Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4

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

Computational Research Division, Lawrence Berkeley National Laboratory; NERSC, Lawrence Berkeley National Laboratory; Computer Science Department, University of California, Berkeley

2009-05-04

We apply auto-tuning to a hybrid MPI-pthreads lattice Boltzmann computation running on the Cray XT4 at National Energy Research Scientific Computing Center (NERSC). Previous work showed that multicore-specific auto-tuning can improve the performance of lattice Boltzmann magnetohydrodynamics (LBMHD) by a factor of 4x when running on dual- and quad-core Opteron dual-socket SMPs. We extend these studies to the distributed memory arena via a hybrid MPI/pthreads implementation. In addition to conventional auto-tuning at the local SMP node, we tune at the message-passing level to determine the optimal aspect ratio as well as the correct balance between MPI tasks and threads permore » MPI task. Our study presents a detailed performance analysis when moving along an isocurve of constant hardware usage: fixed total memory, total cores, and total nodes. Overall, our work points to approaches for improving intra- and inter-node efficiency on large-scale multicore systems for demanding scientific applications.« less

The Hopper System: How the Largest XE6 in the World Went From Requirements to Reality.

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

Antypas, Katie; Butler, Tina; Carter, Jonathan

This paper will discuss the entire process of acquiring and deploying Hopper from the first vendor market surveys to providing 3.8 million hours of production cycles per day for NERSC users. Installing the latest system at NERSC has been both a logistical and technical adventure. Balancing compute requirements with power, cooling, and space limitations drove the initial choice and configuration of the XE6, and a number of first-of- a-kind features implemented in collaboration with Cray have resulted in a high performance, usable, and reliable system.

ArrayBridge: Interweaving declarative array processing with high-performance computing

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

Xing, Haoyuan; Floratos, Sofoklis; Blanas, Spyros

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aimsmore » to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.« less

ASCR Cybersecurity for Scientific Computing Integrity - Research Pathways and Ideas Workshop

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

Peisert, Sean; Potok, Thomas E.; Jones, Todd

At the request of the U.S. Department of Energy's (DOE) Office of Science (SC) Advanced Scientific Computing Research (ASCR) program office, a workshop was held June 2-3, 2015, in Gaithersburg, MD, to identify potential long term (10 to +20 year) cybersecurity fundamental basic research and development challenges, strategies and roadmap facing future high performance computing (HPC), networks, data centers, and extreme-scale scientific user facilities. This workshop was a follow-on to the workshop held January 7-9, 2015, in Rockville, MD, that examined higher level ideas about scientific computing integrity specific to the mission of the DOE Office of Science. Issues includedmore » research computation and simulation that takes place on ASCR computing facilities and networks, as well as network-connected scientific instruments, such as those run by various DOE Office of Science programs. Workshop participants included researchers and operational staff from DOE national laboratories, as well as academic researchers and industry experts. Participants were selected based on the submission of abstracts relating to the topics discussed in the previous workshop report [1] and also from other ASCR reports, including "Abstract Machine Models and Proxy Architectures for Exascale Computing" [27], the DOE "Preliminary Conceptual Design for an Exascale Computing Initiative" [28], and the January 2015 machine learning workshop [29]. The workshop was also attended by several observers from DOE and other government agencies. The workshop was divided into three topic areas: (1) Trustworthy Supercomputing, (2) Extreme-Scale Data, Knowledge, and Analytics for Understanding and Improving Cybersecurity, and (3) Trust within High-end Networking and Data Centers. Participants were divided into three corresponding teams based on the category of their abstracts. The workshop began with a series of talks from the program manager and workshop chair, followed by the leaders for each of the three topics and a representative of each of the four major DOE Office of Science Advanced Scientific Computing Research Facilities: the Argonne Leadership Computing Facility (ALCF), the Energy Sciences Network (ESnet), the National Energy Research Scientific Computing Center (NERSC), and the Oak Ridge Leadership Computing Facility (OLCF). The rest of the workshop consisted of topical breakout discussions and focused writing periods that produced much of this report.« less

Relativistic Collisions of Highly-Charged Ions

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

Ionescu, Dorin; Belkacem, Ali

1998-11-19

The physics of elementary atomic processes in relativistic collisions between highly-charged ions and atoms or other ions is briefly discussed, and some recent theoretical and experimental results in this field are summarized. They include excitation, capture, ionization, and electron-positron pair creation. The numerical solution of the two-center Dirac equation in momentum space is shown to be a powerful nonperturbative method for describing atomic processes in relativistic collisions involving heavy and highly-charged ions. By propagating negative-energy wave packets in time the evolution of the QED vacuum around heavy ions in relativistic motion is investigated. Recent results obtained from numerical calculations usingmore » massively parallel processing on the Cray-T3E supercomputer of the National Energy Research Scientific Computer Center (NERSC) at Berkeley National Laboratory are presented.« less

First-Principles Thermodynamics Study of Spinel MgAl 2 O 4 Surface Stability

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

Cai, Qiuxia; Wang, Jian-guo; Wang, Yong

The surface stability of all possible terminations for three low-index (111, 110, 100) structures of the spinel MgAl2O4 has been studied using first-principles based thermodynamic approach. The surface Gibbs free energy results indicate that the 100_AlO2 termination is the most stable surface structure under ultra-high vacuum at T=1100 K regardless of Al-poor or Al-rich environment. With increasing oxygen pressure, the 111_O2(Al) termination becomes the most stable surface in the Al-rich environment. The oxygen vacancy formation is thermodynamically favorable over the 100_AlO2, 111_O2(Al) and the (111) structure with Mg/O connected terminations. On the basis of surface Gibbs free energies for bothmore » perfect and defective surface terminations, the 100_AlO2 and 111_O2(Al) are the most dominant surfaces in Al-rich environment under atmospheric condition. This is also consistent with our previously reported experimental observation. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computing time was granted by the National Energy Research Scientific Computing Center (NERSC). Part of computing time was also granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington.« less

Performance Analysis Tool for HPC and Big Data Applications on Scientific Clusters

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

Yoo, Wucherl; Koo, Michelle; Cao, Yu

Big data is prevalent in HPC computing. Many HPC projects rely on complex workflows to analyze terabytes or petabytes of data. These workflows often require running over thousands of CPU cores and performing simultaneous data accesses, data movements, and computation. It is challenging to analyze the performance involving terabytes or petabytes of workflow data or measurement data of the executions, from complex workflows over a large number of nodes and multiple parallel task executions. To help identify performance bottlenecks or debug the performance issues in large-scale scientific applications and scientific clusters, we have developed a performance analysis framework, using state-ofthe-more » art open-source big data processing tools. Our tool can ingest system logs and application performance measurements to extract key performance features, and apply the most sophisticated statistical tools and data mining methods on the performance data. It utilizes an efficient data processing engine to allow users to interactively analyze a large amount of different types of logs and measurements. To illustrate the functionality of the big data analysis framework, we conduct case studies on the workflows from an astronomy project known as the Palomar Transient Factory (PTF) and the job logs from the genome analysis scientific cluster. Our study processed many terabytes of system logs and application performance measurements collected on the HPC systems at NERSC. The implementation of our tool is generic enough to be used for analyzing the performance of other HPC systems and Big Data workows.« less

Evaluating the networking characteristics of the Cray XC-40 Intel Knights Landing-based Cori supercomputer at NERSC

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

Doerfler, Douglas; Austin, Brian; Cook, Brandon

There are many potential issues associated with deploying the Intel Xeon Phi™ (code named Knights Landing [KNL]) manycore processor in a large-scale supercomputer. One in particular is the ability to fully utilize the high-speed communications network, given that the serial performance of a Xeon Phi TM core is a fraction of a Xeon®core. In this paper, we take a look at the trade-offs associated with allocating enough cores to fully utilize the Aries high-speed network versus cores dedicated to computation, e.g., the trade-off between MPI and OpenMP. In addition, we evaluate new features of Cray MPI in support of KNL,more » such as internode optimizations. We also evaluate one-sided programming models such as Unified Parallel C. We quantify the impact of the above trade-offs and features using a suite of National Energy Research Scientific Computing Center applications.« less

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

Fadika, Zacharia; Dede, Elif; Govindaraju, Madhusudhan

MapReduce is increasingly becoming a popular framework, and a potent programming model. The most popular open source implementation of MapReduce, Hadoop, is based on the Hadoop Distributed File System (HDFS). However, as HDFS is not POSIX compliant, it cannot be fully leveraged by applications running on a majority of existing HPC environments such as Teragrid and NERSC. These HPC environments typicallysupport globally shared file systems such as NFS and GPFS. On such resourceful HPC infrastructures, the use of Hadoop not only creates compatibility issues, but also affects overall performance due to the added overhead of the HDFS. This paper notmore » only presents a MapReduce implementation directly suitable for HPC environments, but also exposes the design choices for better performance gains in those settings. By leveraging inherent distributed file systems' functions, and abstracting them away from its MapReduce framework, MARIANE (MApReduce Implementation Adapted for HPC Environments) not only allows for the use of the model in an expanding number of HPCenvironments, but also allows for better performance in such settings. This paper shows the applicability and high performance of the MapReduce paradigm through MARIANE, an implementation designed for clustered and shared-disk file systems and as such not dedicated to a specific MapReduce solution. The paper identifies the components and trade-offs necessary for this model, and quantifies the performance gains exhibited by our approach in distributed environments over Apache Hadoop in a data intensive setting, on the Magellan testbed at the National Energy Research Scientific Computing Center (NERSC).« less

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

Koniges, A.E.

The author describes the new T3D parallel computer at NERSC. The adaptive mesh ICF3D code is one of the current applications being ported and developed for use on the T3D. It has been stressed in other papers in this proceedings that the development environment and tools available on the parallel computer is similar to any planned for the future including networks of workstations.

Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex

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

Bhattacharya, Papri; Heiden, Zachariah M.; Wiedner, Eric S.

We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo-15NH3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo=15NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo=15NR generates a terminal Mo≡N nitride, and a [Mo-15NH]+ complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo-15NH3 complex and the formation of Mo=15NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Officemore » of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.« less

Dehydration of 1-octadecanol over H-BEA: A combined experimental and computational study

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

Song, Wenji; Liu, Yuanshuai; Barath, Eszter

Liquid phase dehydration of 1-octdecanol, which is intermediately formed during the hydrodeoxygenation of microalgae oil, has been explored in a combined experimental and computational study. The alkyl chain of C18 alcohol interacts with acid sites during diffusion inside the zeolite pores, resulting in an inefficient utilization of the Brønsted acid sites for samples with high acid site concentrations. The parallel intra- and inter- molecular dehydration pathways having different activation energies pass through alternative reaction intermediates. Formation of surface-bound alkoxide species is the rate-limiting step during intramolecular dehydration, whereas intermolecular dehydration proceeds via a bulky dimer intermediate. Octadecene is the primarymore » dehydration product over H-BEA at 533 K. Despite of the main contribution of Brønsted acid sites towards both dehydration pathways, Lewis acid sites are also active in the formation of dioctadecyl ether. The intramolecular dehydration to octadecene and cleavage of the intermediately formed ether, however, require strong BAS. L. Wang, D. Mei and J. A. Lercher, acknowledge the partial support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Are Cloud Environments Ready for Scientific Applications?

NASA Astrophysics Data System (ADS)

Mehrotra, P.; Shackleford, K.

2011-12-01

Cloud computing environments are becoming widely available both in the commercial and government sectors. They provide flexibility to rapidly provision resources in order to meet dynamic and changing computational needs without the customers incurring capital expenses and/or requiring technical expertise. Clouds also provide reliable access to resources even though the end-user may not have in-house expertise for acquiring or operating such resources. Consolidation and pooling in a cloud environment allow organizations to achieve economies of scale in provisioning or procuring computing resources and services. Because of these and other benefits, many businesses and organizations are migrating their business applications (e.g., websites, social media, and business processes) to cloud environments-evidenced by the commercial success of offerings such as the Amazon EC2. In this paper, we focus on the feasibility of utilizing cloud environments for scientific workloads and workflows particularly of interest to NASA scientists and engineers. There is a wide spectrum of such technical computations. These applications range from small workstation-level computations to mid-range computing requiring small clusters to high-performance simulations requiring supercomputing systems with high bandwidth/low latency interconnects. Data-centric applications manage and manipulate large data sets such as satellite observational data and/or data previously produced by high-fidelity modeling and simulation computations. Most of the applications are run in batch mode with static resource requirements. However, there do exist situations that have dynamic demands, particularly ones with public-facing interfaces providing information to the general public, collaborators and partners, as well as to internal NASA users. In the last few months we have been studying the suitability of cloud environments for NASA's technical and scientific workloads. We have ported several applications to multiple cloud environments including NASA's Nebula environment, Amazon's EC2, Magellan at NERSC, and SGI's Cyclone system. We critically examined the performance of the applications on these systems. We also collected information on the usability of these cloud environments. In this talk we will present the results of our study focusing on the efficacy of using clouds for NASA's scientific applications.

Multi-threaded ATLAS simulation on Intel Knights Landing processors

NASA Astrophysics Data System (ADS)

Farrell, Steven; Calafiura, Paolo; Leggett, Charles; Tsulaia, Vakhtang; Dotti, Andrea; ATLAS Collaboration

2017-10-01

The Knights Landing (KNL) release of the Intel Many Integrated Core (MIC) Xeon Phi line of processors is a potential game changer for HEP computing. With 72 cores and deep vector registers, the KNL cards promise significant performance benefits for highly-parallel, compute-heavy applications. Cori, the newest supercomputer at the National Energy Research Scientific Computing Center (NERSC), was delivered to its users in two phases with the first phase online at the end of 2015 and the second phase now online at the end of 2016. Cori Phase 2 is based on the KNL architecture and contains over 9000 compute nodes with 96GB DDR4 memory. ATLAS simulation with the multithreaded Athena Framework (AthenaMT) is a good potential use-case for the KNL architecture and supercomputers like Cori. ATLAS simulation jobs have a high ratio of CPU computation to disk I/O and have been shown to scale well in multi-threading and across many nodes. In this paper we will give an overview of the ATLAS simulation application with details on its multi-threaded design. Then, we will present a performance analysis of the application on KNL devices and compare it to a traditional x86 platform to demonstrate the capabilities of the architecture and evaluate the benefits of utilizing KNL platforms like Cori for ATLAS production.

First-principles Studies of Ferroelectricity in BiMnO3 Thin Films

NASA Astrophysics Data System (ADS)

Wang, Yun-Peng; Cheng, Hai-Ping

The ferroelectricity in BiMnO3 thin films is a long-standing problem. We employed a first-principles density functional theory with inclusion of the local Hubbard Coulomb (U) and exchange (J) terms. The parameters U and J are optimized to reproduce the atomic structure and the energy gap of bulk C2/c BiMnO3. With these optimal U and J parameters, the calculated ferromagnetic Curie temperature and lattice dynamics properties agree with experiments. We then studied the ferroelectricity in few-layer BiMnO3 thin films on SrTiO3(001) substrates. Our calculations identified ferroelectricity in monolayer, bilayer and trilayer BiMnO3 thin films. We find that the energy barrier for 90° rotation of electric polarization is about 3 - 4 times larger than that of conventional ferroelectric materials. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences (BES), under Contract No. DE-FG02-02ER45995. Computations were done using the utilities of the National Energy Research Scientific Computing Center (NERSC).

Understanding the I/O Performance Gap Between Cori KNL and Haswell

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

Liu, Jialin; Koziol, Quincey; Tang, Houjun

2017-05-01

The Cori system at NERSC has two compute partitions with different CPU architectures: a 2,004 node Haswell partition and a 9,688 node KNL partition, which ranked as the 5th most powerful and fastest supercomputer on the November 2016 Top 500 list. The compute partitions share a common storage configuration, and understanding the IO performance gap between them is important, impacting not only to NERSC/LBNL users and other national labs, but also to the relevant hardware vendors and software developers. In this paper, we have analyzed performance of single core and single node IO comprehensively on the Haswell and KNL partitions,more » and have discovered the major bottlenecks, which include CPU frequencies and memory copy performance. We have also extended our performance tests to multi-node IO and revealed the IO cost difference caused by network latency, buffer size, and communication cost. Overall, we have developed a strong understanding of the IO gap between Haswell and KNL nodes and the lessons learned from this exploration will guide us in designing optimal IO solutions in many-core era.« less

Multigrid treatment of implicit continuum diffusion

NASA Astrophysics Data System (ADS)

Francisquez, Manaure; Zhu, Ben; Rogers, Barrett

2017-10-01

Implicit treatment of diffusive terms of various differential orders common in continuum mechanics modeling, such as computational fluid dynamics, is investigated with spectral and multigrid algorithms in non-periodic 2D domains. In doubly periodic time dependent problems these terms can be efficiently and implicitly handled by spectral methods, but in non-periodic systems solved with distributed memory parallel computing and 2D domain decomposition, this efficiency is lost for large numbers of processors. We built and present here a multigrid algorithm for these types of problems which outperforms a spectral solution that employs the highly optimized FFTW library. This multigrid algorithm is not only suitable for high performance computing but may also be able to efficiently treat implicit diffusion of arbitrary order by introducing auxiliary equations of lower order. We test these solvers for fourth and sixth order diffusion with idealized harmonic test functions as well as a turbulent 2D magnetohydrodynamic simulation. It is also shown that an anisotropic operator without cross-terms can improve model accuracy and speed, and we examine the impact that the various diffusion operators have on the energy, the enstrophy, and the qualitative aspect of a simulation. This work was supported by DOE-SC-0010508. This research used resources of the National Energy Research Scientific Computing Center (NERSC).

LLNL Scientists Use NERSC to Advance Global Aerosol Simulations

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

Bergmann, D J; Chuang, C; Rotman, D

2004-10-13

While ''greenhouse gases'' have been the focus of climate change research for a number of years, DOE's ''Aerosol Initiative'' is now examining how aerosols (small particles of approximately micron size) affect the climate on both a global and regional scale. Scientists in the Atmospheric Science Division at Lawrence Livermore National Laboratory (LLNL) are using NERSC's IBM supercomputer and LLNL's IMPACT (atmospheric chemistry) model to perform simulations showing the historic effects of sulfur aerosols at a finer spatial resolution than ever done before. Simulations were carried out for five decades, from the 1950s through the 1990s. The results clearly show themore » effects of the changing global pattern of sulfur emissions. Whereas in 1950 the United States emitted 41 percent of the world's sulfur aerosols, this figure had dropped to 15 percent by 1990, due to conservation and anti-pollution policies. By contrast, the fraction of total sulfur emissions of European origin has only dropped by a factor of 2 and the Asian emission fraction jumped six fold during the same time, from 7 percent in 1950 to 44 percent in 1990. Under a special allocation of computing time provided by the Office of Science INCITE (Innovative and Novel Computational Impact on Theory and Experiment) program, Dan Bergmann, working with a team of LLNL scientists including Cathy Chuang, Philip Cameron-Smith, and Bala Govindasamy, was able to carry out a large number of calculations during the past month, making the aerosol project one of the largest users of NERSC resources. The applications ran on 128 and 256 processors. The objective was to assess the effects of anthropogenic (man-made) sulfate aerosols. The IMPACT model calculates the rate at which SO{sub 2} (a gas emitted by industrial activity) is oxidized and forms particles known as sulfate aerosols. These particles have a short lifespan in the atmosphere, often washing out in about a week. This means that their effects on climate tend to be more regional, occurring near the area where the SO{sub 2} is emitted. To accurately study these regional effects, Bergmann needed to run the simulations at a finer horizontal resolution, as the coarser resolution (typically 300km by 300km) of other climate models are insufficient for studying changes on a regional scale. Livermore's use of CAM3, the Community Atmospheric Model which is a high-resolution climate model developed at NCAR (with collaboration from DOE), allows a 100km by 100km grid to be applied. NERSC's terascale computing capability provided the needed computational horsepower to run the application at the finer level.« less

Analysis, tuning and comparison of two general sparse solvers for distributed memory computers

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

Amestoy, P.R.; Duff, I.S.; L'Excellent, J.-Y.

2000-06-30

We describe the work performed in the context of a Franco-Berkeley funded project between NERSC-LBNL located in Berkeley (USA) and CERFACS-ENSEEIHT located in Toulouse (France). We discuss both the tuning and performance analysis of two distributed memory sparse solvers (superlu from Berkeley and mumps from Toulouse) on the 512 processor Cray T3E from NERSC (Lawrence Berkeley National Laboratory). This project gave us the opportunity to improve the algorithms and add new features to the codes. We then quite extensively analyze and compare the two approaches on a set of large problems from real applications. We further explain the main differencesmore » in the behavior of the approaches on artificial regular grid problems. As a conclusion to this activity report, we mention a set of parallel sparse solvers on which this type of study should be extended.« less

Evaluating and optimizing the NERSC workload on Knights Landing

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

Barnes, T; Cook, B; Deslippe, J

2017-01-30

NERSC has partnered with 20 representative application teams to evaluate performance on the Xeon-Phi Knights Landing architecture and develop an application-optimization strategy for the greater NERSC workload on the recently installed Cori system. In this article, we present early case studies and summarized results from a subset of the 20 applications highlighting the impact of important architecture differences between the Xeon-Phi and traditional Xeon processors. We summarize the status of the applications and describe the greater optimization strategy that has formed.

Evaluating and Optimizing the NERSC Workload on Knights Landing

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

Barnes, Taylor; Cook, Brandon; Doerfler, Douglas

2016-01-01

NERSC has partnered with 20 representative application teams to evaluate performance on the Xeon-Phi Knights Landing architecture and develop an application-optimization strategy for the greater NERSC workload on the recently installed Cori system. In this article, we present early case studies and summarized results from a subset of the 20 applications highlighting the impact of important architecture differences between the Xeon-Phi and traditional Xeon processors. We summarize the status of the applications and describe the greater optimization strategy that has formed.

First-principles characterization of formate and carboxyl adsorption on the stoichiometric CeO2(111) and CeO2(110) surfaces

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

Mei, Donghai

2013-05-20

Molecular adsorption of formate and carboxyl on the stoichiometric CeO2(111) and CeO2(110) surfaces was studied using periodic density functional theory (DFT+U) calculations. Two distinguishable adsorption modes (strong and weak) of formate are identified. The bidentate configuration is more stable than the monodentate adsorption configuration. Both formate and carboxyl bind at the more open CeO2(110) surface are stronger. The calculated vibrational frequencies of two adsorbed species are consistent with experimental measurements. Finally, the effects of U parameters on the adsorption of formate and carboxyl over both CeO2 surfaces were investigated. We found that the geometrical configurations of two adsorbed species aremore » not affected by using different U parameters (U=0, 5, and 7). However, the calculated adsorption energy of carboxyl pronouncedly increases with the U value while the adsorption energy of formate only slightly changes (<0.2 eV). The Bader charge analysis shows the opposite charge transfer occurs for formate and carboxyl adsorption where the adsorbed formate is negatively charge whiled the adsorbed carboxyl is positively charged. Interestingly, with the increasing U parameter, the amount of charge is also increased. This work was supported by the Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL) and by a Cooperative Research and Development Agreement (CRADA) with General Motors. The computations were performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington. Part of the computing time was also granted by the National Energy Research Scientific Computing Center (NERSC)« less

Crosscut report: Exascale Requirements Reviews, March 9–10, 2017 – Tysons Corner, Virginia. An Office of Science review sponsored by: Advanced Scientific Computing Research, Basic Energy Sciences, Biological and Environmental Research, Fusion Energy Sciences, High Energy Physics, Nuclear Physics

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

Gerber, Richard; Hack, James; Riley, Katherine

The mission of the U.S. Department of Energy Office of Science (DOE SC) is the delivery of scientific discoveries and major scientific tools to transform our understanding of nature and to advance the energy, economic, and national security missions of the United States. To achieve these goals in today’s world requires investments in not only the traditional scientific endeavors of theory and experiment, but also in computational science and the facilities that support large-scale simulation and data analysis. The Advanced Scientific Computing Research (ASCR) program addresses these challenges in the Office of Science. ASCR’s mission is to discover, develop, andmore » deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to DOE. ASCR supports research in computational science, three high-performance computing (HPC) facilities — the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and Leadership Computing Facilities at Argonne (ALCF) and Oak Ridge (OLCF) National Laboratories — and the Energy Sciences Network (ESnet) at Berkeley Lab. ASCR is guided by science needs as it develops research programs, computers, and networks at the leading edge of technologies. As we approach the era of exascale computing, technology changes are creating challenges for science programs in SC for those who need to use high performance computing and data systems effectively. Numerous significant modifications to today’s tools and techniques will be needed to realize the full potential of emerging computing systems and other novel computing architectures. To assess these needs and challenges, ASCR held a series of Exascale Requirements Reviews in 2015–2017, one with each of the six SC program offices,1 and a subsequent Crosscut Review that sought to integrate the findings from each. Participants at the reviews were drawn from the communities of leading domain scientists, experts in computer science and applied mathematics, ASCR facility staff, and DOE program managers in ASCR and the respective program offices. The purpose of these reviews was to identify mission-critical scientific problems within the DOE Office of Science (including experimental facilities) and determine the requirements for the exascale ecosystem that would be needed to address those challenges. The exascale ecosystem includes exascale computing systems, high-end data capabilities, efficient software at scale, libraries, tools, and other capabilities. This effort will contribute to the development of a strategic roadmap for ASCR compute and data facility investments and will help the ASCR Facility Division establish partnerships with Office of Science stakeholders. It will also inform the Office of Science research needs and agenda. The results of the six reviews have been published in reports available on the web at http://exascaleage.org/. This report presents a summary of the individual reports and of common and crosscutting findings, and it identifies opportunities for productive collaborations among the DOE SC program offices.« less

2009 ALCF annual report.

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

Beckman, P.; Martin, D.; Drugan, C.

2010-11-23

This year the Argonne Leadership Computing Facility (ALCF) delivered nearly 900 million core hours of science. The research conducted at their leadership class facility touched our lives in both minute and massive ways - whether it was studying the catalytic properties of gold nanoparticles, predicting protein structures, or unearthing the secrets of exploding stars. The authors remained true to their vision to act as the forefront computational center in extending science frontiers by solving pressing problems for our nation. Our success in this endeavor was due mainly to the Department of Energy's (DOE) INCITE (Innovative and Novel Computational Impact onmore » Theory and Experiment) program. The program awards significant amounts of computing time to computationally intensive, unclassified research projects that can make high-impact scientific advances. This year, DOE allocated 400 million hours of time to 28 research projects at the ALCF. Scientists from around the world conducted the research, representing such esteemed institutions as the Princeton Plasma Physics Laboratory, National Institute of Standards and Technology, and European Center for Research and Advanced Training in Scientific Computation. Argonne also provided Director's Discretionary allocations for research challenges, addressing such issues as reducing aerodynamic noise, critical for next-generation 'green' energy systems. Intrepid - the ALCF's 557-teraflops IBM Blue/Gene P supercomputer - enabled astounding scientific solutions and discoveries. Intrepid went into full production five months ahead of schedule. As a result, the ALCF nearly doubled the days of production computing available to the DOE Office of Science, INCITE awardees, and Argonne projects. One of the fastest supercomputers in the world for open science, the energy-efficient system uses about one-third as much electricity as a machine of comparable size built with more conventional parts. In October 2009, President Barack Obama recognized the excellence of the entire Blue Gene series by awarding it to the National Medal of Technology and Innovation. Other noteworthy achievements included the ALCF's collaboration with the National Energy Research Scientific Computing Center (NERSC) to examine cloud computing as a potential new computing paradigm for scientists. Named Magellan, the DOE-funded initiative will explore which science application programming models work well within the cloud, as well as evaluate the challenges that come with this new paradigm. The ALCF obtained approval for its next-generation machine, a 10-petaflops system to be delivered in 2012. This system will allow us to resolve ever more pressing problems, even more expeditiously through breakthrough science in the years to come.« less

User and Performance Impacts from Franklin Upgrades

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

He, Yun

2009-05-10

The NERSC flagship computer Cray XT4 system"Franklin" has gone through three major upgrades: quad core upgrade, CLE 2.1 upgrade, and IO upgrade, during the past year. In this paper, we will discuss the various aspects of the user impacts such as user access, user environment, and user issues etc from these upgrades. The performance impacts on the kernel benchmarks and selected application benchmarks will also be presented.

