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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Cooperative Research and Development Agreement With Georgetown University Report: National Institutes of Health, National Center for Advancing Translational Sciences Clinical and Translational Science Award

Oak Ridge National Laboratory (ORNL) is participating with Georgetown University (GU) as a subrecipient in response to the National Institutes of Health (NIH), National Center for Advancing Translational Sciences (NCATS) Clinical and Translational Science Award (CTSA) (U54 Clinical Trial Optional) funding opportunity announcement. This Cooperative Research and Development Agreement is put in to place to facilitate the development and implementation of clinical interventions that demonstrably improve human health is currently a complex, recursive, and inefficient process that leads to delays of years or decades before discoveries in biomedical research result in health benefits for patients and communities. NCATS conducts and supports research in the science of translation, to discover the mechanistic and operational principles of the intervention development and dissemination process, thereby providing the scientific foundation for improvements in translational efficiency that will accelerate the realization of interventions that improve human health. Under NCATS’ leadership, the CTSA Program supports a national network of medical research institutions called hubs. GU is the lead institution in one of the NIH hubs that was created as a result of a previous NIH CTSA. The missions of the GU have historically included the advancement of health through research in the clinical and biomedical sciences, the education of future leaders in medical and nursing practice and academia, and the provision of compassionate and scientifically competent patient care and service to the Washington, DC community and the nation. GU is the lead institution for the Georgetown-Howard Universities Center for Clinical and Translational Science (GHUCCTS), a multi-institutional partnership of medical research institutions forged from a desire to promote clinical research and translational science. Through multiple collaborations among these institutions, GHUCCTS is transforming clinical research and translational science in order to bring new scientific advances to health care. Oak Ridge National Laboratory is the Department of Energy's (DOE) largest science and energy laboratory. Managed since April 2000 by a partnership of the University of Tennessee and Battelle, ORNL was established in 1943 as a part of the secret Manhattan Project to pioneer a method for producing and separating plutonium. During the 1950s and 1960s, ORNL became an international center for the study of nuclear energy and related research in the physical and life sciences. With the creation of DOE in the 1970s, ORNL's mission broadened to include a variety of energy technologies and strategies. Today the laboratory supports the nation with a peacetime science and technology mission that is just as important as, but very different from, its role during the Manhattan Project. ORNL is home to the world's premier center for high performance supercomputing to enable scientific discovery. ORNL has extensive expertise in various areas of computer science that are uniquely situated to support GU. Additionally, ORNL’s leading computational user facilities present a unique opportunity to leverage the largest scale machines for open science in support of the stated mission of the NCATS CTSA. ORNL's partnership with GU will offer unparalleled opportunity in data analytics, deep-learning, artificial intelligence, and urban dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sensitive Resources Assessment and Forest Analysis for the Proposed Versatile Test Reactor, Oak Ridge, Tennessee

