on the local environment, measurements of direct radiation and a variety of radionuclides and chemical compounds in ambient air, soil, sewage effluent surface water, groundwater, vegetation, and foodstuff were made at both the Livermore site and at Site 300 nearly. LLNL's compliance with all applicable guides, standards, and limits for radiological and nonradiological emissions to the environment was evaluated. Aside from an August 13 observation of silvermore » concentrations slightly above guidelines for discharges to the sanitary sewer, all the monitoring data demonstrated LLNL compliance with environmental laws and regulations governing emission and discharge of materials to the environment. In addition, the monitoring data demonstrated that the environmental impacts of LLNL are minimal and pose no threat to the public to or to the environment. 114 refs., 46 figs., 79 tabs.« less

ALMA Correlator Real-Time Data Processor

NASA Astrophysics Data System (ADS)

Pisano, J.; Amestica, R.; Perez, J.

2005-10-01

The design of a real-time Linux application utilizing Real-Time Application Interface (RTAI) to process real-time data from the radio astronomy correlator for the Atacama Large Millimeter Array (ALMA) is described. The correlator is a custom-built digital signal processor which computes the cross-correlation function of two digitized signal streams. ALMA will have 64 antennas with 2080 signal streams each with a sample rate of 4 giga-samples per second. The correlator's aggregate data output will be 1 gigabyte per second. The software is defined by hard deadlines with high input and processing data rates, while requiring interfaces to non real-time external computers. The designed computer system - the Correlator Data Processor or CDP, consists of a cluster of 17 SMP computers, 16 of which are compute nodes plus a master controller node all running real-time Linux kernels. Each compute node uses an RTAI kernel module to interface to a 32-bit parallel interface which accepts raw data at 64 megabytes per second in 1 megabyte chunks every 16 milliseconds. These data are transferred to tasks running on multiple CPUs in hard real-time using RTAI's LXRT facility to perform quantization corrections, data windowing, FFTs, and phase corrections for a processing rate of approximately 1 GFLOPS. Highly accurate timing signals are distributed to all seventeen computer nodes in order to synchronize them to other time-dependent devices in the observatory array. RTAI kernel tasks interface to the timing signals providing sub-millisecond timing resolution. The CDP interfaces, via the master node, to other computer systems on an external intra-net for command and control, data storage, and further data (image) processing. The master node accesses these external systems utilizing ALMA Common Software (ACS), a CORBA-based client-server software infrastructure providing logging, monitoring, data delivery, and intra-computer function invocation. The software is being developed in tandem with the correlator hardware which presents software engineering challenges as the hardware evolves. The current status of this project and future goals are also presented.

The LINC-NIRVANA fringe and flexure tracker: Linux real-time solutions

NASA Astrophysics Data System (ADS)

Wang, Yeping; Bertram, Thomas; Straubmeier, Christian; Rost, Steffen; Eckart, Andreas

2006-06-01

The correction of atmospheric differential piston and instrumental flexure effects is mandatory for optimum interferometric performance of the LBT NIR interferometric imaging camera LINC-NIRVANA. The task of the Fringe and Flexure Tracking System (FFTS) is to detect and correct these effects in a real-time closed loop. On a timescale of milliseconds, image data of the order of 4K bytes has to be retrieved from the FFTS detector, analyzed, and the results have to be sent to the control system. The need for a reliable communication between several processes within a confined period of time calls for solutions with good real-time performance. We investigated two soft real-time options for the Linux platform. The design we present takes advantage of several features that follow the POSIX standard with improved real-time performance, which were implemented in the new Linux kernel (2.6.12). Several concepts, such as synchronization, shared memory, and preemptive scheduling are considered and the performance of the most time-critical parts of the FFTS software is tested.

Testing Task Schedulers on Linux System

NASA Astrophysics Data System (ADS)

Jelenković, Leonardo; Groš, Stjepan; Jakobović, Domagoj

Testing task schedulers on Linux operating system proves to be a challenging task. There are two main problems. The first one is to identify which properties of the scheduler to test. The second problem is how to perform it, e.g., which API to use that is sufficiently precise and in the same time supported on most platforms. This paper discusses the problems in realizing test framework for testing task schedulers and presents one potential solution. Observed behavior of the scheduler is the one used for “normal” task scheduling (SCHED_OTHER), unlike one used for real-time tasks (SCHED_FIFO, SCHED_RR).

Comparative Analysis of Active and Passive Mapping Techniques in an Internet-Based Local Area Network

DTIC Science & Technology

2004-03-01

PIII/500 (K) 512 A11 3C905 Honeynet PIII/1000 (C) 512 A11 3C905 Generator PIII/800 (C) 256 A11 3C905 Each system is running Debian GNU / Linux “unstable...Network,” September 2000. http://www.issues.af.mil/notams/notam00-5.html; accessed January 16, 2004. 5. “Debian GNU / Linux 3.0 Released,” Debian News...interact with those servers. 1.5 Summary The remainder of this document is organized into four chapters. Chapter 2 con - tains the literature review where

Dataset for forensic analysis of B-tree file system.

PubMed

Wani, Mohamad Ahtisham; Bhat, Wasim Ahmad

2018-06-01

Since B-tree file system (Btrfs) is set to become de facto standard file system on Linux (and Linux based) operating systems, Btrfs dataset for forensic analysis is of great interest and immense value to forensic community. This article presents a novel dataset for forensic analysis of Btrfs that was collected using a proposed data-recovery procedure. The dataset identifies various generalized and common file system layouts and operations, specific node-balancing mechanisms triggered, logical addresses of various data structures, on-disk records, recovered-data as directory entries and extent data from leaf and internal nodes, and percentage of data recovered.

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chinn, D J

This month's issue has the following articles: (1) The Edward Teller Centennial--Commentary by George H. Miller; (2) Edward Teller's Century: Celebrating the Man and His Vision--Colleagues at the Laboratory remember Edward Teller, cofounder of Lawrence Livermore, adviser to U.S. presidents, and physicist extraordinaire, on the 100th anniversary of his birth; (3) Quark Theory and Today's Supercomputers: It's a Match--Thanks to the power of BlueGene/L, Livermore has become an epicenter for theoretical advances in particle physics; and (4) The Role of Dentin in Tooth Fracture--Studies on tooth dentin show that its mechanical properties degrade with age.

Institute of Geophysics and Planetary Physics (IGPP), Lawrence Livermore National Laboratory (LLNL): Quinquennial report, November 14-15, 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tweed, J.

1996-10-01

This Quinquennial Review Report of the Lawrence Livermore National Laboratory (LLNL) branch of the Institute for Geophysics and Planetary Physics (IGPP) provides an overview of IGPP-LLNL, its mission, and research highlights of current scientific activities. This report also presents an overview of the University Collaborative Research Program (UCRP), a summary of the UCRP Fiscal Year 1997 proposal process and the project selection list, a funding summary for 1993-1996, seminars presented, and scientific publications. 2 figs., 3 tabs.

Additional deployment of ocean bottom gravity meter and ocean bottom electro-magnetic meter for the multidisciplinary cabled observation in Sagami Bay, Japan

NASA Astrophysics Data System (ADS)

Mitsuzawa, K.; Goto, T.; Araki, E.; Watanabe, T.; Sugioka, H.; Kasaya, T.; Sayanagi, K.; Mikada, H.; Fujimoto, H.; Nagao, T.; Koizumi, K.; Asakawa, K.

2005-12-01

Western part of the Sagami Bay central Pacific side of Japan, is known as one of the high active tectonic areas. In this area, Teishi Knoll, volcanic seamount, erupted in 1989 and the earthquake swarms occurs repeatedly every few years in the eastern coast of the Izu Peninsula. The real-time deep sea floor observatory was deployed about 7 km off Hatsushima Island, Sagami Bay, at a depth of 1174 m in 1993 to monitor seismic activities, underwater pressure, water temperature and deep currents. The video camera and lights were also mounted in the observatory to monitor the relations among biological activities associated with the tectonic activities. The observation system including submarine electro-optical cable with a length of 8 km was completely renewed in 2000. The several underwater-mateable connectors are installed in the new observatory for additional observation instruments. A precise pressure sensor, ocean bottom gravity meter and ocean bottom electro-magnetic meter were installed using ROV Hyper-Dolphin in the cruise of R/V Natsushima from January 9 to 14, 2005. We start to operate them at February 10, 2005 after checking those of data qualities. We also installed an underwater internet interface, which is called Linux Box, as a prototype of underwater network system which was operated by Linux operating system. The Linux Box is a key network system for multidisciplinary observation network. It will be able to connect much kind of observation instruments as using internet connection. We put the precise pressure sensor as a sensor of the Linux Box in this experiment.

Initial Results of the SSPX Transient Internal Probe System for Measuring Toroidal Field Profiles

NASA Astrophysics Data System (ADS)

Holcomb, C. T.; Jarboe, T. R.; Mattick, A. T.; Hill, D. N.; McLean, H. S.; Wood, R. D.; Cellamare, V.

2000-10-01

Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. The Sustained Spheromak Physics Experiment (SSPX) is using a field profile diagnostic called the Transient Internal Probe (TIP). TIP consists of a verdet-glass bullet that is used to measure the magnetic field by Faraday rotation. This probe is shot through the spheromak by a light gas gun at speeds near 2 km/s. An argon laser is aligned along the path of the probe. The light passes through the probe and is retro-reflected to an ellipsometer that measures the change in polarization angle. The measurement is spatially resolved down to the probes’ 1 cm length to within 15 Gauss. Initial testing results are given. This and future data will be used to determine the field profile for equilibrium reconstruction. TIP can also be used in conjunction with wall probes to map out toroidal mode amplitudes and phases internally. This work was performed under the auspices of US DOE by the University of California Lawrence Livermore National Laboratory under Contract No. W-7405-ENG-48.

Proceedings of the 3rd US-Japan Workshop on Plasma Polarization Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beiersdorfer, P; Flyimoto, T

The third US-Japan Workshop on Plasma Polarization Spectroscopy was held at the Lawrence Livermore National Laboratory in Livermore, California, on June 18-21, 2001. The talks presented at this workshop are summarized in these proceedings. The papers cover both experimental investigation and applications of plasma polarization spectroscopy as well as the theoretical foundation and formalisms to understand and describe the polarization phenomena. The papers give an overview of the history of plasma polarization spectroscopy, derive the formal aspects of polarization spectroscopy, including the effects of electric and magnetic fields, discuss spectra perturbed by intense microwave fields, charge exchange, and dielectronic recombination,more » and present calculations of various collisional excitation and ionization cross sections and the modeling of plasma polarization spectroscopy phenomena. Experimental results are given from the WT-3 tokamak, the MST reverse field pinch, the Large Helical Device, the GAMMA 10 mirror machine, the Nevada Terrawatt Facility, the Livermore EBIT-II electron beam ion trap, and beam-foil spectroscopy. In addition, results were presented from studies of several laser-produced plasma experiments and new instrumental techniques were demonstrated.« less

LHCb Dockerized Build Environment

NASA Astrophysics Data System (ADS)

Clemencic, M.; Belin, M.; Closier, J.; Couturier, B.