Theoretical Comparison Between Candidates for Dark Matter

NASA Astrophysics Data System (ADS)

McKeough, James; Hira, Ajit; Valdez, Alexandra

2017-01-01

Since the generally-accepted view among astrophysicists is that the matter component of the universe is mostly dark matter, the search for dark matter particles continues unabated. The Large Underground Xenon (LUX) improvements, aided by advanced computer simulations at the U.S. Department of Energy's Lawrence Berkeley National Laboratory's (Berkeley Lab) National Energy Research Scientific Computing Center (NERSC) and Brown University's Center for Computation and Visualization (CCV), can potentially eliminate some particle models of dark matter. Generally, the proposed candidates can be put in three categories: baryonic dark matter, hot dark matter, and cold dark matter. The Lightest Supersymmetric Particle(LSP) of supersymmetric models is a dark matter candidate, and is classified as a Weakly Interacting Massive Particle (WIMP). Similar to the cosmic microwave background radiation left over from the Big Bang, there is a background of low-energy neutrinos in our Universe. According to some researchers, these may be the explanation for the dark matter. One advantage of the Neutrino Model is that they are known to exist. Dark matter made from neutrinos is termed ``hot dark matter''. We formulate a novel empirical function for the average density profile of cosmic voids, identified via the watershed technique in ΛCDM N-body simulations. This function adequately treats both void size and redshift, and describes the scale radius and the central density of voids. We started with a five-parameter model. Our research is mainly on LSP and Neutrino models.

Enabling Efficient Climate Science Workflows in High Performance Computing Environments

NASA Astrophysics Data System (ADS)

Krishnan, H.; Byna, S.; Wehner, M. F.; Gu, J.; O'Brien, T. A.; Loring, B.; Stone, D. A.; Collins, W.; Prabhat, M.; Liu, Y.; Johnson, J. N.; Paciorek, C. J.

2015-12-01

A typical climate science workflow often involves a combination of acquisition of data, modeling, simulation, analysis, visualization, publishing, and storage of results. Each of these tasks provide a myriad of challenges when running on a high performance computing environment such as Hopper or Edison at NERSC. Hurdles such as data transfer and management, job scheduling, parallel analysis routines, and publication require a lot of forethought and planning to ensure that proper quality control mechanisms are in place. These steps require effectively utilizing a combination of well tested and newly developed functionality to move data, perform analysis, apply statistical routines, and finally, serve results and tools to the greater scientific community. As part of the CAlibrated and Systematic Characterization, Attribution and Detection of Extremes (CASCADE) project we highlight a stack of tools our team utilizes and has developed to ensure that large scale simulation and analysis work are commonplace and provide operations that assist in everything from generation/procurement of data (HTAR/Globus) to automating publication of results to portals like the Earth Systems Grid Federation (ESGF), all while executing everything in between in a scalable environment in a task parallel way (MPI). We highlight the use and benefit of these tools by showing several climate science analysis use cases they have been applied to.

Development of a fast framing detector for electron microscopy

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

Johnson, Ian J.; Bustillo, Karen C.; Ciston, Jim

2016-10-01

A high frame rate detector system is described that enables fast real-time data analysis of scanning diffraction experiments in scanning transmission electron microscopy (STEM). This is an end-to-end development that encompasses the data producing detector, data transportation, and real-time processing of data. The detector will consist of a central pixel sensor that is surrounded by annular silicon diodes. Both components of the detector system will synchronously capture data at almost 100 kHz frame rate, which produces an approximately 400 Gb/s data stream. Low-level preprocessing will be implemented in firmware before the data is streamed from the National Center for Electronmore » Microscopy (NCEM) to the National Energy Research Scientific Computing Center (NERSC). Live data processing, before it lands on disk, will happen on the Cori supercomputer and aims to present scientists with prompt experimental feedback. This online analysis will provide rough information of the sample that can be utilized for sample alignment, sample monitoring and verification that the experiment is set up correctly. Only a compressed version of the relevant data is then selected for more in-depth processing.« less

Toward Exascale Earthquake Ground Motion Simulations for Near-Fault Engineering Analysis

DOE PAGES

Johansen, Hans; Rodgers, Arthur; Petersson, N. Anders; ...

2017-09-01

Modernizing SW4 for massively parallel time-domain simulations of earthquake ground motions in 3D earth models increases resolution and provides ground motion estimates for critical infrastructure risk evaluations. Simulations of ground motions from large (M ≥ 7.0) earthquakes require domains on the order of 100 to500 km and spatial granularity on the order of 1 to5 m resulting in hundreds of billions of grid points. Surface-focused structured mesh refinement (SMR) allows for more constant grid point per wavelength scaling in typical Earth models, where wavespeeds increase with depth. In fact, MR allows for simulations to double the frequency content relative tomore » a fixed grid calculation on a given resource. The authors report improvements to the SW4 algorithm developed while porting the code to the Cori Phase 2 (Intel Xeon Phi) systems at the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. As a result, investigations of the performance of the innermost loop of the calculations found that reorganizing the order of operations can improve performance for massive problems.« less

Toward Exascale Earthquake Ground Motion Simulations for Near-Fault Engineering Analysis

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

Johansen, Hans; Rodgers, Arthur; Petersson, N. Anders

Modernizing SW4 for massively parallel time-domain simulations of earthquake ground motions in 3D earth models increases resolution and provides ground motion estimates for critical infrastructure risk evaluations. Simulations of ground motions from large (M ≥ 7.0) earthquakes require domains on the order of 100 to500 km and spatial granularity on the order of 1 to5 m resulting in hundreds of billions of grid points. Surface-focused structured mesh refinement (SMR) allows for more constant grid point per wavelength scaling in typical Earth models, where wavespeeds increase with depth. In fact, MR allows for simulations to double the frequency content relative tomore » a fixed grid calculation on a given resource. The authors report improvements to the SW4 algorithm developed while porting the code to the Cori Phase 2 (Intel Xeon Phi) systems at the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. As a result, investigations of the performance of the innermost loop of the calculations found that reorganizing the order of operations can improve performance for massive problems.« less

Opening Comments: SciDAC 2008

NASA Astrophysics Data System (ADS)

Strayer, Michael

2008-07-01

Welcome to Seattle and the 2008 SciDAC Conference. This conference, the fourth in the series, is a continuation of the PI meetings we first began under SciDAC-1. I would like to start by thanking the organizing committee, and Rick Stevens in particular, for organizing this year's meeting. This morning I would like to look briefly at SciDAC, to give you a brief history of SciDAC and also look ahead to see where we plan to go over the next few years. I think the best description of SciDAC, at least the simulation part, comes from a quote from Dr Ray Orbach, DOE's Under Secretary for Science and Director of the Office of Science. In an interview that appeared in the SciDAC Review magazine, Dr Orbach said, `SciDAC is unique in the world. There isn't any other program like it anywhere else, and it has the remarkable ability to do science by bringing together physical scientists, mathematicians, applied mathematicians, and computer scientists who recognize that computation is not something you do at the end, but rather it needs to be built into the solution of the very problem that one is addressing'. Of course, that is extended not just to physical scientists, but also to biological scientists. This is a theme of computational science, this partnership among disciplines, which goes all the way back to the early 1980s and Ken Wilson. It's a unique thread within the Department of Energy. SciDAC-1, launched around the turn of the millennium, created a new generation of scientific simulation codes. It advocated building out mathematical and computing system software in support of science and a new collaboratory software environment for data. The original concept for SciDAC-1 had topical centers for the execution of the various science codes, but several corrections and adjustments were needed. The ASCR scientific computing infrastructure was also upgraded, providing the hardware facilities for the program. The computing facility that we had at that time was the big 3 teraflop/s center at NERSC and that had to be shared with the programmatic side supporting research across DOE. At the time, ESnet was just slightly over half a gig per sec of bandwidth; and the science being addressed was accelerator science, climate, chemistry, fusion, astrophysics, materials science, and QCD. We built out the national collaboratories from the ASCR office, and in addition we built Integrated Software Infrastructure Centers (ISICs). Of these, three were in applied mathematics, four in computer science (including a performance evaluation research center), and four were collaboratories or Grid projects having to do with data management. For science, there were remarkable breakthroughs in simulation, such as full 3D laboratory scale flame simulation. There were also significant improvements in application codes - from factors of almost 3 to more than 100 - and code improvement as people began to realize they had to integrate mathematics tools and computer science tools into their codes to take advantage of the parallelism of the day. The SciDAC data-mining tool, Sapphire, received a 2006 R&D 100 award. And the community as a whole worked well together and began building a publication record that was substantial. In 2006, we recompeted the program with similar goals - SciDAC-1 was very successful, and we wanted to continue that success and extend what was happening under SciDAC to the broader science community. We opened up the partnership to all of the Offices of Science and the NSF and the NNSA. The goal was to create comprehensive scientific computing software and the infrastructure for the software to enable scientific discovery in the physical, biological, and environmental sciences and take the simulations to an extreme scale, in this case petascale. We would also build out a new generation of data management tools. What we observed during SciDAC-1 was that the data and the data communities - both experimental data from large experimental facilities and observational data, along with simulation data - were expanding at a rate significantly faster than Moore's law. In the past few weeks, the FastBit indexing technology software tool for data analyses and data mining developed under SciDAC's Scientific Data Management project was recognized with an R&D 100 Award, selected by an independent judging panel and editors of R&D Magazine as one of the 100 most technologically significant products introduced into the marketplace over the past year. For SciDAC-2 we had nearly 250 proposals requesting a total of slightly over 1 billion in funding. Of course, we had nowhere near 1 billion. The facilities and the science we ended up with were not significantly different from what we had in SciDAC-1. But we had put in place substantially increased facilities for science. When SciDAC-1 was originally executed with the facilities at NERSC, there was significant impact on the resources at NERSC, because not only did we have an expanding portfolio of programmatic science, but we had the SciDAC projects that also needed to run at NERSC. Suddenly, NERSC was incredibly oversubscribed. With SciDAC-2, we had in place leadership-class computing facilities at Argonne with slightly more than half a petaflop and at Oak Ridge with slightly more than a quarter petaflop with an upgrade planned at the end of this year for a petaflop. And we increased the production computing capacity at NERSC to 104 teraflop/s just so that we would not impact the programmatic research and so that we would have a startup facility for SciDAC. At the end of the summer, NERSC will be at 360 teraflop/s. Both the Oak Ridge system and the principal resource at NERSC are Cray systems; Argonne has a different architecture, an IBM Blue Gene/P. At the same time, ESnet has been built out, and we are on a path where we will have dual rings around the country, from 10 to 40 gigabits per second - a factor of 20 to 80 over what was available during SciDAC-1. The science areas include accelerator science and simulation, astrophysics, climate modeling and simulation, computational biology, fusion science, high-energy physics, petabyte high-energy/ nuclear physics, materials science and chemistry, nuclear physics, QCD, radiation transport, turbulence, and groundwater reactive transport modeling and simulation. They were supported by new enabling technology centers and university-based institutes to develop an educational thread for the SciDAC program. There were four mathematics projects and four computer science projects; and under data management, we see a significant difference in that we are bringing up new visualization projects to support and sustain data-intensive science. When we look at the budgets, we see growth in the budget from just under 60 million for SciDAC-1 to just over 80 for SciDAC-2. Part of the growth is due to bringing in NSF and NNSA as new partners, and some of the growth is due to some program offices increasing their investment in SciDAC, while other program offices are constant or have decreased their investment. This is not a reflection of their priorities per se but, rather, a reflection of the budget process and the difficult times in Washington during the past two years. New activities are under way in SciDAC - the annual PI meeting has turned into what I would describe as the premier interdisciplinary computational science meeting, one of the best in the world. Doing interdisciplinary meetings is difficult because people tend to develop a focus for their particular subject area. But this is the fourth in the series; and since the first meeting in San Francisco, these conferences have been remarkably successful. For SciDAC-2 we also created an outreach magazine, SciDAC Review, which highlights scientific discovery as well as high-performance computing. It's been very successful in telling the non-practitioners what SciDAC and computational science are all about. The other new instrument in SciDAC-2 is an outreach center. As we go from computing at the terascale to computing at the petascale, we face the problem of narrowing our research community. The number of people who are `literate' enough to compute at the terascale is more than the number of those who can compute at the petascale. To address this problem, we established the SciDAC Outreach Center to bring people into the fold and educate them as to how we do SciDAC, how the teams are composed, and what it really means to compute at scale. The resources I have mentioned don't come for free. As part of the HECRTF law of 2005, Congress mandated that the Secretary would ensure that leadership-class facilities would be open to everyone across all agencies. So we took Congress at its word, and INCITE is our instrument for making allocations at the leadership-class facilities at Argonne and Oak Ridge, as well as smaller allocations at NERSC. Therefore, the selected proposals are very large projects that are computationally intensive, that compute at scale, and that have a high science impact. An important feature is that INCITE is completely open to anyone - there is no requirement of DOE Office of Science funding, and proposals are rigorously reviewed for both the science and the computational readiness. In 2008, more than 100 proposals were received, requesting about 600 million processor-hours. We allocated just over a quarter of a billion processor-hours. Astrophysics, materials science, lattice gauge theory, and high energy and nuclear physics were the major areas. These were the teams that were computationally ready for the big machines and that had significant science they could identify. In 2009, there will be a significant increase amount of time to be allocated, over half a billion processor-hours. The deadline is August 11 for new proposals and September 12 for renewals. We anticipate a significant increase in the number of requests this year. We expect you - as successful SciDAC centers, institutes, or partnerships - to compete for and win INCITE program allocation awards. If you have a successful SciDAC proposal, we believe it will make you successful in the INCITE review. We have the expectation that you will among those most prepared and most ready to use the machines and to compute at scale. Over the past 18 months, we have assembled a team to look across our computational science portfolio and to judge what are the 10 most significant science accomplishments. The ASCR office, as it goes forward with OMB, the new administration, and Congress, will be judged by the science we have accomplished. All of our proposals - such as for increasing SciDAC, increasing applied mathematics, and so on - are tied to what have we accomplished in science. And so these 10 big accomplishments are key to establishing credibility for new budget requests. Tony Mezzacappa, who chaired the committee, will also give a presentation on the ranking of these top 10, how they got there, and what the science is all about. Here is the list - numbers 2, 5, 6, 7, 9, and 10 are all SciDAC projects. RankTitle 1Modeling the Molecular Basis of Parkinson's Disease (Tsigelny) 2Discovery of the Standing Accretion Shock Instability and Pulsar Birth Mechanism in a Core-Collapse Supernova Evolution and Explosion (Blondin) 3Prediction and Design of Macromolecular Structures and Functions (Baker) 4Understanding How Lifted Flame Stabilized in a Hot Coflow (Yoo) 5New Insights from LCF-enabled Advanced Kinetic Simulations of Global Turbulence in Fusion Systems (Tang) 6High Transition Temperature Superconductivity: A High-Temperature Superconductive State and a Pairing Mechanism in 2-D Hubbard Model (Scalapino) 7 PETsc: Providing the Solvers for DOE High-Performance Simulations (Smith) 8 Via Lactea II, A Billion Particle Simulation of the Dark Matter Halo of the Milky Way (Madau) 9Probing the Properties of Water through Advanced Computing (Galli) 10First Provably Scalable Maxwell Solver Enables Scalable Electromagnetic Simulations (Kovel) So, what's the future going to look like for us? The office is putting together an initiative with the community, which we call the E3 Initiative. We're looking for a 10-year horizon for what's going to happen. Through the series of town hall meetings, which many of you participated in, we have produced a document on `Transforming Energy, the Environment and Science through simulations at the eXtreme Scale'; it can be found at http://www.science.doe.gov/ascr/ProgramDocuments/TownHall.pdf . We sometimes call it the Exascale initiative. Exascale computing is the gold-ring level of computing that seems just out of reach; but if we work hard and stretch, we just might be able to reach it. We envision that there will be a SciDAC-X, working at the extreme scale, with SciDAC teams that will perform and carry out science in the areas that will have a great societal impact, such as alternative fuels and transportation, combustion, climate, fusion science, high-energy physics, advanced fuel cycles, carbon management, and groundwater. We envision institutes for applied mathematics and computer science that probably will segue into algorithms because, at the extreme scale, we see the distinction between the applied math and the algorithm per se and its implementation in computer science as being inseparable. We envision an INCITE-X with multi-petaflop platforms, perhaps even exaflop computing resources. ESnet will be best in class - our 10-year plan calls for having 400 terabits per second capacity available in dual rings around the country, an enormously fast data communications network for moving large amounts of data. In looking at where we've been and where we are going, we can see that the gigaflops and teraflops era was a regime where we were following Moore's law through advances in clock speed. In the current regime, we're introducing massive parallelism, which I think is exemplified by Intel's announcement of their teraflop chip, where they envision more than a thousand cores on a chip. But in order to reach exascale, extrapolations talk about machines that require 100 megawatts of power in terms of current architectures. It's clearly going to require novel architectures, things we have perhaps not yet envisioned. It is of course an era of challenge. There will be an unpredictable evolution of hardware if we are to reach the exascale; and there will clearly be multilevel heterogeneous parallelism, including multilevel memory hierarchies. We have no idea right now as to the programming models needed to execute at such an extreme scale. We have been incredibly successful at the petascale - we know that already. Managing data and just getting communications to scale is an enormous challenge. And it's not just the extreme scaling. It's the rapid increase in complexity that represents the challenge. Let me end with a metaphor. In previous meetings we have talked about the road to petascale. Indeed, we have seen in hindsight that it was a road well traveled. But perhaps the road to exascale is not a road at all. Perhaps the metaphor will be akin to scaling the south face of K2. That's clearly not something all of us will be able to do, and probably computing at the exascale is not something all of us will do. But if we achieve that goal, perhaps the words of Emily Dickinson will best summarize where we will be. Perhaps in her words, looking backward and down, you will say: I climb the `Hill of Science' I view the landscape o'er; Such transcendental prospect I ne'er beheld before!

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

Jing Yanfei, E-mail: yanfeijing@uestc.edu.c; Huang Tingzhu, E-mail: tzhuang@uestc.edu.c; Duan Yong, E-mail: duanyong@yahoo.c

This study is mainly focused on iterative solutions with simple diagonal preconditioning to two complex-valued nonsymmetric systems of linear equations arising from a computational chemistry model problem proposed by Sherry Li of NERSC. Numerical experiments show the feasibility of iterative methods to some extent when applied to the problems and reveal the competitiveness of our recently proposed Lanczos biconjugate A-orthonormalization methods to other classic and popular iterative methods. By the way, experiment results also indicate that application specific preconditioners may be mandatory and required for accelerating convergence.

Toward Rational Design of Cu/SSZ-13 Selective Catalytic Reduction Catalysts: Implications from Atomic-Level Understanding of Hydrothermal Stability

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

Song, James; Wang, Yilin; Walter, Eric D.

The hydrothermal stability of Cu/SSZ-13 SCR catalysts has been extensively studied, yet atomic level understanding of changes to the zeolite support and the Cu active sites during hydrothermal aging are still lacking. In this work, via the utilization of spectroscopic methods including solid-state 27Al and 29Si NMR, EPR, DRIFTS, and XPS, together with imaging and elemental mapping using STEM, detailed kinetic analyses, and theoretical calculations with DFT, various Cu species, including two types of isolated active sites and CuOx clusters, were precisely quantified for samples hydrothermally aged under varying conditions. This quantification convincingly confirms the exceptional hydrothermal stability of isolatedmore » Cu2+-2Z sites, and the gradual conversion of [Cu(OH)]+-Z to CuOx clusters with increasing aging severity. This stability difference is rationalized from the hydrolysis activation barrier difference between the two isolated sites via DFT. Discussions are provided on the nature of the CuOx clusters, and their possible detrimental roles on catalyst stability. Finally, a few rational design principles for Cu/SSZ-13 are derived rigorously from the atomic-level understanding of this catalyst obtained here. The authors gratefully acknowledge the US Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office for the support of this work. Computing time was granted by a user proposal at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). The experimental studies described in this paper were performed in the EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.« less

Double photoionization of Be-like (Be-F5+) ions

NASA Astrophysics Data System (ADS)

Abdel Naby, Shahin; Pindzola, Michael; Colgan, James

2015-04-01

The time-dependent close-coupling method is used to study the single photon double ionization of Be-like (Be - F5+) ions. Energy and angle differential cross sections are calculated to fully investigate the correlated motion of the two photoelectrons. Symmetric and antisymmetric amplitudes are presented along the isoelectronic sequence for different energy sharing of the emitted electrons. Our total double photoionization cross sections are in good agreement with available theoretical results and experimental measurements along the Be-like ions. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California and the National Institute for Computational Sciences in Knoxville, Tennessee.

A classical reactive potential for molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2015-10-12

We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, itmore » is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.« less

Visualizing staggered fields and analyzing electromagnetic data with PerceptEM

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

Shasharina, Svetlana

This project resulted in VSimSP: a software for simulating large photonic devices of high-performance computers. It includes: GUI for Photonics Simulations; High-Performance Meshing Algorithm; 2d Order Multimaterials Algorithm; Mode Solver for Waveguides; 2d Order Material Dispersion Algorithm; S Parameters Calculation; High-Performance Workflow at NERSC ; and Large Photonic Devices Simulation Setups We believe we became the only company in the world which can simulate large photonics devices in 3D on modern supercomputers without the need to split them into subparts or do low-fidelity modeling. We started commercial engagement with a manufacturing company.

Flux-driven turbulence GDB simulations of the IWL Alcator C-Mod L-mode edge compared with experiment

NASA Astrophysics Data System (ADS)

Francisquez, Manaure; Zhu, Ben; Rogers, Barrett

2017-10-01

Prior to predicting confinement regime transitions in tokamaks one may need an accurate description of L-mode profiles and turbulence properties. These features determine the heat-flux width upon which wall integrity depends, a topic of major interest for research aid to ITER. To this end our work uses the GDB model to simulate the Alcator C-Mod edge and contributes support for its use in studying critical edge phenomena in current and future tokamaks. We carried out 3D electromagnetic flux-driven two-fluid turbulence simulations of inner wall limited (IWL) C-Mod shots spanning closed and open flux surfaces. These simulations are compared with gas puff imaging (GPI) and mirror Langmuir probe (MLP) data, examining global features and statistical properties of turbulent dynamics. GDB reproduces important qualitative aspects of the C-Mod edge regarding global density and temperature profiles, within reasonable margins, and though the turbulence statistics of the simulated turbulence follow similar quantitative trends questions remain about the code's difficulty in exactly predicting quantities like the autocorrelation time A proposed breakpoint in the near SOL pressure and the posited separation between drift and ballooning dynamics it represents are examined This work was supported by DOE-SC-0010508. This research used resources of the National Energy Research Scientific Computing Center (NERSC).

Spark and HPC for High Energy Physics Data Analyses

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

Sehrish, Saba; Kowalkowski, Jim; Paterno, Marc

A full High Energy Physics (HEP) data analysis is divided into multiple data reduction phases. Processing within these phases is extremely time consuming, therefore intermediate results are stored in files held in mass storage systems and referenced as part of large datasets. This processing model limits what can be done with interactive data analytics. Growth in size and complexity of experimental datasets, along with emerging big data tools are beginning to cause changes to the traditional ways of doing data analyses. Use of big data tools for HEP analysis looks promising, mainly because extremely large HEP datasets can be representedmore » and held in memory across a system, and accessed interactively by encoding an analysis using highlevel programming abstractions. The mainstream tools, however, are not designed for scientific computing or for exploiting the available HPC platform features. We use an example from the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in Geneva, Switzerland. The LHC is the highest energy particle collider in the world. Our use case focuses on searching for new types of elementary particles explaining Dark Matter in the universe. We use HDF5 as our input data format, and Spark to implement the use case. We show the benefits and limitations of using Spark with HDF5 on Edison at NERSC.« less

In Situ Fabrication of PtCo Alloy Embedded in Nitrogen-Doped Graphene Nanopores as Synergistic Catalyst for Oxygen Reduction Reaction

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

Zhong, Xing; Wang, Lei; Zhou, Hu

A novel PtCo alloy in situ etched and embedded in graphene nanopores (PtCo/NPG) as a high-performance catalyst for ORR was reported. Graphene nanopores were fabricated in situ while forming PtCo nanoparticles that were uniformly embedded in the graphene nanopores. Given the synergistic effect between PtCo alloy and nanopores, PtCo/NPG exhibited 11.5 times higher mass activity than that of the commercial Pt/C cathode electrocatalyst. DFT calculations indicated that the nanopores in NPG cannot only stabilize PtCo nanoparticles but can also definitely change the electronic structures, thereby change its adsorption abilities. This enhancement can lead to a favorable reaction pathway on PtCo/NPGmore » for ORR. This study showed that PtCo/NPG is a potential candidate for the next generation of Pt-based catalysts in fuel cells. This study also offered a promising alternative strategy and enabled the fabrication of various kinds of metal/graphene nanopore nanohybrids with potential applications in catalysts and potential use for other technological devices. The authors acknowledge the financial support from the National Basic Research Program (973 program, No. 2013CB733501), Zhejiang Provincial Education Department Research Program (Y201326554) and the National Natural Science Foundation of China (No. 21306169, 21101137, 21136001, 21176221 and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC).« less

Deploying Server-side File System Monitoring at NERSC

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

Uselton, Andrew

2009-05-01

The Franklin Cray XT4 at the NERSC center was equipped with the server-side I/O monitoring infrastructure Cerebro/LMT, which is described here in detail. Insights gained from the data produced include a better understanding of instantaneous data rates during file system testing, file system behavior during regular production time, and long-term average behaviors. Information and insights gleaned from this monitoring support efforts to proactively manage the I/O infrastructure on Franklin. A simple model for I/O transactions is introduced and compared with the 250 million observations sent to the LMT database from August 2008 to February 2009.

Nuclear-Recoil Differential Cross Sections for the Two Photon Double Ionization of Helium

NASA Astrophysics Data System (ADS)

Abdel Naby, Shahin; Ciappina, M. F.; Lee, T. G.; Pindzola, M. S.; Colgan, J.

2013-05-01

In support of the reaction microscope measurements at the free-electron laser facility at Hamburg (FLASH), we use the time-dependent close-coupling method (TDCC) to calculate fully differential nuclear-recoil cross sections for the two-photon double ionization of He at photon energy of 44 eV. The total cross section for the double ionization is in good agreement with previous calculations. The nuclear-recoil distribution is in good agreement with the experimental measurements. In contrast to the single-photon double ionization, maximum nuclear recoil triple differential cross section is obtained at small nuclear momenta. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California and the National Institute for Computational Sciences in Knoxville, Tennessee.

Tuning HDF5 subfiling performance on parallel file systems

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

Byna, Suren; Chaarawi, Mohamad; Koziol, Quincey

Subfiling is a technique used on parallel file systems to reduce locking and contention issues when multiple compute nodes interact with the same storage target node. Subfiling provides a compromise between the single shared file approach that instigates the lock contention problems on parallel file systems and having one file per process, which results in generating a massive and unmanageable number of files. In this paper, we evaluate and tune the performance of recently implemented subfiling feature in HDF5. In specific, we explain the implementation strategy of subfiling feature in HDF5, provide examples of using the feature, and evaluate andmore » tune parallel I/O performance of this feature with parallel file systems of the Cray XC40 system at NERSC (Cori) that include a burst buffer storage and a Lustre disk-based storage. We also evaluate I/O performance on the Cray XC30 system, Edison, at NERSC. Our results show performance benefits of 1.2X to 6X performance advantage with subfiling compared to writing a single shared HDF5 file. We present our exploration of configurations, such as the number of subfiles and the number of Lustre storage targets to storing files, as optimization parameters to obtain superior I/O performance. Based on this exploration, we discuss recommendations for achieving good I/O performance as well as limitations with using the subfiling feature.« less

Planck Surveyor On Its Way to Orbit

ScienceCinema

None

2017-12-09

An Ariane 5 rocket carried the Planck Surveyor and a companion satellite into space May 14, 2009 from the European Space Agency (ESA) base on the northwest coast of South America. Once in orbit beyond the moon, Planck will produce the most accurate measurements ever made of the relic radiation from the big bang, plus the largest set of CMB data ever recorded. Berkeley Labs long and continuing involvement with Planck began when George Smoot of the Physics Division proposed Plancks progenitor to ESA and continues with preparations for ongoing data analysis for the U.S. Planck team at NERSC, led by Julian Borrill, co-leader of the Computational Cosmology Center

Instrumented SSH

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

Campbell, Scott; Campbell, Scott

NERSC recently undertook a project to access and analyze Secure Shell (SSH) related data. This includes authentication data such as user names and key fingerprints, interactive session data such as keystrokes and responses, and information about noninteractive sessions such as commands executed and files transferred. Historically, this data has been inaccessible with traditional network monitoring techniques, but with a modification to the SSH daemon, this data can be passed directly to intrusion detection systems for analysis. The instrumented version of SSH is now running on all NERSC production systems. This paper describes the project, details about how SSH was instrumented,more » and the initial results of putting this in production.« less

Extreme I/O on HPC for HEP using the Burst Buffer at NERSC

NASA Astrophysics Data System (ADS)

Bhimji, Wahid; Bard, Debbie; Burleigh, Kaylan; Daley, Chris; Farrell, Steve; Fasel, Markus; Friesen, Brian; Gerhardt, Lisa; Liu, Jialin; Nugent, Peter; Paul, Dave; Porter, Jeff; Tsulaia, Vakho

2017-10-01

In recent years there has been increasing use of HPC facilities for HEP experiments. This has initially focussed on less I/O intensive workloads such as generator-level or detector simulation. We now demonstrate the efficient running of I/O-heavy analysis workloads on HPC facilities at NERSC, for the ATLAS and ALICE LHC collaborations as well as astronomical image analysis for DESI and BOSS. To do this we exploit a new 900 TB NVRAM-based storage system recently installed at NERSC, termed a Burst Buffer. This is a novel approach to HPC storage that builds on-demand filesystems on all-SSD hardware that is placed on the high-speed network of the new Cori supercomputer. We describe the hardware and software involved in this system, and give an overview of its capabilities, before focusing in detail on how the ATLAS, ALICE and astronomical workflows were adapted to work on this system. We describe these modifications and the resulting performance results, including comparisons to other filesystems. We demonstrate that we can meet the challenging I/O requirements of HEP experiments and scale to many thousands of cores accessing a single shared storage system.

