SEARCH · Search NASA

Results for “Computer Science - Distributed”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18

All sources NASA NTRS DOE OSTI

DOE OSTI2023

An Implicit Approach to Phase Field Modeling of Solidification for Additively Manufactured Alloys [Slides]

We are leveraging modern algorithms and computational science to provide a route to predictive simulation of microstructure evolution on emerging exascale architectures. We are utilizing the fastest supercomputers in the world for modeling and simulation of microstructure evolution for generation of data under AM conditions. Solidification conditions in AM can be tailored for the reliable design of materials to specific performance requirements. Developing computational tools to further characterize alloys and correlate the processing-structure-properties-performance (PSPP) relationship.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Compiler and Runtime Approaches to Enable Large-Scale Irregular Programs. Final report, July 2013 - July 2019

While regular algorithms, characterized by operations on dense matrices and arrays, have long been the mainstay of scientific, high-performance computing, irregular algorithms, which feature unpredictable accesses to pointer-based data structures, are becoming increasingly common in high performance computing, arising in graph analysis, data mining and visualization, among other domains. Unfortunately, the defining characteristics of irregular applications, their dynamic, unpredictable, data-dependent access patterns and data layouts, make achieving high performance on large scale systems difficult. Scaling applications to peta- and exa-scale requires carefully controlling communication and data movement and placement, an inherently difficult task when access patterns and data layouts are unpredictable! Most irregular applications that attain high performance must be painstakingly hand-written and hand-tuned, with few common principles or paradigms uniting various implementations and easing future development. Despite the increasing importance of irregular applications, there is little programmer knowledge, and even less compiler ability, devoted to optimizing them. This project aims to solve these problems. By allowing programmers to write irregular applications in high level forms, with at most a few annotations highlighting key structural properties, programmers can focus on developing their algorithms and methods. The compiler and run-time system can take on the tedious task of optimizing the application for execution at large scales, and can automatically provide efficient implementations. This will provide portability and ease maintenance for existing irregular applications, but, more importantly, open up whole new domains of computational science to large-scale, high-performance simulation codes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Sandia's Research in Support of COVID-19 Pandemic Response: Computing and Information Sciences

This report summarizes the goals and findings of eight research projects conducted under the Computing and Information Sciences (CIS) Research Foundation and related to the COVID- 19 pandemic. The projects were all formulated in response to Sandia's call for proposals for rapid-response research with the potential to have a positive impact on the global health emergency. Six of the projects in the CIS portfolio focused on modeling various facets of disease spread, resource requirements, testing programs, and economic impact. The two remaining projects examined the use of web-crawlers and text analytics to allow rapid identification of articles relevant to specific technical questions, and categorization of the reliability of content. The portfolio has collectively produced methods and findings that are being applied by a range of state, regional, and national entities to support enhanced understanding and prediction of the pandemic's spread and its impacts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Generating Protein Structures for Pathway Discovery Using Deep Learning

Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE’s modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Distinguished honors for LANL ASC program associates: E.O. Lawrence Awards and Laboratory Fellow Appointments

LANL ASC program associates have been honored as recipients of highly competitive scientific achievement awards. Luis Chacon and Dana Dattelbaum received DOE E.O. Lawrence awards in 2021 and 2020, respectively. Tim Germann, Lin Yin, Ricardo Lebensohn and Hui Li were four of nine LANL Laboratory Fellows appointed for membership in 2022. Each of these awardees has been an influential technical leader in computational sciences impacting both the ASC program and international scientific communities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter]

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particles and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

Fusion Energy Sciences Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Fusion Energy Sciences, January 27-29, 2016, Gaithersburg, Maryland