The US Department of Energy’s (DOE’s) Oak Ridge National Laboratory (ORNL) is a leading institution in advanced materials, supercomputing, neutrons, and nuclear science. As a research laboratory managed by UT-Battelle, LLC for DOE, ORNL has national priorities in energy, security, and scientific discovery that necessitate facility improvements and expansions. DOE is also committed to environmental stewardship. The laboratory is located on the ~32,000-acre (~13,000-ha) Oak Ridge Reservation (ORR), much of which is categorized as a National Environmental Research Park (NERP) and a state Wildlife Management Area. DOE works with the Tennessee Wildlife Resources Agency (TWRA), Tennessee Department of Environment and Conservation (TDEC), US Fish and Wildlife Service (USFWS), US Department of Agriculture, and other agencies to serve as an effective steward of the ORR. Accordingly, project managers must conform to environmental regulations, agreements, and policies at the federal, state, and institutional levels. Per 40 CFR (Code of Federal Regulations) 1508.14, potential effects on research and science education also represent potential effects of federal actions on the NERP, and impacts on, e.g., deer harvest, must be considered on the Oak Ridge Wildlife Management Area when other aspects of the human environment are affected. The United States currently has no fast neutron testing capability to support advanced nuclear research and development. The proposed Versatile Test Reactor (VTR) will take advantage of current investments by the US government and private industry in nuclear reactors to expedite the design and construction process, using proven technology to create a world-class scientific infrastructure. The VTR will take advantage of fast neutrons provided by this proven technology, along with a capability to rapidly insert, conduct, and remove state-of-the-art experiments. An advantage of the VTR is that it can support future innovations in experimental capabilities without modifying the facility. The VTR will support progress in a variety of science and technology areas, including testing and qualification of advanced reactor fuels; testing and qualification of innovative structural materials; testing of innovative components and instruments; validation of advanced modeling and simulation tools; and versatility for future technical missions. Through proven technology, the VTR can take advantage of existing reactor designs and operating experience to reduce the risk, cost, and time for design and construction. The top available resources of DOE laboratories, industry, and universities will be used to expedite reactor design and construction toward developing the scientific infrastructure that affords a strong testing capability that can be sustained over many years. This report summarizes current knowledge of natural and cultural resources primarily within the VTR construction area. At the time of this report, the proposed VTR site design includes a construction area of ~150.4 acres (~69.9 ha), which contains an ~51.3-acre (~20.8-ha) operations area, located within forested natural areas of the ORR. The primary goal of the work presented here was to evaluate potential effects on sensitive resources that might result from development and construction activities associated with VTR. In addition to on-the-ground surveys during spring and summer 2020 by the ORNL Natural Resources Management Program and Aquatic Ecology Group staff, this report makes use of historical (pre-1995) and contemporary (1995 to present) data from additional confirmed sources (e.g., TDEC). Likewise, forest conditions were compiled from a 2011 forest inventory and supplemented with limited ground observations in 2020. The individuals who obtained and compiled the data presented here are familiar with and routinely assess sensitive resources on the ORR. Anyone who references this report must consider that the timing of surveys did not permit a complete delineation of the resources that will be affected. If the VTR project proceeds, additional surveys will be required to account for the seasonal patterns of various threatened and endangered species. Data deficiencies and potential resources that likely went undetected are indicated where possible. Accordingly, this report should facilitate more environmentally sound decisions during planning and 2 development of the VTR site, provide a foundation for further assessment of sensitive and cultural resources, and help project managers better address regulatory guidance and DOE policies on sustainable development in compliance with, for example, the US Endangered Species Act (ESA), Migratory Bird Treaty Act (MBTA), Tennessee Rare Plant Protection and Conservation Act of 1985, Tennessee Nongame and Endangered or Threatened Wildlife Species Conservation Act of 1974, several federal and state regulations regarding aquatic resource protection, and site-specific policies as outlined in various ORR management plans developed by ORNL and TWRA for DOE.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Two new SciDAC institutes promote mathematical tools and software technology for high-performance computing

Bigger is often said to be better, and the newest extreme-scale computers certainly are bigger, with millions of processing units. Moreover, the breadth of science performed on the U.S. Department of Energy (DOE) computing facilities is expanding, with new technology such as artificial intelligence emerging. These advances are exciting, creating new opportunities for scientific discovery; however, they also raise new questions for scientists who want to exploit these advances for tackling more complex problems. Will my simulation code be able to utilize the accelerators in extreme-scale computing systems? Can I take advantage of the deepening memory hierarchy in heterogeneous processors? Is there a way around bottlenecks caused by the widening ratio of peak floating-point operations per second to I/0 bandwidth? How can I manage my huge amounts of data effectively? Can I analyze data in situ, or must I transfer it to offline storage for later analysis? To address such questions, DOE announced that it is providing $57.5 million over the next five years for two multidisciplinary teams — FASTMath and RAPIDS2 — to develop new tools and techniques to harness supercomputers for scientific discovery. The teams, called SciDAC Institutes, are part of the Scientific Discovery through Advanced Computing program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