Challenges in scaling NLO generators to leadership computers

NASA Astrophysics Data System (ADS)

Benjamin, D.; Childers, JT; Hoeche, S.; LeCompte, T.; Uram, T.

2017-10-01

Exascale computing resources are roughly a decade away and will be capable of 100 times more computing than current supercomputers. In the last year, Energy Frontier experiments crossed a milestone of 100 million core-hours used at the Argonne Leadership Computing Facility, Oak Ridge Leadership Computing Facility, and NERSC. The Fortran-based leading-order parton generator called Alpgen was successfully scaled to millions of threads to achieve this level of usage on Mira. Sherpa and MadGraph are next-to-leading order generators used heavily by LHC experiments for simulation. Integration times for high-multiplicity or rare processes can take a week or more on standard Grid machines, even using all 16-cores. We will describe our ongoing work to scale the Sherpa generator to thousands of threads on leadership-class machines and reduce run-times to less than a day. This work allows the experiments to leverage large-scale parallel supercomputers for event generation today, freeing tens of millions of grid hours for other work, and paving the way for future applications (simulation, reconstruction) on these and future supercomputers.

Inner-shell photoionization of atomic chlorine near the 2p-1 edge: a Breit-Pauli R-matrix calculation

NASA Astrophysics Data System (ADS)

Felfli, Z.; Deb, N. C.; Manson, S. T.; Hibbert, A.; Msezane, A. Z.

2009-05-01

An R-matrix calculation which takes into account relativistic effects via the Breit-Pauli (BP) operator is performed for photoionization cross sections of atomic Cl near the 2p threshold. The wavefunctions are constructed with orbitals generated from a careful large scale configuration interaction (CI) calculation with relativistic corrections using the CIV3 code of Hibbert [1] and Glass and Hibbert [2]. The results are contrasted with the calculation of Martins [3], which uses a CI with relativistic corrections, and compared with the most recent measurements [4]. [1] A. Hibbert, Comput. Phys. Commun. 9, 141 (1975) [2] R. Glass and A. Hibbert, Comput. Phys. Commun. 16, 19 (1978) [3] M. Martins, J. Phys. B 34, 1321 (2001) [4] D. Lindle et al (private communication) Research supported by U.S. DOE, Division of Chemical Sciences, NSF and CAU CFNM, NSF-CREST Program. Computing facilities at Queen's University of Belfast, UK and of DOE Office of Science, NERSC are appreciated.

Photoionization of Li2

NASA Astrophysics Data System (ADS)

Li, Y.; Pindzola, M. S.; Ballance, C. P.; Colgan, J.

2014-05-01

Single and double photoionization cross sections for Li2 are calculated using a time-dependent close-coupling method. The correlation between the outer two electrons of Li2 is obtained by relaxation of the close-coupled equations in imaginary time. Propagation of the close-coupled equations in real time yields single and double photoionization cross sections for Li2. The two active electron cross sections are compared with one active electron distorted-wave and close-coupling results for both Li and Li2. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California, NICS in Knoxville, Tennessee, and OLCF in Oak Ridge, Tennessee.

Simulating contrast inversion in atomic force microscopy imaging with real-space pseudopotentials

NASA Astrophysics Data System (ADS)

Lee, Alex; Sakai, Yuki; Chelikowsky, James

Atomic force microscopy measurements have reported contrast inversions for systems such as Cu2N and graphene that can hamper image interpretation and characterization. Here, we apply a simulation method based on ab initio real-space pseudopotentials to gain an understanding of the tip-sample interactions that influence the inversion. We find that chemically reactive tips induce an attractive binding force that results in the contrast inversion. The inversion is tip height dependent and not observed when using less reactive CO-functionalized tips. Work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Spectroscopy of organic semiconductors from first principles

NASA Astrophysics Data System (ADS)

Sharifzadeh, Sahar; Biller, Ariel; Kronik, Leeor; Neaton, Jeffery

2011-03-01

Advances in organic optoelectronic materials rely on an accurate understanding their spectroscopy, motivating the development of predictive theoretical methods that accurately describe the excited states of organic semiconductors. In this work, we use density functional theory and many-body perturbation theory (GW/BSE) to compute the electronic and optical properties of two well-studied organic semiconductors, pentacene and PTCDA. We carefully compare our calculations of the bulk density of states with available photoemission spectra, accounting for the role of finite temperature and surface effects in experiment, and examining the influence of our main approximations -- e.g. the GW starting point and the application of the generalized plasmon-pole model -- on the predicted electronic structure. Moreover, our predictions for the nature of the exciton and its binding energy are discussed and compared against optical absorption data. We acknowledge DOE, NSF, and BASF for financial support and NERSC for computational resources.

First-Principles Studies of the Excited States and Optical Properties of Xanthene Derivative Chromophores

NASA Astrophysics Data System (ADS)

Hamed, Samia; Sharifzadeh, Sahar; Neaton, Jeffrey

2014-03-01

Elucidation of the energy transfer mechanism in natural photosynthetic systems remains an exciting challenge. In particular, biomimetic protein-pigment complexes provide a unique study space in which individual parameters are adjusted and the impact of those changes captured. Here, we compute the excited state properties of a group of xanthene-derivative chromophores to be employed in the construction of new biomimetic light harvesting frameworks. Excitation energies, transition dipoles, and natural transition orbitals for the low-lying singlet and triplet states of these experimentally-relevant chromophores are obtained from first-principles density functional theory. The performance of several exchange-correlation functionals, including an optimally-tuned range-separated hybrid, are evaluated and compared with many body perturbation theory and experiment. Finally, we will discuss the implication of our results for the bottom-up design of new chromophores. This work is supported by the DOE and computational resources are provided by NERSC.

Understanding Singlet and Triplet Excitons in Acene Crystals from First Principles

NASA Astrophysics Data System (ADS)

Rangel Gordillo, Tonatiuh; Sharifzadeh, Sahar; Kronik, Leeor; Neaton, Jeffrey

2014-03-01

Singlet fission, a process in which two triplet excitons are formed from a singlet exciton, has the potential to increase the solar cell efficiencies above 100%. Efficient singlet fission has been reported in larger acene crystals, such as tetracene and pentacene, in part attributable to their low-lying triplet energies. In this work, we use many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation approach to compute quasiparticle gaps, low-lying singlet and and triplet excitations, and optical absorption spectra across the entire acene family of crystals, from benzene to hexacene. We closely examine the degree of localization and charge-transfer character of the low-lying singlets and triplets, and their sensitivity to crystal environment, and discuss implications for the efficiency of singlet fission in this systems. This work supported by DOE and computational resources provided by NERSC.

DEEP: Database of Energy Efficiency Performance

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

A database of energy efficiency performance (DEEP) is a presimulated database to enable quick and accurate assessment of energy retrofit of commercial buildings. DEEP was compiled from results of about 10 million EnergyPlus simulations. DEEP provides energy savings for screening and evaluation of retrofit measures targeting the small and medium-sized office and retail buildings in California. The prototype building models are developed for a comprehensive assessment of building energy performance based on DOE commercial reference buildings and the California DEER [sic] prototype buildings. The prototype buildings represent seven building types across six vintages of constructions and 16 California climate zones.more » DEEP uses these prototypes to evaluate energy performance of about 100 energy conservation measures covering envelope, lighting, heating, ventilation, air conditioning, plug loads, and domestic hot war. DEEP consists the energy simulation results for individual retrofit measures as well as packages of measures to consider interactive effects between multiple measures. The large scale EnergyPlus simulations are being conducted on the super computers at the National Energy Research Scientific Computing Center (NERSC) of Lawrence Berkeley National Laboratory. The pre-simulation database is a part of the CEC PIER project to develop a web-based retrofit toolkit for small and medium-sized commercial buildings in California, which provides real-time energy retrofit feedback by querying DEEP with recommended measures, estimated energy savings and financial payback period based on users' decision criteria of maximizing energy savings, energy cost savings, carbon reduction, or payback of investment. The pre-simulated database and associated comprehensive measure analysis enhances the ability to performance assessments of retrofits to reduce energy use for small and medium buildings and business owners who typically do not have resources to conduct costly building energy audit.« less

Mechanisms of selective cleavage of C–O bonds in di-aryl ethers in aqueous phase

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

He, Jiayue; Zhao, Chen; Mei, Donghai

2014-01-01

A novel route for cleaving the C-O aryl ether bonds of p-substituted H-, CH 3-, and OH- diphenyl ethers has been explored over Ni/SiO 2 catalysts at very mild conditions. The C-O bond of diphenyl ether is cleaved by parallel hydrogenolysis and hydrolysis (hydrogenolysis combined with HO* addition) on Ni. The rates as a function of H 2 pressure from 0 to 10 MPa indicate that the rate-determining step is the C-O bond cleavage on Ni. H* atoms compete with the organic reactant for adsorption leading to a maximum in the rate with increasing H 2 pressure. In contrast tomore » diphenyl ether, hydrogenolysis is the exclusive route for cleaving an ether C-O bond of di-p-tolyl ether to form p-cresol and toluene. 4,4'-dihydroxydiphenyl ether undergoes sequential surface hydrogenolysis, first to phenol and HOC 6H 4O* (adsorbed), which is then cleaved to phenol (C 6H 5O* with added H*) and H 2O (O* with two added H*) in a second step. Density function theory supports the operation of this pathway. Notably, addition of H* to HOC 6H 4O* is less favorable than a further hydrogenolytic C-O bond cleavage. The TOFs of three aryl ethers with Ni/SiO 2 in water followed the order 4,4'-dihydroxydiphenyl ether (69 h -1) > diphenyl ether (26 h -1) > di-p-tolyl ether (1.3 h -1), in line with the increasing apparent activation energies, ranging from 93 kJ∙mol -1 (4,4'-dihydroxydiphenyl ether) < diphenyl ether (98 kJ∙mol -1) to di-p-tolyl ether (105 kJ∙mol -1). D.M. thanks the support from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase

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

Yoon, Yeohoon; Rousseau, Roger J.; Weber, Robert S.

2014-07-23

The effects of aqueous phase on the reactivity of phenol hydrogenation over Pt and Ni catalysts were investigated using density functional theory based ab initio molecular dynamics (AIMD) calculations. The adsorption of phenol and the first hydrogenation steps via three carbon positions (ortho, meta and para) with respect to the phenolic OH group were studied in both vacuum and liquid phase conditions. To gain insight into how the aqueous phase affects the metal catalyst surface, increasing water environments including singly adsorbed water molecule, mono- (9 water molecules), double layers (24 water molecules), and the bulk liquid water which (52 watermore » molecules) on the Pt(111) and the Ni(111) surfaces were modeled. Compared to the vacuum/metal interfaces, AIMD simulation results suggest that the aqueous Pt(111) and Ni(111) interfaces have a lower metal work function in the order of 0.8 - 0.9 eV, thus, making the metals in aqueous phase stronger reducing agents and poorer oxidizing agents. Phenol adsorption from the aqueous phase is found to be slightly weaker that from the vapor phase. The first hydrogenation step of phenol at the ortho position of the phenolic ring is slightly favored over the other two positions. The polarization induced by the surrounding water molecules and the solvation effect play important roles in stabilizing the transition states associated with phenol hydrogenation by lowering the barriers of 0.1 - 0.4 eV. The detailed discussion on the basis of the interfacial electrostatics from the current study is very useful to understand the nature of a broader class of metal catalyzed reactions in liquid solution phase. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences and Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Catalytic N 2 Reduction to Silylamines and Thermodynamics of N 2 Binding at Square Planar Fe

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

Prokopchuk, Demyan E.; Wiedner, Eric S.; Walter, Eric D.

The geometric constraints imposed by a tetradentate P 4N 2 ligand play an essential role in stabilizing square planar Fe complexes with changes in metal oxidation state. A combination of high-pressure electrochemistry and variable temperature UV-vis spectroscopy were used to obtain these thermodynamic measurements, while X-ray crystallography, 57Fe Mössbauer spectroscopy, and EPR spectroscopy were used to fully characterize these new compounds. Analysis of Fe 0, FeI, and FeII complexes reveals that the free energy of N 2 binding across three oxidation states spans more than 37 kcal mol -1. The square pyramidal Fe0(N 2)(P 4N 2) complex catalyzes the conversionmore » of N 2 to N(SiR 3) 3 (R = Me, Et) at room temperature, representing the highest turnover number (TON) of any Fe-based N 2 silylation catalyst to date (up to 65 equiv N(SiMe 3) 3 per Fe center). Elevated N 2 pressures (> 1 atm) have a dramatic effect on catalysis, increasing N 2 solubility and the thermodynamic N 2 binding affinity at Fe0(N 2)(P 4N 2). Acknowledgment. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. EPR experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. DOE. Computational resources were provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. The authors thank Prof. Yisong Alex Guo at Carnegie Mellon University for recording Mössbauer data for some complexes and Emma Wellington and Kaye Kuphal for their assistance with the collection of Mössbauer data at Colgate University, Dr. Katarzyna Grubel for X-ray assistance, and Dr. Rosalie Chu for mass spectrometry assistance. The authors also thank Dr. Aaron Appel and Dr. Alex Kendall for helpful discussions.« less

Effect of Graphene with Nanopores on Metal Clusters

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

Zhou, Hu; Chen, Xianlang; Wang, Lei

Porous graphene, which is a novel type of defective graphene, shows excellent potential as a support material for metal clusters. In this work, the stability and electronic structures of metal clusters (Pd, Ir, Rh) supported on pristine graphene and graphene with different sizes of nanopore were investigated by first-principle density functional theory (DFT) calculations. Thereafter, CO adsorption and oxidation reaction on the Pd-graphene system were chosen to evaluate its catalytic performance. Graphene with nanopore can strongly stabilize the metal clusters and cause a substantial downshift of the d-band center of the metal clusters, thus decreasing CO adsorption. All binding energies,more » d-band centers, and adsorption energies show a linear change with the size of the nanopore: a bigger size of nanopore corresponds to a stronger metal clusters bond to the graphene, lower downshift of the d-band center, and weaker CO adsorption. By using a suitable size nanopore, supported Pd clusters on the graphene will have similar CO and O2 adsorption ability, thus leading to superior CO tolerance. The DFT calculated reaction energy barriers show that graphene with nanopore is a superior catalyst for CO oxidation reaction. These properties can play an important role in instructing graphene-supported metal catalyst preparation to prevent the diffusion or agglomeration of metal clusters and enhance catalytic performance. This work was supported by National Basic Research Program of China (973Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21176221, 21136001, 21101137, 21306169, and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC).« less

Energy Efficient Supercomputing

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

Anypas, Katie

2014-10-17

Katie Anypas, Head of NERSC's Services Department discusses the Lab's research into developing increasingly powerful and energy efficient supercomputers at our '8 Big Ideas' Science at the Theater event on October 8th, 2014, in Oakland, California.

Energy Efficient Supercomputing

ScienceCinema

Anypas, Katie

2018-05-07

Katie Anypas, Head of NERSC's Services Department discusses the Lab's research into developing increasingly powerful and energy efficient supercomputers at our '8 Big Ideas' Science at the Theater event on October 8th, 2014, in Oakland, California.

Efficient Calculation of Exact Exchange Within the Quantum Espresso Software Package

NASA Astrophysics Data System (ADS)

Barnes, Taylor; Kurth, Thorsten; Carrier, Pierre; Wichmann, Nathan; Prendergast, David; Kent, Paul; Deslippe, Jack

Accurate simulation of condensed matter at the nanoscale requires careful treatment of the exchange interaction between electrons. In the context of plane-wave DFT, these interactions are typically represented through the use of approximate functionals. Greater accuracy can often be obtained through the use of functionals that incorporate some fraction of exact exchange; however, evaluation of the exact exchange potential is often prohibitively expensive. We present an improved algorithm for the parallel computation of exact exchange in Quantum Espresso, an open-source software package for plane-wave DFT simulation. Through the use of aggressive load balancing and on-the-fly transformation of internal data structures, our code exhibits speedups of approximately an order of magnitude for practical calculations. Additional optimizations are presented targeting the many-core Intel Xeon-Phi ``Knights Landing'' architecture, which largely powers NERSC's new Cori system. We demonstrate the successful application of the code to difficult problems, including simulation of water at a platinum interface and computation of the X-ray absorption spectra of transition metal oxides.

Exploring the Influence of Dynamic Disorder on Excitons in Solid Pentacene

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Sharifzadeh, Sahar; Doak, Peter; Lu, Zhenfei; Neaton, Jeffrey

2014-03-01

A complete understanding of the spectroscopic and charge transport properties of organic semiconductors requires knowledge of the role of thermal fluctuations and dynamic disorder. We present a first-principles theoretical study aimed at understanding the degree to which dynamic disorder at room temperature results in energy level broadening and excited-state localization within bulk crystalline pentacene. Ab initio molecular dynamics simulations are well-equilibrated for 7-9 ps and tens of thousands of structural snapshots, taken at 0.5 fs intervals, provide input for many-body perturbation theory within the GW approximation and Bethe-Salpeter equation (BSE) approach. The GW-corrected density of states, including thousands of snapshots, indicates that thermal fluctuations significantly broaden the valence and conduction states by >0.2 eV. Additionally, we investigate the nature and energy of the lowest energy singlet and triplet excitons, computed for a set of uncorrelated and energetically preferred structures. This work supported by DOE; computational resources provided by NERSC.

Single and Double Photoionization of Mg

NASA Astrophysics Data System (ADS)

Abdel-Naby, Shahin; Pindzola, M. S.; Colgan, J.

2014-05-01

Single and double photoionization cross sections for Mg are calculated using a time-dependent close-coupling method. The correlation between the two 3 s subshell electrons of Mg is obtained by relaxation of the close-coupled equations in imaginary time. An implicit method is used to propagate the close-coupled equations in real time to obtain single and double ionization cross sections for Mg. Energy and angle triple differential cross sections for double photoionization at equal energy sharing of E1 =E2 = 16 . 4 eV are compared with Elettra experiments and previous theoretical calculations. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California, NICS in Knoxville, Tennessee, and OLCF in Oak Ridge, Tennessee.

Photoionization of Ne8+

NASA Astrophysics Data System (ADS)

Pindzola, M. S.; Abdel-Naby, Sh. A.; Robicheaux, F.; Colgan, J.

2014-05-01

Single and double photoionization cross sections for Ne8+ are calculated using a non-perturbative fully relativistic time-dependent close-coupling method. A Bessel function expansion is used to include both dipole and quadrupole effects in the radiation field interaction and the repulsive interaction between electrons includes both the Coulomb and Gaunt interactions. The fully correlated ground state of Ne8+ is obtained by solving a time-independent inhomogeneous set of close-coupled equations. Propagation of the time-dependent close-coupled equations yields single and double photoionization cross sections for Ne8+ at energies easily accessible at advanced free electron laser facilities. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California, NICS in Knoxville, Tennessee, and OLCF in Oak Ridge, Tennessee.

Neutron-Impact Ionization of H and He

NASA Astrophysics Data System (ADS)

Lee, T.-G.; Ciappina, M. F.; Robicheaux, F.; Pindzola, M. S.

2014-05-01

Perturbative distorted-wave and non-perturbative close-coupling methods are used to study neutron-impact ionization of H and He. For single ionization of H, we find excellent agreement between the distorted-wave and close-coupling results at all incident energies. For double ionization of He, we find poor agreement between the distorted-wave and close-coupling results, except at the highest incident energies. We present the ratio of double to single ionization for He as a guide to experimental checks of theory at low energies and experimental confirmation of the rapid rise of the ratio at high energies. This work was supported in part by grants from NSF and US DoE. Computational work was carried out at NERSC in Oakland, California, NICS in Knoxville, Tennessee, and OLCF in Oak Ridge, Tennessee.

Large Scale GW Calculations on the Cori System

NASA Astrophysics Data System (ADS)

Deslippe, Jack; Del Ben, Mauro; da Jornada, Felipe; Canning, Andrew; Louie, Steven

The NERSC Cori system, powered by 9000+ Intel Xeon-Phi processors, represents one of the largest HPC systems for open-science in the United States and the world. We discuss the optimization of the GW methodology for this system, including both node level and system-scale optimizations. We highlight multiple large scale (thousands of atoms) case studies and discuss both absolute application performance and comparison to calculations on more traditional HPC architectures. We find that the GW method is particularly well suited for many-core architectures due to the ability to exploit a large amount of parallelism across many layers of the system. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division, as part of the Computational Materials Sciences Program.

Graphics Processing Unit Acceleration of Gyrokinetic Turbulence Simulations

NASA Astrophysics Data System (ADS)

Hause, Benjamin; Parker, Scott

2012-10-01

We find a substantial increase in on-node performance using Graphics Processing Unit (GPU) acceleration in gyrokinetic delta-f particle-in-cell simulation. Optimization is performed on a two-dimensional slab gyrokinetic particle simulation using the Portland Group Fortran compiler with the GPU accelerator compiler directives. We have implemented the GPU acceleration on a Core I7 gaming PC with a NVIDIA GTX 580 GPU. We find comparable, or better, acceleration relative to the NERSC DIRAC cluster with the NVIDIA Tesla C2050 computing processor. The Tesla C 2050 is about 2.6 times more expensive than the GTX 580 gaming GPU. Optimization strategies and comparisons between DIRAC and the gaming PC will be presented. We will also discuss progress on optimizing the comprehensive three dimensional general geometry GEM code.

Auger recombination in sodium iodide

NASA Astrophysics Data System (ADS)

McAllister, Andrew; Kioupakis, Emmanouil; Åberg, Daniel; Schleife, André

2014-03-01

Scintillators are an important tool used to detect high energy radiation - both in the interest of national security and in medicine. However, scintillator detectors currently suffer from lower energy resolutions than expected from basic counting statistics. This has been attributed to non-proportional light yield compared to incoming radiation, but the specific mechanism for this non-proportionality has not been identified. Auger recombination is a non-radiative process that could be contributing to the non-proportionality of scintillating materials. Auger recombination comes in two types - direct and phonon-assisted. We have used first-principles calculations to study Auger recombination in sodium iodide, a well characterized scintillating material. Our findings indicate that phonon-assisted Auger recombination is stronger in sodium iodide than direct Auger recombination. Computational resources provided by LLNL and NERSC. Funding provided by NA-22.

The PRISM project

NASA Astrophysics Data System (ADS)

Guilyardi, E.

2003-04-01

The European Union's PRISM infrastructure project (PRogram for Integrated earth System Modelling) aims at designing a flexible environment to easily assemble and run Earth System Models (http://prism.enes.org). Europe's widely distributed modelling expertise is both a strength and a challenge. Recognizing this, the PRISM project aims at developing an efficient shared modelling software infrastructure for climate scientists, providing them with an opportunity for greater focus on scientific issues, including the necessary scientific diversity (models and approaches). The proposed PRISM system includes 1) the use - or definition - and promotion of scientific and technical standards to increase component modularity, 2) an end-to-end software environment (coupler, user interface, diagnostics) to launch, monitor and analyze complex Earth System Models built around the existing and future community models, 3) testing and quality standards to ensure HPC performance on a variety of platforms and 4) community wide inputs and requirements capture in all stages of system specifications and design through user/developers meetings, workshops and thematic schools. This science driven project, led by 22 institutes* and started December 1st 2001, benefits from a unique gathering of scientific and technical expertise. More than 30 models (both global and regional) have expressed interest to be part of the PRISM system and 6 types of components have been identified: atmosphere, atmosphere chemistry, land surface, ocean, sea ice and ocean biochemistry. Progress and overall architecture design will be presented. * MPI-Met (Coordinator), KNMI (co-coordinator), MPI-M&D, Met Office, University of Reading, IPSL, Meteo-France, CERFACS, DMI, SMHI, NERSC, ETH Zurich, INGV, MPI-BGC, PIK, ECMWF, UCL-ASTR, NEC, FECIT, SGI, SUN, CCRLE

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.

Structure, dynamics and stability of water/scCO 2/mineral interfaces from ab initio molecular dynamics simulations

DOE PAGES

Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; ...

2015-10-12

Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.« less

Anharmonicity and confinement in zeolites: Structure, spectroscopy, and adsorption free energy of ethanol in H-ZSM-5

DOE PAGES

Alexopoulos, Konstantinos; Lee, Mal -Soon; Liu, Yue; ...

2016-03-21

Here, to account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Brønsted acid site of the H-ZSM-5 catalyst has been studied at different temperatures and ethanol loadings using ab initio molecular dynamics (AIMD) simulations, infrared (IR) spectroscopy and calorimetric measurements. At low temperatures (T ≤ 400 K) and ethanol loading, a single ethanol molecule adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alcohol. At higher ethanol loading, a second ethanol molecule helpsmore » to stabilize the protonated ethanol at all temperatures by acting as a solvating agent. The vibrational density of states (VDOS), as calculated from the AIMD simulations, are in excellent agreement with measured IR spectra for C 2H 5OH, C 2H 5OD and C 2D 5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approximation (QHA), applied to the VDOS obtained from the AIMD simulations, provides estimates of adsorption free energy within ~10 kJ/mol of the experimentally determined quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state minimum, strongly overestimates the adsorption free energy by at least ~30 kJ/mol. This discrepancy is traced back to the inability of the harmonic approximation to represent the contributions to the vibrational motions of the ethanol molecule upon confinement in the zeolite. KA, MFR, GBM were supported by the Long Term Structural Methusalem Funding by the Flemish Government – grant number BOF09/01M00409. MSL, VAG, RR and JAL were supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated for DOE by Battelle. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL, the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and the Stevin Supercomputer Infrastructure at Ghent University.« less

Effect of polar surfaces on organic molecular crystals

NASA Astrophysics Data System (ADS)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

Efficacy of Code Optimization on Cache-Based Processors

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob F.; Saphir, William C.; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

In this paper a number of techniques for improving the cache performance of a representative piece of numerical software is presented. Target machines are popular processors from several vendors: MIPS R5000 (SGI Indy), MIPS R8000 (SGI PowerChallenge), MIPS R10000 (SGI Origin), DEC Alpha EV4 + EV5 (Cray T3D & T3E), IBM RS6000 (SP Wide-node), Intel PentiumPro (Ames' Whitney), Sun UltraSparc (NERSC's NOW). The optimizations all attempt to increase the locality of memory accesses. But they meet with rather varied and often counterintuitive success on the different computing platforms. We conclude that it may be genuinely impossible to obtain portable performance on the current generation of cache-based machines. At the least, it appears that the performance of modern commodity processors cannot be described with parameters defining the cache alone.

Transport properties of two-dimensional metal-phthalocyanine junctions: An ab initio study

NASA Astrophysics Data System (ADS)

Liu, Shuang-Long; Wang, Yun-Peng; Li, Xiang-Guo; Cheng, Hai-Ping

We study two dimensional (2D) electronic/spintronic junctions made of metal-organic frameworks via first-principles simulation. The system consists of two Mn-phthalocyanine leads and a Ni-phthalocyanine center. A 2D Mn phthalocyanine sheet is ferromagnetic half metal and a 2D Ni phthalocyanine sheet is nonmagnetic semiconductor. Our results show that this system has a large tunnel magnetic resistance. The transmission coefficient at Fermi energy decays exponentially with the length of the central region which is not surprising. However, the transmission of the junction can be tuned using gate voltage by up to two orders of magnitude. The origin of the change lies in the mode matching between the lead and the center electronic states. Moreover, the threshold gate voltage varies with the length of the center region which provides a way of engineering the transport properties. Finally, we combine non-equilibrium Green's function and Boltzmann transport equation to compute conductance of the junction. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences (BES), under Contract No. DE-FG02-02ER45995. Computations were done using the utilities of NERSC and University of Florida Research Computing.