2017-10-01

Used as lightweight virtual machines or as enhanced chroot environments, Linux containers, and in particular the Docker abstraction over them, are more and more popular in the virtualization communities. The LHCb Core Software team decided to investigate how to use Docker containers to provide stable and reliable build environments for the different supported platforms, including the obsolete ones which cannot be installed on modern hardware, to be used in integration builds, releases and by any developer. We present here the techniques and procedures set up to define and maintain the Docker images and how these images can be used to develop on modern Linux distributions for platforms otherwise not accessible.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

Millisecond accuracy video display using OpenGL under Linux.

PubMed

Stewart, Neil

2006-02-01

To measure people's reaction times to the nearest millisecond, it is necessary to know exactly when a stimulus is displayed. This article describes how to display stimuli with millisecond accuracy on a normal CRT monitor, using a PC running Linux. A simple C program is presented to illustrate how this may be done within X Windows using the OpenGL rendering system. A test of this system is reported that demonstrates that stimuli may be consistently displayed with millisecond accuracy. An algorithm is presented that allows the exact time of stimulus presentation to be deduced, even if there are relatively large errors in measuring the display time.

Image Capture and Display Based on Embedded Linux

NASA Astrophysics Data System (ADS)

Weigong, Zhang; Suran, Di; Yongxiang, Zhang; Liming, Li

For the requirement of building a highly reliable communication system, SpaceWire was selected in the integrated electronic system. There was a need to test the performance of SpaceWire. As part of the testing work, the goal of this paper is to transmit image data from CMOS camera through SpaceWire and display real-time images on the graphical user interface with Qt in the embedded development platform of Linux & ARM. A point-to-point mode of transmission was chosen; the running result showed the two communication ends basically reach a consensus picture in succession. It suggests that the SpaceWire can transmit the data reliably.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bearinger, J P

This months issue has the following articles: (1) Science Translated for the Greater Good--Commentary by Steven D. Liedle; (2) The New Face of Industrial Partnerships--An entrepreneurial spirit is blossoming at Lawrence Livermore; (3) Monitoring a Nuclear Weapon from the Inside--Livermore researchers are developing tiny sensors to warn of detrimental chemical and physical changes inside nuclear warheads; (4) Simulating the Biomolecular Structure of Nanometer-Size Particles--Grand Challenge simulations reveal the size and structure of nanolipoprotein particles used to study membrane proteins; and (5) Antineutrino Detectors Improve Reactor Safeguards--Antineutrino detectors track the consumption and production of fissile materials inside nuclear reactors.

Development of a Landmine Detection Sensor Final Report CRADA No. TC02133.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romero, C. E.; Sheppard, C.

2017-09-06

This was one of two CRADAs between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and First Alliance Technologies, LLC (First Alliance), to conduct research and development activity toward an integrated system for the detecting, locating, and destroying of landmines and unexploded ordinance using a laser to destroy landmines and unexploded ordinance and First Alliance’s Land Mine Locator (LML) system. The focus of this CRADA was on developing a sensor system that accurately detects landmines, and provides exact location information in a timely manner with extreme reliability.

Human-factors engineering control-room design review/audit: Waterford 3 SES Generating Station, Louisiana Power and Light Company

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savage, J.W.

1983-03-10

A human factors engineering design review/audit of the Waterford-3 control room was performed at the site on May 10 through May 13, 1982. The report was prepared on the basis of the HFEB's review of the applicant's Preliminary Human Engineering Discrepancy (PHED) report and the human factors engineering design review performed at the site. This design review was carried out by a team from the Human Factors Engineering Branch, Division of Human Factors Safety. The review team was assisted by consultants from Lawrence Livermore National Laboratory (University of California), Livermore, California.

Science & Technology Review September 2005

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aufderheide III, M B

2005-07-19

This month's issue has the following articles: (1) The Pursuit of Fusion Energy--Commentary by William H. Goldstein; (2) A Dynamo of a Plasma--The self-organizing magnetized plasmas in a Livermore fusion energy experiment are akin to solar flares and galactic jets; (3) How One Equation Changed the World--A three-page paper by Albert Einstein revolutionized physics by linking mass and energy; (4) Recycled Equations Help Verify Livermore Codes--New analytic solutions for imploding spherical shells give scientists additional tools for verifying codes; and (5) Dust That.s Worth Keeping--Scientists have solved the mystery of an astronomical spectral feature in interplanetary dust particles.

Enhancing Scalability and Efficiency of the TOUGH2_MP for LinuxClusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Wu, Yu-Shu

2006-04-17

TOUGH2{_}MP, the parallel version TOUGH2 code, has been enhanced by implementing more efficient communication schemes. This enhancement is achieved through reducing the amount of small-size messages and the volume of large messages. The message exchange speed is further improved by using non-blocking communications for both linear and nonlinear iterations. In addition, we have modified the AZTEC parallel linear-equation solver to nonblocking communication. Through the improvement of code structuring and bug fixing, the new version code is now more stable, while demonstrating similar or even better nonlinear iteration converging speed than the original TOUGH2 code. As a result, the new versionmore » of TOUGH2{_}MP is improved significantly in its efficiency. In this paper, the scalability and efficiency of the parallel code are demonstrated by solving two large-scale problems. The testing results indicate that speedup of the code may depend on both problem size and complexity. In general, the code has excellent scalability in memory requirement as well as computing time.« less

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ligand.Info small-molecule Meta-Database.

PubMed

von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek

2004-12-01

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

ParDRe: faster parallel duplicated reads removal tool for sequencing studies.

PubMed

González-Domínguez, Jorge; Schmidt, Bertil

2016-05-15

Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/ jgonzalezd@udc.es. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Large-Scale NASA Science Applications on the Columbia Supercluster

NASA Technical Reports Server (NTRS)

Brooks, Walter

2005-01-01

Columbia, NASA's newest 61 teraflops supercomputer that became operational late last year, is a highly integrated Altix cluster of 10,240 processors, and was named to honor the crew of the Space Shuttle lost in early 2003. Constructed in just four months, Columbia increased NASA's computing capability ten-fold, and revitalized the Agency's high-end computing efforts. Significant cutting-edge science and engineering simulations in the areas of space and Earth sciences, as well as aeronautics and space operations, are already occurring on this largest operational Linux supercomputer, demonstrating its capacity and capability to accelerate NASA's space exploration vision. The presentation will describe how an integrated environment consisting not only of next-generation systems, but also modeling and simulation, high-speed networking, parallel performance optimization, and advanced data analysis and visualization, is being used to reduce design cycle time, accelerate scientific discovery, conduct parametric analysis of multiple scenarios, and enhance safety during the life cycle of NASA missions. The talk will conclude by discussing how NAS partnered with various NASA centers, other government agencies, computer industry, and academia, to create a national resource in large-scale modeling and simulation.

Recent advances in automatic alignment system for the National Ignition Facility

NASA Astrophysics Data System (ADS)

Wilhelmsen, Karl; Awwal, Abdul A. S.; Kalantar, Dan; Leach, Richard; Lowe-Webb, Roger; McGuigan, David; Miller Kamm, Vicki

2011-03-01

The automatic alignment system for the National Ignition Facility (NIF) is a large-scale parallel system that directs all 192 laser beams along the 300-m optical path to a 50-micron focus at target chamber in less than 50 minutes. The system automatically commands 9,000 stepping motors to adjust mirrors and other optics based upon images acquired from high-resolution digital cameras viewing beams at various locations. Forty-five control loops per beamline request image processing services running on a LINUX cluster to analyze these images of the beams and references, and automatically steer the beams toward the target. This paper discusses the upgrades to the NIF automatic alignment system to handle new alignment needs and evolving requirements as related to various types of experiments performed. As NIF becomes a continuously-operated system and more experiments are performed, performance monitoring is increasingly important for maintenance and commissioning work. Data, collected during operations, is analyzed for tuning of the laser and targeting maintenance work. Handling evolving alignment and maintenance needs is expected for the planned 30-year operational life of NIF.

Hubble Sees 'Island Universe' in the Coma Cluster

NASA Image and Video Library

2017-12-08

NASA image release August 10, 2010 A long-exposure Hubble Space Telescope image shows a majestic face-on spiral galaxy located deep within the Coma Cluster of galaxies, which lies 320 million light-years away in the northern constellation Coma Berenices. The galaxy, known as NGC 4911, contains rich lanes of dust and gas near its center. These are silhouetted against glowing newborn star clusters and iridescent pink clouds of hydrogen, the existence of which indicates ongoing star formation. Hubble has also captured the outer spiral arms of NGC 4911, along with thousands of other galaxies of varying sizes. The high resolution of Hubble's cameras, paired with considerably long exposures, made it possible to observe these faint details. NGC 4911 and other spirals near the center of the cluster are being transformed by the gravitational tug of their neighbors. In the case of NGC 4911, wispy arcs of the galaxy's outer spiral arms are being pulled and distorted by forces from a companion galaxy (NGC 4911A), to the upper right. The resultant stripped material will eventually be dispersed throughout the core of the Coma Cluster, where it will fuel the intergalactic populations of stars and star clusters. The Coma Cluster is home to almost 1,000 galaxies, making it one of the densest collections of galaxies in the nearby universe. It continues to transform galaxies at the present epoch, due to the interactions of close-proximity galaxy systems within the dense cluster. Vigorous star formation is triggered in such collisions. Galaxies in this cluster are so densely packed that they undergo frequent interactions and collisions. When galaxies of nearly equal masses merge, they form elliptical galaxies. Merging is more likely to occur in the center of the cluster where the density of galaxies is higher, giving rise to more elliptical galaxies. This natural-color Hubble image, which combines data obtained in 2006, 2007, and 2009 from the Wide Field Planetary Camera 2 and the Advanced Camera for Surveys, required 28 hours of exposure time. The Hubble Space Telescope is a project of international cooperation between NASA and the European Space Agency. NASA's Goddard Space Flight Center manages the telescope. The Space Telescope Science Institute (STScI) conducts Hubble science operations. STScI is operated for NASA by the Association of Universities for Research in Astronomy, Inc. in Washington, D.C. Credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA) Acknowledgment: K. Cook (Lawrence Livermore National Laboratory) To learn more about Hubble go to: www.nasa.gov/mission_pages/hubble/main/index.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

MCdevelop - a universal framework for Stochastic Simulations

NASA Astrophysics Data System (ADS)

Slawinska, M.; Jadach, S.

2011-03-01

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools.

Impact on TRMM Products of Conversion to Linux

NASA Technical Reports Server (NTRS)

Stocker, Erich Franz; Kwiatkowski, John

2008-01-01

In June 2008, TRMM data processing will be assumed by the Precipitation Processing System (PPS). This change will also mean a change in the hardware production environment from an SGI 32 bit IRIX processing environment to a Linux (Beowulf) 64 bit processing environment. This change of platform and operating system addressing (32 to 64) has some influence on data values in the TRMM data products. This paper will describe the transition architecture and scheduling. It will also provide an analysis of what the nature of the product differences will be. It will demonstrate that the differences are not scientifically significant and are generally not visible. However, they are not always identical with those which the SGI would produce.

NanoPack: visualizing and processing long read sequencing data.