The additional computing power offered by the planned exascale facilities could be transformational across the spectrum of plasma and fusion research — provided that the new architectures can be efficiently applied to our problem space. The collaboration that will be required to succeed should be viewed as an opportunity to identify and exploit cross-disciplinary synergies. To assess the opportunities and requirements as part of the development of an overall strategy for computing in the exascale era, the Exascale Requirements Review meeting of the Fusion Energy Sciences (FES) community was convened January 27–29, 2016, with participation from a broad range of fusion and plasma scientists, specialists in applied mathematics and computer science, and representatives from the U.S. Department of Energy (DOE) and its major computing facilities. This report is a summary of that meeting and the preparatory activities for it and includes a wealth of detail to support the findings. Technical opportunities, requirements, and challenges are detailed in this report (and in the recent report on the Workshop on Integrated Simulation). Science applications are described, along with mathematical and computational enabling technologies. Also see http://exascaleage.org/fes/ for more information.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

DOE FAIR Surrogate Benchmarks Supporting AI and Simulation Research (SBI Surrogate Benchmark Initiative) (Final Report)

Computational Science is being revolutionized by integrating AI and simulation and, in particular, by deep learning surrogate models that can replace all or part of traditional large‐scale HPC computations. Such surrogates can achieve remarkable performance improvements, as much as several orders of magnitude, and save both compute time and energy. The Surrogate Benchmark Initiative (SBI) project creates a community repository and FAIR (Findable, Accessible, Interoperable, and Reusable) data ecosystem for HPC application surrogate benchmarks. The SBI team comes from Argonne National Laboratory (ANL), Indiana University (IU), Rutgers University, the University of Tennessee, Knoxville (UTK), and the University of Virginia(UVA). SBI repositories include data, code, and all relevant collateral artifacts, that the science and engineering community needs to use and reuse these data sets and surrogates. SBI repositories generate active research from both participants in SBI and the broader AI and domain science communities. This project develops surrogates that use several different neural nets to learn and quickly infer the results of simulations and data systems and capture them as surrogate benchmarks with a rich set of metadata, covering. Data; Model; Metrics specification; Machine specification; Science, Speed, Power Results, We research FAIR metadata for these benchmarks. We develop application surrogate examples as benchmarks across many fields (ANL, UTK, IU, UVA). We also study non Surrogate benchmarks that have many common features and similar issues regarding FAIRness. We work with MLCommons (UVA, UTK), which is a major machine learning benchmarking activity where we get metadata ontologies, software, and benchmarks, benchmarks have datasets, models, and metadata, and they need a technical framework developed by UTK and Rutgers and deployed by UVA. We study features of Surrogates, including performance, training set size, and uncertainty quantification (Rutgers, UVA and IU).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

FAIR Surrogate Benchmarks Supporting AI and Simulation Research (Final Report)

Computational Science is being revolutionized by integrating AI and simulation and, in particular, by deep learning surrogate models that can replace all or part of traditional large‐scale HPC computations. Such surrogates can achieve remarkable performance improvements, as much as several orders of magnitude, and save both compute time and energy. The Surrogate Benchmark Initiative (SBI) project creates a community repository and FAIR (Findable, Accessible, Interoperable, and Reusable) data ecosystem for HPC application surrogate benchmarks. The SBI team comes from Argonne National Laboratory (ANL), Indiana University (IU), Rutgers University, the University of Tennessee, Knoxville (UTK), and the University of Virginia (UVA). SBI repositories include data, code, and all relevant collateral artifacts that the science and engineering community need to use and reuse these data sets and surrogates. SBI repositories generate active research from both the participants in SBI and the broad community of AI and domain scientists. This project develops surrogates that use several different neural nets to learn and quickly infer the results of simulations and data systems and captures them as surrogate benchmarks with a rich set of metadata covering: Data; Model; Metrics specification; Machine specification; and Science, Speed, and Power Results. We research FAIR metadata for these benchmarks. We develop application surrogate examples as benchmarks across many fields (ANL, UTK, IU, UVA). We also study non-Surrogate benchmarks that have many common features and similar issues as regards FAIRness. We work with MLCommons (UVA, UTK), which is a major machine learning benchmarking activity where we get metadata ontologies, software, and benchmarks, Benchmarks have datasets, models, and metadata and they need a technical framework developed by UTK and Rutgers and deployed by UVA. We study features of Surrogates including performance, training set size, and uncertainty quantification (Rutgers, UVA and IU).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactions methods, analytic gradients, and taking advantage of new hardware.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Smoky Mountain Data Challenge 2021: An Open Call to Solve Scientific Data Challenges Using Advanced Data Analytics and Edge Computing