The Hardware of Smaller Clusters (V.3.0)

Chris Saunders and three technologists are in high demand from Sandia’s deep learning teams, and they’re kept busy by building new clusters of computer nodes for researchers who need the power of supercomputing on a smaller scale. Sandia researchers working on Laboratory Directed Research & Development (LDRD) projects, or innovative ideas for solutions on short timeframes, formulate new ideas on old themes and frequently rely on smaller cluster machines to help solve problems before introducing their code to larger HPC resources. These research teams need an agile hardware and software environment where nascent ideas can be tested and cultivated on a smaller scale.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Initial full core SMR simulations with NekRS

This document describes the completion of a recent milestone of the ExaSMR program concerning "Full core simulations". The ExaSMR project is developing tools for coupling Monte Carlo (MC) radiation transport solvers to a computational fluid dynamics (CFD) solver. Work is based on the Shift MC, OpenMC MC, and Nek5000/NekRS CFD codes. As part of this milestone, a novel set of pin-resolved CFD full-core simulations have been performed for the first time. These simulations represent a significant increase in capability in what is now possible with CFD on pre-Exascale systems. The simulations have been performed with the spectral element solvers NekRS on the supercomputer Summit. Multiple simulations campaigns have been conducted: (1) LES simulations in bare bundle, (2) RANS simulations in bare bundles, (3) RANS simulations with momentum sources and (4) Conjugate heat transfer calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

SST-GPU: A Scalable SST GPU Component for Performance Modeling and Profiling

Programmable accelerators have become commonplace in modern computing systems. Advances in programming models and the availability of unprecedented amounts of data have created a space for massively parallel accelerators capable of maintaining context for thousands of concurrent threads resident on-chip. These threads are grouped and interleaved on a cycle-by-cycle basis among several massively parallel computing cores. One path for the design of future supercomputers relies on an ability to model the performance of these massively parallel cores at scale. The SST framework has been proven to scale up to run simulations containing tens of thousands of nodes. A previous report described the initial integration of the open-source, execution-driven GPU simulator, GPGPU-Sim, into the SST framework. This report discusses the results of the integration and how to use the new GPU component in SST. It also provides examples of what it can be used to analyze and a correlation study showing how closely the execution matches that of a Nvidia V100 GPU when running kernels and mini-apps.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

IC reports (2021)

We requested HPC support to continue research on the seismic waves generated by impacts. We used the following codes: (1) the Hybrid Optimization Software Suite (HOSS), developed at LANL. HOSS is based on a combined Finite and Discrete Element Method (FDEM). New material models are developed for the sedimentary rocks. HOSS has been recently benchmarked to iSale and FLAG codes. SPECFEM3D is an open-source code developed since the last 90s. It won the Gordon Bell award for best performance in 2003, was finalist again in 2008 for a run at 0.16 petaflops on 149,784 cores on the ‘Jaguar’ Cray system at Oak Ridge National Laboratory. It also won the BULL Joseph Fourier supercomputing award in 2010.; SW4 is a 4th-order finite difference code developed at LLNL which is currently actively developed to handle complex 3D models and to be ported on future exascale platforms. We assessed our need to a total of 3.9M CPU-hrs for year 1 and and 3.1 M for year 2.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Validation of energetic particle transport models for time-dependent integrated simulations of burning plasmas (Final ST Report)

The major goal of this project is to deliver a suite of validated energetic particle (EP) modeling tools for time-dependent integrated tokamak simulations (with the code TRANSP) that can be used for modeling plasma discharges featuring a substantial EP content, such as burning plasmas. During FY20, issues were resolved with an energetic particle transport model called TGLF-EP, with improvements made to the TGLF-EP workflow, generation of input files, and interpretation of runs on the NERSC supercomputing cluster. The recipient also gave input on simulations with the code TRANSP to reproduce the reference JET discharge, and assessed the accuracy and uncertainties of the simulated B field, current evolution, thermal plasma profiles, stored energy, etc. Input was also given on interpretation of fast-ion instability calculations and recommendations for modifications to JET afterglow discharge for the upcoming DT campaign.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Milestone M6 Report: Reducing Excess Data Movement Part 1