PubMed

De Coster, Wouter; D'Hert, Svenn; Schultz, Darrin T; Cruts, Marc; Van Broeckhoven, Christine

2018-03-14

Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. wouter.decoster@molgen.vib-ua.be. Supplementary tables and figures are available at Bioinformatics online.

Real-time head movement system and embedded Linux implementation for the control of power wheelchairs.

PubMed

Nguyen, H T; King, L M; Knight, G

2004-01-01

Mobility has become very important for our quality of life. A loss of mobility due to an injury is usually accompanied by a loss of self-confidence. For many individuals, independent mobility is an important aspect of self-esteem. Head movement is a natural form of pointing and can be used to directly replace the joystick whilst still allowing for similar control. Through the use of embedded LINUX and artificial intelligence, a hands-free head movement wheelchair controller has been designed and implemented successfully. This system provides for severely disabled users an effective power wheelchair control method with improved posture, ease of use and attractiveness.

Real-time Experiment Interface for Biological Control Applications

PubMed Central

Lin, Risa J.; Bettencourt, Jonathan; White, John A.; Christini, David J.; Butera, Robert J.

2013-01-01

The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux. RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when using the Live CD). RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology. RTXI includes standard plug-ins for implementing commonly used electrophysiology protocols with synchronized stimulation, event detection, and online analysis. These and other user-contributed plug-ins can be found on the website (http://www.rtxi.org). PMID:21096883

Software for Processing of Digitized Astronegatives from Archives and Databases of Virtual Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu. I.; Andruk, V. N.; Kazantseva, L. V.

The paper discusses and illustrates the steps of basic processing of digitized image of astro negatives. Software for obtaining of a rectangular coordinates and photometric values of objects on photographic plates was created in the environment LINUX / MIDAS / ROMAFOT. The program can automatically process the specified number of files in FITS format with sizes up to 20000 x 20000 pixels. Other programs were made in FORTRAN and PASCAL with the ability to work in an environment of LINUX or WINDOWS. They were used for: identification of stars, separation and exclusion of diffraction satellites and double and triple exposures, elimination of image defects, reduction to the equatorial coordinates and magnitudes of a reference catalogs.

Directed self-assembly of virus particles at nanoscale chemical templates

NASA Astrophysics Data System (ADS)

Chung, Sung-Wook; Cheung, Chin Li; Chatterji, Anju; Lin, Tianwei; Johnson, Jack; de Yoreo, Jim

2006-03-01

Because viruses can be site-specifically engineered to present catalytic, electronic, and optical moieties, they are attractive as building blocks for hierarchical nanostructures. We report results using scanned probe nanolithography to direct virus organization into 1D and 2D patterns and in situ AFM investigations of organization dynamics as pattern geometry, inter-viral potential, virus flux, and virus-pattern interaction are varied. Cowpea Mosaic Virus was modified to present surface sites with histidine (His) or cysteine (Cys) groups. Flat gold substrates were patterned with 10-100nm features of alkyl thiols terminated by Ni-NTA or meleimide groups to reversibly and irreversibly bind to the Hys and Cys groups, respectively. We show how assembly kinetics, degree of ordering and cluster-size distribution at these templates depend on the control parameters and present a physical picture of virus assembly at templates that incorporates growth dynamics of small-molecule epitaxial systems and condensation dynamics of colloidal systems. This work was performed under the auspices of the U. S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.

Development of Carbon-14 Waste Destruction and Recovery System Using AC Plasma Torch Technology Final Report CRADA No. TC02108.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Althouse, P.; McKannay, R. H.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and ISOFLEX USA (ISOFLEX), to 1) develop and test a prototype waste destruction system ("System") using AC plasma torch technology to break down and drastically reduce the volume of Carbon-14 (C-14) contaminated medical laboratory wastes while satisfying all environmental regulations, and 2) develop and demonstrate methods for recovering 99%+ of the carbon including the C-14 allowing for possible re-use as a tagging and labeling tool in the biomedical industry.

Lawrence Livermore National Laboratories Perspective on Code Development and High Performance Computing Resources in Support of the National HED/ICF Effort

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clouse, C. J.; Edwards, M. J.; McCoy, M. G.

2015-07-07

Through its Advanced Scientific Computing (ASC) and Inertial Confinement Fusion (ICF) code development efforts, Lawrence Livermore National Laboratory (LLNL) provides a world leading numerical simulation capability for the National HED/ICF program in support of the Stockpile Stewardship Program (SSP). In addition the ASC effort provides high performance computing platform capabilities upon which these codes are run. LLNL remains committed to, and will work with, the national HED/ICF program community to help insure numerical simulation needs are met and to make those capabilities available, consistent with programmatic priorities and available resources.

Nuclear security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dingell, J.D.

1991-02-01

The Department of Energy's (DOE) Lawrence Livermore National Laboratory, located in Livermore, California, generates and controls large numbers of classified documents associated with the research and testing of nuclear weapons. Concern has been raised about the potential for espionage at the laboratory and the national security implications of classified documents being stolen. This paper determines the extent of missing classified documents at the laboratory and assesses the adequacy of accountability over classified documents in the laboratory's custody. Audit coverage was limited to the approximately 600,000 secret documents in the laboratory's custody. The adequacy of DOE's oversight of the laboratory's secretmore » document control program was also assessed.« less

322-R2U2 Engineering Assessment - August 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abri, M.; Griffin, D.

This Engineering Assessment and Certification of Integrity of retention tank system 322-R2 has been prepared for tank systems that store and neutralizes hazardous waste and have secondary containment. The regulations require that this assessment be completed periodically and certified by an independent, qualified, California-registered professional engineer. Abri Environmental Engineering performed an inspection of the 322-R2 Tank system at the Lawrence Livermore National Laboratory (LLNL) in Livermore, CA. Mr. William W. Moore, P.E., conducted this inspection on March 16, 2015. Mr. Moore is a California Registered Civil Engineer, with extensive experience in civil engineering, and hazardous waste management.

Rethinking Approaches to Strategic Stability in the 21st Century

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rose, Brian

Lawrence Livermore National Laboratory (LLNL) hosted a two-day conference on rethinking approaches to strategic stability in the 21st century on October 20-21, 2016 in Livermore, CA. The conference was jointly convened by Lawrence Livermore, Los Alamos, and Sandia National Laboratories, and was held in partnership with the United States Department of State’s Bureau of Arms Control, Verification and Compliance. The conference took place at LLNL’s Center for Global Security Research (CGSR) and included a range of representatives from U.S. government, academic, and private institutions, as well as representatives from U.S. allies in Europe and Asia.The following summary covers topics andmore » discussions from each of the panels. It is not intended to capture every point in detail, but seeks to outline the range of views on these complex and inter-related issues while providing a general overview of the panel topics and discussions that took place. The conference was held under the Chatham House rule and does not attribute any remarks to any specific individual or institution. The views reflected in this report do not represent the United States Government, Department of State, or the national laboratories.« less

Site safety plan for Lawrence Livermore National Laboratory CERCLA investigations at site 300. Revision 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kilmer, J.

Various Department of Energy Orders incorporate by reference, health and safety regulations promulgated by the Occupational Safety and Health Administration (OSHA). One of the OSHA regulations, 29 CFR 1910.120, Hazardous Waste Operations and Emergency Response, requires that site safety plans are written for activities such as those covered by work plans for Site 300 environmental investigations. Based upon available data, this Site Safety Plan (Plan) for environmental restoration has been prepared specifically for the Lawrence Livermore National Laboratory Site 300, located approximately 15 miles east of Livermore, California. As additional facts, monitoring data, or analytical data on hazards are provided,more » this Plan may need to be modified. It is the responsibility of the Environmental Restoration Program and Division (ERD) Site Safety Officer (SSO), with the assistance of Hazards Control, to evaluate data which may impact health and safety during these activities and to modify the Plan as appropriate. This Plan is not `cast-in-concrete.` The SSO shall have the authority, with the concurrence of Hazards Control, to institute any change to maintain health and safety protection for workers at Site 300.« less

Cross-scale MD simulations of dynamic strength of tantalum

NASA Astrophysics Data System (ADS)

Bulatov, Vasily

2017-06-01

Dislocations are ubiquitous in metals where their motion presents the dominant and often the only mode of plastic response to straining. Over the last 25 years computational prediction of plastic response in metals has relied on Discrete Dislocation Dynamics (DDD) as the most fundamental method to account for collective dynamics of moving dislocations. Here we present first direct atomistic MD simulations of dislocation-mediated plasticity that are sufficiently large and long to compute plasticity response of single crystal tantalum while tracing the underlying dynamics of dislocations in all atomistic details. Where feasible, direct MD simulations sidestep DDD altogether thus reducing uncertainties of strength predictions to those of the interatomic potential. In the specific context of shock-induced material dynamics, the same MD models predict when, under what conditions and how dislocations interact and compete with other fundamental mechanisms of dynamic response, e.g. twinning, phase-transformations, fracture. In collaboration with: Luis Zepeda-Ruiz, Lawrence Livermore National Laboratory; Alexander Stukowski, Technische Universitat Darmstadt; Tomas Oppelstrup, Lawrence Livermore National Laboratory. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Lawrence Livermore National Laboratory Environmental Report 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Henry E.; Armstrong, Dave; Blake, Rick G.

Lawrence Livermore National Laboratory (LLNL) is a premier research laboratory that is part of the National Nuclear Security Administration (NNSA) within the U.S. Department of Energy (DOE). As a national security laboratory, LLNL is responsible for ensuring that the nation’s nuclear weapons remain safe, secure, and reliable. The Laboratory also meets other pressing national security needs, including countering the proliferation of weapons of mass destruction and strengthening homeland security, and conducting major research in atmospheric, earth, and energy sciences; bioscience and biotechnology; and engineering, basic science, and advanced technology. The Laboratory is managed and operated by Lawrence Livermore National Security,more » LLC (LLNS), and serves as a scientific resource to the U.S. government and a partner to industry and academia. LLNL operations have the potential to release a variety of constituents into the environment via atmospheric, surface water, and groundwater pathways. Some of the constituents, such as particles from diesel engines, are common at many types of facilities while others, such as radionuclides, are unique to research facilities like LLNL. All releases are highly regulated and carefully monitored. LLNL strives to maintain a safe, secure and efficient operational environment for its employees and neighboring communities. Experts in environment, safety and health (ES&H) support all Laboratory activities. LLNL’s radiological control program ensures that radiological exposures and releases are reduced to as low as reasonably achievable to protect the health and safety of its employees, contractors, the public, and the environment. LLNL is committed to enhancing its environmental stewardship and managing the impacts its operations may have on the environment through a formal Environmental Management System. The Laboratory encourages the public to participate in matters related to the Laboratory’s environmental impact on the community by soliciting citizens’ input on matters of significant public interest and through various communications. The Laboratory also provides public access to information on its ES&H activities. LLNL consists of two sites—an urban site in Livermore, California, referred to as the “Livermore Site,” which occupies 1.3 square miles; and a rural Experimental Test Site, referred to as “Site 300,” near Tracy, California, which occupies 10.9 square miles. In 2012 the Laboratory had a staff of approximately 7000.« less

Lawrence Livermore National Laboratory Environmental Report 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, H. E.; Bertoldo, N. A.; Blake, R. G.