The 2021 Smoky Mountains Computational Sciences and Engineering Conference enlists scientists from across Oak Ridge National Laboratory (ORNL) and industry to be data sponsors and help create data analytics and edge computing challenges for eminent datasets in a variety of scientific domains. This work describes the significance of each of the eight datasets and their associated challenge questions. The challenge questions for each dataset were required to cover multiple difficulty levels. An international call for participation was sent to students, asking them to form teams of up to six people and apply novel data analytics and edge computing methods to solve these challenges.

Devineni, Pravallika↗

DOE OSTI2015

Ultrafast dynamics of liquid water: Energy relaxation and transfer processes of the OH stretch and the HOH bend

The vibrational energy relaxation and transfer processes of the OH stretching and the HOH bending vibrations in liquid water are investigated via the theoretical calculation of the pump-probe spectra obtained from non-equilibrium molecular dynamics simulations with the TTM3-F interaction potential. The excitation of the OH stretch induces an instantaneous response of the high frequency librational motions in the 600-1000 cm-1 range. In addition, the excess energy of the OH stretch of a water molecule quickly transfers to the OH stretches of molecules in its first hydration shell with a time constant of ~50 fs, followed by relaxation to the HOH bends of the surrounding molecules with a time constant of 230 fs. The excitation of the HOH bend also results in the ultrafast excitation of the high frequency librational motions. The energy of the excited HOH bend of a water molecule decays, with a time constant of 200 fs, mainly to the relaxation of the HOH bends of its surrounding molecules. The energies of the HOH bends were found to transfer quickly to the intermolecular motions via the coupling with the high frequency librational motions. The excess energy of the OH stretch or the HOH bend relaxes to the high frequency intermolecular librational motions and eventually to the hot ground state with a time scale of ~1 ps via the coupling with the librational and translational motions. The energy relaxation and transfer processes were found to depend on the local hydrogen bonding network; the relaxations of the excess energy of the OH stretch and the HOH bend of four- and five-coordinated molecules are faster than those of a three-coordinated molecule due to the delocalization of the vibrational motions of the former (four- and five-coordinated molecules) compared to those of the later (three-coordinated molecules). The present results highlight the importance of the high frequency intermolecular librational modes in facilitating the ultrafast energy relaxation process in liquid water via their strong nonlinear couplings with the intramolecular OH stretching and HOH bending vibrations. S.S.X. acknowledges the support of the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The calculation was carried out using the computing resources at the Research Center for Computational Science in Okazaki, Japan.

Imoto, Sho↗

DOE OSTI2020

In-Situ Inference: Bringing Advanced Data Science Into Exascale Simulations

As simulations generate ever-increasing amounts of data, there are correspondingly richer opportunities for analysis and scientific discovery - discoveries that will be missed if most of the data must be discarded before it is analyzed. Because future exascale architectures will be increasingly storage-limited, it will not be possible to save the vast majority of simulation data for later analysis, requiring analysis to occur “in-situ” within the simulation. However, existing in-situ data analysis frameworks provide little or no support for one of the most sophisticated forms of data science: probabilistic statistical modeling or uncertainty quantification (UQ), and the accompanying challenge of inference - fitting those statistical models to massive simulation output. Our goal is to develop the fundamental statistical algorithms and computer science needed to perform statistical inference in-situ (in HPC simulations) to the full stream of data those simulations generate.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Brookhaven Lab Hosts Hackathon Focused on Graphics Processing Units (GPUs)

For five days in June 2017, Brookhaven Lab’s Computational Science Initiative hosted “Brookathon”—a programming workshop where teams of researchers, students, and software developers worked with mentors to accelerate scientific applications on GPUs for high-performance computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Center for Computing Research Summer Research Proceedings 2015.

The Center for Computing Research (CCR) at Sandia National Laboratories organizes a summer student program each summer, in coordination with the Computer Science Research Institute (CSRI) and Cyber Engineering Research Institute (CERI).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