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At least 73 records · Page 4

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

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.

Oliker, Leonid↗

Persistent Memory Object Storage and Indexing for Scientific Computing

This paper presents Mosiqs, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design Mosiqs based on the key idea that memory objects on shared PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. Mosiqs provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects. Mosiqs uses a lightweight persistent memory key-value store to manage the metadata of memory objects such as persistent pointer mappings, which enables memory object sharing for effective scientific collaborations. Mosiqs is implemented atop PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. The preliminary evaluation confirms a 100% improvement for write and 30% in read performance against a PM-aware file system approach.

Khan, Awais↗

The InSAR Scientific Computing Environment 3.0: A Flexible Framework for NISAR Operational and User-Led Science Processing

The InSAR Scientific Computing Environment (ISCE) was first developed under the NASA Advanced Information Systems Technology as a flexible, extensible object-oriented framework for Interferometric Synthetic Aperture Radar (InSAR) processing. The ISCE framework uses Python 3 at the workflow level, controlling modules of compiled code for functional processing, and managing inputs, outputs, and other flow control services. The currently released version, called ISCE 2.1, is distributed to the research community through the Western North America InSAR Consortium under a research license. The ISCE team is working on the next generation of the code in order to prepare for the NASAISRO SAR (NISAR) mission operational processing. Innovations in this code include augmentation or conversion of the custom Python framework elements in ISCE with the Pyre framework, new workflows for interferometric and polarimetric stack processing, a more intuitive and graphically based user interface, and flow control for hybrid computing environments including CPU/GPU clusters, logging and error tracking facilities, and new more efficient computational modules that exploit graphical processor units (GPUs) when available. The ISCE 3.0 framework is designed to work in an operational environment as well as on a single user’s laptop or compute cluster, with services to discover capabilities and scale computations accordingly.

Buckley, Sean M.↗

Approximation algorithms in combinatorial scientific computing

We survey recent work on approximation algorithms for computing degree-constrained subgraphs in graphs and their applications in combinatorial scientific computing. The problems we consider include maximization versions of cardinality matching, edge-weighted matching, vertex-weighted matching and edge-weighted $b$ -matching, and minimization versions of weighted edge cover and $b$ -edge cover. Exact algorithms for these problems are impractical for massive graphs with several millions of edges. For each problem we discuss theoretical foundations, the design of several linear or near-linear time approximation algorithms, their implementations on serial and parallel computers, and applications. Our focus is on practical algorithms that yield good performance on modern computer architectures with multiple threads and interconnected processors. We also include information about the software available for these problems.

Mathematics↗

Environmental and Energy Research at the Texas Center for Advanced Scientific Computing and Modeling (CASCaM)

The funding enabled the creation of the (University of North) Texas Center for Advanced Scientific Computing and Modeling (CASCaM). Due to its success, CASCaM has continued to grow beyond the initial team focused on the biological and environmental research discussed herein, with investments by the University of North Texas in new faculty and researchers who contribute to CASCaM research. CASCaM is now a sustainable effort, with researchers across multiple fields including chemistry, physics, biology, mechanical engineering, materials science, and other fields, with multiple researchers engaged in a broad variety of research, including other DOE projects. Over 20 PI’s and ~100 researchers are engaged in CASCaM research. The overall goal of the research effort was to provide greater understanding about carbon capture, storage, and utilization. As part of this effort, the development of computational methods and identification of novel strategies to support the CO2 and CO studies were necessary. Three primary themes were investigated: carbon dioxide and CO catalysis; protein- and amino acid-based strategies towards carbon dioxide capture, storage, and utilization; and, finally, the methodology improvements for modeling carbon dioxide chemistry

54 ENVIRONMENTAL SCIENCES↗

Reimagining Codesign for Advanced Scientific Computing: Report for the ASCR Workshop on Reimagining Codesign

In March 2021, the U.S. Department of Energy’s Advanced Scientific Computing Research program convened the Workshop on Reimagining Codesign. The workshop, also known as ReCoDe, was organized around discussions on eight topic areas: (1) codesign for traditional high-performance computing workloads; (2) codesign of memory/storage systems; (3) codesign of machine learning, neuromorphic, quantum, and other non-von Neumann accelerators; (4) codesign for edge computing and processing at experimental instruments; (5) codesign for security and privacy; (6) hardware design tools and open-source hardware for high-productivity codesign; (7) tools, software stack, and programming languages for high-productivity codesign; and (8) quantitative tools and data collection for modeling and simulation for codesign. The panels identified four Priority Research Directions from these deliberations: (1) breakthrough computing capabilities with targeted heterogeneity and rapid design; (2) software and applications that embrace radical architecture diversity; (3) engineered security and integrity, from transistors to applications; and (4) design with data-rich processes.