This is the second in a sequence of three Hardware Evaluation milestones that provide insight into the following questions: What are the sources of excess data movement across all levels of the memory hierarchy, going out to the network fabric? What can be done at various levels of the hardware/software hierarchy to reduce excess data movement? How does reduced data movement track application performance? The results of this study can be used to suggest where the DOE supercomputing facilities, working with their hardware vendors, can optimize aspects of the system to reduce excess data movement. Quantitative analysis will also benefit systems software and applications to optimize caching and data layout strategies. Another potential avenue is to answer cost-benefit questions, such as those involving memory capacity versus latency and bandwidth. This milestone focuses on techniques to reduce data movement, quantitatively evaluates the efficacy of the techniques in accomplishing that goal, and measures how performance tracks data movement reduction. We study a small collection of benchmarks and proxy mini-apps that run on pre-exascale GPUs and on the Accelsim GPU simulator. Our approach has two thrusts: to measure advanced data movement reduction directives and techniques on the newest available GPUs, and to evaluate our benchmark set on simulated GPUs configured with architectural refinements to reduce data movement.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

FY 2021 Mid-Year HPC Utilization Report M3UF-21IN0701018

Idaho National Laboratory (INL), supported by the Department of Energy Office of Nuclear Energy (DOE-NE) through the Nuclear Science User Facilities, provides access to supercomputer systems and data storage along with support staff for system management, software installation, cybersecurity and user support to the broader DOE-NE user community. Users include individuals at universities, industry, and government laboratories enabling a wide range of research and development and mission-supporting activities. The availability of high-performance computing (HPC) capabilities is a key foundation of collaboration and innovation in nuclear energy systems research. HPC resources and INL directly support the mission and objectives of DOE-NE. From October 2020 through March 2021, INL HPC capabilities were utilized by a diverse set of computing and applied researchers, for a wide range of research and engineering activities. This report focuses on current INL HPC systems and utilization from October 1, 2020 through March 31, 2021.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Report on the LLNL Global Full-waveform Inversion Workflow and Progress

LLNL has developed the SPiRaL global seismic tomography model based upon millions of body wave travel times and surface wave dispersion curves in the period range of 25-200 seconds (Simmons et al., 2021). The motivation to construct the SPiRaL model (which stands for S-, P-, Rayleigh, and Love waves) is based upon the guidance provided by a 3-D model workshop held in Berkeley in 2007 and documented in a paper by Zucca et al. (2009). It was concluded in Zucca et al. (2009) that a “practical and obtainable” model is one that predicts body wave travel times for event location while also predicting surface wave velocities for moment tensor estimation. We have largely followed that guidance which has led to the construction of SPiRaL. Looking forward, we now seek to improve the global model through full waveform inversion (FWI). This necessitates the development/customization of an efficient and flexible modeling workflow to automate the process using LLNL’s supercomputing platforms. This report briefly outlines the work that being performed at LLNL to develop the necessary tools and framework to update the SPiRaL global model with full waveform information.