Preface: SciDAC 2009

NASA Astrophysics Data System (ADS)

Simon, Horst

2009-07-01

By almost any measure, the SciDAC community has come a long way since DOE launched the SciDAC program back in 2001. At the time, we were grappling with how to efficiently run applications on terascale systems (the November 2001 TOP500 list was led by DOE's ASCI White IBM system at Lawrence Livermore achieving 7.2 teraflop/s). And the results stemming from the first round of SciDAC projects were summed up in two-page reports. The scientific results were presented at annual meetings, which were by invitation only and typically were attended by about 75 researchers. Fast forward to 2009 and we now have SciDAC Review, a quarterly magazine showcasing the scientific computing contributions of SciDAC projects and related programs, all focused on presenting a comprehensive look at Scientific Discovery through Advanced Computing. That is also the motivation behind the annual SciDAC conference that in 2009 was held from June 14-18 in San Diego. The annual conference, which can also be described as a celebration of all things SciDAC, grew out those meetings organized in the early days of the program. In 2005, the meeting was held in San Francisco and attendance was opened up to all members of the SciDAC community. The schedule was also expanded to include a keynote address, plenary speakers and other features found in a conference format. This year marks the fifth such SciDAC conference, which now comprises four days of computational science presentations, multiple poster sessions and, since last year, an evening event showcasing simulations and modeling runs resulting from SciDAC projects. The fifth annual SciDAC conference was remarkable on several levels. The primary purpose, of course, is to showcase the research accomplishments resulting from SciDAC programs in particular and computational science in general. It is these accomplishments, represented in 38 papers and 52 posters, that comprise this set of conference proceedings. These proceedings can stand alone as evidence of the success of DOE's innovative SciDAC efforts. But from the outset, a critical driver for the program was to foster increased collaboration among researchers across disciplines and organizations. In particular, SciDAC wanted to engage scientists at universities in the projects, both to expand the community and to develop the next generation of computational scientists. At the meeting in San Diego, the fruits of this emphasis were clearly visible, from the special poster session highlighting the work of the DOE Computational Science Graduate Fellows, to the informal discussions in hotel hallways, to focused side meetings apart from the main presentations. A highlight of the meeting was the keynote address by Dr Ray Orbach, until recently the DOE Under Secretary for Science and head of the Office of Science. It was during his tenure that the first round of projects matured and the second set of SciDAC projects were launched. And complementing these research projects was Dr Orbach's vision for INCITE, DOE's Innovative and Novel Computational Impact on Theory and Experiment program, inaugurated in 2003. This program allocated significant HPC resources to scientists tackling high-impact problems, including some of those addressed by SciDAC teams. Together, SciDAC and INCITE are dramatically accelerating the field of computational science. As has been noted before, the SciDAC conference celebrates progress in advancing science through large-scale modeling and simulation. Over 400 people registered to attend this year's talks, poster sessions and tutorials, all spanning the disciplines supported by DOE. While the principal focus was on SciDAC accomplishments, this year's conference also included invited presentations and posters from colleagues whose research is supported by other agencies. At the 2009 meeting we also formalized a developing synergy with the Department of Defense's HPC Users Group Meeting, which has occasionally met in parallel with the SciDAC meeting. But in San Diego, we took the additional steps of organizing a joint poster session and a joint plenary session, further advancing opportunities for broader networking. Throughout the four-day program, attendees at both meetings had the option of sitting in on sessions at either conference. We also included several of the NSF Petascale applications in the program, and have also extended invitations to our computational colleagues in other federal agencies, including the National Science Foundation, NASA, and the National Oceanographic and Atmospheric Administration, as well as international collaborators to join us in San Diego. In 2009 we also reprised one of the more popular sessions from Seattle in 2008, the Electronic Visualization and Poster Night, during which 29 scientific visualizations were presented on high-resolution large-format displays. The best entries were awarded one of the coveted 'OASCR Awards.' The conference also featured a session about breakthroughs in computational science, based on the 'Breakthrough Report' that was published in 2008, led by Tony Mezzacappa (ORNL). Tony was also the chair of the SciDAC 2005 conference. For the third consecutive year, the conference was followed by a day of tutorials organized by the SciDAC Outreach Center and aimed primarily at students interested in scientific computing. This year, nearly 100 participants attended the tutorials, hosted by the San Diego Supercomputer Center and General Atomics. This outreach to the broader community is really what SciDAC is all about - Scientific Discovery through Advanced Computing. Such discoveries are not confined by organizational lines, but rather are often the result of researchers reaching out and collaborating with others, using their combined expertise to push our boundaries of knowledge. I am happy to see that this vision is shared by so many researchers in computational science, who all decided to join SciDAC 2009. While credit for the excellent presentations and posters goes to the teams of researchers, the success of this year's conference is due to the strong efforts and support from members of the 2009 SciDAC Program Committee and Organizing Committee, and I would like to extend my heartfelt thanks to them for helping to make the 2009 meeting the largest and most successful to date. Program Committee members were: David Bader, LLNL; Pete Beckman, ANL; John Bell, LBNL; John Boisseau, University of Texas; Paul Bonoli, MIT; Hank Childs, LBNL; Bill Collins, LBNL; Jim Davenport, BNL; David Dean, ORNL; Thom Dunning, NCSA; Peg Folta, LLNL; Glenn Hammond, PNNL; Maciej Haranczyk, LBNL; Robert Harrison, ORNL; Paul Hovland, ANL; Paul Kent, ORNL; Aram Kevorkian, SPAWAR; David Keyes, Columbia University; Kwok Ko, SLAC; Felice Lightstone, LLNL; Bob Lucas, ISI/USC; Paul Mackenzie, Fermilab; Tony Mezzacappa, ORNL; John Negele, MIT; Jeff Nichols, ORNL; Mike Norman, UCSD; Joe Oefelein, SNL; Jeanie Osburn, NRL; Peter Ostroumov, ANL; Valerio Pascucci, University of Utah; Ruth Pordes, Fermilab; Rob Ross, ANL; Nagiza Samatova, ORNL; Martin Savage, University of Washington; Tim Scheibe, PNNL; Ed Seidel, NSF; Arie Shoshani, LBNL; Rick Stevens, ANL; Bob Sugar, UCSB; Bill Tang, PPPL; Bob Wilhelmson, NCSA; Kathy Yelick, NERSC/LBNL; Dave Zachmann, Vista Computational Technology LLC. Organizing Committee members were: Communications: Jon Bashor, LBNL. Contracts/Logistics: Mary Spada and Cheryl Zidel, ANL. Posters: David Bailey, LBNL. Proceedings: John Hules, LBNL. Proceedings Database Developer: Beth Cerny Patino, ANL. Program Committee Liaison/Conference Web Site: Yeen Mankin, LBNL. Tutorials: David Skinner, NERSC/LBNL. Visualization Night: Hank Childs, LBNL; Valerio Pascucci, Chems Touati, Nathan Galli, and Erik Jorgensen, University of Utah. Again, my thanks to all. Horst Simon San Diego, California June 18, 2009

Performance Analysis, Modeling and Scaling of HPC Applications and Tools

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

Bhatele, Abhinav

2016-01-13

E cient use of supercomputers at DOE centers is vital for maximizing system throughput, mini- mizing energy costs and enabling science breakthroughs faster. This requires complementary e orts along several directions to optimize the performance of scienti c simulation codes and the under- lying runtimes and software stacks. This in turn requires providing scalable performance analysis tools and modeling techniques that can provide feedback to physicists and computer scientists developing the simulation codes and runtimes respectively. The PAMS project is using time allocations on supercomputers at ALCF, NERSC and OLCF to further the goals described above by performing research alongmore » the following fronts: 1. Scaling Study of HPC applications; 2. Evaluation of Programming Models; 3. Hardening of Performance Tools; 4. Performance Modeling of Irregular Codes; and 5. Statistical Analysis of Historical Performance Data. We are a team of computer and computational scientists funded by both DOE/NNSA and DOE/ ASCR programs such as ECRP, XStack (Traleika Glacier, PIPER), ExaOSR (ARGO), SDMAV II (MONA) and PSAAP II (XPACC). This allocation will enable us to study big data issues when analyzing performance on leadership computing class systems and to assist the HPC community in making the most e ective use of these resources.« less

Many-Body Perturbation Theory for Understanding Optical Excitations in Organic Molecules and Solids

NASA Astrophysics Data System (ADS)

Sharifzadeh, Sahar

Organic semiconductors are promising as light-weight, flexible, and strongly absorbing materials for next-generation optoelectronics. The advancement of such technologies relies on understanding the fundamental excited-state properties of organic molecules and solids, motivating the development of accurate computational approaches for this purpose. Here, I will present first-principles many-body perturbation theory (MBPT) calculations aimed at understanding the spectroscopic properties of select organic molecules and crystalline semiconductors, and improving these properties for enhanced photovoltaic performance. We show that for both gas-phase molecules and condensed-phase crystals, MBPT within the GW/BSE approximation provides quantitative accuracy of transport gaps extracted from photoemission spectroscopy and conductance measurements, as well as with measured polarization-dependent optical absorption spectra. We discuss the implications of standard approximations within GW/BSE on accuracy of these results. Additionally, we demonstrate significant exciton binding energies and charge-transfer character in the crystalline systems, which can be controlled through solid-state morphology or change of conjugation length, suggesting a new strategy for the design of optoelectronic materials. We acknowledge NSF for financial support; NERSC and Boston University for computational resources.

GYROKINETIC PARTICLE SIMULATION OF TURBULENT TRANSPORT IN BURNING PLASMAS

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

Horton, Claude Wendell

2014-06-10

The SciDAC project at the IFS advanced the state of high performance computing for turbulent structures and turbulent transport. The team project with Prof Zhihong Lin [PI] at Univ California Irvine produced new understanding of the turbulent electron transport. The simulations were performed at the Texas Advanced Computer Center TACC and the NERSC facility by Wendell Horton, Lee Leonard and the IFS Graduate Students working in that group. The research included a Validation of the electron turbulent transport code using the data from a steady state university experiment at the University of Columbia in which detailed probe measurements of themore » turbulence in steady state were used for wide range of temperature gradients to compare with the simulation data. These results were published in a joint paper with Texas graduate student Dr. Xiangrong Fu using the work in his PhD dissertation. X.R. Fu, W. Horton, Y. Xiao, Z. Lin, A.K. Sen and V. Sokolov, “Validation of electron Temperature gradient turbulence in the Columbia Linear Machine, Phys. Plasmas 19, 032303 (2012).« less

Structure and Dynamics Ionic Block co-Polymer Melts: Computational Study

NASA Astrophysics Data System (ADS)

Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

Tethering ionomer blocks into co-polymers enables engineering of polymeric systems designed to encompass transport while controlling structure. Here the structure and dynamics of symmetric pentablock copolymers melts are probed by fully atomistic molecular dynamics simulations. The center block consists of randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55 tethered to a hydrogenated polyisoprene (PI), end caped with poly(t-butyl styrene). We find that melts with f = 0.15 and 0.30 consist of isolated ionic clusters whereas melts with f = 0.55 exhibit a long-range percolating ionic network. Similar to polystyrene sulfonate, a small number of ionic clusters slow the mobility of the center of mass of the co-polymer, however, formation of the ionic clusters is slower and they are often intertwined with PI segments. Surprisingly, the segmental dynamics of the other blocks are also affected. NSF DMR-1611136; NERSC; Palmetto Cluster Clemson University; Kraton Polymers US, LLC.

Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-03-01

Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

ESnet authentication services and trust federations

NASA Astrophysics Data System (ADS)

Muruganantham, Dhivakaran; Helm, Mike; Genovese, Tony

2005-01-01

ESnet provides authentication services and trust federation support for SciDAC projects, collaboratories, and other distributed computing applications. The ESnet ATF team operates the DOEGrids Certificate Authority, available to all DOE Office of Science programs, plus several custom CAs, including one for the National Fusion Collaboratory and one for NERSC. The secure hardware and software environment developed to support CAs is suitable for supporting additional custom authentication and authorization applications that your program might require. Seamless, secure interoperation across organizational and international boundaries is vital to collaborative science. We are fostering the development of international PKI federations by founding the TAGPMA, the American regional PMA, and the worldwide IGTF Policy Management Authority (PMA), as well as participating in European and Asian regional PMAs. We are investigating and prototyping distributed authentication technology that will allow us to support the "roaming scientist" (distributed wireless via eduroam), as well as more secure authentication methods (one-time password tokens).

OPENING REMARKS: Scientific Discovery through Advanced Computing

NASA Astrophysics Data System (ADS)

Strayer, Michael

2006-01-01

Good morning. Welcome to SciDAC 2006 and Denver. I share greetings from the new Undersecretary for Energy, Ray Orbach. Five years ago SciDAC was launched as an experiment in computational science. The goal was to form partnerships among science applications, computer scientists, and applied mathematicians to take advantage of the potential of emerging terascale computers. This experiment has been a resounding success. SciDAC has emerged as a powerful concept for addressing some of the biggest challenges facing our world. As significant as these successes were, I believe there is also significance in the teams that achieved them. In addition to their scientific aims these teams have advanced the overall field of computational science and set the stage for even larger accomplishments as we look ahead to SciDAC-2. I am sure that many of you are expecting to hear about the results of our current solicitation for SciDAC-2. I’m afraid we are not quite ready to make that announcement. Decisions are still being made and we will announce the results later this summer. Nearly 250 unique proposals were received and evaluated, involving literally thousands of researchers, postdocs, and students. These collectively requested more than five times our expected budget. This response is a testament to the success of SciDAC in the community. In SciDAC-2 our budget has been increased to about 70 million for FY 2007 and our partnerships have expanded to include the Environment and National Security missions of the Department. The National Science Foundation has also joined as a partner. These new partnerships are expected to expand the application space of SciDAC, and broaden the impact and visibility of the program. We have, with our recent solicitation, expanded to turbulence, computational biology, and groundwater reactive modeling and simulation. We are currently talking with the Department’s applied energy programs about risk assessment, optimization of complex systems - such as the national and regional electricity grid, carbon sequestration, virtual engineering, and the nuclear fuel cycle. The successes of the first five years of SciDAC have demonstrated the power of using advanced computing to enable scientific discovery. One measure of this success could be found in the President’s State of the Union address in which President Bush identified ‘supercomputing’ as a major focus area of the American Competitiveness Initiative. Funds were provided in the FY 2007 President’s Budget request to increase the size of the NERSC-5 procurement to between 100-150 teraflops, to upgrade the LCF Cray XT3 at Oak Ridge to 250 teraflops and acquire a 100 teraflop IBM BlueGene/P to establish the Leadership computing facility at Argonne. We believe that we are on a path to establish a petascale computing resource for open science by 2009. We must develop software tools, packages, and libraries as well as the scientific application software that will scale to hundreds of thousands of processors. Computer scientists from universities and the DOE’s national laboratories will be asked to collaborate on the development of the critical system software components such as compilers, light-weight operating systems and file systems. Standing up these large machines will not be business as usual for ASCR. We intend to develop a series of interconnected projects that identify cost, schedule, risks, and scope for the upgrades at the LCF at Oak Ridge, the establishment of the LCF at Argonne, and the development of the software to support these high-end computers. The critical first step in defining the scope of the project is to identify a set of early application codes for each leadership class computing facility. These codes will have access to the resources during the commissioning phase of the facility projects and will be part of the acceptance tests for the machines. Applications will be selected, in part, by breakthrough science, scalability, and ability to exercise key hardware and software components. Possible early applications might include climate models; studies of the magnetic properties of nanoparticles as they relate to ultra-high density storage media; the rational design of chemical catalysts, the modeling of combustion processes that will lead to cleaner burning coal, and fusion and astrophysics research. I have presented just a few of the challenges that we look forward to on the road to petascale computing. Our road to petascale science might be paraphrased by the quote from e e cummings, ‘somewhere I have never traveled, gladly beyond any experience . . .’

HF Surface Wave Radar for Oceanography -- A Review of Activities in Germany

DTIC Science & Technology

2005-04-14

Environmental and Remote Sensing Center (NERSC). The model and data assimilation technique is described by Breivik and Sætra [2]. Figure 10 shows a...forecasts with the measurements taken at that time, the rms error increases to 20 cm/s. Breivik and Sætra, 2001, present scatter plots and correlations

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, P.; Benveniste, J.

2011-07-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

Effective Hamiltonian approach to bright and dark excitons in single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Choi, Sangkook; Deslippe, Jack; Louie, Steven G.

2009-03-01

Recently, excitons in single-walled carbon nanotubes (SWCNTs) have generated great research interest due to the large binding energies and unique screening properties associated with one-dimensional (1D) materials. Considerable progress in their theoretical understanding has been achieved by studies employing the ab initio GW-Bethe-Salpeter equation methodology. For example, the presence of bright and dark excitons with binding energies of a large fraction of an eV has been predicted and subsequently verified by experiment. Some of these results have also been quantitatively reproduced by recent model calculations using a spatially dependent screened Coulomb interaction between the excited electron and hole, an approach that would be useful for studying large diameter and chiral nanotubes with many atoms per unit cell. However, this previous model neglects the degeneracy of the band states and hence the dark excitons. We present an extension of this exciton model for the SWCNT, incorporating the screened Coulomb interaction as well as state degeneracy, to understand and compute the characteristics of the bright and dark excitons, such as the bright and dark level splittings. Supported by NSF #DMR07-05941, DOE #De-AC02-05CH11231 and computational resources from Teragrid and NERSC.

Extended Subject Access to Hypertext Online Documentation. Parts I and II: The Search-Support and Maintenance Problems.

ERIC Educational Resources Information Center

Girill, T. R.; And Others

1991-01-01

Describes enhancements made to a hypertext information retrieval system at the National Energy Research Supercomputer Center (NERSC) called DFT (Document, Find, and Theseus). The enrichment of DFT's entry vocabulary is described, DFT and other hypertext systems are compared, and problems that occur due to the need for frequent updates are…

Protonation Studies of a Tungsten Dinitrogen Complex Supported by a Diphosphine Ligand Containing a Pendant Amine

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

Weiss, Charles J.; Egbert, Jonathan D.; Chen, Shentan

2014-04-28

Treatment of trans-[W(N2)2(dppe)(PEtNMePEt)] (dppe = Ph2PCH2CH2PPh2; PEtNMePEt = Et2PCH2N(Me)CH2PEt2) with three equivalents of tetrafluoroboric acid (HBF4∙Et2O) at -78 °C generated the seven-coordinate tungsten hydride trans-[W(N2)2(H)(dppe)(PEtNMePEt)][BF4]. Depending on the temperature of the reaction, protonation of a pendant amine is also observed, affording trans-[W(N2)2(H)(dppe)(PEtNMe(H)PEt)][BF4]2, with formation of the hydrazido complex, [W(NNH2)(dppe)(PEtNMe(H)PEt)][BF4]2, as a minor product. Similar product mixtures were obtained using triflic acid (HOTf). Upon acid addition to the carbonyl analogue, cis-[W(CO)2(dppe)(PEtNMePEt)], the seven-coordinate carbonyl-hydride complex, trans-[W(CO)2(H)(dppe)(PEtN(H)MePEt)][OTf]2 was generated. The mixed diphosphine complex without the pendant amine in the ligand backbone, trans-[W(N2)2(dppe)(depp)] (depp = Et2P(CH2)3PEt2), was synthesized and treated with HBF4∙Et2O, selectivelymore » generating a hydrazido complex, [W(NNH2)(F)(dppe)(depp)][BF4]. Computational analysis was used to probe proton affinity of three sites of protonation, the metal, pendant amine, and N2 ligand in these complexes. Room temperature reactions with 100 equivalents of HOTf produced NH4+ from reduction of the N2 ligand (electrons come from W). The addition of 100 equivalents HOTf to trans-[W(N2)2(dppe)(PEtNMePEt)] afforded 0.88 ± 0.02 equivalents NH4+, while 0.36 ± 0.02 equivalents of NH4+was formed upon treatment of trans-[W(N2)2(dppe)(depp)], the complex without the pendant amine. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy Office of Science, Office of Basic Energy Sciences. Computational resources were provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for DOE.« less

Electronic and steric influences of pendant amine groups on the protonation of molybdenum bis (dinitrogen) complexes

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

Labios, Liezel A.; Heiden, Zachariah M.; Mock, Michael T.

2015-05-04

The synthesis of a series of P EtP NRR' (P EtP NRR' = Et₂PCH₂CH₂P(CH₂NRR')₂, R = H, R' = Ph or 2,4-difluorophenyl; R = R' = Ph or iPr) diphosphine ligands containing mono- and disubstituted pendant amine groups, and the preparation of their corresponding molybdenum bis(dinitrogen) complexes trans-Mo(N₂)₂(PMePh₂)₂(P EtP NRR') is described. In situ IR and multinuclear NMR spectroscopic studies monitoring the stepwise addition of (HOTf) to trans-Mo(N₂)₂(PMePh₂)₂(P EtP NRR') complexes in THF at -40 °C show that the electronic and steric properties of the R and R' groups of the pendant amines influence whether the complexes are protonated atmore » Mo, a pendant amine, a coordinated N2 ligand, or a combination of these sites. For example, complexes containing mono-aryl substituted pendant amines are protonated at Mo and pendant amine to generate mono- and dicationic Mo–H species. Protonation of the complex containing less basic diphenyl-substituted pendant amines exclusively generates a monocationic hydrazido (Mo(NNH₂)) product, indicating preferential protonation of an N₂ ligand. Addition of HOTf to the complex featuring more basic diisopropyl amines primarily produces a monocationic product protonated at a pendant amine site, as well as a trace amount of dicationic Mo(NNH₂) product that contain protonated pendant amines. In addition, trans-Mo(N₂)₂(PMePh₂)₂(depe) (depe = Et₂PCH₂CH₂PEt₂) without a pendant amine was synthesized and treated with HOTf, generating a monocationic Mo(NNH₂) product. Protonolysis experiments conducted on select complexes in the series afforded trace amounts of NH₄⁺. Computational analysis of the series of trans-Mo(N₂)₂(PMePh₂)₂(P EtP NRR') complexes provides further insight into the proton affinity values of the metal center, N₂ ligand, and pendant amine sites to rationalize the differing reactivity profiles. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Computational resources provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Hydraulic Jumps, Waves and Other Flow Features Found by Modeling Stably-Stratified Flows in the Salt Lake Valley

NASA Astrophysics Data System (ADS)

Chen, Y.; Ludwig, F.; Street, R.

2003-12-01

The Advanced Regional Prediction System (ARPS) was used to simulate weak synoptic wind conditions with stable stratification and pronounced drainage flow at night in the vicinity of the Jordan Narrows at the south end of Salt Lake Valley. The simulations showed the flow to be quite complex with hydraulic jumps and internal waves that make it essential to use a complete treatment of the fluid dynamics. Six one-way nested grids were used to resolve the topography; they ranged from 20-km grid spacing, initialized by ETA 40-km operational analyses down to 250-m horizontal resolution and 200 vertically stretched levels to a height of 20 km, beginning with a 10-m cell at the surface. Most of the features of interest resulted from interactions with local terrain features, so that little was lost by using one-way nesting. Canyon, gap, and over-terrain flows have a large effect on mixing and vertical transport, especially in the regions where hydraulic jumps are likely. Our results also showed that the effect of spatial resolution on simulation performance is profound. The horizontal resolution must be such that the smallest features that are likely to have important impact on the flow are spanned by at least a few grid points. Thus, the 250 m minimum resolution of this study is appropriate for treating the effects of features of about 1 km or greater extent. To be consistent, the vertical cell dimension must resolve the same terrain features resolved by the horizontal grid. These simulations show that many of the interesting flow features produce observable wind and temperature gradients at or near the surface. Accordingly, some relatively simple field measurements might be made to confirm that the mixing phenomena that were simulated actually take place in the real atmosphere, which would be very valuable for planning large, expensive field campaigns. The work was supported by the Atmospheric Sciences Program, Office of Biological and Environmental Research, U.S. Department of Energy. The National Energy Research Scientific Computing Center (NERSC) provided computational time. We thank Professor Ming Xue and others at the University of Oklahoma for their help.

Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2014-01-14

The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems.more » The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy, Office of Science of the under Contract No. DE-AC02-05CH11231.« less

Excitonic Effects and Optical Absorption Spectrum of Doped Graphene

NASA Astrophysics Data System (ADS)

Jornada, Felipe; Deslippe, Jack; Louie, Steven

2012-02-01

First-principles calculations based on the GW-Bethe-Salpeter Equation (GW-BSE) approach and subsequent experiments have shown large excitonic effects in the optical absorbance of graphene. Here we employ the GW-BSE formalism to probe the effects of charge carrier doping and of having an external electric field on the absorption spectrum of graphene. We show that the absorbance peak due to the resonant exciton exhibits systematic changes in both its position and profile when graphene is gate doped by carriers, in excellent agreement to very recent measurementsootnotetextTony F. Heinz, private communications.. We analyze the various contributions to these changes in the absorption spectrum, such as the effects of screening by carriers to the quasiparticle energies and electron-hole interactions. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and the U.S. DOD - Office of Naval Research under RTC Grant No. N00014-09-1-1066. Computer time was provided by NERSC.

Electronic and Optical Properties of Novel Phases of Silicon and Silicon-Based Derivatives

NASA Astrophysics Data System (ADS)

Ong, Chin Shen; Choi, Sangkook; Louie, Steven

2014-03-01

The vast majority of solar cells in the market today are made from crystalline silicon in the diamond-cubic phase. Nonetheless, diamond-cubic Si has an intrinsic disadvantage: it has an indirect band gap with a large energy difference between the direct gap and the indirect gap. In this work, we perform a careful study of the electronic and optical properties of a newly discovered cubic-Si20 phase of Si that is found to sport a direct band gap. In addition, other silicon-based derivatives have also been discovered and found to be thermodynamically metastable. We carry out ab initio GW and GW-BSE calculations for the quasiparticle excitations and optical spectra, respectively, of these new phases of silicon and silicon-based derivatives. This work was supported by NSF grant No. DMR10-1006184 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at Lawrence Berkeley National Laboratory's NERSC facility and the NSF through XSEDE resources at NICS.

Towards real-time detection and tracking of spatio-temporal features: Blob-filaments in fusion plasma

DOE PAGES

Wu, Lingfei; Wu, Kesheng; Sim, Alex; ...

2016-06-01

A novel algorithm and implementation of real-time identification and tracking of blob-filaments in fusion reactor data is presented. Similar spatio-temporal features are important in many other applications, for example, ignition kernels in combustion and tumor cells in a medical image. This work presents an approach for extracting these features by dividing the overall task into three steps: local identification of feature cells, grouping feature cells into extended feature, and tracking movement of feature through overlapping in space. Through our extensive work in parallelization, we demonstrate that this approach can effectively make use of a large number of compute nodes tomore » detect and track blob-filaments in real time in fusion plasma. Here, on a set of 30GB fusion simulation data, we observed linear speedup on 1024 processes and completed blob detection in less than three milliseconds using Edison, a Cray XC30 system at NERSC.« less

High Performance Data Transfer for Distributed Data Intensive Sciences

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

Fang, Chin; Cottrell, R 'Les' A.; Hanushevsky, Andrew B.

We report on the development of ZX software providing high performance data transfer and encryption. The design scales in: computation power, network interfaces, and IOPS while carefully balancing the available resources. Two U.S. patent-pending algorithms help tackle data sets containing lots of small files and very large files, and provide insensitivity to network latency. It has a cluster-oriented architecture, using peer-to-peer technologies to ease deployment, operation, usage, and resource discovery. Its unique optimizations enable effective use of flash memory. Using a pair of existing data transfer nodes at SLAC and NERSC, we compared its performance to that of bbcp andmore » GridFTP and determined that they were comparable. With a proof of concept created using two four-node clusters with multiple distributed multi-core CPUs, network interfaces and flash memory, we achieved 155Gbps memory-to-memory over a 2x100Gbps link aggregated channel and 70Gbps file-to-file with encryption over a 5000 mile 100Gbps link.« less

Connecting Restricted, High-Availability, or Low-Latency Resources to a Seamless Global Pool for CMS

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Hufnagel, D.; Hurtado Anampa, K.; Jayatilaka, B.; Khan, F.; Larson, K.; Letts, J.; Mascheroni, M.; Mohapatra, A.; Marra Da Silva, J.; Mason, D.; Perez-Calero Yzquierdo, A.; Piperov, S.; Tiradani, A.; Verguilov, V.; CMS Collaboration

2017-10-01

The connection of diverse and sometimes non-Grid enabled resource types to the CMS Global Pool, which is based on HTCondor and glideinWMS, has been a major goal of CMS. These resources range in type from a high-availability, low latency facility at CERN for urgent calibration studies, called the CAF, to a local user facility at the Fermilab LPC, allocation-based computing resources at NERSC and SDSC, opportunistic resources provided through the Open Science Grid, commercial clouds, and others, as well as access to opportunistic cycles on the CMS High Level Trigger farm. In addition, we have provided the capability to give priority to local users of beyond WLCG pledged resources at CMS sites. Many of the solutions employed to bring these diverse resource types into the Global Pool have common elements, while some are very specific to a particular project. This paper details some of the strategies and solutions used to access these resources through the Global Pool in a seamless manner.