Lawrence Livermore National Laboratory (LLNL) is a premier research laboratory that is part of the National Nuclear Security Administration (NNSA) within the U.S. Department of Energy (DOE). As a national security laboratory, LLNL is responsible for ensuring that the nation’s nuclear weapons remain safe, secure, and reliable. The Laboratory also meets other pressing national security needs, including countering the proliferation of weapons of mass destruction and strengthening homeland security, and conducting major research in atmospheric, earth, and energy sciences; bioscience and biotechnology; and engineering, basic science, and advanced technology. The Laboratory is managed and operated by Lawrence Livermore National Security,more » LLC (LLNS), and serves as a scientific resource to the U.S. government and a partner to industry and academia. LLNL operations have the potential to release a variety of constituents into the environment via atmospheric, surface water, and groundwater pathways. Some of the constituents, such as particles from diesel engines, are common at many types of facilities while others, such as radionuclides, are unique to research facilities like LLNL. All releases are highly regulated and carefully monitored. LLNL strives to maintain a safe, secure and efficient operational environment for its employees and neighboring communities. Experts in environment, safety and health (ES&H) support all Laboratory activities. LLNL’s radiological control program ensures that radiological exposures and releases are reduced to as low as reasonably achievable to protect the health and safety of its employees, contractors, the public, and the environment. LLNL is committed to enhancing its environmental stewardship and managing the impacts its operations may have on the environment through a formal Environmental Management System. The Laboratory encourages the public to participate in matters related to the Laboratory’s environmental impact on the community by soliciting citizens’ input on matters of significant public interest and through various communications. The Laboratory also provides public access to information on its ES&H activities. LLNL consists of two sites—an urban site in Livermore, California, referred to as the “Livermore Site,” which occupies 1.3 square miles; and a rural Experimental Test Site, referred to as “Site 300,” near Tracy, California, which occupies 10.9 square miles. In 2013 the Laboratory had a staff of approximately 6,300.« less

Development and application of remote video monitoring system for combine harvester based on embedded Linux

NASA Astrophysics Data System (ADS)

Chen, Jin; Wang, Yifan; Wang, Xuelei; Wang, Yuehong; Hu, Rui

2017-01-01

Combine harvester usually works in sparsely populated areas with harsh environment. In order to achieve the remote real-time video monitoring of the working state of combine harvester. A remote video monitoring system based on ARM11 and embedded Linux is developed. The system uses USB camera for capturing working state video data of the main parts of combine harvester, including the granary, threshing drum, cab and cut table. Using JPEG image compression standard to compress video data then transferring monitoring screen to remote monitoring center over the network for long-range monitoring and management. At the beginning of this paper it describes the necessity of the design of the system. Then it introduces realization methods of hardware and software briefly. And then it describes detailedly the configuration and compilation of embedded Linux operating system and the compiling and transplanting of video server program are elaborated. At the end of the paper, we carried out equipment installation and commissioning on combine harvester and then tested the system and showed the test results. In the experiment testing, the remote video monitoring system for combine harvester can achieve 30fps with the resolution of 800x600, and the response delay in the public network is about 40ms.

Transitioning to Intel-based Linux Servers in the Payload Operations Integration Center

NASA Technical Reports Server (NTRS)

Guillebeau, P. L.

2004-01-01

The MSFC Payload Operations Integration Center (POIC) is the focal point for International Space Station (ISS) payload operations. The POIC contains the facilities, hardware, software and communication interface necessary to support payload operations. ISS ground system support for processing and display of real-time spacecraft and telemetry and command data has been operational for several years. The hardware components were reaching end of life and vendor costs were increasing while ISS budgets were becoming severely constrained. Therefore it has been necessary to migrate the Unix portions of our ground systems to commodity priced Intel-based Linux servers. hardware architecture including networks, data storage, and highly available resources. This paper will concentrate on the Linux migration implementation for the software portion of our ground system. The migration began with 3.5 million lines of code running on Unix platforms with separate servers for telemetry, command, Payload information management systems, web, system control, remote server interface and databases. The Intel-based system is scheduled to be available for initial operational use by August 2004 The overall migration to Intel-based Linux servers in the control center involves changes to the This paper will address the Linux migration study approach including the proof of concept, criticality of customer buy-in and importance of beginning with POSlX compliant code. It will focus on the development approach explaining the software lifecycle. Other aspects of development will be covered including phased implementation, interim milestones and metrics measurements and reporting mechanisms. This paper will also address the testing approach covering all levels of testing including development, development integration, IV&V, user beta testing and acceptance testing. Test results including performance numbers compared with Unix servers will be included. need for a smooth transition while maintaining real-time support. An important aspect of the paper will involve challenges and lessons learned. product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support. This paper will also address the deployment approach including user involvement in testing and the , This includes COTS product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support.

Cluster Computing For Real Time Seismic Array Analysis.

NASA Astrophysics Data System (ADS)

Martini, M.; Giudicepietro, F.

A seismic array is an instrument composed by a dense distribution of seismic sen- sors that allow to measure the directional properties of the wavefield (slowness or wavenumber vector) radiated by a seismic source. Over the last years arrays have been widely used in different fields of seismological researches. In particular they are applied in the investigation of seismic sources on volcanoes where they can be suc- cessfully used for studying the volcanic microtremor and long period events which are critical for getting information on the volcanic systems evolution. For this reason arrays could be usefully employed for the volcanoes monitoring, however the huge amount of data produced by this type of instruments and the processing techniques which are quite time consuming limited their potentiality for this application. In order to favor a direct application of arrays techniques to continuous volcano monitoring we designed and built a small PC cluster able to near real time computing the kinematics properties of the wavefield (slowness or wavenumber vector) produced by local seis- mic source. The cluster is composed of 8 Intel Pentium-III bi-processors PC working at 550 MHz, and has 4 Gigabytes of RAM memory. It runs under Linux operating system. The developed analysis software package is based on the Multiple SIgnal Classification (MUSIC) algorithm and is written in Fortran. The message-passing part is based upon the LAM programming environment package, an open-source imple- mentation of the Message Passing Interface (MPI). The developed software system includes modules devote to receiving date by internet and graphical applications for the continuous displaying of the processing results. The system has been tested with a data set collected during a seismic experiment conducted on Etna in 1999 when two dense seismic arrays have been deployed on the northeast and the southeast flanks of this volcano. A real time continuous acquisition system has been simulated by a pro- gram which reads data from disk files and send them to a remote host by using the Internet protocols.

High-Performance, Multi-Node File Copies and Checksums for Clustered File Systems

NASA Technical Reports Server (NTRS)

Kolano, Paul Z.; Ciotti, Robert B.

2012-01-01

Modern parallel file systems achieve high performance using a variety of techniques, such as striping files across multiple disks to increase aggregate I/O bandwidth and spreading disks across multiple servers to increase aggregate interconnect bandwidth. To achieve peak performance from such systems, it is typically necessary to utilize multiple concurrent readers/writers from multiple systems to overcome various singlesystem limitations, such as number of processors and network bandwidth. The standard cp and md5sum tools of GNU coreutils found on every modern Unix/Linux system, however, utilize a single execution thread on a single CPU core of a single system, and hence cannot take full advantage of the increased performance of clustered file systems. Mcp and msum are drop-in replacements for the standard cp and md5sum programs that utilize multiple types of parallelism and other optimizations to achieve maximum copy and checksum performance on clustered file systems. Multi-threading is used to ensure that nodes are kept as busy as possible. Read/write parallelism allows individual operations of a single copy to be overlapped using asynchronous I/O. Multinode cooperation allows different nodes to take part in the same copy/checksum. Split-file processing allows multiple threads to operate concurrently on the same file. Finally, hash trees allow inherently serial checksums to be performed in parallel. Mcp and msum provide significant performance improvements over standard cp and md5sum using multiple types of parallelism and other optimizations. The total speed-ups from all improvements are significant. Mcp improves cp performance over 27x, msum improves md5sum performance almost 19x, and the combination of mcp and msum improves verified copies via cp and md5sum by almost 22x. These improvements come in the form of drop-in replacements for cp and md5sum, so are easily used and are available for download as open source software at http://mutil.sourceforge.net.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

Cloud prediction of protein structure and function with PredictProtein for Debian.

PubMed

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

PubMed Central

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

Evaluating the ISDN line to deliver interactive multimedia experiences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michaels, D.K.

1994-05-06

We will use the 128 kilobit/sec ISDN connection from the Lawrence Livermore National Laboratory to the Livermore High School Math Learning Center to provide students there with interactive multimedia educational experiences. These experiences may consist of tutorials, exercises, and interactive puzzles to teach students` course material. We will determine if it is possible to store the multimedia files at LLNL and deliver them to the student machines via FTP as they are needed. An evaluation of the effect of the ISDN data rate is a substantial component of our research and suggestions on how to best use the ISDN linemore » in this capacity will be given.« less

Lawrence Livermore National Laboratory`s Computer Security Short Subjects Videos: Hidden Password, The Incident, Dangerous Games and The Mess; Computer Security Awareness Guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

A video on computer security is described. Lonnie Moore, the Computer Security Manager, CSSM/CPPM at Lawrence Livermore National Laboratory (LLNL) and Gale Warshawsky, the Coordinator for Computer Security Education and Awareness at LLNL, wanted to share topics such as computer ethics, software piracy, privacy issues, and protecting information in a format that would capture and hold an audience`s attention. Four Computer Security Short Subject videos were produced which ranged from 1--3 minutes each. These videos are very effective education and awareness tools that can be used to generate discussions about computer security concerns and good computing practices.

Emergency Response Capability Baseline Needs Assessment Compliance Assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharry, John A.

2013-09-16

This document is the second of a two-part analysis of Emergency Response Capabilities of Lawrence Livermore National Laboratory. The first part, 2013 Baseline Needs Assessment Requirements Document established the minimum performance criteria necessary to meet mandatory requirements. This second part analyses the performance of Lawrence Livermore Laboratory Emergency Management Department to the contents of the Requirements Document. The document was prepared based on an extensive review of information contained in the 2009 BNA, the 2012 BNA document, a review of Emergency Planning Hazards Assessments, a review of building construction, occupancy, fire protection features, dispatch records, LLNL alarm system records, firemore » department training records, and fire department policies and procedures.« less

Livermore study says oil leaks not severe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patrick, L.

The Petroleum Marketers Association of America (PMAA), which is working to reform the federal Leaking Underground Storage Tank program, got some strong ammunition last month. A study that the Lawrence Livermore National Laboratory performed for the California State Water Resources Control Board has found that the environmental threat of leaks is not as severe as formerly thought. The study said: such leaks rarely jeopardize drinking water; fuel hydrocarbons have limited impacts on health, the environment, and groundwater; and cleanups often are done contrary to the knowledge and experience gained from prior remediations. As a result of the study, Gov. Petemore » Wilson ordered California cleanups halted at sites more than 250 feet from drinking water supplies.« less

Mosaic Transparent Armor System Final Report CRADA No. TC02162.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuntz, J. D.; Breslin, M.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and The Protective Group, Inc. (TPG) to improve the performance of the mosaic transparent armor system (MTAS) for transparent armor applications, military and civilian. LLNL was to provide the unique MTAS technology and designs to TPG for innovative construction and ballistic testing of improvements needed for current and near future application of the armor windows on vehicles and aircraft. The goal of the project was to advance the technology of MTAS to the point that these mosaic transparent windowsmore » would be introduced and commercially manufactured for military vehicles and aircraft.« less

Slurry Coating System Statement of Work and Specification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, S. M.