58 GEOSCIENCES↗
DOE OSTI2021

Advances in Mixed Precision Algorithms: 2021 Edition

Over the last year, the ECP xSDK-multiprecision effort has made tremendous progress in developing and deploying new mixed precision technology and customizing the algorithms for the hardware deployed in the ECP flagship supercomputers. The effort also has succeeded in creating a cross-laboratory community of scientists interested in mixed precision technology and now working together in deploying this technology for ECP applications. In this report, we highlight some of the most promising and impactful achievements of the last year. Among the highlights we present are: Mixed precision IR using a dense LU factorization and achieving a 1.8× speedup on Spock; results and strategies for mixed precision IR using a sparse LU factorization; a mixed precision eigenvalue solver; Mixed Precision GMRES-IR being deployed in Trilinos, and achieving a speedup of 1.4× over standard GMRES; compressed Basis (CB) GMRES being deployed in Ginkgo and achieving an average 1.4× speedup over standard GMRES; preparing hypre for mixed precision execution; mixed precision sparse approximate inverse preconditioners achieving an average speedup of 1.2×; and detailed description of the memory accessor separating the arithmetic precision from the memory precision, and enabling memory-bound low precision BLAS 1/2 operations to increase the accuracy by using high precision in the computations without degrading the performance. We emphasize that many of the highlights presented here have also been submitted to peer-reviewed journals or established conferences, and are under peer-review or have already been published.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Advances in Mixed Precision Algorithms: 2021 Edition

Over the last year, the ECP xSDK-multiprecision effort has made tremendous progress in developing and deploying new mixed precision technology and customizing the algorithms for the hardware deployed in the ECP flagship supercomputers. The effort also has succeeded in creating a cross-laboratory community of scientists interested in mixed precision technology and now working together in deploying this technology for ECP applications. In this report, we highlight some of the most promising and impactful achievements of the last year. Among the highlights we present are • Mixed precision IR using a dense LU factorization and achieving a 1.8× speedup on Spock; • Results and strategies for mixed precision IR using a sparse LU factorization; • A mixed precision eigenvalue solver; • Mixed Precision GMRES-IR being deployed in Trilinos, and achieving a speedup of 1.4× over standard GMRES; • Compressed Basis (CB) GMRES being deployed in Ginkgo and achieving an average 1.4× speedup over standard GMRES; • Preparing hypre for mixed precision execution; • Mixed precision sparse approximate inverse preconditioners achieving an average speedup of 1.2×; • Detailed description of the memory accessor separating the arithmetic precision from the memory precision, and enabling memory-bound low precision BLAS 1/2 operations to increase the accuracy by using high precision in the computations without degrading the performance. We emphasize that many of the highlights presented here have also been submitted to peer-reviewed journals or established conferences, and are under peer-review or have already been published.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Using Pilot Jobs and CernVM File System for Simplified Use of Containers and Software Distribution

High Energy Physics (HEP) experiments entail an abundance of computing resources, i.e. sites, to run simulations and analyses by processing data. This requirement is fulfilled by local batch farms, grid sites, private/commercial clouds, and supercomputing centers via High Throughput Computing (HTC). The growing needs of such experiments and resources being prone to trends of heterogeneity make it difficult for physicists to handle these resources directly. Additionally, HEP collaborations heavily rely on data and software releases, typically in the order of tens of gigabytes, while conducting simulations and analyses. Hence, aspects of scalability, reliability, and maintenance become crucial with regards to the distribution of the necessary data and software stack. The GlideinWMS [4] framework helps with the resource management problem by using pilot jobs, aka Glideins, to provision reliable elastic virtual clusters. Glideins are submitted to unreliable heterogeneous resources which are validated and customized by the Glideins to make the worker nodes available for end-user job execution. On the other hand, the CernVM File System (CernVM-FS or CVMFS) [1] helps with data distribution. It is a write-once, read-everywhere filesystem used to deploy scientific software to thousands of nodes on a worldwide distributed computing infrastructure. CVMFS is based on the Hyper Text Transfer Protocol and has been widely used within the particle physics community for (1) distributing experiment software and data such as calibrations, and (2) facilitating containerization by efficiently hosting container images along with providing containerization software, especially Singularity [3] GlideinWMS relies on CVMFS installed locally on the computing resources to satisfy the experiments' software needs. This requires system administrators' effort to install and maintain CVMFS at the sites and limits the use of sites, especially HPC resources, that do not have CVMFS installed. This poster presents a solution, taking advantage of Glideins to provide CVMFS at most sites without the need for a local installation. Doing so expands the pool of resources available for HEP experiments and reduces the effort of system administrators for current resources. Additionally, the proposed solution allows GlideinWMS to also start Singularity [3], a containerization software that can run unprivileged, on sites where neither CVMFS nor Singularity are available, including HPC sites. The benefits provided by this solution are: (1) lower overhead for site administrators in that they have less software to install, (2) an expanded pool of resources that run user jobs with easy access to software and data provided by CVMFS, thus making life easier for the scientists, and (3) improved flexibility to use HPC resources by enabling GlideinWMS pilot jobs to support HPC sites.