97 MATHEMATICS AND COMPUTING↗

A data management system for engineering and scientific computing

Data elements and relationship definition capabilities for this data management system are explicitly tailored to the needs of engineering and scientific computing. System design was based upon studies of data management problems currently being handled through explicit programming. The system-defined data element types include real scalar numbers, vectors, arrays and special classes of arrays such as sparse arrays and triangular arrays. The data model is hierarchical (tree structured). Multiple views of data are provided at two levels. Subschemas provide multiple structural views of the total data base and multiple mappings for individual record types are supported through the use of a REDEFINES capability. The data definition language and the data manipulation language are designed as extensions to FORTRAN. Examples of the coding of real problems taken from existing practice in the data definition language and the data manipulation language are given.

Elliot, L.↗

High Energy Physics Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and High Energy Physics, June 10-12, 2015, Bethesda, Maryland

The U.S. Department of Energy (DOE) Office of Science (SC) Offices of High Energy Physics (HEP) and Advanced Scientific Computing Research (ASCR) convened a programmatic Exascale Requirements Review on June 10–12, 2015, in Bethesda, Maryland. This report summarizes the findings, results, and recommendations derived from that meeting. The high-level findings and observations are as follows. Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude — and in some cases greater — than that available currently. The growth rate of data produced by simulations is overwhelming the current ability of both facilities and researchers to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. Data rates and volumes from experimental facilities are also straining the current HEP infrastructure in its ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. A close integration of high-performance computing (HPC) simulation and data analysis will greatly aid in interpreting the results of HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. Long-range planning between HEP and ASCR will be required to meet HEP’s research needs. To best use ASCR HPC resources, the experimental HEP program needs (1) an established, long-term plan for access to ASCR computational and data resources, (2) the ability to map workflows to HPC resources, (3) the ability for ASCR facilities to accommodate workflows run by collaborations potentially comprising thousands of individual members, (4) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, (5) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.

97 MATHEMATICS AND COMPUTING↗

Parallel Time Integration: An Approaching Paradigm Shift for Scientific Computing

This note argues that parallel-in-time methods will be necessary for doing high-fidelity time-dependent simulations in the future. A “proof” is given to support the argument and to provide a framework for debate. The effect of a parallel-in-time paradigm on scientific computing practice is also discussed.

97 MATHEMATICS AND COMPUTING↗

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

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, and 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.

97 MATHEMATICS AND COMPUTING↗

Basic Energy Sciences Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Basic Energy Sciences, November 3-5, 2015, Rockville, Maryland

Computers have revolutionized every aspect of our lives. Yet in science, the most tantalizing applications of computing lie just beyond our reach. The current quest to build an exascale computer with one thousand times the capability of today’s fastest machines (and more than a million times that of a laptop) will take researchers over the next horizon. The field of materials, chemical reactions, and compounds is inherently complex. Imagine millions of new materials with new functionalities waiting to be discovered — while researchers also seek to extend those materials that are known to a dizzying number of new forms. We could translate massive amounts of data from high precision experiments into new understanding through data mining and analysis. We could have at our disposal the ability to predict the properties of these materials, to follow their transformations during reactions on an atom-by-atom basis, and to discover completely new chemical pathways or physical states of matter. Extending these predictions from the nanoscale to the mesoscale, from the ultrafast world of reactions to long-time simulations to predict the lifetime performance of materials, and to the discovery of new materials and processes will have a profound impact on energy technology. In addition, discovery of new materials is vital to move computing beyond Moore’s law. To realize this vision, more than hardware is needed. New algorithms to take advantage of the increase in computing power, new programming paradigms, and new ways of mining massive data sets are needed as well. This report summarizes the opportunities and the requisite computing ecosystem needed to realize the potential before us. In addition to pursuing new and more complete physical models and theoretical frameworks, this review found that the following broadly grouped areas relevant to the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR) would directly affect the Basic Energy Sciences (BES) mission need. Simulation, visualization, and data analysis are crucial for advances in energy science and technology. Revolutionary mathematical, software, and algorithm developments are required in all areas of BES science to take advantage of exascale computing architectures and to meet data analysis, management, and workflow needs. In partnership with ASCR, BES has an emerging and pressing need to develop new and disruptive capabilities in data science. More capable and larger high-performance computing (HPC) and data ecosystems are required to support priority research in BES. Continued success in BES research requires developing the next-generation workforce through education and training and by providing sustained career opportunities.