DESCQA: Synthetic Sky Catalog Validation Framework

NASA Astrophysics Data System (ADS)

Mao, Yao-Yuan; Uram, Thomas D.; Zhou, Rongpu; Kovacs, Eve; Ricker, Paul M.; Kalmbach, J. Bryce; Padilla, Nelson; Lanusse, François; Zu, Ying; Tenneti, Ananth; Vikraman, Vinu; DeRose, Joseph

2018-04-01

The DESCQA framework provides rigorous validation protocols for assessing the quality of high-quality simulated sky catalogs in a straightforward and comprehensive way. DESCQA enables the inspection, validation, and comparison of an inhomogeneous set of synthetic catalogs via the provision of a common interface within an automated framework. An interactive web interface is also available at portal.nersc.gov/project/lsst/descqa.

Opening Remarks: SciDAC 2007

NASA Astrophysics Data System (ADS)

Strayer, Michael

2007-09-01

Good morning. Welcome to Boston, the home of the Red Sox, Celtics and Bruins, baked beans, tea parties, Robert Parker, and SciDAC 2007. A year ago I stood before you to share the legacy of the first SciDAC program and identify the challenges that we must address on the road to petascale computing—a road E E Cummins described as `. . . never traveled, gladly beyond any experience.' Today, I want to explore the preparations for the rapidly approaching extreme scale (X-scale) generation. These preparations are the first step propelling us along the road of burgeoning scientific discovery enabled by the application of X- scale computing. We look to petascale computing and beyond to open up a world of discovery that cuts across scientific fields and leads us to a greater understanding of not only our world, but our universe. As part of the President's America Competitiveness Initiative, the ASCR Office has been preparing a ten year vision for computing. As part of this planning the LBNL together with ORNL and ANL hosted three town hall meetings on Simulation and Modeling at the Exascale for Energy, Ecological Sustainability and Global Security (E3). The proposed E3 initiative is organized around four programmatic themes: Engaging our top scientists, engineers, computer scientists and applied mathematicians; investing in pioneering large-scale science; developing scalable analysis algorithms, and storage architectures to accelerate discovery; and accelerating the build-out and future development of the DOE open computing facilities. It is clear that we have only just started down the path to extreme scale computing. Plan to attend Thursday's session on the out-briefing and discussion of these meetings. The road to the petascale has been at best rocky. In FY07, the continuing resolution provided 12% less money for Advanced Scientific Computing than either the President, the Senate, or the House. As a consequence, many of you had to absorb a no cost extension for your SciDAC work. I am pleased that the President's FY08 budget restores the funding for SciDAC. Quoting from Advanced Scientific Computing Research description in the House Energy and Water Development Appropriations Bill for FY08, "Perhaps no other area of research at the Department is so critical to sustaining U.S. leadership in science and technology, revolutionizing the way science is done and improving research productivity." As a society we need to revolutionize our approaches to energy, environmental and global security challenges. As we go forward along the road to the X-scale generation, the use of computation will continue to be a critical tool along with theory and experiment in understanding the behavior of the fundamental components of nature as well as for fundamental discovery and exploration of the behavior of complex systems. The foundation to overcome these societal challenges will build from the experiences and knowledge gained as you, members of our SciDAC research teams, work together to attack problems at the tera- and peta- scale. If SciDAC is viewed as an experiment for revolutionizing scientific methodology, then a strategic goal of ASCR program must be to broaden the intellectual base prepared to address the challenges of the new X-scale generation of computing. We must focus our computational science experiences gained over the past five years on the opportunities introduced with extreme scale computing. Our facilities are on a path to provide the resources needed to undertake the first part of our journey. Using the newly upgraded 119 teraflop Cray XT system at the Leadership Computing Facility, SciDAC research teams have in three days performed a 100-year study of the time evolution of the atmospheric CO2 concentration originating from the land surface. The simulation of the El Nino/Southern Oscillation which was part of this study has been characterized as `the most impressive new result in ten years' gained new insight into the behavior of superheated ionic gas in the ITER reactor as a result of an AORSA run on 22,500 processors that achieved over 87 trillion calculations per second (87 teraflops) which is 74% of the system's theoretical peak. Tomorrow, Argonne and IBM will announce that the first IBM Blue Gene/P, a 100 teraflop system, will be shipped to the Argonne Leadership Computing Facility later this fiscal year. By the end of FY2007 ASCR high performance and leadership computing resources will include the 114 teraflop IBM Blue Gene/P; a 102 teraflop Cray XT4 at NERSC and a 119 teraflop Cray XT system at Oak Ridge. Before ringing in the New Year, Oak Ridge will upgrade to 250 teraflops with the replacement of the dual core processors with quad core processors and Argonne will upgrade to between 250-500 teraflops, and next year, a petascale Cray Baker system is scheduled for delivery at Oak Ridge. The multidisciplinary teams in our SciDAC Centers for Enabling Technologies and our SciDAC Institutes must continue to work with our Scientific Application teams to overcome the barriers that prevent effective use of these new systems. These challenges include: the need for new algorithms as well as operating system and runtime software and tools which scale to parallel systems composed of hundreds of thousands processors; program development environments and tools which scale effectively and provide ease of use for developers and scientific end users; and visualization and data management systems that support moving, storing, analyzing, manipulating and visualizing multi-petabytes of scientific data and objects. The SciDAC Centers, located primarily at our DOE national laboratories will take the lead in ensuring that critical computer science and applied mathematics issues are addressed in a timely and comprehensive fashion and to address issues associated with research software lifecycle. In contrast, the SciDAC Institutes, which are university-led centers of excellence, will have more flexibility to pursue new research topics through a range of research collaborations. The Institutes will also work to broaden the intellectual and researcher base—conducting short courses and summer schools to take advantage of new high performance computing capabilities. The SciDAC Outreach Center at Lawrence Berkeley National Laboratory complements the outreach efforts of the SciDAC Institutes. The Outreach Center is our clearinghouse for SciDAC activities and resources and will communicate with the high performance computing community in part to understand their needs for workshops, summer schools and institutes. SciDAC is not ASCR's only effort to broaden the computational science community needed to meet the challenges of the new X-scale generation. I hope that you were able to attend the Computational Science Graduate Fellowship poster session last night. ASCR developed the fellowship in 1991 to meet the nation's growing need for scientists and technology professionals with advanced computer skills. CSGF, now jointly funded between ASCR and NNSA, is more than a traditional academic fellowship. It has provided more than 200 of the best and brightest graduate students with guidance, support and community in preparing them as computational scientists. Today CSGF alumni are bringing their diverse top-level skills and knowledge to research teams at DOE laboratories and in industries such as Proctor and Gamble, Lockheed Martin and Intel. At universities they are working to train the next generation of computational scientists. To build on this success, we intend to develop a wholly new Early Career Principal Investigator's (ECPI) program. Our objective is to stimulate academic research in scientific areas within ASCR's purview especially among faculty in early stages of their academic careers. Last February, we lost Ken Kennedy, one of the leading lights of our community. As we move forward into the extreme computing generation, his vision and insight will be greatly missed. In memorial to Ken Kennedy, we shall designate the ECPI grants to beginning faculty in Computer Science as the Ken Kennedy Fellowship. Watch the ASCR website for more information about ECPI and other early career programs in the computational sciences. We look to you, our scientists, researchers, and visionaries to take X-scale computing and use it to explode scientific discovery in your fields. We at SciDAC will work to ensure that this tool is the sharpest and most precise and efficient instrument to carve away the unknown and reveal the most exciting secrets and stimulating scientific discoveries of our time. The partnership between research and computing is the marriage that will spur greater discovery, and as Spencer said to Susan in Robert Parker's novel, `Sudden Mischief', `We stick together long enough, and we may get as smart as hell'. Michael Strayer

Computational Investigations of Rovibrational Quenching of HD due to Collisions in the Interstellar Medium

NASA Astrophysics Data System (ADS)

Goodman Veazey, Clark; Wan, Yier; Yang, Benhui H.; Stancil, P.

2017-06-01

When conducting an examination of distant astronomical objects, scientists rely on measurements derived from astronomical observations of these objects, which are primarily collected using spectroscopy. In order to interpret spectroscopic data collected on astronomical objects, it is necessary to have a background of accurate dynamical information on interstellar molecules at one’s disposal. Seeing as most of the observable infrared radiation in the universe is emitted by molecules excited by collisional processes in the interstellar gas, generating accurate data on the rate of molecular collisions is of salient interest to astronomical endeavors.The collisional system we will be focusing on here is He-HD, an atom-diatom system in which He collides with HD. We are primarily interested in the cooling capabilities of this system, as these species are predicted to have played an important role in the formation of primordial stars, which emerged from a background composed solely of Hydrogen, Helium, and their compounds. HD is being investigated because it has a finite dipole moment and is hence a powerful radiator, and He due to its relative abundance in the early universe. Using a hybrid OpenMP/MPI adaption (vrrm) of a public-domain scattering package, cross sections for He-HD collisions are computed for a swathe of both rotational and vibrational states across a range of relevant kinetic energies, then integrated to produce rate coefficients. Due to the vast computational requirements for performing these operations, the use of high-powered computational resources is necessary.The work of CV was funded by a UGA Center for Undergraduate Research Opportunities award. We thank the University of Georgia GACRC and NERSC at Lawrence-Berkeley for computational resources and Brendan McLaughlin for assistance.

Impact of Weak Agostic Interactions in Nickel Electrocatalysts for Hydrogen Oxidation

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

Klug, Christina M.; O’Hagan, Molly; Bullock, R. Morris

To understand how H2 binding and oxidation is influenced by [Ni(PR2NR'2)2]2+ PR2NR'2 catalysts with H2 binding energies close to thermoneutral, two [Ni(PPh2NR'2)2]2+ (R = Me or C14H29) complexes with phenyl substituents on phosphorous and varying alkyl chain lengths on the pendant amine were studied. In the solid state, [Ni(PPh2NMe2)2]2+ exhibits an anagostic interaction between the Ni(II) center and the α-CH3 of the pendant amine, and DFT and variable-temperature 31P NMR experiments suggest than the anagostic interaction persists in solution. The equilibrium constants for H2 addition to these complexes was measured by 31P NMR spectroscopy, affording free energies of H2 additionmore » (ΔG°H2) of –0.8 kcal mol–1 in benzonitrile and –1.6 to –2.3 kcal mol–1 in THF. The anagostic interaction contributes to the low driving force for H2 binding by stabilizing the four-coordinate Ni(II) species prior to binding of H2. The pseudo-first order rate constants for H2 addition at 1 atm were measured by variable scan rate cyclic voltammetry, and were found to be similar for both complexes, less than 0.2 s–1 in benzonitrile and 3 –6 s–1 in THF. In the presence of exogenous base and H2 , turnover frequencies of electrocatalytic H2 oxidation were measured to be less than 0.2 s–1 in benzonitrile and 4 –9 s–1 in THF. These complexes are slower electrocatalysts for H2 oxidation than previously studied [Ni(PR2NR'2)2]2+ complexes due to a competition between H2 binding and formation of the anagostic interaction. However, the decrease in catalytic rate is accompanied by a beneficial 130 mV decrease in overpotential. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Computational resources were provided at the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Mass spectrometry experiments were performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located and the Pacific Northwest National Laboratory (PNNL). The authors thank Dr. Rosalie Chu for mass spectroscopy analysis. PNNL is operated by Battelle for DOE.« less

Conformational Dynamics and Proton Relay Positioning in Nickel Catalysts for Hydrogen Production and Oxidation

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

Franz, James A.; O'Hagan, Molly J.; Ho, Ming-Hsun

2013-12-09

The [Ni(PR2NR’2)2]2+ catalysts, (where PR2NR´2 is 1,5-R´-3,7-R-1,5-diaza-3,7-diphosphacyclooctane), are some of the fastest reported for hydrogen production and oxidation, however, chair/boat isomerization and the presence of a fifth solvent ligand have the potential to slow catalysis by incorrectly positioning the pendant amines or blocking the addition of hydrogen. Here, we report the structural dynamics of a series of [Ni(PR2NR’2)2]n+ complexes, characterized by NMR spectroscopy and theoretical modeling. A fast exchange process was observed for the [Ni(CH3CN)(PR2NR’2)2]2+ complexes which depends on the ligand. This exchange process was identified to occur through a three step mechanism including dissociation of the acetonitrile, boat/chair isomerizationmore » of each of the four rings identified by the phosphine ligands (including nitrogen inversion), and reassociation of acetonitrile on the opposite side of the complex. The rate of the chair/boat inversion can be influenced by varying the substituent on the nitrogen atom, but the rate of the overall exchange process is at least an order of magnitude faster than the catalytic rate in acetonitrile demonstrating that the structural dynamics of the [Ni(PR2NR´2)2]2+ complexes does not hinder catalysis. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under FWP56073. Research by J.A.F., M.O., M-H. H., M.L.H, D.L.D. A.M.A., S. R. and R.M.B. was carried out in the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. W.J.S. and S.L. were funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. T.L. was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory; the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory; and the Jaguar supercomputer at Oak Ridge National Laboratory (INCITE 2008-2011 award supported by the Office of Science of the U.S. DOE under Contract No. DE-AC0500OR22725).« less

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

Churchill, R. Michael

Apache Spark is explored as a tool for analyzing large data sets from the magnetic fusion simulation code XGCI. Implementation details of Apache Spark on the NERSC Edison supercomputer are discussed, including binary file reading, and parameter setup. Here, an unsupervised machine learning algorithm, k-means clustering, is applied to XGCI particle distribution function data, showing that highly turbulent spatial regions do not have common coherent structures, but rather broad, ring-like structures in velocity space.

76 FR 41234 - Advanced Scientific Computing Advisory Committee Charter Renewal

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-13

... Secretariat, General Services Administration, notice is hereby given that the Advanced Scientific Computing... advice and recommendations concerning the Advanced Scientific Computing program in response only to... Advanced Scientific Computing Research program and recommendations based thereon; --Advice on the computing...

Soft Functionals for Hard Matter

NASA Astrophysics Data System (ADS)

Cooper, Valentino R.; Yuk, Simuck F.; Krogel, Jaron T.

Theory and computation are critical to the materials discovery process. While density functional theory (DFT) has become the standard for predicting materials properties, it is often plagued by inaccuracies in the underlying exchange-correlation functionals. Using high-throughput DFT calculations we explore the accuracy of various exchange-correlation functionals for modeling the structural and thermodynamic properties of a wide range of complex oxides. In particular, we examine the feasibility of using the nonlocal van der Waals density correlation functional with C09 exchange (C09x), which was designed for sparsely packed soft matter, for investigating the properties of hard matter like bulk oxides. Preliminary results show unprecedented performance for some prototypical bulk ferroelectrics, which can be correlated with similarities between C09x and PBEsol. This effort lays the groundwork for understanding how these soft functionals can be employed as general purpose functionals for studying a wide range of materials where strong internal bonds and nonlocal interactions coexist. Research was sponsored by the US DOE, Office of Science, BES, MSED and Early Career Research Programs and used resources at NERSC.

76 FR 31945 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-02

... DEPARTMENT OF ENERGY Advanced Scientific Computing Advisory Committee AGENCY: Department of Energy... teleconference meeting of the Advanced Scientific Computing Advisory Committee (ASCAC). The Federal [email protected] . FOR FURTHER INFORMATION CONTACT: Melea Baker, Office of Advanced Scientific Computing...

Highly Active and Stable MgAl2O4 Supported Rh and Ir Catalysts for Methane Steam Reforming: A Combined Experimental and Theoretical Study

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

Mei, Donghai; Glezakou, Vassiliki Alexandra; Lebarbier, Vanessa MC

2014-07-01

In this work we present a combined experimental and theoretical investigation of stable MgAl2O4 spinel-supported Rh and Ir catalysts for the steam methane reforming (SMR) reaction. Firstly, catalytic performance for a series of noble metal catalysts supported on MgAl2O4 spinel was evaluated for SMR at 600-850°C. Turnover rate at 850°C follows the order: Pd > Pt > Ir > Rh > Ru > Ni. However, Rh and Ir were found to have the best combination of activity and stability for methane steam reforming in the presence of simulated biomass-derived syngas. It was found that highly dispersed ~2 nm Rh andmore » ~1 nm Ir clusters were formed on the MgAl2O4 spinel support. Scanning Transition Electron Microscopy (STEM) images show that excellent dispersion was maintained even under challenging high temperature conditions (e.g. at 850°C in the presence of steam) while Ir and Rh catalysts supported on Al2O3 were observed to sinter at increased rates under the same conditions. These observations were further confirmed by ab initio molecular dynamics (AIMD) simulations which find that ~1 nm Rh and Ir particles (50-atom cluster) bind strongly to the MgAl2O4 surfaces via a redox process leading to a strong metal-support interaction, thus helping anchor the metal clusters and reduce the tendency to sinter. Density functional theory (DFT) calculations suggest that these supported smaller Rh and Ir particles have a lower work function than larger more bulk-like ones, which enables them to activate both water and methane more effectively than larger particles, yet have a minimal influence on the relative stability of coke precursors. In addition, theoretical mechanistic studies were used to probe the relationship between structure and reactivity. Consistent with the experimental observations, our theoretical modeling results also suggest that the small spinel-supported Ir particle catalyst is more active than the counterpart of Rh catalyst for SMR. This work was financially supported by the United States Department of Energy (DOE)’s Bioenergy Technologies Office (BETO) and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle Memorial Institute. Computing time was granted by a user proposal at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) located at PNNL. Part of the computational time was provided by the National Energy Research Scientific Computing Center (NERSC).« less

75 FR 9887 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... DEPARTMENT OF ENERGY Advanced Scientific Computing Advisory Committee AGENCY: Department of Energy... Advanced Scientific Computing Advisory Committee (ASCAC). Federal Advisory Committee Act (Pub. L. 92-463... INFORMATION CONTACT: Melea Baker, Office of Advanced Scientific Computing Research; SC-21/Germantown Building...

76 FR 9765 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-22

... DEPARTMENT OF ENERGY Advanced Scientific Computing Advisory Committee AGENCY: Office of Science... Advanced Scientific Computing Advisory Committee (ASCAC). The Federal Advisory Committee Act (Pub. L. 92... INFORMATION CONTACT: Melea Baker, Office of Advanced Scientific Computing Research, SC-21/Germantown Building...

77 FR 45345 - DOE/Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-31

... Recompetition results for Scientific Discovery through Advanced Computing (SciDAC) applications Co-design Public... DEPARTMENT OF ENERGY DOE/Advanced Scientific Computing Advisory Committee AGENCY: Office of... the Advanced Scientific Computing Advisory Committee (ASCAC). The Federal Advisory Committee Act (Pub...

75 FR 64720 - DOE/Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-20

... DEPARTMENT OF ENERGY DOE/Advanced Scientific Computing Advisory Committee AGENCY: Department of... the Advanced Scientific Computing Advisory Committee (ASCAC). Federal Advisory Committee Act (Pub. L.... FOR FURTHER INFORMATION CONTACT: Melea Baker, Office of Advanced Scientific Computing Research; SC-21...

Computing through Scientific Abstractions in SysBioPS

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

Chin, George; Stephan, Eric G.; Gracio, Deborah K.

2004-10-13

Today, biologists and bioinformaticists have a tremendous amount of computational power at their disposal. With the availability of supercomputers, burgeoning scientific databases and digital libraries such as GenBank and PubMed, and pervasive computational environments such as the Grid, biologists have access to a wealth of computational capabilities and scientific data at hand. Yet, the rapid development of computational technologies has far exceeded the typical biologist’s ability to effectively apply the technology in their research. Computational sciences research and development efforts such as the Biology Workbench, BioSPICE (Biological Simulation Program for Intra-Cellular Evaluation), and BioCoRE (Biological Collaborative Research Environment) are importantmore » in connecting biologists and their scientific problems to computational infrastructures. On the Computational Cell Environment and Heuristic Entity-Relationship Building Environment projects at the Pacific Northwest National Laboratory, we are jointly developing a new breed of scientific problem solving environment called SysBioPSE that will allow biologists to access and apply computational resources in the scientific research context. In contrast to other computational science environments, SysBioPSE operates as an abstraction layer above a computational infrastructure. The goal of SysBioPSE is to allow biologists to apply computational resources in the context of the scientific problems they are addressing and the scientific perspectives from which they conduct their research. More specifically, SysBioPSE allows biologists to capture and represent scientific concepts and theories and experimental processes, and to link these views to scientific applications, data repositories, and computer systems.« 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.

75 FR 43518 - Advanced Scientific Computing Advisory Committee; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-26

... DEPARTMENT OF ENERGY Advanced Scientific Computing Advisory Committee; Meeting AGENCY: Office of... Scientific Computing Advisory Committee (ASCAC). Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770...: Melea Baker, Office of Advanced Scientific Computing Research; SC-21/Germantown Building; U. S...

Intercomparison of Operational Ocean Forecasting Systems in the framework of GODAE

NASA Astrophysics Data System (ADS)

Hernandez, F.

2009-04-01

One of the main benefits of the GODAE 10-year activity is the implementation of ocean forecasting systems in several countries. In 2008, several systems are operated routinely, at global or basin scale. Among them, the BLUElink (Australia), HYCOM (USA), MOVE/MRI.COM (Japan), Mercator (France), FOAM (United Kingdom), TOPAZ (Norway) and C-NOOFS (Canada) systems offered to demonstrate their operational feasibility by performing an intercomparison exercise during a three months period (February to April 2008). The objectives were: a) to show that operational ocean forecasting systems are operated routinely in different countries, and that they can interact; b) to perform in a similar way a scientific validation aimed to assess the quality of the ocean estimates, the performance, and forecasting capabilities of each system; and c) to learn from this intercomparison exercise to increase inter-operability and collaboration in real time. The intercomparison relies on the assessment strategy developed for the EU MERSEA project, where diagnostics over the global ocean have been revisited by the GODAE contributors. This approach, based on metrics, allow for each system: a) to verify if ocean estimates are consistent with the current general knowledge of the dynamics; and b) to evaluate the accuracy of delivered products, compared to space and in-situ observations. Using the same diagnostics also allows one to intercompare the results from each system consistently. Water masses and general circulation description by the different systems are consistent with WOA05 Levitus climatology. The large scale dynamics (tropical, subtropical and subpolar gyres ) are also correctly reproduced. At short scales, benefit of high resolution systems can be evidenced on the turbulent eddy field, in particular when compared to eddy kinetic energy deduced from satellite altimetry of drifter observations. Comparisons to high resolution SST products show some discrepancies on ocean surface representation, either due to model and forcing fields errors, or assimilation scheme efficiency. Comparisons to sea-ice satellite products also evidence discrepancies linked to model, forcing and assimilation strategies of each forecasting system. Key words: Intercomparison, ocean analysis, operational oceanography, system assessment, metrics, validation GODAE Intercomparison Team: L. Bertino (NERSC/Norway), G. Brassington (BMRC/Australia), E. Chassignet (FSU/USA), J. Cummings (NRL/USA), F. Davidson (DFO/Canda), M. Drévillon (CERFACS/France), P. Hacker (IPRC/USA), M. Kamachi (MRI/Japan), J.-M. Lellouche (CERFACS/France), K. A. Lisæter (NERSC/Norway), R. Mahdon (UKMO/UK), M. Martin (UKMO/UK), A. Ratsimandresy (DFO/Canada), and C. Regnier (Mercator Ocean/France)

Bellerophon

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

Lingerfelt, Eric J; Messer, II, Otis E

2017-01-02

The Bellerophon software system supports CHIMERA, a production-level HPC application that simulates the evolution of core-collapse supernovae. Bellerophon enables CHIMERA's geographically dispersed team of collaborators to perform job monitoring and real-time data analysis from multiple supercomputing resources, including platforms at OLCF, NERSC, and NICS. Its multi-tier architecture provides an encapsulated, end-to-end software solution that enables the CHIMERA team to quickly and easily access highly customizable animated and static views of results from anywhere in the world via a cross-platform desktop application.

Many-electron effects in the optical properties of single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Spataru, Catalin D.; Ismail-Beigi, Sohrab; Capaz, Rodrigo B.; Louie, Steven G.

2005-03-01

Recent optical measurements on single-wall carbon nanotubes (SWCNT) showed anomalous behaviors that are indicative of strong many-electron effects. To understand these data, we performed ab initio calculation of self-energy and electron-hole interaction (excitonic) effects on the optical spectra of several SWCNTs. We employed a many-electron Green's function approach that determines both the quasiparticle and optical excitations from first principles. We found important many-electron effects that explain many of the puzzling experimental findings in the optical spectrum of these quasi-one dimensional systems, and are in excellent quantitative agreement with measurements. We have also calculated the radiative lifetime of the bright excitons in these tubes. Taking into account temperature effects and the existence of dark excitons, our results explain the radiative lifetime of excited nanotubes measured in time- resolved fluorescence experiments. This work was supported by the NSF under Grant No. DMR04-39768, and the U.S. DOE under Contract No. DE-AC03-76SF00098. Computational resources have been provided by NERSC and NPACI. RBC acknowledges financial support from the Guggenheim Foundation and Brazilian funding agencies CNPq, CAPES, FAPERJ, Instituto de Nanociências, FUJB-UFRJ and PRONEX-MCT.

PATHA: Performance Analysis Tool for HPC Applications

DOE PAGES

Yoo, Wucherl; Koo, Michelle; Cao, Yi; ...

2016-02-18

Large science projects rely on complex workflows to analyze terabytes or petabytes of data. These jobs are often running over thousands of CPU cores and simultaneously performing data accesses, data movements, and computation. It is difficult to identify bottlenecks or to debug the performance issues in these large workflows. In order to address these challenges, we have developed Performance Analysis Tool for HPC Applications (PATHA) using the state-of-art open source big data processing tools. Our framework can ingest system logs to extract key performance measures, and apply the most sophisticated statistical tools and data mining methods on the performance data.more » Furthermore, it utilizes an efficient data processing engine to allow users to interactively analyze a large amount of different types of logs and measurements. To illustrate the functionality of PATHA, we conduct a case study on the workflows from an astronomy project known as the Palomar Transient Factory (PTF). This study processed 1.6 TB of system logs collected on the NERSC supercomputer Edison. Using PATHA, we were able to identify performance bottlenecks, which reside in three tasks of PTF workflow with the dependency on the density of celestial objects.« less

Substrate Screening Effects in ab initio Many-body Green's Function Calculations of Doped Graphene on SiC

NASA Astrophysics Data System (ADS)

Vigil-Fowler, Derek; Lischner, Johannes; Louie, Steven

2013-03-01

Understanding many-electron interaction effects and the influence of the substrate in graphene-on-substrate systems is of great theoretical and practical interest. Thus far, both model Hamiltonian and ab initio GW calculations for the quasiparticle properties of such systems have employed crude models for the effect of the substrate, often approximating the complicated substrate dielectric matrix by a single constant. We develop a method in which the spatially-dependent dielectric matrix of the substrate (e.g., SiC) is incorporated into that of doped graphene to obtain an accurate total dielectric matrix. We present ab initio GW + cumulant expansion calculations, showing that both the cumulant expansion (to include higher-order electron correlations) and a proper account of the substrate screening are needed to achieve agreement with features seen in ARPES. We discuss how this methodology could be used in other systems. This work was supported by NSF Grant No. DMR10-1006184 and U.S. DOE Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NERSC and NICS. D.V-F. acknowledges funding from the DOD's NDSEG fellowship.

Investigation of energetic particle induced geodesic acoustic mode

NASA Astrophysics Data System (ADS)

Schneller, Mirjam; Fu, Guoyong; Chavdarovski, Ilija; Wang, Weixing; Lauber, Philipp; Lu, Zhixin

2017-10-01

Energetic particles are ubiquitous in present and future tokamaks due to heating systems and fusion reactions. Anisotropy in the distribution function of the energetic particle population is able to excite oscillations from the continuous spectrum of geodesic acoustic modes (GAMs), which cannot be driven by plasma pressure gradients due to their toroidally and nearly poloidally symmetric structures. These oscillations are known as energetic particle-induced geodesic acoustic modes (EGAMs) [G.Y. Fu'08] and have been observed in recent experiments [R. Nazikian'08]. EGAMs are particularly attractive in the framework of turbulence regulation, since they lead to an oscillatory radial electric shear which can potentially saturate the turbulence. For the presented work, the nonlinear gyrokinetic, electrostatic, particle-in-cell code GTS [W.X. Wang'06] has been extended to include an energetic particle population following either bump-on-tail Maxwellian or slowing-down [Stix'76] distribution function. With this new tool, we study growth rate, frequency and mode structure of the EGAM in an ASDEX Upgrade-like scenario. A detailed understanding of EGAM excitation reveals essential for future studies of EGAM interaction with micro-turbulence. Funded by the Max Planck Princeton Research Center. Computational resources of MPCDF and NERSC are greatefully acknowledged.