Urs, Namratha↗
DOE OSTI2021

Legacy of Metropolis continues through new materials donated to classified library collections

“From the very beginning of the Los Alamos project, it was inevitable that the Laboratory would suffer total immersion in computing,” said Nicholas Constantine Metropolis in 1976, reflecting his characteristic humor. Metropolis had succinctly summarized the prominent place of computing in Los Alamos’s mission and history. Metropolis himself played no small role in that “total immersion,” exemplified by the Lab’s supercomputing center, a postdoctoral fellowship, and the world-famous algorithm that carry his name. So does a collection of legacy materials in the National Security Research Center (NSRC). The NSRC, the Lab’s classified library, which also houses unclassified artifacts, recently received a new addition to the Metropolis Collections. This donation, 22 years after his death on October 17, 1999, provides tangible evidence of Metropolis’s continuing legacy at Los Alamos.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Distributed Training for High Resolution Images: A Domain and Spatial Decomposition Approach

In this work we developed two Pytorch libraries using the PyTorch RPC interface for distributed deep learning approaches on high resolution images. The spatial decomposition library allows for distributedtraining on very large images, which otherwise won’t be possible on a single GPU. The domain parallelism library allows for distributed training across multiple domain unlabeled data, by leveraging the domain separation architecture. Both of those libraries were tested on the Summit supercomputer at a moderate scale, and we are releasing the code for both of them.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Dipolar molecule emulator of lattice gauge theories (Final Report)

The quantum many-body problem is a great unsolved, cross-cutting challenge in physics that is of fundamental importance. Our understanding of phenomena related to dense quark matter, in particular, is challenged by this practical intractability of classical simulations. Because of the sheer cost and challenge of performing experiments that probe the length and energy scales relevant to such physics, there are practical motivations for finding theoretical methods to address the many-body problem. One promising approach is based on the use of a programmable and controllable analog quantum systems to emulate the physics of many-body problems of interest. While there are currently broad efforts to develop mid- to large-scale quantum computers, we are still likely many years away from such devices outperforming classical supercomputers for useful calculations. Even though digital quantum computers are still at a stage too premature for such tasks, approaches based on analog quantum simulators have advanced rapidly over the past two decades and can now treat many-body problems of interest on small- to medium-scale systems. Tackling the challenging many-body problems of relevance to high energy physics represents one of the great new opportunities and challenges for the field of analog quantum simulation. To address this challenge, this award brought together an interdisciplinary team of physicists with expertise in high energy theory (El-Khadra and Draper), computational and condensed matter physics (Clark), and experimental quantum and atomic, molecular, optical (AMO) science (DeMarco and Gadway), with the goal of developing realistic and optimized strategies for the analog quantum simulation of lattice gauge theories using cold atoms and molecules. This track 1 project included both theoretical and experimental goals, stated as follows. The theory goals were to "develop and verify a novel approach to quantum emulation of (1+1)d quantum link models, based on arrays of trapped quantum spins with long-range interactions." This final project report details the progress made under this award, as well as new research directions developed under this award.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

2022 Agnew and Metropolis Postdoc Fellow Showcase Event Book

Agnew National Security Postdoc Fellows pursue cutting-edge experimental, theoretical, computational science, and engineering research aligned with the national security mission. Metropolis Postdoc Fellows pursue cutting-edge research in the areas of computational and computer science, physics, and engineering. Computer simulation capabilities are developed in support of the stockpile stewardship program together with broader national nuclear security needs. Fellows have access to some of the most powerful supercomputers in the world to perform pioneering research.

42 ENGINEERING↗