2017-02-06

The Slurry Coating System will be used to coat crystals with a polymer to support Lawrence Livermore National Security, LLC (LLNS) research and development at Lawrence Livermore National Laboratory (LLNL). The crystals will be suspended in water in a kettle. A polymer solution is added, temperature of the kettle is raised and aggregates of the crystals and polymer form. The slurry is heated under vacuum to drive off the solvents and slowly cooled while mixing to room temperature. The resulting aggregates are then filtered and dried. The performance characteristics and fielding constraints define a unique set of requirements for amore » new system. This document presents the specifications and requirements for the system.« less

2DRMP: A suite of two-dimensional R-matrix propagation codes

NASA Astrophysics Data System (ADS)

Scott, N. S.; Scott, M. P.; Burke, P. G.; Stitt, T.; Faro-Maza, V.; Denis, C.; Maniopoulou, A.

2009-12-01

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionise the target. In this paper we describe 2DRMP, a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Program summaryProgram title: 2DRMP Catalogue identifier: AEEA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 196 717 No. of bytes in distributed program, including test data, etc.: 3 819 727 Distribution format: tar.gz Programming language: Fortran 95, MPI Computer: Tested on CRAY XT4 [1]; IBM eServer 575 [2]; Itanium II cluster [3] Operating system: Tested on UNICOS/lc [1]; IBM AIX [2]; Red Hat Linux Enterprise AS [3] Has the code been vectorised or parallelised?: Yes. 16 cores were used for small test run Classification: 2.4 External routines: BLAS, LAPACK, PBLAS, ScaLAPACK Subprograms used: ADAZ_v1_1 Nature of problem: 2DRMP is a suite of programs aimed at creating virtual experiments on high performance architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Solution method: Two-dimensional R-matrix propagation theory. The (r,r) space of the internal region is subdivided into a number of subregions. Local R-matrices are constructed within each subregion and used to propagate a global R-matrix, ℜ, across the internal region. On the boundary of the internal region ℜ is transformed onto the IERM target state basis. Thus, the two-dimensional R-matrix propagation technique transforms an intractable problem into a series of tractable problems enabling the internal region to be extended far beyond that which is possible with the standard one-sector codes. A distinctive feature of the method is that both electrons are treated identically and the R-matrix basis states are constructed to allow for both electrons to be in the continuum. The subregion size is flexible and can be adjusted to accommodate the number of cores available. Restrictions: The implementation is currently restricted to electron scattering from H-like atoms and ions. Additional comments: The programs have been designed to operate on serial computers and to exploit the distributed memory parallelism found on tightly coupled high performance clusters and supercomputers. 2DRMP has been systematically and comprehensively documented using ROBODoc [4] which is an API documentation tool that works by extracting specially formatted headers from the program source code and writing them to documentation files. Running time: The wall clock running time for the small test run using 16 cores and performed on [3] is as follows: bp (7 s); rint2 (34 s); newrd (32 s); diag (21 s); amps (11 s); prop (24 s). References:HECToR, CRAY XT4 running UNICOS/lc, http://www.hector.ac.uk/, accessed 22 July, 2009. HPCx, IBM eServer 575 running IBM AIX, http://www.hpcx.ac.uk/, accessed 22 July, 2009. HP Cluster, Itanium II cluster running Red Hat Linux Enterprise AS, Queen s University Belfast, http://www.qub.ac.uk/directorates/InformationServices/Research/HighPerformanceComputing/Services/Hardware/HPResearch/, accessed 22 July, 2009. Automating Software Documentation with ROBODoc, http://www.xs4all.nl/~rfsber/Robo/, accessed 22 July, 2009.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

PubMed

Parker, Nicolas J; Parker, Andrew G

2008-04-18

The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.

The Effect of NUMA Tunings on CPU Performance

NASA Astrophysics Data System (ADS)

Hollowell, Christopher; Caramarcu, Costin; Strecker-Kellogg, William; Wong, Antonio; Zaytsev, Alexandr

2015-12-01

Non-Uniform Memory Access (NUMA) is a memory architecture for symmetric multiprocessing (SMP) systems where each processor is directly connected to separate memory. Indirect access to other CPU's (remote) RAM is still possible, but such requests are slower as they must also pass through that memory's controlling CPU. In concert with a NUMA-aware operating system, the NUMA hardware architecture can help eliminate the memory performance reductions generally seen in SMP systems when multiple processors simultaneously attempt to access memory. The x86 CPU architecture has supported NUMA for a number of years. Modern operating systems such as Linux support NUMA-aware scheduling, where the OS attempts to schedule a process to the CPU directly attached to the majority of its RAM. In Linux, it is possible to further manually tune the NUMA subsystem using the numactl utility. With the release of Red Hat Enterprise Linux (RHEL) 6.3, the numad daemon became available in this distribution. This daemon monitors a system's NUMA topology and utilization, and automatically makes adjustments to optimize locality. As the number of cores in x86 servers continues to grow, efficient NUMA mappings of processes to CPUs/memory will become increasingly important. This paper gives a brief overview of NUMA, and discusses the effects of manual tunings and numad on the performance of the HEPSPEC06 benchmark, and ATLAS software.

Status and Roadmap of CernVM

NASA Astrophysics Data System (ADS)

Berzano, D.; Blomer, J.; Buncic, P.; Charalampidis, I.; Ganis, G.; Meusel, R.

2015-12-01

Cloud resources nowadays contribute an essential share of resources for computing in high-energy physics. Such resources can be either provided by private or public IaaS clouds (e.g. OpenStack, Amazon EC2, Google Compute Engine) or by volunteers computers (e.g. LHC@Home 2.0). In any case, experiments need to prepare a virtual machine image that provides the execution environment for the physics application at hand. The CernVM virtual machine since version 3 is a minimal and versatile virtual machine image capable of booting different operating systems. The virtual machine image is less than 20 megabyte in size. The actual operating system is delivered on demand by the CernVM File System. CernVM 3 has matured from a prototype to a production environment. It is used, for instance, to run LHC applications in the cloud, to tune event generators using a network of volunteer computers, and as a container for the historic Scientific Linux 5 and Scientific Linux 4 based software environments in the course of long-term data preservation efforts of the ALICE, CMS, and ALEPH experiments. We present experience and lessons learned from the use of CernVM at scale. We also provide an outlook on the upcoming developments. These developments include adding support for Scientific Linux 7, the use of container virtualization, such as provided by Docker, and the streamlining of virtual machine contextualization towards the cloud-init industry standard.

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

PubMed

Yu, Jen-Shiang K; Yu, Chin-Hui

2002-01-01

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

High speed real-time wavefront processing system for a solid-state laser system

NASA Astrophysics Data System (ADS)

Liu, Yuan; Yang, Ping; Chen, Shanqiu; Ma, Lifang; Xu, Bing

2008-03-01

A high speed real-time wavefront processing system for a solid-state laser beam cleanup system has been built. This system consists of a core2 Industrial PC (IPC) using Linux and real-time Linux (RT-Linux) operation system (OS), a PCI image grabber, a D/A card. More often than not, the phase aberrations of the output beam from solid-state lasers vary fast with intracavity thermal effects and environmental influence. To compensate the phase aberrations of solid-state lasers successfully, a high speed real-time wavefront processing system is presented. Compared to former systems, this system can improve the speed efficiently. In the new system, the acquisition of image data, the output of control voltage data and the implementation of reconstructor control algorithm are treated as real-time tasks in kernel-space, the display of wavefront information and man-machine conversation are treated as non real-time tasks in user-space. The parallel processing of real-time tasks in Symmetric Multi Processors (SMP) mode is the main strategy of improving the speed. In this paper, the performance and efficiency of this wavefront processing system are analyzed. The opened-loop experimental results show that the sampling frequency of this system is up to 3300Hz, and this system can well deal with phase aberrations from solid-state lasers.

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

SlideSort: all pairs similarity search for short reads

PubMed Central

Shimizu, Kana; Tsuda, Koji

2011-01-01

Motivation: Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses. Results: In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing. Availability: Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows. Contact: slidesort@m.aist.go.jp; shimizu-kana@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21148542

JaSTA-2: Second version of the Java Superposition T-matrix Application

NASA Astrophysics Data System (ADS)

Halder, Prithish; Das, Himadri Sekhar

2017-12-01

In this article, we announce the development of a new version of the Java Superposition T-matrix App (JaSTA-2), to study the light scattering properties of porous aggregate particles. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precision superposition T-matrix codes for multi-sphere clusters in random orientation, developed by Mackowski and Mischenko (1996). The new version consists of two options as part of the input parameters: (i) single wavelength and (ii) multiple wavelengths. The first option (which retains the applicability of older version of JaSTA) calculates the light scattering properties of aggregates of spheres for a single wavelength at a given instant of time whereas the second option can execute the code for a multiple numbers of wavelengths in a single run. JaSTA-2 provides convenient and quicker data analysis which can be used in diverse fields like Planetary Science, Atmospheric Physics, Nanoscience, etc. This version of the software is developed for Linux platform only, and it can be operated over all the cores of a processor using the multi-threading option.

Resource Isolation Method for Program’S Performance on CMP

NASA Astrophysics Data System (ADS)

Guan, Ti; Liu, Chunxiu; Xu, Zheng; Li, Huicong; Ma, Qiang

2017-10-01

Data center and cloud computing are more popular, which make more benefits for customers and the providers. However, in data center or clusters, commonly there is more than one program running on one server, but programs may interference with each other. The interference may take a little effect, however, the interference may cause serious drop down of performance. In order to avoid the performance interference problem, the mechanism of isolate resource for different programs is a better choice. In this paper we propose a light cost resource isolation method to improve program’s performance. This method uses Cgroups to set the dedicated CPU and memory resource for a program, aiming at to guarantee the program’s performance. There are three engines to realize this method: Program Monitor Engine top program’s resource usage of CPU and memory and transfer the information to Resource Assignment Engine; Resource Assignment Engine calculates the size of CPU and memory resource should be applied for the program; Cgroups Control Engine divide resource by Linux tool Cgroups, and drag program in control group for execution. The experiment result show that making use of the resource isolation method proposed by our paper, program’s performance can be improved.

In silico reconstitution of Listeria propulsion exhibits nano-saltation.