National Storage Laboratory: a collaborative research project

NASA Astrophysics Data System (ADS)

Coyne, Robert A.; Hulen, Harry; Watson, Richard W.

1993-01-01

The grand challenges of science and industry that are driving computing and communications have created corresponding challenges in information storage and retrieval. An industry-led collaborative project has been organized to investigate technology for storage systems that will be the future repositories of national information assets. Industry participants are IBM Federal Systems Company, Ampex Recording Systems Corporation, General Atomics DISCOS Division, IBM ADSTAR, Maximum Strategy Corporation, Network Systems Corporation, and Zitel Corporation. Industry members of the collaborative project are funding their own participation. Lawrence Livermore National Laboratory through its National Energy Research Supercomputer Center (NERSC) will participate in the project as the operational site and provider of applications. The expected result is the creation of a National Storage Laboratory to serve as a prototype and demonstration facility. It is expected that this prototype will represent a significant advance in the technology for distributed storage systems capable of handling gigabyte-class files at gigabit-per-second data rates. Specifically, the collaboration expects to make significant advances in hardware, software, and systems technology in four areas of need, (1) network-attached high performance storage; (2) multiple, dynamic, distributed storage hierarchies; (3) layered access to storage system services; and (4) storage system management.

Interplay between Self-Assembled Structures and Energy Level Alignment of Benzenediamine on Au(111) Surfaces

NASA Astrophysics Data System (ADS)

Li, Guo; Neaton, Jeffrey

2015-03-01

Using van der Waals-corrected density functional theory (DFT) calculations, we study the adsorption of benzene-diamine (BDA) molecules on Au(111) surfaces. We find that at low surface coverage, the adsorbed molecules prefer to stay isolated from each other in a monomer phase, due to the inter-molecular dipole-dipole repulsions. However, when the coverage rises above a critical value of 0.9nm-2, the adsorbed molecules aggregate into linear structures via hydrogen bonding between amine groups, consistent with recent experiments [Haxton, Zhou, Tamblyn, et al, Phys. Rev. Lett. 111, 265701 (2013)]. Moreover, we find that these linear structures at high density considerably reduces the Au work function (relative to a monomer phase). Due to reduced surface polarization effects, we estimate that the resonance energy of the highest occupied molecular orbital of the adsorbed BDA molecule relative to the Au Fermi level is significantly lower than the monomer phase by more than 0.5 eV, consistent with the experimental measurements [DellAngela, Kladnik, and Cossaro, et al., Nano Lett. 10, 2470 (2010)]. This work supported by DOE (the JCAP under Award Number DE-SC000499 and the Molecular Foundry of LBNL), and computational resources provided by NERSC.

Scaling Optimization of the SIESTA MHD Code

NASA Astrophysics Data System (ADS)

Seal, Sudip; Hirshman, Steven; Perumalla, Kalyan

2013-10-01

SIESTA is a parallel three-dimensional plasma equilibrium code capable of resolving magnetic islands at high spatial resolutions for toroidal plasmas. Originally designed to exploit small-scale parallelism, SIESTA has now been scaled to execute efficiently over several thousands of processors P. This scaling improvement was accomplished with minimal intrusion to the execution flow of the original version. First, the efficiency of the iterative solutions was improved by integrating the parallel tridiagonal block solver code BCYCLIC. Krylov-space generation in GMRES was then accelerated using a customized parallel matrix-vector multiplication algorithm. Novel parallel Hessian generation algorithms were integrated and memory access latencies were dramatically reduced through loop nest optimizations and data layout rearrangement. These optimizations sped up equilibria calculations by factors of 30-50. It is possible to compute solutions with granularity N/P near unity on extremely fine radial meshes (N > 1024 points). Grid separation in SIESTA, which manifests itself primarily in the resonant components of the pressure far from rational surfaces, is strongly suppressed by finer meshes. Large problem sizes of up to 300 K simultaneous non-linear coupled equations have been solved on the NERSC supercomputers. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

Graphics Processing Unit Acceleration of Gyrokinetic Turbulence Simulations

NASA Astrophysics Data System (ADS)

Hause, Benjamin; Parker, Scott; Chen, Yang

2013-10-01

We find a substantial increase in on-node performance using Graphics Processing Unit (GPU) acceleration in gyrokinetic delta-f particle-in-cell simulation. Optimization is performed on a two-dimensional slab gyrokinetic particle simulation using the Portland Group Fortran compiler with the OpenACC compiler directives and Fortran CUDA. Mixed implementation of both Open-ACC and CUDA is demonstrated. CUDA is required for optimizing the particle deposition algorithm. We have implemented the GPU acceleration on a third generation Core I7 gaming PC with two NVIDIA GTX 680 GPUs. We find comparable, or better, acceleration relative to the NERSC DIRAC cluster with the NVIDIA Tesla C2050 computing processor. The Tesla C 2050 is about 2.6 times more expensive than the GTX 580 gaming GPU. We also see enormous speedups (10 or more) on the Titan supercomputer at Oak Ridge with Kepler K20 GPUs. Results show speed-ups comparable or better than that of OpenMP models utilizing multiple cores. The use of hybrid OpenACC, CUDA Fortran, and MPI models across many nodes will also be discussed. Optimization strategies will be presented. We will discuss progress on optimizing the comprehensive three dimensional general geometry GEM code.

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem: Mid-year report FY17 Q2

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

Moreland, Kenneth D.; Pugmire, David; Rogers, David

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressingmore » four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.« less

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem: Year-end report FY17.

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

Moreland, Kenneth D.; Pugmire, David; Rogers, David

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressingmore » four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.« less

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem. Mid-year report FY16 Q2

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

Moreland, Kenneth D.; Sewell, Christopher; Childs, Hank

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressingmore » four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.« less

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem: Year-end report FY15 Q4.

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

Moreland, Kenneth D.; Sewell, Christopher; Childs, Hank

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressingmore » four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.« less

Scientific Services on the Cloud

NASA Astrophysics Data System (ADS)

Chapman, David; Joshi, Karuna P.; Yesha, Yelena; Halem, Milt; Yesha, Yaacov; Nguyen, Phuong

Scientific Computing was one of the first every applications for parallel and distributed computation. To this date, scientific applications remain some of the most compute intensive, and have inspired creation of petaflop compute infrastructure such as the Oak Ridge Jaguar and Los Alamos RoadRunner. Large dedicated hardware infrastructure has become both a blessing and a curse to the scientific community. Scientists are interested in cloud computing for much the same reason as businesses and other professionals. The hardware is provided, maintained, and administrated by a third party. Software abstraction and virtualization provide reliability, and fault tolerance. Graduated fees allow for multi-scale prototyping and execution. Cloud computing resources are only a few clicks away, and by far the easiest high performance distributed platform to gain access to. There may still be dedicated infrastructure for ultra-scale science, but the cloud can easily play a major part of the scientific computing initiative.

Center for Center for Technology for Advanced Scientific Component Software (TASCS)

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

Kostadin, Damevski

A resounding success of the Scientific Discovery through Advanced Computing (SciDAC) program is that high-performance computational science is now universally recognized as a critical aspect of scientific discovery [71], complementing both theoretical and experimental research. As scientific communities prepare to exploit unprecedented computing capabilities of emerging leadership-class machines for multi-model simulations at the extreme scale [72], it is more important than ever to address the technical and social challenges of geographically distributed teams that combine expertise in domain science, applied mathematics, and computer science to build robust and flexible codes that can incorporate changes over time. The Center for Technologymore » for Advanced Scientific Component Software (TASCS)1 tackles these these issues by exploiting component-based software development to facilitate collaborative high-performance scientific computing.« less

XVIS: Visualization for the Extreme-Scale Scientific-Computation Ecosystem Final Scientific/Technical Report

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

Geveci, Berk; Maynard, Robert

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. The XVis project brought together collaborators from predominant DOE projects for visualization on accelerators and combining their respectivemore » features into a new visualization toolkit called VTK-m.« less

Joint the Center for Applied Scientific Computing

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

Gamblin, Todd; Bremer, Timo; Van Essen, Brian

The Center for Applied Scientific Computing serves as Livermore Lab’s window to the broader computer science, computational physics, applied mathematics, and data science research communities. In collaboration with academic, industrial, and other government laboratory partners, we conduct world-class scientific research and development on problems critical to national security. CASC applies the power of high-performance computing and the efficiency of modern computational methods to the realms of stockpile stewardship, cyber and energy security, and knowledge discovery for intelligence applications.

78 FR 41046 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-09

... Services Administration, notice is hereby given that the Advanced Scientific Computing Advisory Committee will be renewed for a two-year period beginning on July 1, 2013. The Committee will provide advice to the Director, Office of Science (DOE), on the Advanced Scientific Computing Research Program managed...

Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture

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

Shan, Hongzhang; Williams, Samuel; Jong, Wibe de

In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments.more » In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in tt native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant effort was required to safely and efficiently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI OpenMP hybrid implementations attain up to 65x better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6x better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.« less

Thread-level parallelization and optimization of NWChem for the Intel MIC architecture

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

Shan, Hongzhang; Williams, Samuel; de Jong, Wibe

In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments.more » In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant e ort was required to safely and efeciently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI+OpenMP hybrid implementations attain up to 65× better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6× better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.« less

Whole earth modeling: developing and disseminating scientific software for computational geophysics.

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

Historically, a great deal of specialized scientific software for modeling and data analysis has been developed by individual researchers or small groups of scientists working on their own specific research problems. As the magnitude of available data and computer power has increased, so has the complexity of scientific problems addressed by computational methods, creating both a need to sustain existing scientific software, and expand its development to take advantage of new algorithms, new software approaches, and new computational hardware. To that end, communities like the Computational Infrastructure for Geodynamics (CIG) have been established to support the use of best practices in scientific computing for solid earth geophysics research and teaching. Working as a scientific community enables computational geophysicists to take advantage of technological developments, improve the accuracy and performance of software, build on prior software development, and collaborate more readily. The CIG community, and others, have adopted an open-source development model, in which code is developed and disseminated by the community in an open fashion, using version control and software repositories like Git. One emerging issue is how to adequately identify and credit the intellectual contributions involved in creating open source scientific software. The traditional method of disseminating scientific ideas, peer reviewed publication, was not designed for review or crediting scientific software, although emerging publication strategies such software journals are attempting to address the need. We are piloting an integrated approach in which authors are identified and credited as scientific software is developed and run. Successful software citation requires integration with the scholarly publication and indexing mechanisms as well, to assign credit, ensure discoverability, and provide provenance for software.

Integrating Data Base into the Elementary School Science Program.

ERIC Educational Resources Information Center

Schlenker, Richard M.

This document describes seven science activities that combine scientific principles and computers. The objectives for the activities are to show students how the computer can be used as a tool to store and arrange scientific data, provide students with experience using the computer as a tool to manage scientific data, and provide students with…

A high performance scientific cloud computing environment for materials simulations

NASA Astrophysics Data System (ADS)

Jorissen, K.; Vila, F. D.; Rehr, J. J.

2012-09-01

We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials science codes, together with essential interface tools (an SCC toolset) that offers functionality comparable to local compute clusters. In particular, our SCC toolset provides automatic creation of virtual clusters for parallel computing, including tools for execution and monitoring performance, as well as efficient I/O utilities that enable seamless connections to and from the cloud. Our SCC platform is optimized for the Amazon Elastic Compute Cloud (EC2). We present benchmarks for prototypical scientific applications and demonstrate performance comparable to local compute clusters. To facilitate code execution and provide user-friendly access, we have also integrated cloud computing capability in a JAVA-based GUI. Our SCC platform may be an alternative to traditional HPC resources for materials science or quantum chemistry applications.

Constructing Scientific Arguments Using Evidence from Dynamic Computational Climate Models

ERIC Educational Resources Information Center

Pallant, Amy; Lee, Hee-Sun

2015-01-01

Modeling and argumentation are two important scientific practices students need to develop throughout school years. In this paper, we investigated how middle and high school students (N = 512) construct a scientific argument based on evidence from computational models with which they simulated climate change. We designed scientific argumentation…

Highly Efficient Parallel Multigrid Solver For Large-Scale Simulation of Grain Growth Using the Structural Phase Field Crystal Model

NASA Astrophysics Data System (ADS)

Guan, Zhen; Pekurovsky, Dmitry; Luce, Jason; Thornton, Katsuyo; Lowengrub, John

The structural phase field crystal (XPFC) model can be used to model grain growth in polycrystalline materials at diffusive time-scales while maintaining atomic scale resolution. However, the governing equation of the XPFC model is an integral-partial-differential-equation (IPDE), which poses challenges in implementation onto high performance computing (HPC) platforms. In collaboration with the XSEDE Extended Collaborative Support Service, we developed a distributed memory HPC solver for the XPFC model, which combines parallel multigrid and P3DFFT. The performance benchmarking on the Stampede supercomputer indicates near linear strong and weak scaling for both multigrid and transfer time between multigrid and FFT modules up to 1024 cores. Scalability of the FFT module begins to decline at 128 cores, but it is sufficient for the type of problem we will be examining. We have demonstrated simulations using 1024 cores, and we expect to achieve 4096 cores and beyond. Ongoing work involves optimization of MPI/OpenMP-based codes for the Intel KNL Many-Core Architecture. This optimizes the code for coming pre-exascale systems, in particular many-core systems such as Stampede 2.0 and Cori 2 at NERSC, without sacrificing efficiency on other general HPC systems.

Simulations of laser-driven ion acceleration from a thin CH target

NASA Astrophysics Data System (ADS)

Park, Jaehong; Bulanov, Stepan; Ji, Qing; Steinke, Sven; Treffert, Franziska; Vay, Jean-Luc; Schenkel, Thomas; Esarey, Eric; Leemans, Wim; Vincenti, Henri

2017-10-01

2D and 3D computer simulations of laser driven ion acceleration from a thin CH foil using code WARP were performed. As the foil thickness varies from a few nm to μm, the simulations confirm that the acceleration mechanism transitions from the RPA (radiation pressure acceleration) to the TNSA (target normal sheath acceleration). In the TNSA regime, with the CH target thickness of 1 μ m and a pre-plasma ahead of the target, the simulations show the production of the collimated proton beam with the maximum energy of about 10 MeV. This agrees with the experimental results obtained at the BELLA laser facility (I 5 × 18 W / cm2 , λ = 800 nm). Furthermore, the maximum proton energy dependence on different setups of the initialization, i.e., different angles of the laser incidence from the target normal axis, different gradient scales and distributions of the pre-plasma, was explored. This work was supported by LDRD funding from LBNL, provided by the U.S. DOE under Contract No. DE-AC02-05CH11231, and used resources of the NERSC, a DOE office of Science User Facility supported by the U.S. DOE under Contract No. DE-AC02-05CH11231.

Understanding the spin-driven polarizations in Bi MO3 (M = 3 d transition metals) multiferroics

NASA Astrophysics Data System (ADS)

Kc, Santosh; Lee, Jun Hee; Cooper, Valentino R.

Bismuth ferrite (BiFeO3) , a promising multiferroic, stabilizes in a perovskite type rhombohedral crystal structure (space group R3c) at room temperature. Recently, it has been reported that in its ground state it possess a huge spin-driven polarization. To probe the underlying mechanism of this large spin-phonon response, we examine these couplings within other Bi based 3 d transition metal oxides Bi MO3 (M = Ti, V, Cr, Mn, Fe, Co, Ni) using density functional theory. Our results demonstrate that this large spin-driven polarization is a consequence of symmetry breaking due to competition between ferroelectric distortions and anti-ferrodistortive octahedral rotations. Furthermore, we find a strong dependence of these enhanced spin-driven polarizations on the crystal structure; with the rhombohedral phase having the largest spin-induced atomic distortions along [111]. These results give us significant insights into the magneto-electric coupling in these materials which is essential to the magnetic and electric field control of electric polarization and magnetization in multiferroic based devices. Research is supported by the US Department of Energy, Office of Science, Basic Energy Sciences, Materials Science and Engineering Division and the Office of Science Early Career Research Program (V.R.C) and used computational resources at NERSC.

Parallel processing for scientific computations

NASA Technical Reports Server (NTRS)

Alkhatib, Hasan S.

1995-01-01

The scope of this project dealt with the investigation of the requirements to support distributed computing of scientific computations over a cluster of cooperative workstations. Various experiments on computations for the solution of simultaneous linear equations were performed in the early phase of the project to gain experience in the general nature and requirements of scientific applications. A specification of a distributed integrated computing environment, DICE, based on a distributed shared memory communication paradigm has been developed and evaluated. The distributed shared memory model facilitates porting existing parallel algorithms that have been designed for shared memory multiprocessor systems to the new environment. The potential of this new environment is to provide supercomputing capability through the utilization of the aggregate power of workstations cooperating in a cluster interconnected via a local area network. Workstations, generally, do not have the computing power to tackle complex scientific applications, making them primarily useful for visualization, data reduction, and filtering as far as complex scientific applications are concerned. There is a tremendous amount of computing power that is left unused in a network of workstations. Very often a workstation is simply sitting idle on a desk. A set of tools can be developed to take advantage of this potential computing power to create a platform suitable for large scientific computations. The integration of several workstations into a logical cluster of distributed, cooperative, computing stations presents an alternative to shared memory multiprocessor systems. In this project we designed and evaluated such a system.

Introduction to the LaRC central scientific computing complex

NASA Technical Reports Server (NTRS)

Shoosmith, John N.

1993-01-01

The computers and associated equipment that make up the Central Scientific Computing Complex of the Langley Research Center are briefly described. The electronic networks that provide access to the various components of the complex and a number of areas that can be used by Langley and contractors staff for special applications (scientific visualization, image processing, software engineering, and grid generation) are also described. Flight simulation facilities that use the central computers are described. Management of the complex, procedures for its use, and available services and resources are discussed. This document is intended for new users of the complex, for current users who wish to keep appraised of changes, and for visitors who need to understand the role of central scientific computers at Langley.

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

Scientific Computing Paradigm

NASA Technical Reports Server (NTRS)

VanZandt, John

1994-01-01

The usage model of supercomputers for scientific applications, such as computational fluid dynamics (CFD), has changed over the years. Scientific visualization has moved scientists away from looking at numbers to looking at three-dimensional images, which capture the meaning of the data. This change has impacted the system models for computing. This report details the model which is used by scientists at NASA's research centers.

Commentary: Considerations in Pedagogy and Assessment in the Use of Computers to Promote Learning about Scientific Models

ERIC Educational Resources Information Center

Adams, Stephen T.

2004-01-01

Although one role of computers in science education is to help students learn specific science concepts, computers are especially intriguing as a vehicle for fostering the development of epistemological knowledge about the nature of scientific knowledge--what it means to "know" in a scientific sense (diSessa, 1985). In this vein, the…

High-End Scientific Computing

EPA Pesticide Factsheets

EPA uses high-end scientific computing, geospatial services and remote sensing/imagery analysis to support EPA's mission. The Center for Environmental Computing (CEC) assists the Agency's program offices and regions to meet staff needs in these areas.

Using the High-Level Based Program Interface to Facilitate the Large Scale Scientific Computing

PubMed Central

Shang, Yizi; Shang, Ling; Gao, Chuanchang; Lu, Guiming; Ye, Yuntao; Jia, Dongdong

2014-01-01

This paper is to make further research on facilitating the large-scale scientific computing on the grid and the desktop grid platform. The related issues include the programming method, the overhead of the high-level program interface based middleware, and the data anticipate migration. The block based Gauss Jordan algorithm as a real example of large-scale scientific computing is used to evaluate those issues presented above. The results show that the high-level based program interface makes the complex scientific applications on large-scale scientific platform easier, though a little overhead is unavoidable. Also, the data anticipation migration mechanism can improve the efficiency of the platform which needs to process big data based scientific applications. PMID:24574931

Defining Computational Thinking for Mathematics and Science Classrooms

ERIC Educational Resources Information Center

Weintrop, David; Beheshti, Elham; Horn, Michael; Orton, Kai; Jona, Kemi; Trouille, Laura; Wilensky, Uri

2016-01-01

Science and mathematics are becoming computational endeavors. This fact is reflected in the recently released Next Generation Science Standards and the decision to include "computational thinking" as a core scientific practice. With this addition, and the increased presence of computation in mathematics and scientific contexts, a new…

Ermittlung von Wortstaemmen in russischen wissenschaftlichen Fachsprachen mit Hilfe des Computers (Establishing Word Stems in Scientific Russian With the Aid of a Computer)

ERIC Educational Resources Information Center

Halbauer, Siegfried

1976-01-01

It was considered that students of intensive scientific Russian courses could learn vocabulary more efficiently if they were taught word stems and how to combine them with prefixes and suffixes to form scientific words. The computer programs developed to identify the most important stems is discussed. (Text is in German.) (FB)

Scientific Visualization: The Modern Oscilloscope for "Seeing the Unseeable" (LBNL Summer Lecture Series)

ScienceCinema

Bethel, E. Wes [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division and Scientific Visualization Group

2018-05-07

Summer Lecture Series 2008: Scientific visualization transforms abstract data into readily comprehensible images, provide a vehicle for "seeing the unseeable," and play a central role in both experimental and computational sciences. Wes Bethel, who heads the Scientific Visualization Group in the Computational Research Division, presents an overview of visualization and computer graphics, current research challenges, and future directions for the field.

Scientific Visualization, Seeing the Unseeable

ScienceCinema

LBNL

2017-12-09

June 24, 2008 Berkeley Lab lecture: Scientific visualization transforms abstract data into readily comprehensible images, provide a vehicle for "seeing the unseeable," and play a central role in bo... June 24, 2008 Berkeley Lab lecture: Scientific visualization transforms abstract data into readily comprehensible images, provide a vehicle for "seeing the unseeable," and play a central role in both experimental and computational sciences. Wes Bethel, who heads the Scientific Visualization Group in the Computational Research Division, presents an overview of visualization and computer graphics, current research challenges, and future directions for the field.

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

Parallel computing works

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

Not Available

An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of manymore » computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.« less

Exploring Cloud Computing for Large-scale Scientific Applications

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

Lin, Guang; Han, Binh; Yin, Jian

This paper explores cloud computing for large-scale data-intensive scientific applications. Cloud computing is attractive because it provides hardware and software resources on-demand, which relieves the burden of acquiring and maintaining a huge amount of resources that may be used only once by a scientific application. However, unlike typical commercial applications that often just requires a moderate amount of ordinary resources, large-scale scientific applications often need to process enormous amount of data in the terabyte or even petabyte range and require special high performance hardware with low latency connections to complete computation in a reasonable amount of time. To address thesemore » challenges, we build an infrastructure that can dynamically select high performance computing hardware across institutions and dynamically adapt the computation to the selected resources to achieve high performance. We have also demonstrated the effectiveness of our infrastructure by building a system biology application and an uncertainty quantification application for carbon sequestration, which can efficiently utilize data and computation resources across several institutions.« less

An Overview of the Computational Physics and Methods Group at Los Alamos National Laboratory

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

Baker, Randal Scott

CCS Division was formed to strengthen the visibility and impact of computer science and computational physics research on strategic directions for the Laboratory. Both computer science and computational science are now central to scientific discovery and innovation. They have become indispensable tools for all other scientific missions at the Laboratory. CCS Division forms a bridge between external partners and Laboratory programs, bringing new ideas and technologies to bear on today’s important problems and attracting high-quality technical staff members to the Laboratory. The Computational Physics and Methods Group CCS-2 conducts methods research and develops scientific software aimed at the latest andmore » emerging HPC systems.« less

[Earth Science Technology Office's Computational Technologies Project

NASA Technical Reports Server (NTRS)

Fischer, James (Technical Monitor); Merkey, Phillip

2005-01-01

This grant supported the effort to characterize the problem domain of the Earth Science Technology Office's Computational Technologies Project, to engage the Beowulf Cluster Computing Community as well as the High Performance Computing Research Community so that we can predict the applicability of said technologies to the scientific community represented by the CT project and formulate long term strategies to provide the computational resources necessary to attain the anticipated scientific objectives of the CT project. Specifically, the goal of the evaluation effort is to use the information gathered over the course of the Round-3 investigations to quantify the trends in scientific expectations, the algorithmic requirements and capabilities of high-performance computers to satisfy this anticipated need.

Computers and Computation. Readings from Scientific American.

ERIC Educational Resources Information Center

Fenichel, Robert R.; Weizenbaum, Joseph

A collection of articles from "Scientific American" magazine has been put together at this time because the current period in computer science is one of consolidation rather than innovation. A few years ago, computer science was moving so swiftly that even the professional journals were more archival than informative; but today it is…

Using OFI libfabric on Cori/Edison

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

Pritchard, Howard Porter; Choi, Sung-Eun

2016-08-22

These are slides from a presentation during an NERSC site visit to Los Alamos National Laboratory. The following topics are covered: building/installing libfabric, OpenMPI using libfabric, MPICH using libfabric, Open SHMEM (Sandia), other applications, and what is next. The next steps are: get a libfabric 1.4 out, it would be nice to have libfabric 1.4 installed in system space on Cori, add libfabric modules on Cori, might be a good idea to have a SLURM PMI module to simplify its use when building/using Open MPI and MPICH built to use libfabric, and upgrade Edison to CLE 5.2 UP04 or newer.

