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DOE OSTI2019

A Shift Selection Strategy for Parallel Shift-Invert Spectrum Slicing in Symmetric Self-Consistent Eigenvalue Computation

The central importance of large scale eigenvalue problems in scientific computation necessitates the development massively parallel algorithms for their solution. Recent advances in dense numerical linear algebra have enabled the routine treatment of eigenvalue problems with dimensions on the order of hundreds of thousands on the world's largest supercomputers. In cases where dense treatments are not feasible, Krylov subspace methods offer an attractive alternative due to the fact that they do not require storage of the problem matrices. However, demonstration of scalability of either of these classes of eigenvalue algorithms on computing architectures capable of expressing excessive parallelism is non-trivial due to communication requirements and serial bottlenecks, respectively. In this work, we introduce the SISLICE method: a parallel shift-invert algorithm for the solution of the symmetric self-consistent field (SCF) eigenvalue problem. The SISLICE method drastically reduces the communication requirement of current parallel shift-invert eigenvalue algorithms through various shift selection and migration techniques based on density of states estimation and k-means clustering, respectively. This work demonstrates the robustness and parallel performance of the SISLICE method on a representative set of SCF eigenvalue problems and outlines research directions which will be explored in future work.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Compiler-based code generation and autotuning for geometric multigrid on GPU-accelerated supercomputers

GPUs, with their high bandwidths and computational capabilities are an increasingly popular target for scientific computing. Unfortunately, to date, harnessing the power of the GPU has required use of a GPU-specific programming model like CUDA, OpenCL, or OpenACC. Thus, in order to deliver portability across CPU-based and GPU-accelerated supercomputers, programmers are forced to write and maintain two versions of their applications or frameworks. In this paper, we explore the use of a compiler-based autotuning framework based on CUDA-CHiLL to deliver not only portability, but also performance portability across CPU- and GPU-accelerated platforms for the geometric multigrid linear solvers found in many scientific applications. We also show that with autotuning we can attain near Roofline (a performance bound for a computation and target architecture) performance across the key operations in the miniGMG benchmark for both CPU- and GPU-based architectures as well as for a multiple stencil discretizations and smoothers. We show that our technology is readily interoperable with MPI resulting in performance at scale equal to that obtained via hand-optimized MPI+CUDA implementation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

High Performance Computing Facility Operational Assessment 2015: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable systems; creating innovative solutions for high-performance computing (HPC) needs; and managing risks, safety, and security aspects associated with operating one of the most powerful computers in the world. The results can be seen in the cutting-edge science delivered by users and the praise from the research community. Calendar year (CY) 2015 was filled with outstanding operational results and accomplishments: a very high rating from users on overall satisfaction that ties the highest-ever mark set in CY 2014; the greatest number of core-hours delivered to research projects; the largest percentage of capability usage since the OLCF began tracking the metric in 2009; and success in delivering on the allocation of 60, 30, and 10% of core hours offered for the INCITE (Innovative and Novel Computational Impact on Theory and Experiment), ALCC (Advanced Scientific Computing Research Leadership Computing Challenge), and Director’s Discretionary programs, respectively. These accomplishments, coupled with the extremely high utilization rate, represent the fulfillment of the promise of Titan: maximum use by maximum-size simulations. The impact of all of these successes and more is reflected in the accomplishments of OLCF users, with publications this year in notable journals Nature, Nature Materials, Nature Chemistry, Nature Physics, Nature Climate Change, ACS Nano, Journal of the American Chemical Society, and Physical Review Letters, as well as many others. The achievements included in the 2015 OLCF Operational Assessment Report reflect first-ever or largest simulations in their communities; for example Titan enabled engineers in Los Angeles and the surrounding region to design and begin building improved critical infrastructure by enabling the highest-resolution Cybershake map for Southern California to date. The Titan system provides the largest extant heterogeneous architecture for computing and computational science. Usage is high, delivering on the promise of a system well-suited for capability simulations for science. This success is due in part to innovations in tracking and reporting the activity on the compute nodes, and using this information to further enable and optimize applications, extending and balancing workload across the entire node. The OLCF continues to invest in innovative processes, tools, and resources necessary to meet continuing user demand. The facility’s leadership in data analysis and workflows was featured at the Department of Energy (DOE) booth at SC15, for the second year in a row, highlighting work with researchers from the National Library of Medicine coupled with unique computational and data resources serving experimental and observational data across facilities. Effective operations of the OLCF play a key role in the scientific missions and accomplishments of its users. Building on the exemplary year of 2014, as shown by the 2014 Operational Assessment Report (OAR) review committee response in Appendix A, this OAR delineates the policies, procedures, and innovations implemented by the OLCF to continue delivering a multi-petaflop resource for cutting-edge research. This report covers CY 2015, which, unless otherwise specified, denotes January 1, 2015, through December 31, 2015.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2012