97 MATHEMATICS AND COMPUTING↗

Scientific Computing Paradigm

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.

VanZandt, John↗

Scientific Computation Application Partnerships in Materials and Chemical Sciences, Charge Transfer and Charge Transport in Photoactivated Systems, Developing Electron-Correlated Methods for Excited State Structure and Dynamics in the NWChem Software Suite

Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.

14 SOLAR ENERGY↗

Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation

Achieving performance portability for high-performance computing (HPC) applications in scientific fields has become an increasingly important initiative due to large differences in emerging supercomputer architectures. Here we test some key kernels from molecular dynamics (MD) to determine whether the use of the OpenACC directive-based programming model when applied to these kernels can result in performance within an acceptable range for these types of programs in the HPC setting. We find that for easily parallelizable kernels, performance on the GPU remains within this range. On the CPU, OpenACC-parallelized pairwise distance kernels would not meet the performance standards required, when using AMD Opteron “Interlagos” processors, but with IBM Power 9 processors, performance remains within an acceptable range for small batch sizes. These kernels provide a test for achieving performance portability with compiler directives for problems with memory-intensive components as are often found in scientific applications.

Sedova, Ada↗

QSCOUT Progress Report, June 2022 [Quantum Scientific Computing Open User Testbed]

Quantum information processing has reached an inflection point, transitioning from proof-of-principle scientific experiments to small, noisy quantum processors. To accelerate this process and eventually move to fault-tolerant quantum computing, it is necessary to provide the scientific community with access to whitebox testbed systems. The Quantum Scientific Computing Open User Testbed (QSCOUT) provides scientists unique access to an innovative system to help advance quantum computing science.

97 MATHEMATICS AND COMPUTING↗

Scientific computing

Our research generates a vast amount of data that scientists must gather, store, analyze and interpret. These activities require expertise and the right tools. Fermilab is home to one of the largest tape robotic systems available today, providing more than 800 petabytes of storage capability. The lab is growing the tape facilities to meet expected demands of over 1,000 petabytes of additional data per year by the end of the decade. Fermilab also has the technology and computing power to efficiently pr ocess these data to facilitate scientific discoveries. Our computation al experts work closely with experimenters and the scientific commu - nity at large to provide and facilitate the use of the cutting-edge computing tools necessary for these discoveries.

Fermilab, Fermilab↗

Combinatorial Algorithms in Scientific Computing

We provide the final report for this grant, detailing the publications, software produced, students trained who have joined the DOE workforce, and the impact our work has had on computational mathematics and related disciplines.

97 MATHEMATICS AND COMPUTING↗

Double Diffusion Maps and their Latent Harmonics for scientific computations in latent space

In this work, we introduce a data-driven approach to building reduced dynamical models through manifold learning; the reduced latent space is discovered using Diffusion Maps (a manifold learning technique) on time series data. A second round of Diffusion Maps on those latent coordinates allows the approximation of the reduced dynamical models. This second round enables mapping the latent space coordinates back to the full ambient space (what is called lifting); it also enables the approximation of full state functions of interest in terms of the reduced coordinates. In our work, we develop and test three different reduced numerical simulation methodologies, either through pre-tabulation in the latent space and integration on the fly or by going back and forth between the ambient space and the latent space. The data-driven latent space simulation results, based on the three different approaches, are validated through (a) the latent space observation of the full simulation through the Nyström Extension formula, or through (b) lifting the reduced trajectory back to the full ambient space, via Latent Harmonics. Latent space modeling often involves additional regularization to favor certain properties of the space over others, and the mapping back to the ambient space is then constructed mostly independently from these properties; here, we use the same data-driven approach to construct the latent space and then map back to the ambient space.

97 MATHEMATICS AND COMPUTING↗