Preface: SciDAC 2008

NASA Astrophysics Data System (ADS)

Stevens, Rick

2008-07-01

The fourth annual Scientific Discovery through Advanced Computing (SciDAC) Conference was held June 13-18, 2008, in Seattle, Washington. The SciDAC conference series is the premier communitywide venue for presentation of results from the DOE Office of Science's interdisciplinary computational science program. Started in 2001 and renewed in 2006, the DOE SciDAC program is the country's - and arguably the world's - most significant interdisciplinary research program supporting the development of advanced scientific computing methods and their application to fundamental and applied areas of science. SciDAC supports computational science across many disciplines, including astrophysics, biology, chemistry, fusion sciences, and nuclear physics. Moreover, the program actively encourages the creation of long-term partnerships among scientists focused on challenging problems and computer scientists and applied mathematicians developing the technology and tools needed to address those problems. The SciDAC program has played an increasingly important role in scientific research by allowing scientists to create more accurate models of complex processes, simulate problems once thought to be impossible, and analyze the growing amount of data generated by experiments. To help further the research community's ability to tap into the capabilities of current and future supercomputers, Under Secretary for Science, Raymond Orbach, launched the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program in 2003. The INCITE program was conceived specifically to seek out computationally intensive, large-scale research projects with the potential to significantly advance key areas in science and engineering. The program encourages proposals from universities, other research institutions, and industry. During the first two years of the INCITE program, 10 percent of the resources at NERSC were allocated to INCITE awardees. However, demand for supercomputing resources far exceeded available systems; and in 2003, the Office of Science identified increasing computing capability by a factor of 100 as the second priority on its Facilities of the Future list. The goal was to establish leadership-class computing resources to support open science. As a result of a peer reviewed competition, the first leadership computing facility was established at Oak Ridge National Laboratory in 2004. A second leadership computing facility was established at Argonne National Laboratory in 2006. This expansion of computational resources led to a corresponding expansion of the INCITE program. In 2008, Argonne, Lawrence Berkeley, Oak Ridge, and Pacific Northwest national laboratories all provided resources for INCITE. By awarding large blocks of computer time on the DOE leadership computing facilities, the INCITE program enables the largest-scale computations to be pursued. In 2009, INCITE will award over half a billion node-hours of time. The SciDAC conference celebrates progress in advancing science through large-scale modeling and simulation. Over 350 participants attended this year's talks, poster sessions, and tutorials, spanning the disciplines supported by DOE. While the principal focus was on SciDAC accomplishments, this year's conference also included invited presentations and posters from DOE INCITE awardees. Another new feature in the SciDAC conference series was an electronic theater and video poster session, which provided an opportunity for the community to see over 50 scientific visualizations in a venue equipped with many high-resolution large-format displays. To highlight the growing international interest in petascale computing, this year's SciDAC conference included a keynote presentation by Herman Lederer from the Max Planck Institut, one of the leaders of DEISA (Distributed European Infrastructure for Supercomputing Applications) project and a member of the PRACE consortium, Europe's main petascale project. We also heard excellent talks from several European groups, including Laurent Gicquel of CERFACS, who spoke on `Large-Eddy Simulations of Turbulent Reacting Flows of Real Burners: Status and Challenges', and Jean-Francois Hamelin from EDF, who presented a talk on `Getting Ready for Petaflop Capacities and Beyond: A Utility Perspective'. Two other compelling addresses gave attendees a glimpse into the future. Tomas Diaz de la Rubia of Lawrence Livermore National Laboratory spoke on a vision for a fusion/fission hybrid reactor known as the `LIFE Engine' and discussed some of the materials and modeling challenges that need to be overcome to realize the vision for a 1000-year greenhouse-gas-free power source. Dan Reed from Microsoft gave a capstone talk on the convergence of technology, architecture, and infrastructure for cloud computing, data-intensive computing, and exascale computing (1018 flops/sec). High-performance computing is making rapid strides. The SciDAC community's computational resources are expanding dramatically. In the summer of 2008 the first general purpose petascale system (IBM Cell-based RoadRunner at Los Alamos National Laboratory) was recognized in the top 500 list of fastest machines heralding in the dawning of the petascale era. The DOE's leadership computing facility at Argonne reached number three on the Top 500 and is at the moment the most capable open science machine based on an IBM BG/P system with a peak performance of over 550 teraflops/sec. Later this year Oak Ridge is expected to deploy a 1 petaflops/sec Cray XT system. And even before the scientific community has had an opportunity to make significant use of petascale systems, the computer science research community is forging ahead with ideas and strategies for development of systems that may by the end of the next decade sustain exascale performance. Several talks addressed barriers to, and strategies for, achieving exascale capabilities. The last day of the conference was devoted to tutorials hosted by Microsoft Research at a new conference facility in Redmond, Washington. Over 90 people attended the tutorials, which covered topics ranging from an introduction to BG/P programming to advanced numerical libraries. The SciDAC and INCITE programs and the DOE Office of Advanced Scientific Computing Research core program investments in applied mathematics, computer science, and computational and networking facilities provide a nearly optimum framework for advancing computational science for DOE's Office of Science. At a broader level this framework also is benefiting the entire American scientific enterprise. As we look forward, it is clear that computational approaches will play an increasingly significant role in addressing challenging problems in basic science, energy, and environmental research. It takes many people to organize and support the SciDAC conference, and I would like to thank as many of them as possible. The backbone of the conference is the technical program; and the task of selecting, vetting, and recruiting speakers is the job of the organizing committee. I thank the members of this committee for all the hard work and the many tens of conference calls that enabled a wonderful program to be assembled. This year the following people served on the organizing committee: Jim Ahrens, LANL; David Bader, LLNL; Bryan Barnett, Microsoft; Peter Beckman, ANL; Vincent Chan, GA; Jackie Chen, SNL; Lori Diachin, LLNL; Dan Fay, Microsoft; Ian Foster, ANL; Mark Gordon, Ames; Mohammad Khaleel, PNNL; David Keyes, Columbia University; Bob Lucas, University of Southern California; Tony Mezzacappa, ORNL; Jeff Nichols, ORNL; David Nowak, ANL; Michael Papka, ANL; Thomas Schultess, ORNL; Horst Simon, LBNL; David Skinner, LBNL; Panagiotis Spentzouris, Fermilab; Bob Sugar, UCSB; and Kathy Yelick, LBNL. I owe a special thanks to Mike Papka and Jim Ahrens for handling the electronic theater. I also thank all those who submitted videos. It was a highly successful experiment. Behind the scenes an enormous amount of work is required to make a large conference go smoothly. First I thank Cheryl Zidel for her tireless efforts as organizing committee liaison and posters chair and, in general, handling all of my end of the program and keeping me calm. I also thank Gail Pieper for her work in editing the proceedings, Beth Cerny Patino for her work on the Organizing Committee website and electronic theater, and Ken Raffenetti for his work in keeping that website working. Jon Bashor and John Hules did an excellent job in handling conference communications. I thank Caitlin Youngquist for the striking graphic design; Dan Fay for tutorials arrangements; and Lynn Dory, Suzanne Stevenson, Sarah Pebelske and Sarah Zidel for on-site registration and conference support. We all owe Yeen Mankin an extra-special thanks for choosing the hotel, handling contracts, arranging menus, securing venues, and reassuring the chair that everything was under control. We are pleased to have obtained corporate sponsorship from Cray, IBM, Intel, HP, and SiCortex. I thank all the speakers and panel presenters. I also thank the former conference chairs Tony Metzzacappa, Bill Tang, and David Keyes, who were never far away for advice and encouragement. Finally, I offer my thanks to Michael Strayer, without whose leadership, vision, and persistence the SciDAC program would not have come into being and flourished. I am honored to be part of his program and his friend. Rick Stevens Seattle, Washington July 18, 2008

Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

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

Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.

2014-07-03

Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinitiesmore » and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL.« less

Scientific Inquiry Self-Efficacy and Computer Game Self-Efficacy as Predictors and Outcomes of Middle School Boys' and Girls' Performance in a Science Assessment in a Virtual Environment

NASA Astrophysics Data System (ADS)

Bergey, Bradley W.; Ketelhut, Diane Jass; Liang, Senfeng; Natarajan, Uma; Karakus, Melissa

2015-10-01

The primary aim of the study was to examine whether performance on a science assessment in an immersive virtual environment was associated with changes in scientific inquiry self-efficacy. A secondary aim of the study was to examine whether performance on the science assessment was equitable for students with different levels of computer game self-efficacy, including whether gender differences were observed. We examined 407 middle school students' scientific inquiry self-efficacy and computer game self-efficacy before and after completing a computer game-like assessment about a science mystery. Results from path analyses indicated that prior scientific inquiry self-efficacy predicted achievement on end-of-module questions, which in turn predicted change in scientific inquiry self-efficacy. By contrast, computer game self-efficacy was neither predictive of nor predicted by performance on the science assessment. While boys had higher computer game self-efficacy compared to girls, multi-group analyses suggested only minor gender differences in how efficacy beliefs related to performance. Implications for assessments with virtual environments and future design and research are discussed.

Exploring Electric Polarization Mechanisms in Multiferroic Oxides

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

Tyson, Trevor A.

2017-01-24

Multiferroic oxides are a class of systems which exhibit coupling between the electrical polarization and the magnetization. These materials show promise to lead to devices in which ferromagnetic memory can be written with magnetic fields or magnetic bits can be written by an electric field. The work conducted in our research focuses on single phase materials. We studied the detailed coupling of the spin and lattice correlations in these systems. In the first phase of the proposal, we explored the complex spin spiral systems and low temperature behavior of hexagonal layered REMnO 3 (RE= rare earth, Y and Sc) systemmore » following the detailed structural changes which occurred on crossing into the magnetic states. The techniques were applied to other layered materials such as superconductors and thermoelectric where the same layered motif exists. The second phase of the proposal focused on understanding the mechanisms involved in the onset high temperature ferroelectricity ion hexagonal REMnO 3 and at low temperature in E-Type magnetic ordered perovskite REMnO 3. We wsynthesized preovskite small A site multiferroics by high pressure and high temperature methods. Detailed measurement of the structural properties and dynamics were conducted over a range of length scales from atomic to mesoscopic scale using, x-ray absorption spectroscopy, x-ray diffuse scattering, x-ray and neutron pair distribution analysis and high resolution x-ray diffraction. Changes in vibration modes which occur with the onset of polarization were probed with temperature and pressure dependent infrared absorption spectroscopy. In addition the orthorhombic system (small radius RE ions) which is believed to exhibit electronically driven ferroelectricity and is also not understood was examined. The multiple length scale synchrotron based measurements may assist in developing more detailed models of these materials and possibly lead to device applications. The experimental work was complemented by density functional methods to determine the magnetic ground states and ab initio molecular dynamics methods (AIMD) to determine the high temperature structures. Simulation were carried out on supercomputers at the National Energy Research Scientific Computing Center (NERSC). An important contribution of this work was the training of graduate students and postdoctoral researchers in materials synthesis, high pressure methods and synchrotron based spectroscopy and x-ray scattering techniques.« less

Hypergraph-Based Combinatorial Optimization of Matrix-Vector Multiplication

ERIC Educational Resources Information Center

Wolf, Michael Maclean

2009-01-01

Combinatorial scientific computing plays an important enabling role in computational science, particularly in high performance scientific computing. In this thesis, we will describe our work on optimizing matrix-vector multiplication using combinatorial techniques. Our research has focused on two different problems in combinatorial scientific…

The Versatile Terminal.

ERIC Educational Resources Information Center

Evans, C. D.

This paper describes the experiences of the industrial research laboratory of Kodak Ltd. in finding and providing a computer terminal most suited to its very varied requirements. These requirements include bibliographic and scientific data searching and access to a number of worldwide computing services for scientific computing work. The provision…

Amplify scientific discovery with artificial intelligence

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

Gil, Yolanda; Greaves, Mark T.; Hendler, James

Computing innovations have fundamentally changed many aspects of scientific inquiry. For example, advances in robotics, high-end computing, networking, and databases now underlie much of what we do in science such as gene sequencing, general number crunching, sharing information between scientists, and analyzing large amounts of data. As computing has evolved at a rapid pace, so too has its impact in science, with the most recent computing innovations repeatedly being brought to bear to facilitate new forms of inquiry. Recently, advances in Artificial Intelligence (AI) have deeply penetrated many consumer sectors, including for example Apple’s Siri™ speech recognition system, real-time automatedmore » language translation services, and a new generation of self-driving cars and self-navigating drones. However, AI has yet to achieve comparable levels of penetration in scientific inquiry, despite its tremendous potential in aiding computers to help scientists tackle tasks that require scientific reasoning. We contend that advances in AI will transform the practice of science as we are increasingly able to effectively and jointly harness human and machine intelligence in the pursuit of major scientific challenges.« less

A distributed computing environment with support for constraint-based task scheduling and scientific experimentation

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

Ahrens, J.P.; Shapiro, L.G.; Tanimoto, S.L.

1997-04-01

This paper describes a computing environment which supports computer-based scientific research work. Key features include support for automatic distributed scheduling and execution and computer-based scientific experimentation. A new flexible and extensible scheduling technique that is responsive to a user`s scheduling constraints, such as the ordering of program results and the specification of task assignments and processor utilization levels, is presented. An easy-to-use constraint language for specifying scheduling constraints, based on the relational database query language SQL, is described along with a search-based algorithm for fulfilling these constraints. A set of performance studies show that the environment can schedule and executemore » program graphs on a network of workstations as the user requests. A method for automatically generating computer-based scientific experiments is described. Experiments provide a concise method of specifying a large collection of parameterized program executions. The environment achieved significant speedups when executing experiments; for a large collection of scientific experiments an average speedup of 3.4 on an average of 5.5 scheduled processors was obtained.« less

Computer-Supported Aids to Making Sense of Scientific Articles: Cognitive, Motivational, and Attitudinal Effects

ERIC Educational Resources Information Center

Gegner, Julie A.; Mackay, Donald H. J.; Mayer, Richard E.

2009-01-01

High school students can access original scientific research articles on the Internet, but may have trouble understanding them. To address this problem of online literacy, the authors developed a computer-based prototype for guiding students' comprehension of scientific articles. High school students were asked to read an original scientific…

Scientific Computing for Chemists: An Undergraduate Course in Simulations, Data Processing, and Visualization

ERIC Educational Resources Information Center

Weiss, Charles J.

2017-01-01

The Scientific Computing for Chemists course taught at Wabash College teaches chemistry students to use the Python programming language, Jupyter notebooks, and a number of common Python scientific libraries to process, analyze, and visualize data. Assuming no prior programming experience, the course introduces students to basic programming and…

Computational chemistry in pharmaceutical research: at the crossroads.

PubMed

Bajorath, Jürgen

2012-01-01

Computational approaches are an integral part of pharmaceutical research. However, there are many of unsolved key questions that limit the scientific progress in the still evolving computational field and its impact on drug discovery. Importantly, a number of these questions are not new but date back many years. Hence, it might be difficult to conclusively answer them in the foreseeable future. Moreover, the computational field as a whole is characterized by a high degree of heterogeneity and so is, unfortunately, the quality of its scientific output. In light of this situation, it is proposed that changes in scientific standards and culture should be seriously considered now in order to lay a foundation for future progress in computational research.

[Earth and Space Sciences Project Services for NASA HPCC

NASA Technical Reports Server (NTRS)

Merkey, Phillip

2002-01-01

This grant supported the effort to characterize the problem domain of the Earth Science Technology Office's Computational Technologies Project, to engage the Beowulf Cluster Computing Community as well as the High Performance Computing Research Community so that we can predict the applicability of said technologies to the scientific community represented by the CT project and formulate long term strategies to provide the computational resources necessary to attain the anticipated scientific objectives of the CT project. Specifically, the goal of the evaluation effort is to use the information gathered over the course of the Round-3 investigations to quantify the trends in scientific expectations, the algorithmic requirements and capabilities of high-performance computers to satisfy this anticipated need.

Scholarly literature and the press: scientific impact and social perception of physics computing

NASA Astrophysics Data System (ADS)

Pia, M. G.; Basaglia, T.; Bell, Z. W.; Dressendorfer, P. V.

2014-06-01

The broad coverage of the search for the Higgs boson in the mainstream media is a relative novelty for high energy physics (HEP) research, whose achievements have traditionally been limited to scholarly literature. This paper illustrates the results of a scientometric analysis of HEP computing in scientific literature, institutional media and the press, and a comparative overview of similar metrics concerning representative particle physics measurements. The picture emerging from these scientometric data documents the relationship between the scientific impact and the social perception of HEP physics research versus that of HEP computing. The results of this analysis suggest that improved communication of the scientific and social role of HEP computing via press releases from the major HEP laboratories would be beneficial to the high energy physics community.

Software Reuse Methods to Improve Technological Infrastructure for e-Science

NASA Technical Reports Server (NTRS)

Marshall, James J.; Downs, Robert R.; Mattmann, Chris A.

2011-01-01

Social computing has the potential to contribute to scientific research. Ongoing developments in information and communications technology improve capabilities for enabling scientific research, including research fostered by social computing capabilities. The recent emergence of e-Science practices has demonstrated the benefits from improvements in the technological infrastructure, or cyber-infrastructure, that has been developed to support science. Cloud computing is one example of this e-Science trend. Our own work in the area of software reuse offers methods that can be used to improve new technological development, including cloud computing capabilities, to support scientific research practices. In this paper, we focus on software reuse and its potential to contribute to the development and evaluation of information systems and related services designed to support new capabilities for conducting scientific research.

Multidimensional Environmental Data Resource Brokering on Computational Grids and Scientific Clouds

NASA Astrophysics Data System (ADS)

Montella, Raffaele; Giunta, Giulio; Laccetti, Giuliano

Grid computing has widely evolved over the past years, and its capabilities have found their way even into business products and are no longer relegated to scientific applications. Today, grid computing technology is not restricted to a set of specific grid open source or industrial products, but rather it is comprised of a set of capabilities virtually within any kind of software to create shared and highly collaborative production environments. These environments are focused on computational (workload) capabilities and the integration of information (data) into those computational capabilities. An active grid computing application field is the fully virtualization of scientific instruments in order to increase their availability and decrease operational and maintaining costs. Computational and information grids allow to manage real-world objects in a service-oriented way using industrial world-spread standards.

78 FR 6087 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-29

... INFORMATION CONTACT: Melea Baker, Office of Advanced Scientific Computing Research; SC-21/Germantown Building... Theory and Experiment (INCITE) Public Comment (10-minute rule) Public Participation: The meeting is open...

Computational Science in Armenia (Invited Talk)

NASA Astrophysics Data System (ADS)

Marandjian, H.; Shoukourian, Yu.

This survey is devoted to the development of informatics and computer science in Armenia. The results in theoretical computer science (algebraic models, solutions to systems of general form recursive equations, the methods of coding theory, pattern recognition and image processing), constitute the theoretical basis for developing problem-solving-oriented environments. As examples can be mentioned: a synthesizer of optimized distributed recursive programs, software tools for cluster-oriented implementations of two-dimensional cellular automata, a grid-aware web interface with advanced service trading for linear algebra calculations. In the direction of solving scientific problems that require high-performance computing resources, examples of completed projects include the field of physics (parallel computing of complex quantum systems), astrophysics (Armenian virtual laboratory), biology (molecular dynamics study of human red blood cell membrane), meteorology (implementing and evaluating the Weather Research and Forecast Model for the territory of Armenia). The overview also notes that the Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia has established a scientific and educational infrastructure, uniting computing clusters of scientific and educational institutions of the country and provides the scientific community with access to local and international computational resources, that is a strong support for computational science in Armenia.

Highly parallel computation

NASA Technical Reports Server (NTRS)

Denning, Peter J.; Tichy, Walter F.

1990-01-01

Highly parallel computing architectures are the only means to achieve the computation rates demanded by advanced scientific problems. A decade of research has demonstrated the feasibility of such machines and current research focuses on which architectures designated as multiple instruction multiple datastream (MIMD) and single instruction multiple datastream (SIMD) have produced the best results to date; neither shows a decisive advantage for most near-homogeneous scientific problems. For scientific problems with many dissimilar parts, more speculative architectures such as neural networks or data flow may be needed.

Radiative and Auger recombination of degenerate carriers in InN

NASA Astrophysics Data System (ADS)

McAllister, Andrew; Bayerl, Dylan; Kioupakis, Emmanouil

Group-III nitrides find applications in many fields - energy conversion, sensors, and solid-state lighting. The band gaps of InN, GaN and AlN alloys span the infrared to ultraviolet spectral range. However, nitride optoelectronic devices suffer from a drop in efficiency as carrier density increases. A major component of this decrease is Auger recombination, but its influence is not fully understood, particularly for degenerate carriers. For nondegenerate carriers the radiative rate scales as the carrier density squared, while the Auger rate scales as the density cubed. However, it is unclear how these power laws decrease as carriers become degenerate. Using first-principles calculations we studied the dependence of the radiative and Auger recombination rates on carrier density in InN. We found a more complex dependence on the Auger rate than expected. The power law of the Auger rate changes at different densities depending on the type of Auger process involved and the type of carriers that have become degenerate. In contrast, the power law of the radiative rate changes when either carrier type becomes degenerate. This creates problems in designing devices, as Auger remains a major contributor to carrier recombination at densities for which radiative recombination is suppressed by phase-space filling. This work was supported by NSF (GRFP DGE 1256260 and CAREER DMR-1254314). Computational resources provided by the DOE NERSC facility (DE-AC02-05CH11231).

Visualization Tools for Lattice QCD - Final Report

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

Massimo Di Pierro

2012-03-15

Our research project is about the development of visualization tools for Lattice QCD. We developed various tools by extending existing libraries, adding new algorithms, exposing new APIs, and creating web interfaces (including the new NERSC gauge connection web site). Our tools cover the full stack of operations from automating download of data, to generating VTK files (topological charge, plaquette, Polyakov lines, quark and meson propagators, currents), to turning the VTK files into images, movies, and web pages. Some of the tools have their own web interfaces. Some Lattice QCD visualization have been created in the past but, to our knowledge,more » our tools are the only ones of their kind since they are general purpose, customizable, and relatively easy to use. We believe they will be valuable to physicists working in the field. They can be used to better teach Lattice QCD concepts to new graduate students; they can be used to observe the changes in topological charge density and detect possible sources of bias in computations; they can be used to observe the convergence of the algorithms at a local level and determine possible problems; they can be used to probe heavy-light mesons with currents and determine their spatial distribution; they can be used to detect corrupted gauge configurations. There are some indirect results of this grant that will benefit a broader audience than Lattice QCD physicists.« less

Building Cognition: The Construction of Computational Representations for Scientific Discovery

ERIC Educational Resources Information Center

Chandrasekharan, Sanjay; Nersessian, Nancy J.

2015-01-01

Novel computational representations, such as simulation models of complex systems and video games for scientific discovery (Foldit, EteRNA etc.), are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a…

DOE Advanced Scientific Computing Advisory Committee (ASCAC) Subcommittee Report on Scientific and Technical Information

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

Hey, Tony; Agarwal, Deborah; Borgman, Christine

The Advanced Scientific Computing Advisory Committee (ASCAC) was charged to form a standing subcommittee to review the Department of Energy’s Office of Scientific and Technical Information (OSTI) and to begin by assessing the quality and effectiveness of OSTI’s recent and current products and services and to comment on its mission and future directions in the rapidly changing environment for scientific publication and data. The Committee met with OSTI staff and reviewed available products, services and other materials. This report summaries their initial findings and recommendations.

Computational Scientific Inquiry with Virtual Worlds and Agent-Based Models: New Ways of Doing Science to Learn Science

ERIC Educational Resources Information Center

Jacobson, Michael J.; Taylor, Charlotte E.; Richards, Deborah

2016-01-01

In this paper, we propose computational scientific inquiry (CSI) as an innovative model for learning important scientific knowledge and new practices for "doing" science. This approach involves the use of a "game-like" virtual world for students to experience virtual biological fieldwork in conjunction with using an agent-based…

Using Just-in-Time Information to Support Scientific Discovery Learning in a Computer-Based Simulation

ERIC Educational Resources Information Center

Hulshof, Casper D.; de Jong, Ton

2006-01-01

Students encounter many obstacles during scientific discovery learning with computer-based simulations. It is hypothesized that an effective type of support, that does not interfere with the scientific discovery learning process, should be delivered on a "just-in-time" base. This study explores the effect of facilitating access to…

An Interdisciplinary Guided Inquiry on Estuarine Transport Using a Computer Model in High School Classrooms

ERIC Educational Resources Information Center

Chan, Kit Yu Karen; Yang, Sylvia; Maliska, Max E.; Grunbaum, Daniel

2012-01-01

The National Science Education Standards have highlighted the importance of active learning and reflection for contemporary scientific methods in K-12 classrooms, including the use of models. Computer modeling and visualization are tools that researchers employ in their scientific inquiry process, and often computer models are used in…

Architectural Principles and Experimentation of Distributed High Performance Virtual Clusters

ERIC Educational Resources Information Center

Younge, Andrew J.

2016-01-01

With the advent of virtualization and Infrastructure-as-a-Service (IaaS), the broader scientific computing community is considering the use of clouds for their scientific computing needs. This is due to the relative scalability, ease of use, advanced user environment customization abilities, and the many novel computing paradigms available for…

An Analysis on the Effect of Computer Self-Efficacy over Scientific Research Self-Efficacy and Information Literacy Self-Efficacy

ERIC Educational Resources Information Center

Tuncer, Murat

2013-01-01

Present research investigates reciprocal relations amidst computer self-efficacy, scientific research and information literacy self-efficacy. Research findings have demonstrated that according to standardized regression coefficients, computer self-efficacy has a positive effect on information literacy self-efficacy. Likewise it has been detected…

The Impact of Three-Dimensional Computational Modeling on Student Understanding of Astronomical Concepts: A Quantitative Analysis

ERIC Educational Resources Information Center

Hansen, John; Barnett, Michael; MaKinster, James; Keating, Thomas

2004-01-01

The increased availability of computational modeling software has created opportunities for students to engage in scientific inquiry through constructing computer-based models of scientific phenomena. However, despite the growing trend of integrating technology into science curricula, educators need to understand what aspects of these technologies…

Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Carter, Jonathan; Shalf, John; Skinner, David; Ethier, Stephane; Biswas, Rupak; Djomehri, Jahed; VanderWijngaart, Rob

2003-01-01

The growing gap between sustained and peak performance for scientific applications has become a well-known problem in high performance computing. The recent development of parallel vector systems offers the potential to bridge this gap for a significant number of computational science codes and deliver a substantial increase in computing capabilities. This paper examines the intranode performance of the NEC SX6 vector processor and the cache-based IBM Power3/4 superscalar architectures across a number of key scientific computing areas. First, we present the performance of a microbenchmark suite that examines a full spectrum of low-level machine characteristics. Next, we study the behavior of the NAS Parallel Benchmarks using some simple optimizations. Finally, we evaluate the perfor- mance of several numerical codes from key scientific computing domains. Overall results demonstrate that the SX6 achieves high performance on a large fraction of our application suite and in many cases significantly outperforms the RISC-based architectures. However, certain classes of applications are not easily amenable to vectorization and would likely require extensive reengineering of both algorithm and implementation to utilize the SX6 effectively.

USRA/RIACS

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1992-01-01

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on 6 June 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under a cooperative agreement with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. A flexible scientific staff is provided through a university faculty visitor program, a post doctoral program, and a student visitor program. Not only does this provide appropriate expertise but it also introduces scientists outside of NASA to NASA problems. A small group of core RIACS staff provides continuity and interacts with an ARC technical monitor and scientific advisory group to determine the RIACS mission. RIACS activities are reviewed and monitored by a USRA advisory council and ARC technical monitor. Research at RIACS is currently being done in the following areas: Parallel Computing; Advanced Methods for Scientific Computing; Learning Systems; High Performance Networks and Technology; Graphics, Visualization, and Virtual Environments.

Using Computer Simulations for Promoting Model-based Reasoning. Epistemological and Educational Dimensions

NASA Astrophysics Data System (ADS)

Develaki, Maria

2017-11-01

Scientific reasoning is particularly pertinent to science education since it is closely related to the content and methodologies of science and contributes to scientific literacy. Much of the research in science education investigates the appropriate framework and teaching methods and tools needed to promote students' ability to reason and evaluate in a scientific way. This paper aims (a) to contribute to an extended understanding of the nature and pedagogical importance of model-based reasoning and (b) to exemplify how using computer simulations can support students' model-based reasoning. We provide first a background for both scientific reasoning and computer simulations, based on the relevant philosophical views and the related educational discussion. This background suggests that the model-based framework provides an epistemologically valid and pedagogically appropriate basis for teaching scientific reasoning and for helping students develop sounder reasoning and decision-taking abilities and explains how using computer simulations can foster these abilities. We then provide some examples illustrating the use of computer simulations to support model-based reasoning and evaluation activities in the classroom. The examples reflect the procedure and criteria for evaluating models in science and demonstrate the educational advantages of their application in classroom reasoning activities.

A toolbox and a record for scientific model development

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Scientific computation can benefit from software tools that facilitate construction of computational models, control the application of models, and aid in revising models to handle new situations. Existing environments for scientific programming provide only limited means of handling these tasks. This paper describes a two pronged approach for handling these tasks: (1) designing a 'Model Development Toolbox' that includes a basic set of model constructing operations; and (2) designing a 'Model Development Record' that is automatically generated during model construction. The record is subsequently exploited by tools that control the application of scientific models and revise models to handle new situations. Our two pronged approach is motivated by our belief that the model development toolbox and record should be highly interdependent. In particular, a suitable model development record can be constructed only when models are developed using a well defined set of operations. We expect this research to facilitate rapid development of new scientific computational models, to help ensure appropriate use of such models and to facilitate sharing of such models among working computational scientists. We are testing this approach by extending SIGMA, and existing knowledge-based scientific software design tool.

The Petascale Data Storage Institute

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

Gibson, Garth; Long, Darrell; Honeyman, Peter

2013-07-01

Petascale computing infrastructures for scientific discovery make petascale demands on information storage capacity, performance, concurrency, reliability, availability, and manageability.The Petascale Data Storage Institute focuses on the data storage problems found in petascale scientific computing environments, with special attention to community issues such as interoperability, community buy-in, and shared tools.The Petascale Data Storage Institute is a collaboration between researchers at Carnegie Mellon University, National Energy Research Scientific Computing Center, Pacific Northwest National Laboratory, Oak Ridge National Laboratory, Sandia National Laboratory, Los Alamos National Laboratory, University of Michigan, and the University of California at Santa Cruz.

The need for scientific software engineering in the pharmaceutical industry

NASA Astrophysics Data System (ADS)

Luty, Brock; Rose, Peter W.

2017-03-01

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.

The need for scientific software engineering in the pharmaceutical industry.

PubMed

Luty, Brock; Rose, Peter W

2017-03-01

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.

Understanding the Performance and Potential of Cloud Computing for Scientific Applications

DOE PAGES

Sadooghi, Iman; Martin, Jesus Hernandez; Li, Tonglin; ...