PubMed

Alberts, Jonathan B; Odell, Garrett M

2004-12-01

To understand how the actin-polymerization-mediated movements in cells emerge from myriad individual protein-protein interactions, we developed a computational model of Listeria monocytogenes propulsion that explicitly simulates a large number of monomer-scale biochemical and mechanical interactions. The literature on actin networks and L. monocytogenes motility provides the foundation for a realistic mathematical/computer simulation, because most of the key rate constants governing actin network dynamics have been measured. We use a cluster of 80 Linux processors and our own suite of simulation and analysis software to characterize salient features of bacterial motion. Our "in silico reconstitution" produces qualitatively realistic bacterial motion with regard to speed and persistence of motion and actin tail morphology. The model also produces smaller scale emergent behavior; we demonstrate how the observed nano-saltatory motion of L. monocytogenes,in which runs punctuate pauses, can emerge from a cooperative binding and breaking of attachments between actin filaments and the bacterium. We describe our modeling methodology in detail, as it is likely to be useful for understanding any subcellular system in which the dynamics of many simple interactions lead to complex emergent behavior, e.g., lamellipodia and filopodia extension, cellular organization, and cytokinesis.

Computing with Beowulf

NASA Technical Reports Server (NTRS)

Cohen, Jarrett

1999-01-01

Parallel computers built out of mass-market parts are cost-effectively performing data processing and simulation tasks. The Supercomputing (now known as "SC") series of conferences celebrated its 10th anniversary last November. While vendors have come and gone, the dominant paradigm for tackling big problems still is a shared-resource, commercial supercomputer. Growing numbers of users needing a cheaper or dedicated-access alternative are building their own supercomputers out of mass-market parts. Such machines are generally called Beowulf-class systems after the 11th century epic. This modern-day Beowulf story began in 1994 at NASA's Goddard Space Flight Center. A laboratory for the Earth and space sciences, computing managers there threw down a gauntlet to develop a $50,000 gigaFLOPS workstation for processing satellite data sets. Soon, Thomas Sterling and Don Becker were working on the Beowulf concept at the University Space Research Association (USRA)-run Center of Excellence in Space Data and Information Sciences (CESDIS). Beowulf clusters mix three primary ingredients: commodity personal computers or workstations, low-cost Ethernet networks, and the open-source Linux operating system. One of the larger Beowulfs is Goddard's Highly-parallel Integrated Virtual Environment, or HIVE for short.

Models@Home: distributed computing in bioinformatics using a screensaver based approach.

PubMed

Krieger, Elmar; Vriend, Gert

2002-02-01

Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beck, James B.

National Security Office (NSO) newsletter's main highlight is on the annual Strategic Weapons in the 21st Century that the Los Alamos and Lawrence Livermore National Laboratories host in Washington, DC.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernhardt, A. F.; Smith, P. M.

This project was a collaborative effort between the University of California, Lawrence Livermore National Laboratory (LLNL) and FlexICs, Inc. to develop thin film transistor (TFT) electronics for active matrix displays.

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.

PubMed

Excoffier, Laurent; Lischer, Heidi E L

2010-05-01

We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework. © 2010 Blackwell Publishing Ltd.

RTSPM: real-time Linux control software for scanning probe microscopy.

PubMed

Chandrasekhar, V; Mehta, M M

2013-01-01

Real time computer control is an essential feature of scanning probe microscopes, which have become important tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe data acquisition software uses digital signal processors to handle the real time data processing and control, which adds to the expense and complexity of the control software. We describe here scan control software that uses a single computer and a data acquisition card to acquire scan data. The computer runs an open-source real time Linux kernel, which permits fast acquisition and control while maintaining a responsive graphical user interface. Images from a simulated tuning-fork based microscope as well as a standard topographical sample are also presented, showing some of the capabilities of the software.

PyEPL: a cross-platform experiment-programming library.

PubMed

Geller, Aaron S; Schlefer, Ian K; Sederberg, Per B; Jacobs, Joshua; Kahana, Michael J

2007-11-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.

PyEPL: A cross-platform experiment-programming library

PubMed Central

Geller, Aaron S.; Schleifer, Ian K.; Sederberg, Per B.; Jacobs, Joshua; Kahana, Michael J.

2009-01-01

PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments for spatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL. PMID:18183912

DOE Office of Scientific and Technical Information (OSTI.GOV)

Exercise environment for Introduction to Cyber Technologies class. This software is essentially a collection of short scripts, configuration files, and small executables that form the exercise component of the Sandia Cyber Technologies Academy's Introduction to Cyber Technologies class. It builds upon other open-source technologies, such as Debian Linux and minimega, to provide comprehensive Linux and networking exercises that make learning these topics exciting and fun. Sample exercises: a pre-built set of home directories the student must navigate through to learn about privilege escalation, the creation of a virtual network playground designed to teach the student about the resiliency of themore » Internet, and a two-hour Capture the Flag challenge for the final lesson. There are approximately thirty (30) exercises included for the students to complete as part of the course.« less

Ligand Depot: a data warehouse for ligands bound to macromolecules.

PubMed

Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John

2004-09-01

Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edward Moses

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by NIF Director Edward Moses.

Development of Operational Free-Space-Optical (FSO) Laser Communication Systems Final Report CRADA No. TC02093.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruggiero, A.; Orgren, A.

This project was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of California)/Lawrence Livermore National Laboratory (LLNL) and LGS Innovations, LLC (formerly Lucent Technologies, Inc.), to develop long-range and mobile operational free-space optical (FSO) laser communication systems for specialized government applications. LLNL and LGS Innovations formerly Lucent Bell Laboratories Government Communications Systems performed this work for a United States Government (USG) Intelligence Work for Others (I-WFO) customer, also referred to as "Government Customer", or "Customer" and "Government Sponsor." The CRADA was a critical and required part of the LLNL technology transfer plan formore » the customer.« less

Development of a design basis tornado and structural design criteria for Lawrence Livermore Laboratory's Site 300

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, J.R.; Minor, J.E.; Mehta, K.C.

1975-11-01

Criteria are prescribed and guidance is provided for professional personnel who are involved with the evaluation of existing buildings and facilities at Site 300 near Livermore, California to resist the possible effects of extreme winds and tornadoes. The development of parameters for the effects of tornadoes and extreme winds and guidelines for evaluation and design of structures are presented. The investigations conducted are summarized and the techniques used for arriving at the combined tornado and extreme wind risk model are discussed. The guidelines for structural design methods for calculating pressure distributions on walls and roofs of structures and methods formore » accommodating impact loads from missiles are also presented. (auth)« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, C.; Arsenlis, T.; Bailey, A.

Lawrence Livermore National Laboratory Campus Capability Plan for 2018-2028. Lawrence Livermore National Laboratory (LLNL) is one of three national laboratories that are part of the National Nuclear Security Administration. LLNL provides critical expertise to strengthen U.S. security through development and application of world-class science and technology that: Ensures the safety, reliability, and performance of the U.S. nuclear weapons stockpile; Promotes international nuclear safety and nonproliferation; Reduces global danger from weapons of mass destruction; Supports U.S. leadership in science and technology. Essential to the execution and continued advancement of these mission areas are responsive infrastructure capabilities. This report showcases each LLNLmore » capability area and describes the mission, science, and technology efforts enabled by LLNL infrastructure, as well as future infrastructure plans.« less

Science and Technology Review July/August 2010

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blobaum, K M

2010-05-27

This issue has the following articles: (1) Deterrence with a Minimum Nuclear Stockpile - Commentary by Bruce T. Goodwin; (2) Enhancing Confidence in the Nation's Nuclear Stockpile - Livermore experts are participating in a national effort aimed at predicting how nuclear weapon materials and systems will likely change over time; (3) Narrowing Uncertainties - For climate modeling and many other fields, understanding uncertainty, or margin of error, is critical; (4) Insight into a Deadly Disease - Laboratory experiments reveal the pathogenesis of tularemia in host cells, bringing scientists closer to developing a vaccine for this debilitating disease. (5) Return tomore » Rongelap - On the Rongelap Atoll, Livermore scientists are working to minimize radiological exposure for natives now living on or wishing to return to the islands.« less

Webinar: Delivering Transformational HPC Solutions to Industry

ScienceCinema

Streitz, Frederick

2018-01-16

Dr. Frederick Streitz, director of the High Performance Computing Innovation Center, discusses Lawrence Livermore National Laboratory computational capabilities and expertise available to industry in this webinar.

HARE: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mckie, Jim

2012-01-09

This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. Themore » HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating systems and runtime research follows; we discuss infrastructure software; and close with a description of the new NIX operating system, future work, and conclusions.« less

David Whiteside | NREL

Science.gov Websites

Whiteside David Whiteside HPC System Administrator David.Whiteside@nrel.gov | 303-275-3943 David . David has over 10 years of experience with Linux administration and a strong background in system

Lawrence Livermore National Laboratory Experimental Test Site (Site 300) Potable Water System Operations Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ocampo, Ruben P.; Bellah, Wendy

The existing Lawrence Livermore National Laboratory (LLNL) Site 300 drinking water system operation schematic is shown in Figures 1 and 2 below. The sources of water are from two Site 300 wells (Well #18 and Well #20) and San Francisco Public Utilities Commission (SFPUC) Hetch-Hetchy water through the Thomas shaft pumping station. Currently, Well #20 with 300 gallons per minute (gpm) pump capacity is the primary source of well water used during the months of September through July, while Well #18 with 225 gpm pump capacity is the source of well water for the month of August. The well watermore » is chlorinated using sodium hypochlorite to provide required residual chlorine throughout Site 300. Well water chlorination is covered in the Lawrence Livermore National Laboratory Experimental Test Site (Site 300) Chlorination Plan (“the Chlorination Plan”; LLNL-TR-642903; current version dated August 2013). The third source of water is the SFPUC Hetch-Hetchy Water System through the Thomas shaft facility with a 150 gpm pump capacity. At the Thomas shaft station the pumped water is treated through SFPUC-owned and operated ultraviolet (UV) reactor disinfection units on its way to Site 300. The Thomas Shaft Hetch- Hetchy water line is connected to the Site 300 water system through the line common to Well pumps #18 and #20 at valve box #1.« less

First-Principles Equation of State and Shock Compression of Warm Dense Aluminum and Hydrocarbons

NASA Astrophysics Data System (ADS)

Driver, Kevin; Soubiran, Francois; Zhang, Shuai; Militzer, Burkhard

2017-10-01

Theoretical studies of warm dense plasmas are a key component of progress in fusion science, defense science, and astrophysics programs. Path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD), two state-of-the-art, first-principles, electronic-structure simulation methods, provide a consistent description of plasmas over a wide range of density and temperature conditions. Here, we combine high-temperature PIMC data with lower-temperature DFT-MD data to compute coherent equations of state (EOS) for aluminum and hydrocarbon plasmas. Subsequently, we derive shock Hugoniot curves from these EOSs and extract the temperature-density evolution of plasma structure and ionization behavior from pair-correlation function analyses. Since PIMC and DFT-MD accurately treat effects of atomic shell structure, we find compression maxima along Hugoniot curves attributed to K-shell and L-shell ionization, which provide a benchmark for widely-used EOS tables, such as SESAME and LEOS, and more efficient models. LLNL-ABS-734424. Funding provided by the DOE (DE-SC0010517) and in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Computational resources provided by Blue Waters (NSF ACI1640776) and NERSC. K. Driver's and S. Zhang's current address is Lawrence Livermore Natl. Lab, Livermore, CA, 94550, USA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ronald W.