2015-02-19

In this paper, commercial clouds bring a great opportunity to the scientific computing area. Scientific applications usually require significant resources, however not all scientists have access to sufficient high-end computing systems, may of which can be found in the Top500 list. Cloud Computing has gained the attention of scientists as a competitive resource to run HPC applications at a potentially lower cost. But as a different infrastructure, it is unclear whether clouds are capable of running scientific applications with a reasonable performance per money spent. This work studies the performance of public clouds and places this performance in context tomore » price. We evaluate the raw performance of different services of AWS cloud in terms of the basic resources, such as compute, memory, network and I/O. We also evaluate the performance of the scientific applications running in the cloud. This paper aims to assess the ability of the cloud to perform well, as well as to evaluate the cost of the cloud running scientific applications. We developed a full set of metrics and conducted a comprehensive performance evlauation over the Amazon cloud. We evaluated EC2, S3, EBS and DynamoDB among the many Amazon AWS services. We evaluated the memory sub-system performance with CacheBench, the network performance with iperf, processor and network performance with the HPL benchmark application, and shared storage with NFS and PVFS in addition to S3. We also evaluated a real scientific computing application through the Swift parallel scripting system at scale. Armed with both detailed benchmarks to gauge expected performance and a detailed monetary cost analysis, we expect this paper will be a recipe cookbook for scientists to help them decide where to deploy and run their scientific applications between public clouds, private clouds, or hybrid clouds.« less

Understanding the Performance and Potential of Cloud Computing for Scientific Applications

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

Sadooghi, Iman; Martin, Jesus Hernandez; Li, Tonglin

In this paper, commercial clouds bring a great opportunity to the scientific computing area. Scientific applications usually require significant resources, however not all scientists have access to sufficient high-end computing systems, may of which can be found in the Top500 list. Cloud Computing has gained the attention of scientists as a competitive resource to run HPC applications at a potentially lower cost. But as a different infrastructure, it is unclear whether clouds are capable of running scientific applications with a reasonable performance per money spent. This work studies the performance of public clouds and places this performance in context tomore » price. We evaluate the raw performance of different services of AWS cloud in terms of the basic resources, such as compute, memory, network and I/O. We also evaluate the performance of the scientific applications running in the cloud. This paper aims to assess the ability of the cloud to perform well, as well as to evaluate the cost of the cloud running scientific applications. We developed a full set of metrics and conducted a comprehensive performance evlauation over the Amazon cloud. We evaluated EC2, S3, EBS and DynamoDB among the many Amazon AWS services. We evaluated the memory sub-system performance with CacheBench, the network performance with iperf, processor and network performance with the HPL benchmark application, and shared storage with NFS and PVFS in addition to S3. We also evaluated a real scientific computing application through the Swift parallel scripting system at scale. Armed with both detailed benchmarks to gauge expected performance and a detailed monetary cost analysis, we expect this paper will be a recipe cookbook for scientists to help them decide where to deploy and run their scientific applications between public clouds, private clouds, or hybrid clouds.« less

75 FR 65639 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-26

...: Computational Biology Special Emphasis Panel A. Date: October 29, 2010. Time: 2 p.m. to 3:30 p.m. Agenda: To.... Name of Committee: Center for Scientific Review Special Emphasis Panel; Member Conflict: Computational...

The Effects of Inquiry-Based Computer Simulation with Cooperative Learning on Scientific Thinking and Conceptual Understanding of Gas Laws

ERIC Educational Resources Information Center

Abdullah, Sopiah; Shariff, Adilah

2008-01-01

The purpose of the study was to investigate the effects of inquiry-based computer simulation with heterogeneous-ability cooperative learning (HACL) and inquiry-based computer simulation with friendship cooperative learning (FCL) on (a) scientific reasoning (SR) and (b) conceptual understanding (CU) among Form Four students in Malaysian Smart…

RIACS/USRA

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1993-01-01

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on 6 June 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under contract with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. A flexible scientific staff is provided through a university faculty visitor program, a post doctoral program, and a student visitor program. Not only does this provide appropriate expertise but it also introduces scientists outside of NASA to NASA problems. A small group of core RIACS staff provides continuity and interacts with an ARC technical monitor and scientific advisory group to determine the RIACS mission. RIACS activities are reviewed and monitored by a USRA advisory council and ARC technical monitor. Research at RIACS is currently being done in the following areas: Parallel Computing, Advanced Methods for Scientific Computing, High Performance Networks and Technology, and Learning Systems. Parallel compiler techniques, adaptive numerical methods for flows in complicated geometries, and optimization were identified as important problems to investigate for ARC's involvement in the Computational Grand Challenges of the next decade.

The emergence of spatial cyberinfrastructure.

PubMed

Wright, Dawn J; Wang, Shaowen

2011-04-05

Cyberinfrastructure integrates advanced computer, information, and communication technologies to empower computation-based and data-driven scientific practice and improve the synthesis and analysis of scientific data in a collaborative and shared fashion. As such, it now represents a paradigm shift in scientific research that has facilitated easy access to computational utilities and streamlined collaboration across distance and disciplines, thereby enabling scientific breakthroughs to be reached more quickly and efficiently. Spatial cyberinfrastructure seeks to resolve longstanding complex problems of handling and analyzing massive and heterogeneous spatial datasets as well as the necessity and benefits of sharing spatial data flexibly and securely. This article provides an overview and potential future directions of spatial cyberinfrastructure. The remaining four articles of the special feature are introduced and situated in the context of providing empirical examples of how spatial cyberinfrastructure is extending and enhancing scientific practice for improved synthesis and analysis of both physical and social science data. The primary focus of the articles is spatial analyses using distributed and high-performance computing, sensor networks, and other advanced information technology capabilities to transform massive spatial datasets into insights and knowledge.

The emergence of spatial cyberinfrastructure

PubMed Central

Wright, Dawn J.; Wang, Shaowen

2011-01-01

Cyberinfrastructure integrates advanced computer, information, and communication technologies to empower computation-based and data-driven scientific practice and improve the synthesis and analysis of scientific data in a collaborative and shared fashion. As such, it now represents a paradigm shift in scientific research that has facilitated easy access to computational utilities and streamlined collaboration across distance and disciplines, thereby enabling scientific breakthroughs to be reached more quickly and efficiently. Spatial cyberinfrastructure seeks to resolve longstanding complex problems of handling and analyzing massive and heterogeneous spatial datasets as well as the necessity and benefits of sharing spatial data flexibly and securely. This article provides an overview and potential future directions of spatial cyberinfrastructure. The remaining four articles of the special feature are introduced and situated in the context of providing empirical examples of how spatial cyberinfrastructure is extending and enhancing scientific practice for improved synthesis and analysis of both physical and social science data. The primary focus of the articles is spatial analyses using distributed and high-performance computing, sensor networks, and other advanced information technology capabilities to transform massive spatial datasets into insights and knowledge. PMID:21467227

Evolution of the Virtualized HPC Infrastructure of Novosibirsk Scientific Center

NASA Astrophysics Data System (ADS)

Adakin, A.; Anisenkov, A.; Belov, S.; Chubarov, D.; Kalyuzhny, V.; Kaplin, V.; Korol, A.; Kuchin, N.; Lomakin, S.; Nikultsev, V.; Skovpen, K.; Sukharev, A.; Zaytsev, A.

2012-12-01

Novosibirsk Scientific Center (NSC), also known worldwide as Akademgorodok, is one of the largest Russian scientific centers hosting Novosibirsk State University (NSU) and more than 35 research organizations of the Siberian Branch of Russian Academy of Sciences including Budker Institute of Nuclear Physics (BINP), Institute of Computational Technologies, and Institute of Computational Mathematics and Mathematical Geophysics (ICM&MG). Since each institute has specific requirements on the architecture of computing farms involved in its research field, currently we've got several computing facilities hosted by NSC institutes, each optimized for a particular set of tasks, of which the largest are the NSU Supercomputer Center, Siberian Supercomputer Center (ICM&MG), and a Grid Computing Facility of BINP. A dedicated optical network with the initial bandwidth of 10 Gb/s connecting these three facilities was built in order to make it possible to share the computing resources among the research communities, thus increasing the efficiency of operating the existing computing facilities and offering a common platform for building the computing infrastructure for future scientific projects. Unification of the computing infrastructure is achieved by extensive use of virtualization technology based on XEN and KVM platforms. This contribution gives a thorough review of the present status and future development prospects for the NSC virtualized computing infrastructure and the experience gained while using it for running production data analysis jobs related to HEP experiments being carried out at BINP, especially the KEDR detector experiment at the VEPP-4M electron-positron collider.

Position Paper: Applying Machine Learning to Software Analysis to Achieve Trusted, Repeatable Scientific Computing

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

Prowell, Stacy J; Symons, Christopher T

2015-01-01

Producing trusted results from high-performance codes is essential for policy and has significant economic impact. We propose combining rigorous analytical methods with machine learning techniques to achieve the goal of repeatable, trustworthy scientific computing.

Advanced Scientific Computing Research Exascale Requirements Review. An Office of Science review sponsored by Advanced Scientific Computing Research, September 27-29, 2016, Rockville, Maryland

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

Almgren, Ann; DeMar, Phil; Vetter, Jeffrey

The widespread use of computing in the American economy would not be possible without a thoughtful, exploratory research and development (R&D) community pushing the performance edge of operating systems, computer languages, and software libraries. These are the tools and building blocks — the hammers, chisels, bricks, and mortar — of the smartphone, the cloud, and the computing services on which we rely. Engineers and scientists need ever-more specialized computing tools to discover new material properties for manufacturing, make energy generation safer and more efficient, and provide insight into the fundamentals of the universe, for example. The research division of themore » U.S. Department of Energy’s (DOE’s) Office of Advanced Scientific Computing and Research (ASCR Research) ensures that these tools and building blocks are being developed and honed to meet the extreme needs of modern science. See also http://exascaleage.org/ascr/ for additional information.« less

Quantum Testbeds Stakeholder Workshop (QTSW) Report meeting purpose and agenda.

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

Hebner, Gregory A.

Quantum computing (QC) is a promising early-stage technology with the potential to provide scientific computing capabilities far beyond what is possible with even an Exascale computer in specific problems of relevance to the Office of Science. These include (but are not limited to) materials modeling, molecular dynamics, and quantum chromodynamics. However, commercial QC systems are not yet available and the technical maturity of current QC hardware, software, algorithms, and systems integration is woefully incomplete. Thus, there is a significant opportunity for DOE to define the technology building blocks, and solve the system integration issues to enable a revolutionary tool. Oncemore » realized, QC will have world changing impact on economic competitiveness, the scientific enterprise, and citizen well-being. Prior to this workshop, DOE / Office of Advanced Scientific Computing Research (ASCR) hosted a workshop in 2015 to explore QC scientific applications. The goal of that workshop was to assess the viability of QC technologies to meet the computational requirements in support of DOE’s science and energy mission and to identify the potential impact of these technologies.« less

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

DOE PAGES

Haidar, Azzam; Jagode, Heike; Vaccaro, Phil; ...

2018-03-22

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore howmore » different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.« less

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

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

Haidar, Azzam; Jagode, Heike; Vaccaro, Phil

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore howmore » different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.« less

A Computing Environment to Support Repeatable Scientific Big Data Experimentation of World-Wide Scientific Literature

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

Schlicher, Bob G; Kulesz, James J; Abercrombie, Robert K

A principal tenant of the scientific method is that experiments must be repeatable and relies on ceteris paribus (i.e., all other things being equal). As a scientific community, involved in data sciences, we must investigate ways to establish an environment where experiments can be repeated. We can no longer allude to where the data comes from, we must add rigor to the data collection and management process from which our analysis is conducted. This paper describes a computing environment to support repeatable scientific big data experimentation of world-wide scientific literature, and recommends a system that is housed at the Oakmore » Ridge National Laboratory in order to provide value to investigators from government agencies, academic institutions, and industry entities. The described computing environment also adheres to the recently instituted digital data management plan mandated by multiple US government agencies, which involves all stages of the digital data life cycle including capture, analysis, sharing, and preservation. It particularly focuses on the sharing and preservation of digital research data. The details of this computing environment are explained within the context of cloud services by the three layer classification of Software as a Service , Platform as a Service , and Infrastructure as a Service .« less

Idle waves in high-performance computing

NASA Astrophysics Data System (ADS)

Markidis, Stefano; Vencels, Juris; Peng, Ivy Bo; Akhmetova, Dana; Laure, Erwin; Henri, Pierre

2015-01-01

The vast majority of parallel scientific applications distributes computation among processes that are in a busy state when computing and in an idle state when waiting for information from other processes. We identify the propagation of idle waves through processes in scientific applications with a local information exchange between the two processes. Idle waves are nondispersive and have a phase velocity inversely proportional to the average busy time. The physical mechanism enabling the propagation of idle waves is the local synchronization between two processes due to remote data dependency. This study provides a description of the large number of processes in parallel scientific applications as a continuous medium. This work also is a step towards an understanding of how localized idle periods can affect remote processes, leading to the degradation of global performance in parallel scientific applications.

Comparisons of some large scientific computers

NASA Technical Reports Server (NTRS)

Credeur, K. R.

1981-01-01

In 1975, the National Aeronautics and Space Administration (NASA) began studies to assess the technical and economic feasibility of developing a computer having sustained computational speed of one billion floating point operations per second and a working memory of at least 240 million words. Such a powerful computer would allow computational aerodynamics to play a major role in aeronautical design and advanced fluid dynamics research. Based on favorable results from these studies, NASA proceeded with developmental plans. The computer was named the Numerical Aerodynamic Simulator (NAS). To help insure that the estimated cost, schedule, and technical scope were realistic, a brief study was made of past large scientific computers. Large discrepancies between inception and operation in scope, cost, or schedule were studied so that they could be minimized with NASA's proposed new compter. The main computers studied were the ILLIAC IV, STAR 100, Parallel Element Processor Ensemble (PEPE), and Shuttle Mission Simulator (SMS) computer. Comparison data on memory and speed were also obtained on the IBM 650, 704, 7090, 360-50, 360-67, 360-91, and 370-195; the CDC 6400, 6600, 7600, CYBER 203, and CYBER 205; CRAY 1; and the Advanced Scientific Computer (ASC). A few lessons learned conclude the report.

USSR Report: Cybernetics, Computers and Automation Technology. No. 69.

DTIC Science & Technology

1983-05-06

computers in multiprocessor and multistation design , control and scientific research automation systems. The results of comparing the efficiency of...Podvizhnaya, Scientific Research Institute of Control Computers, Severodonetsk] [Text] The most significant change in the design of the SM-2M compared to...UPRAVLYAYUSHCHIYE SISTEMY I MASHINY, Nov-Dec 82) 95 APPLICATIONS Kiev Automated Control System, Design Features and Prospects for Development (V. A

Nuclear Physics Science Network Requirements Workshop, May 2008 - Final Report

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

Tierney, Ed., Brian L; Dart, Ed., Eli; Carlson, Rich

2008-11-10

The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In May 2008, ESnet and the Nuclear Physics (NP) Program Office of the DOEmore » Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the NP Program Office. Most of the key DOE sites for NP related work will require significant increases in network bandwidth in the 5 year time frame. This includes roughly 40 Gbps for BNL, and 20 Gbps for NERSC. Total transatlantic requirements are on the order of 40 Gbps, and transpacific requirements are on the order of 30 Gbps. Other key sites are Vanderbilt University and MIT, which will need on the order of 20 Gbps bandwidth to support data transfers for the CMS Heavy Ion program. In addition to bandwidth requirements, the workshop emphasized several points in regard to science process and collaboration. One key point is the heavy reliance on Grid tools and infrastructure (both PKI and tools such as GridFTP) by the NP community. The reliance on Grid software is expected to increase in the future. Therefore, continued development and support of Grid software is very important to the NP science community. Another key finding is that scientific productivity is greatly enhanced by easy researcher-local access to instrument data. This is driving the creation of distributed repositories for instrument data at collaborating institutions, along with a corresponding increase in demand for network-based data transfers and the tools to manage those transfers effectively. Network reliability is also becoming more important as there is often a narrow window between data collection and data archiving when transfer and analysis can be done. The instruments do not stop producing data, so extended network outages can result in data loss due to analysis pipeline stalls. Finally, as the scope of collaboration continues to increase, collaboration tools such as audio and video conferencing are becoming ever more critical to the productivity of scientific collaborations.« less

Accelerating scientific discovery : 2007 annual report.

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

Beckman, P.; Dave, P.; Drugan, C.

2008-11-14

As a gateway for scientific discovery, the Argonne Leadership Computing Facility (ALCF) works hand in hand with the world's best computational scientists to advance research in a diverse span of scientific domains, ranging from chemistry, applied mathematics, and materials science to engineering physics and life sciences. Sponsored by the U.S. Department of Energy's (DOE) Office of Science, researchers are using the IBM Blue Gene/L supercomputer at the ALCF to study and explore key scientific problems that underlie important challenges facing our society. For instance, a research team at the University of California-San Diego/ SDSC is studying the molecular basis ofmore » Parkinson's disease. The researchers plan to use the knowledge they gain to discover new drugs to treat the disease and to identify risk factors for other diseases that are equally prevalent. Likewise, scientists from Pratt & Whitney are using the Blue Gene to understand the complex processes within aircraft engines. Expanding our understanding of jet engine combustors is the secret to improved fuel efficiency and reduced emissions. Lessons learned from the scientific simulations of jet engine combustors have already led Pratt & Whitney to newer designs with unprecedented reductions in emissions, noise, and cost of ownership. ALCF staff members provide in-depth expertise and assistance to those using the Blue Gene/L and optimizing user applications. Both the Catalyst and Applications Performance Engineering and Data Analytics (APEDA) teams support the users projects. In addition to working with scientists running experiments on the Blue Gene/L, we have become a nexus for the broader global community. In partnership with the Mathematics and Computer Science Division at Argonne National Laboratory, we have created an environment where the world's most challenging computational science problems can be addressed. Our expertise in high-end scientific computing enables us to provide guidance for applications that are transitioning to petascale as well as to produce software that facilitates their development, such as the MPICH library, which provides a portable and efficient implementation of the MPI standard--the prevalent programming model for large-scale scientific applications--and the PETSc toolkit that provides a programming paradigm that eases the development of many scientific applications on high-end computers.« less

Precision searches in dijets at the HL-LHC and HE-LHC

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Childers, J. T.; Proudfoot, J.; Wang, R.; Frizzell, D.

2018-05-01

This paper explores the physics reach of the High-Luminosity Large Hadron Collider (HL-LHC) for searches of new particles decaying to two jets. We discuss inclusive searches in dijets and b-jets, as well as searches in semi-inclusive events by requiring an additional lepton that increases sensitivity to different aspects of the underlying processes. We discuss the expected exclusion limits for generic models predicting new massive particles that result in resonant structures in the dijet mass. Prospects of the Higher-Energy LHC (HE-LHC) collider are also discussed. The study is based on the Pythia8 Monte Carlo generator using representative event statistics for the HL-LHC and HE-LHC running conditions. The event samples were created using supercomputers at NERSC.

The HIBEAM Manual

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

Fawley, William M.

2000-02-01

HIBEAM is a 2 1/2D particle-in-cell (PIC) simulation code developed in the late 1990's in the Heavy-Ion Fusion research program at Lawrence Berkeley National Laboratory. The major purpose of HIBEAM is to simulate the transverse (i.e., X-Y) dynamics of a space-charge-dominated, non-relativistic heavy-ion beam being transported in a static accelerator focusing lattice. HIBEAM has been used to study beam combining systems, effective dynamic apertures in electrostatic quadrupole lattices, and emittance growth due to transverse misalignments. At present, HIBEAM runs on the CRAY vector machines (C90 and J90's) at NERSC, although it would be relatively simple to port the code tomore » UNIX workstations so long as IMSL math routines were available.« less

Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

First-principles quantum-mechanical investigations of biomass conversion at the liquid-solid interfaces

NASA Astrophysics Data System (ADS)

Dang, Hongli; Xue, Wenhua; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

We report first-principles density-functional calculations and ab initio molecular dynamics (MD) simulations for the reactions involving furfural, which is an important intermediate in biomass conversion, at the catalytic liquid-solid interfaces. The different dynamic processes of furfural at the water-Cu(111) and water-Pd(111) interfaces suggest different catalytic reaction mechanisms for the conversion of furfural. Simulations for the dynamic processes with and without hydrogen demonstrate the importance of the liquid-solid interface as well as the presence of hydrogen in possible catalytic reactions including hydrogenation and decarbonylation of furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

RAPPORT: running scientific high-performance computing applications on the cloud.

PubMed

Cohen, Jeremy; Filippis, Ioannis; Woodbridge, Mark; Bauer, Daniela; Hong, Neil Chue; Jackson, Mike; Butcher, Sarah; Colling, David; Darlington, John; Fuchs, Brian; Harvey, Matt

2013-01-28

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.

High-performance scientific computing in the cloud

NASA Astrophysics Data System (ADS)

Jorissen, Kevin; Vila, Fernando; Rehr, John

2011-03-01

Cloud computing has the potential to open up high-performance computational science to a much broader class of researchers, owing to its ability to provide on-demand, virtualized computational resources. However, before such approaches can become commonplace, user-friendly tools must be developed that hide the unfamiliar cloud environment and streamline the management of cloud resources for many scientific applications. We have recently shown that high-performance cloud computing is feasible for parallelized x-ray spectroscopy calculations. We now present benchmark results for a wider selection of scientific applications focusing on electronic structure and spectroscopic simulation software in condensed matter physics. These applications are driven by an improved portable interface that can manage virtual clusters and run various applications in the cloud. We also describe a next generation of cluster tools, aimed at improved performance and a more robust cluster deployment. Supported by NSF grant OCI-1048052.

GRDC. A Collaborative Framework for Radiological Background and Contextual Data Analysis

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

Brian J. Quiter; Ramakrishnan, Lavanya; Mark S. Bandstra

The Radiation Mobile Analysis Platform (RadMAP) is unique in its capability to collect both high quality radiological data from both gamma-ray detectors and fast neutron detectors and a broad array of contextual data that includes positioning and stance data, high-resolution 3D radiological data from weather sensors, LiDAR, and visual and hyperspectral cameras. The datasets obtained from RadMAP are both voluminous and complex and require analyses from highly diverse communities within both the national laboratory and academic communities. Maintaining a high level of transparency will enable analysis products to further enrich the RadMAP dataset. It is in this spirit of openmore » and collaborative data that the RadMAP team proposed to collect, calibrate, and make available online data from the RadMAP system. The Berkeley Data Cloud (BDC) is a cloud-based data management framework that enables web-based data browsing visualization, and connects curated datasets to custom workflows such that analysis products can be managed and disseminated while maintaining user access rights. BDC enables cloud-based analyses of large datasets in a manner that simulates real-time data collection, such that BDC can be used to test algorithm performance on real and source-injected datasets. Using the BDC framework, a subset of the RadMAP datasets have been disseminated via the Gamma Ray Data Cloud (GRDC) that is hosted through the National Energy Research Science Computing (NERSC) Center, enabling data access to over 40 users at 10 institutions.« less

Post-pyrite transition in SiO2

NASA Astrophysics Data System (ADS)

Ho, K.; Wu, S.; Umemoto, K.; Wentzcovitch, R. M.; Ji, M.; Wang, C.

2010-12-01

Here we propose a new phase of SiO2 beyond the pyrite-type phase. SiO2 is one of the most important minerals in Earth and planetary sciences. So far, the pyrite-type phase has been identified experimentally as the highest-pressure form of SiO2. In solar giants and extrasolar planets whose interior pressures are considerably higher than that on Earth, a post-pyrite transition in SiO2 may occur at ~ 1 TPa as a result of the dissociation of MgSiO3 post-perovskite into MgO and SiO2 [Umemtoto et al., Science 311, 983 (2006)]. Several dioxides considered to be low-pressure analogs of SiO2 have a phase with cotunnite-type (PbCl2-type) structure as the post-pyrite phase. However, a first-principles structural search using a genetic algorithm shows that SiO2 should undergo a post-pyrite transition to a hexagonal phase, not to the cotunnite phase. The hexagonal phase is energetically very competitive with the cotunnite-type one. This work was supported by the U.S. Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering and NSF under ATM-0428774 (VLab), EAR-0757903, and EAR-1019853. Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358. The computations were performed at the National Energy Research Supercomputing Centre (NERSC) and the Minnesota Supercomputing Institute (MSI).

Effect of Magnetic Islands on Divertors in Tokamaks and Stellarators

NASA Astrophysics Data System (ADS)

Punjabi, Alkesh; Boozer, Allen

2017-10-01

Divertors are required for handling the plasma particle and heat exhausts on the walls in fusion plasmas. Relatively simple methods, models, and maps from field line Hamiltonian are developed to better understand the interaction of strong plasma shaping and magnetic islands on the size and behavior of the magnetic flux tubes that go from the plasma edge to the wall in non-axisymmetric system. This approach is applicable not only in tokamaks but also in stellarators. Stellarator diverters in which magnetic islands are dominant are called resonant and when shaping is dominant are called non-resonant. Optimized stellarators generally have sharp edges on their surface, but unlike the case for tokamaks these edges do not encircle the entire plasma, so they do not define an edge value for the rotational transform. The approach is used in the DIII-D tokamak. Computation results are consistent with the predictions of the models. Further simulations are being done to understand why the transition from an effective cubic to a linear increase in loss time and area of footprint occurs and whether this increase is discontinuous or not. This work is supported by the US DOE Grants DE-FG02-01ER54624 and DE-FG02-04ER54793 to Hampton University and DE-FG02-95ER54333 to Columbia University. This research used resources of the NERSC, supported by the Office of Science, US DOE, under Contract No. DE-AC02-05CH11231.

Activities of the Research Institute for Advanced Computer Science

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1994-01-01

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under contract with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. Research at RIACS is currently being done in the following areas: (1) parallel computing; (2) advanced methods for scientific computing; (3) high performance networks; and (4) learning systems. RIACS technical reports are usually preprints of manuscripts that have been submitted to research journals or conference proceedings. A list of these reports for the period January 1, 1994 through December 31, 1994 is in the Reports and Abstracts section of this report.

The future of scientific workflows

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

Deelman, Ewa; Peterka, Tom; Altintas, Ilkay

Today’s computational, experimental, and observational sciences rely on computations that involve many related tasks. The success of a scientific mission often hinges on the computer automation of these workflows. In April 2015, the US Department of Energy (DOE) invited a diverse group of domain and computer scientists from national laboratories supported by the Office of Science, the National Nuclear Security Administration, from industry, and from academia to review the workflow requirements of DOE’s science and national security missions, to assess the current state of the art in science workflows, to understand the impact of emerging extreme-scale computing systems on thosemore » workflows, and to develop requirements for automated workflow management in future and existing environments. This article is a summary of the opinions of over 50 leading researchers attending this workshop. We highlight use cases, computing systems, workflow needs and conclude by summarizing the remaining challenges this community sees that inhibit large-scale scientific workflows from becoming a mainstream tool for extreme-scale science.« less

Neuromorphic Computing, Architectures, Models, and Applications. A Beyond-CMOS Approach to Future Computing, June 29-July 1, 2016, Oak Ridge, TN

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

Potok, Thomas; Schuman, Catherine; Patton, Robert

The White House and Department of Energy have been instrumental in driving the development of a neuromorphic computing program to help the United States continue its lead in basic research into (1) Beyond Exascale—high performance computing beyond Moore’s Law and von Neumann architectures, (2) Scientific Discovery—new paradigms for understanding increasingly large and complex scientific data, and (3) Emerging Architectures—assessing the potential of neuromorphic and quantum architectures. Neuromorphic computing spans a broad range of scientific disciplines from materials science to devices, to computer science, to neuroscience, all of which are required to solve the neuromorphic computing grand challenge. In our workshopmore » we focus on the computer science aspects, specifically from a neuromorphic device through an application. Neuromorphic devices present a very different paradigm to the computer science community from traditional von Neumann architectures, which raises six major questions about building a neuromorphic application from the device level. We used these fundamental questions to organize the workshop program and to direct the workshop panels and discussions. From the white papers, presentations, panels, and discussions, there emerged several recommendations on how to proceed.« less

Computational science: shifting the focus from tools to models

PubMed Central

Hinsen, Konrad

2014-01-01

Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication of big data sets or complex models. As a consequence, these crucial pieces of information no longer enter the scientific record. Moreover, they have become prisoners of scientific software: many models exist only as software implementations, and the data are often stored in proprietary formats defined by the software. In this article, I argue that this emphasis on software tools over models and data is detrimental to science in the long term, and I propose a means by which this can be reversed. PMID:25309728

The International Conference on Vector and Parallel Computing (2nd)

DTIC Science & Technology

1989-01-17

Computation of the SVD of Bidiagonal Matrices" ...................................... 11 " Lattice QCD -As a Large Scale Scientific Computation...vectorizcd for the IBM 3090 Vector Facility. In addition, elapsed times " Lattice QCD -As a Large Scale Scientific have been reduced by using 3090...benchmarked Lattice QCD on a large number ofcompu- come from the wavefront solver routine. This was exten- ters: CrayX-MP and Cray 2 (vector

Multi-threading: A new dimension to massively parallel scientific computation

NASA Astrophysics Data System (ADS)

Nielsen, Ida M. B.; Janssen, Curtis L.

2000-06-01

Multi-threading is becoming widely available for Unix-like operating systems, and the application of multi-threading opens new ways for performing parallel computations with greater efficiency. We here briefly discuss the principles of multi-threading and illustrate the application of multi-threading for a massively parallel direct four-index transformation of electron repulsion integrals. Finally, other potential applications of multi-threading in scientific computing are outlined.

Comment on "Most computational hydrology is not reproducible, so is it really science?" by Christopher Hutton et al.

NASA Astrophysics Data System (ADS)

Añel, Juan A.

2017-03-01

Nowadays, the majority of the scientific community is not aware of the risks and problems associated with an inadequate use of computer systems for research, mostly for reproducibility of scientific results. Such reproducibility can be compromised by the lack of clear standards and insufficient methodological description of the computational details involved in an experiment. In addition, the inappropriate application or ignorance of copyright laws can have undesirable effects on access to aspects of great importance of the design of experiments and therefore to the interpretation of results.