With the addition of the 3D volume slicer widget, VERAView now relies on Mayavi and its dependents. Enthought's Canopy Python environment provides everything VERAView needs, and pre-built Canopy versions for Windows, Mac OSX, and Linux can be downloaded.

HEP Computing

Science.gov Websites

Service Request Password Help New Users Back to HEP Computing Mail-Migration Procedure on Linux Mail -Migration Procedure on Windows How to Migrate a Folder to GMail using Pine U.S. Department of Energy The

MISR Level 2 TOA/Cloud Versioning

Atmospheric Science Data Center

2017-10-11

... at this level. Software has been ported over to Linux. The Broadband Albedos have been fixed. New ancillary files: ... Difference Vectors implemented. Block Center Times for AN camera added to product. New ancillary files: ...

FTAP: a Linux-based program for tapping and music experiments.

PubMed

Finney, S A

2001-02-01

This paper describes FTAP, a flexible data collection system for tapping and music experiments. FTAP runs on standard PC hardware with the Linux operating system and can process input keystrokes and auditory output with reliable millisecond resolution. It uses standard MIDI devices for input and output and is particularly flexible in the area of auditory feedback manipulation. FTAP can run a wide variety of experiments, including synchronization/continuation tasks (Wing & Kristofferson, 1973), synchronization tasks combined with delayed auditory feedback (Aschersleben & Prinz, 1997), continuation tasks with isolated feedback perturbations (Wing, 1977), and complex alterations of feedback in music performance (Finney, 1997). Such experiments have often been implemented with custom hardware and software systems, but with FTAP they can be specified by a simple ASCII text parameter file. FTAP is available at no cost in source-code form.

Enhancements to the Sentinel Fireball Network Video Software

NASA Astrophysics Data System (ADS)

Watson, Wayne

2009-05-01

The Sentinel Fireball Network that supports meteor imaging of bright meteors (fireballs) has been in existence for over ten years. Nearly five years ago it moved from gathering meteor data with a camera and VCR video tape to a fisheye lens attached to a hardware device, the Sentinel box, which allowed meteor data to be recorded on a PC operating under real-time Linux. In 2006, that software, sentuser, was made available on Apple, Linux, and Window operating systems using the Python computer language. It provides basic video and management functionality and a small amount of analytic software capability. This paper describes the new and attractive future features of the software, and, additionally, it reviews some of the research and networks from the past and present using video equipment to collect and analyze fireball data that have applicability to sentuser.

Limits, discovery and cut optimization for a Poisson process with uncertainty in background and signal efficiency: TRolke 2.0

NASA Astrophysics Data System (ADS)

Lundberg, J.; Conrad, J.; Rolke, W.; Lopez, A.

2010-03-01

A C++ class was written for the calculation of frequentist confidence intervals using the profile likelihood method. Seven combinations of Binomial, Gaussian, Poissonian and Binomial uncertainties are implemented. The package provides routines for the calculation of upper and lower limits, sensitivity and related properties. It also supports hypothesis tests which take uncertainties into account. It can be used in compiled C++ code, in Python or interactively via the ROOT analysis framework. Program summaryProgram title: TRolke version 2.0 Catalogue identifier: AEFT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 3431 No. of bytes in distributed program, including test data, etc.: 21 789 Distribution format: tar.gz Programming language: ISO C++. Computer: Unix, GNU/Linux, Mac. Operating system: Linux 2.6 (Scientific Linux 4 and 5, Ubuntu 8.10), Darwin 9.0 (Mac-OS X 10.5.8). RAM:˜20 MB Classification: 14.13. External routines: ROOT ( http://root.cern.ch/drupal/) Nature of problem: The problem is to calculate a frequentist confidence interval on the parameter of a Poisson process with statistical or systematic uncertainties in signal efficiency or background. Solution method: Profile likelihood method, Analytical Running time:<10 seconds per extracted limit.

Beamlet diagnostics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theys, M.

1994-05-06

Beamlet is a high power laser currently being built at Lawrence Livermore National Lab as a proof of concept for the National Ignition Facility (NIF). Beamlet is testing several areas of laser advancements, such as a 37cm Pockels cell, square amplifier, and propagation of a square beam. The diagnostics on beamlet tell the operators how much energy the beam has in different locations, the pulse shape, the energy distribution, and other important information regarding the beam. This information is being used to evaluate new amplifier designs, and extrapolate performance to the NIF laser. In my term at Lawrence Livermore Nationalmore » Laboratory I have designed and built a diagnostic, calibrated instruments used on diagnostics, setup instruments, hooked up communication lines to the instruments, and setup computers to control specific diagnostics.« less

Ceramic High Efficiency Particulate Air (HEPA) Filter Final Report CRADA No. TC02102.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, M.; Morse, T.

This was a collaborative effort between Lawrence Livermore National Security, LLC (formerly The Regents of the University of California)/Lawrence Livermor e National Laboratory (LLNL) and Flanders-Precisionaire (Flanders), to develop ceramic HEP A filters under a Thrust II Initiative for Proliferation Prevention (IPP) project. The research was conducted via the IPP Program at Commonwe alth of Independent States (CIS) Institutes, which are handled under a separate agreement. The institutes (collectively referred to as "CIS Institutes") involved with this project were: Bochvar: Federal State Unitarian Enterprise All-Russia Scientific and Research Institute of Inorganic Materials (FSUE VNIINM); Radium Khlopin: Federal State Unitarian Enterprisemore » NPO Radium Institute named (FSUE NPO Radium Institute); and Bakor: Science and Technology Center Bakor (STC Bakor).« less

Emission line spectra of S VII ? S XIV in the 20 ? 75 ? wavelength region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepson, J K; Beiersdorfer, P; Behar, E

As part of a larger project to complete a comprehensive catalogue of astrophysically relevant emission lines in support of new-generation X-ray observatories using the Lawrence Livermore electron beam ion traps EBIT-I and EBIT-II, the authors present observations of sulfur lines in the soft X-ray and extreme ultraviolet regions. The database includes wavelength measurements with standard errors, relative intensities, and line assignments for 127 transitions of S VII through S XIV between 20 and 75 {angstrom}. The experimental data are complemented with a full set of calculations using the Hebrew University Lawrence Livermore Atomic Code (HULLAC). A comparison of the laboratorymore » data with Chandra measurements of Procyon allows them to identify S VII-S XI lines.« less

Commercialization of Ultra-Hard Ceramics for Cutting Tools Final Report CRADA No. TC0279.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Landingham, R.; Neumann, T.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Greenleaf Corporation (Greenleaf) to develop the technology for forming unique precursor nano-powders process that can be consolidated into ceramic products for industry. LLNL researchers have developed a solgel process for forming nano-ceramic powders. The nano powders are highly tailorable, allowing the explicit design of desired properties that lead to ultra hard materials with fine grain size. The present CRADA would allow the two parties to continue the development of the sol-gel process and the consolidation process in ordermore » to develop an industrially sound process for the manufacture of these ultra-hard materials.« less

Kiwi: An Evaluated Library of Uncertainties in Nuclear Data and Package for Nuclear Sensitivity Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruet, J

2007-06-23

This report describes Kiwi, a program developed at Livermore to enable mature studies of the relation between imperfectly known nuclear physics and uncertainties in simulations of complicated systems. Kiwi includes a library of evaluated nuclear data uncertainties, tools for modifying data according to these uncertainties, and a simple interface for generating processed data used by transport codes. As well, Kiwi provides access to calculations of k eigenvalues for critical assemblies. This allows the user to check implications of data modifications against integral experiments for multiplying systems. Kiwi is written in python. The uncertainty library has the same format and directorymore » structure as the native ENDL used at Livermore. Calculations for critical assemblies rely on deterministic and Monte Carlo codes developed by B division.« less

Water Treatment Using Advanced Ultraviolet Light Sources Final Report CRADA No. TC02089.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoppes, W.; Oster, S.

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Teknichal Services, LLC (TkS), to develop water treatment systems using advanced ultraviolet light sources. The Russian institutes involved with this project were The High Current Electronics Institute (HCEI) and Russian Institute of Technical Physics-Institute of Experimental Physics (VNIIEF). HCEI and VNIIEF developed and demonstrated the potential commercial viability of short-wavelength ultraviolet excimer lamps under a Thrust 1 Initiatives for Proliferation Prevention (IPP) Program. The goals of this collaboration were to demonstrate both the commercial viability of excilampbased watermore » disinfection and achieve further substantial operational improvement in the lamps themselves; particularly in the area of energy efficiency.« less

01-NIF Dedication: George Miller

ScienceCinema

George Miller

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Lab Director George Miller.

09-NIF Dedication: Arnold Schwarzenegger

DOE Office of Scientific and Technical Information (OSTI.GOV)

Governor Arnold Schwarzenegger

2009-07-02

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by California Governor Arnold Schwarzenegger.

09-NIF Dedication: Arnold Schwarzenegger

ScienceCinema

Governor Arnold Schwarzenegger

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by California Governor Arnold Schwarzenegger.

01-NIF Dedication: George Miller

DOE Office of Scientific and Technical Information (OSTI.GOV)

George Miller

2009-07-02

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by Lab Director George Miller.

02-NIF Dedication: Edward Moses

ScienceCinema

Edward Moses

2017-12-09

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the remarks by NIF Director Edward Moses.

Global Seismic Cross-Correlation Results: Characterizing Repeating Seismic Events

NASA Astrophysics Data System (ADS)

Vieceli, R.; Dodge, D. A.; Walter, W. R.

2016-12-01

Increases in seismic instrument quality and coverage have led to increased knowledge of earthquakes, but have also revealed the complex and diverse nature of earthquake ruptures. Nonetheless, some earthquakes are sufficiently similar to each other that they produce correlated waveforms. Such repeating events have been used to investigate interplate coupling of subduction zones [e.g. Igarashi, 2010; Yu, 2013], study spatio-temporal changes in slip rate at plate boundaries [e.g. Igarashi et al., 2003], observe variations in seismic wave propagation velocities in the crust [e.g. Schaff and Beroza, 2004; Sawazaki et al., 2015], and assess inner core rotation [e.g. Yu, 2016]. The characterization of repeating events on a global scale remains a very challenging problem. An initial global seismic cross-correlation study used over 310 million waveforms from nearly 3.8 million events recorded between 1970 and 2013 to determine an initial look at global correlated seismicity [Dodge and Walter, 2015]. In this work, we analyze the spatial and temporal distribution of the most highly correlated event clusters or "multiplets" from the Dodge and Walter [2015] study. We examine how the distributions and characteristics of multiplets are effected by tectonic environment, source-station separation, and frequency band. Preliminary results suggest that the distribution of multiplets does not correspond to the tectonic environment in any obvious way, nor do they always coincide with the occurrence of large earthquakes. Future work will focus on clustering correlated pairs and working to reduce the bias introduced by non-uniform seismic station coverage and data availability. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

NASA Astrophysics Data System (ADS)

Rostrup, Scott; De Sterck, Hans

2010-12-01

Increasingly, high-performance computing is looking towards data-parallel computational devices to enhance computational performance. Two technologies that have received significant attention are IBM's Cell Processor and NVIDIA's CUDA programming model for graphics processing unit (GPU) computing. In this paper we investigate the acceleration of parallel hyperbolic partial differential equation simulation on structured grids with explicit time integration on clusters with Cell and GPU backends. The message passing interface (MPI) is used for communication between nodes at the coarsest level of parallelism. Optimizations of the simulation code at the several finer levels of parallelism that the data-parallel devices provide are described in terms of data layout, data flow and data-parallel instructions. Optimized Cell and GPU performance are compared with reference code performance on a single x86 central processing unit (CPU) core in single and double precision. We further compare the CPU, Cell and GPU platforms on a chip-to-chip basis, and compare performance on single cluster nodes with two CPUs, two Cell processors or two GPUs in a shared memory configuration (without MPI). We finally compare performance on clusters with 32 CPUs, 32 Cell processors, and 32 GPUs using MPI. Our GPU cluster results use NVIDIA Tesla GPUs with GT200 architecture, but some preliminary results on recently introduced NVIDIA GPUs with the next-generation Fermi architecture are also included. This paper provides computational scientists and engineers who are considering porting their codes to accelerator environments with insight into how structured grid based explicit algorithms can be optimized for clusters with Cell and GPU accelerators. It also provides insight into the speed-up that may be gained on current and future accelerator architectures for this class of applications. Program summaryProgram title: SWsolver Catalogue identifier: AEGY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v3 No. of lines in distributed program, including test data, etc.: 59 168 No. of bytes in distributed program, including test data, etc.: 453 409 Distribution format: tar.gz Programming language: C, CUDA Computer: Parallel Computing Clusters. Individual compute nodes may consist of x86 CPU, Cell processor, or x86 CPU with attached NVIDIA GPU accelerator. Operating system: Linux Has the code been vectorised or parallelized?: Yes. Tested on 1-128 x86 CPU cores, 1-32 Cell Processors, and 1-32 NVIDIA GPUs. RAM: Tested on Problems requiring up to 4 GB per compute node. Classification: 12 External routines: MPI, CUDA, IBM Cell SDK Nature of problem: MPI-parallel simulation of Shallow Water equations using high-resolution 2D hyperbolic equation solver on regular Cartesian grids for x86 CPU, Cell Processor, and NVIDIA GPU using CUDA. Solution method: SWsolver provides 3 implementations of a high-resolution 2D Shallow Water equation solver on regular Cartesian grids, for CPU, Cell Processor, and NVIDIA GPU. Each implementation uses MPI to divide work across a parallel computing cluster. Additional comments: Sub-program numdiff is used for the test run.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edward Moses

The National Ignition Facility, the world's largest laser system, was dedicated at a ceremony on May 29, 2009 at Lawrence Livermore National Laboratory. These are the concluding remarks by NIF Director Edward Moses, and a brief video presentation.

Small Optics Laser Damage Test Procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolfe, Justin

2017-10-19

This specification defines the requirements and procedure for laser damage testing of coatings and bare surfaces designated for small optics in the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory (LLNL).

Human Health and Ecological Risk Assessment for the Operation of the Explosives Waste Treatment Facility at Site 300 of the Lawrence Livermore National Laboratory Volume 1: Report of Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallegos, G; Daniels, J; Wegrecki, A

2006-04-24

This document contains the human health and ecological risk assessment for the Resource Recovery and Conservation Act (RCRA) permit renewal for the Explosives Waste Treatment Facility (EWTF). Volume 1 is the text of the risk assessment, and Volume 2 (provided on a compact disc) is the supporting modeling data. The EWTF is operated by the Lawrence Livermore National Laboratory (LLNL) at Site 300, which is located in the foothills between the cities of Livermore and Tracy, approximately 17 miles east of Livermore and 8 miles southwest of Tracy. Figure 1 is a map of the San Francisco Bay Area, showingmore » the location of Site 300 and other points of reference. One of the principal activities of Site 300 is to test what are known as ''high explosives'' for nuclear weapons. These are the highly energetic materials that provide the force to drive fissionable material to criticality. LLNL scientists develop and test the explosives and the integrated non-nuclear components in support of the United States nuclear stockpile stewardship program as well as in support of conventional weapons and the aircraft, mining, oil exploration, and construction industries. Many Site 300 facilities are used in support of high explosives research. Some facilities are used in the chemical formulation of explosives; others are locations where explosive charges are mechanically pressed; others are locations where the materials are inspected radiographically for such defects as cracks and voids. Finally, some facilities are locations where the machined charges are assembled before they are sent to the on-site test firing facilities, and additional facilities are locations where materials are stored. Wastes generated from high-explosives research are treated by open burning (OB) and open detonation (OD). OB and OD treatments are necessary because they are the safest methods for treating explosives wastes generated at these facilities, and they eliminate the requirement for further handling and transportation that would be required if the wastes were treated off site.« less

Human Health and Ecological Risk Assessment for the Operation of the Explosives Waste Treatment Facility at Site 300 of the Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallegos, G; Daniels, J; Wegrecki, A

2007-10-01

This document contains the human health and ecological risk assessment for the Resource Recovery and Conservation Act (RCRA) permit renewal for the Explosives Waste Treatment Facility (EWTF). Volume 1 is the text of the risk assessment, and Volume 2 (provided on a compact disc) is the supporting modeling data. The EWTF is operated by the Lawrence Livermore National Laboratory (LLNL) at Site 300, which is located in the foothills between the cities of Livermore and Tracy, approximately 17 miles east of Livermore and 8 miles southwest of Tracy. Figure 1 is a map of the San Francisco Bay Area, showingmore » the location of Site 300 and other points of reference. One of the principal activities of Site 300 is to test what are known as 'high explosives' for nuclear weapons. These are the highly energetic materials that provide the force to drive fissionable material to criticality. LLNL scientists develop and test the explosives and the integrated non-nuclear components in support of the United States nuclear stockpile stewardship program as well as in support of conventional weapons and the aircraft, mining, oil exploration, and construction industries. Many Site 300 facilities are used in support of high explosives research. Some facilities are used in the chemical formulation of explosives; others are locations where explosive charges are mechanically pressed; others are locations where the materials are inspected radiographically for such defects as cracks and voids. Finally, some facilities are locations where the machined charges are assembled before they are sent to the onsite test firing facilities, and additional facilities are locations where materials are stored. Wastes generated from high-explosives research are treated by open burning (OB) and open detonation (OD). OB and OD treatments are necessary because they are the safest methods for treating explosives wastes generated at these facilities, and they eliminate the requirement for further handling and transportation that would be required if the wastes were treated off site.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bauer, Gerry; et al.

The DAQ system of the CMS experiment at CERN collects data from more than 600 custom detector Front-End Drivers (FEDs). During 2013 and 2014 the CMS DAQ system will undergo a major upgrade to address the obsolescence of current hardware and the requirements posed by the upgrade of the LHC accelerator and various detector components. For a loss-less data collection from the FEDs a new FPGA based card implementing the TCP/IP protocol suite over 10Gbps Ethernet has been developed. To limit the TCP hardware implementation complexity the DAQ group developed a simplified and unidirectional but RFC 793 compliant version ofmore » the TCP protocol. This allows to use a PC with the standard Linux TCP/IP stack as a receiver. We present the challenges and protocol modifications made to TCP in order to simplify its FPGA implementation. We also describe the interaction between the simplified TCP and Linux TCP/IP stack including the performance measurements.« less

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

PubMed

Buske, Fabian A; French, Hugh J; Smith, Martin A; Clark, Susan J; Bauer, Denis C

2014-05-15

The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. Denis.Bauer@csiro.au Supplementary data are available at Bioinformatics online.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

4273π: Bioinformatics education on low cost ARM hardware

PubMed Central

2013-01-01

Background Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. Results We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012–2013. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

High-performance data processing using distributed computing on the SOLIS project

NASA Astrophysics Data System (ADS)

Wampler, Stephen

2002-12-01

The SOLIS solar telescope collects data at a high rate, resulting in 500 GB of raw data each day. The SOLIS Data Handling System (DHS) has been designed to quickly process this data down to 156 GB of reduced data. The DHS design uses pools of distributed reduction processes that are allocated to different observations as needed. A farm of 10 dual-cpu Linux boxes contains the pools of reduction processes. Control is through CORBA and data is stored on a fibre channel storage area network (SAN). Three other Linux boxes are responsible for pulling data from the instruments using SAN-based ringbuffers. Control applications are Java-based while the reduction processes are written in C++. This paper presents the overall design of the SOLIS DHS and provides details on the approach used to control the pooled reduction processes. The various strategies used to manage the high data rates are also covered.

Use of Low-Cost Acquisition Systems with an Embedded Linux Device for Volcanic Monitoring

PubMed Central

Moure, David; Torres, Pedro; Casas, Benito; Toma, Daniel; Blanco, María José; Del Río, Joaquín; Manuel, Antoni

2015-01-01

This paper describes the development of a low-cost multiparameter acquisition system for volcanic monitoring that is applicable to gravimetry and geodesy, as well as to the visual monitoring of volcanic activity. The acquisition system was developed using a System on a Chip (SoC) Broadcom BCM2835 Linux operating system (based on DebianTM) that allows for the construction of a complete monitoring system offering multiple possibilities for storage, data-processing, configuration, and the real-time monitoring of volcanic activity. This multiparametric acquisition system was developed with a software environment, as well as with different hardware modules designed for each parameter to be monitored. The device presented here has been used and validated under different scenarios for monitoring ocean tides, ground deformation, and gravity, as well as for monitoring with images the island of Tenerife and ground deformation on the island of El Hierro. PMID:26295394

4273π: bioinformatics education on low cost ARM hardware.

PubMed

Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

2013-08-12

Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

Use of Low-Cost Acquisition Systems with an Embedded Linux Device for Volcanic Monitoring.

PubMed

Moure, David; Torres, Pedro; Casas, Benito; Toma, Daniel; Blanco, María José; Del Río, Joaquín; Manuel, Antoni

2015-08-19

This paper describes the development of a low-cost multiparameter acquisition system for volcanic monitoring that is applicable to gravimetry and geodesy, as well as to the visual monitoring of volcanic activity. The acquisition system was developed using a System on a Chip (SoC) Broadcom BCM2835 Linux operating system (based on DebianTM) that allows for the construction of a complete monitoring system offering multiple possibilities for storage, data-processing, configuration, and the real-time monitoring of volcanic activity. This multiparametric acquisition system was developed with a software environment, as well as with different hardware modules designed for each parameter to be monitored. The device presented here has been used and validated under different scenarios for monitoring ocean tides, ground deformation, and gravity, as well as for monitoring with images the island of Tenerife and ground deformation on the island of El Hierro.

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware

PubMed Central

Zheng, Da; Burns, Randal; Szalay, Alexander S.

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads. PMID:24402052

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware.

PubMed

Zheng, Da; Burns, Randal; Szalay, Alexander S

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooper, J. F.; Berner, J. K.

This was a collaborative effort between The Regents of the University of California, Lawrence Livermore National Laboratory (LLNL) and Contained Energy, Inc. (CEI), to conduct necessary research and to develop, fabricate and test a multi-cell carbon fuel cell.