Evaluating the Efficacy of the Cloud for Cluster Computation

Computing requirements vary by industry, and it follows that NASA and other research organizations have computing demands that fall outside the mainstream. While cloud computing made rapid inroads for tasks such as powering web applications, performance issues on highly distributed tasks hindered early adoption for scientific computation. One venture to address this problem is Nebula, NASA's homegrown cloud project tasked with delivering science-quality cloud computing resources. However, another industry development is Amazon's high-performance computing (HPC) instances on Elastic Cloud Compute (EC2) that promises improved performance for cluster computation. This paper presents results from a series of benchmarks run on Amazon EC2 and discusses the efficacy of current commercial cloud technology for running scientific applications across a cluster. In particular, a 240-core cluster of cloud instances achieved 2 TFLOPS on High-Performance Linpack (HPL) at 70% of theoretical computational performance. The cluster's local network also demonstrated sub-100 ?s inter-process latency with sustained inter-node throughput in excess of 8 Gbps. Beyond HPL, a real-world Hadoop image processing task from NASA's Lunar Mapping and Modeling Project (LMMP) was run on a 29 instance cluster to process lunar and Martian surface images with sizes on the order of tens of gigapixels. These results demonstrate that while not a rival of dedicated supercomputing clusters, commercial cloud technology is now a feasible option for moderately demanding scientific workloads.

Cloud Computing↗

DOE OSTI2020

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory's (ORNL's) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high performance computing (HPC) needs; and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2019 was a big year as OLCF staff ran five world-class resources (the leadershipclass computers Titan and Summit, the large analysis cluster called Eos, and the massive parallel filesystems called Atlas and Alpine)) and also began power and cooling upgrades for a 2021 exascale system called Frontier. While continuing exceptional operation of Titan, Eos, and Rhea, the OLCF released the Summit supercomputer for production on January 1, 2019. Summit debuted as the most capable and efficient system in its class and has been recognized as the most powerful system in the world for its performance on both the high performance linpack (HPL) and conjugate gradient (HPCG) benchmark applications since June 2018 according to TOP500. Summit represents the culmination of a multiyear effort between the OLCF, IBM, NVIDIA, and Mellanox to deliver a system that is unmatched for modeling, simulation, data analysis, and learning. To hit the ground running with science-ready applications on day one, application teams worked closely with the OLCF through the Center for Accelerated Application Readiness (CAAR) program for years in advance of the Summit deployment. CY 2019 was filled with outstanding results and accomplishments: a very high rating from users on overall satisfaction for the sixth year in a row; a tremendous amount of core-hours delivered to researchers from two leadership-class systems; and success in delivering on the allocation split of roughly 60%, 30%, and 10% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director's Discretionary (DD) programs, respectively (see Operational Performance section). These accomplishments, coupled with the high utilization rates (overall and capability usage), represent the fulfillment of the promise of both leadership-class machines: efficient facilitation of leadership-class computational applications. Table ES.1 presents a summary of the 2019 OLCF metric targets and the associated results. More information can be found in the Operational Performance section for each OLCF resource. The scientific accomplishments of OLCF users are a strong indication of long-term operational success, with publications this year in such notable journals and publications as Nature, Nature Physics, Nature Plants, Physical Review X, Journal of the American Physical Society, Cell, Nano Letters, and Trends in Biotechnology. Crucial domain-specific discoveries facilitated by resources at the OLCF are described in the High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility (OAR) Strategic Results section. For example, researchers used Summit to pinpoint and understand the production of proteins from genetic information, including mutations and the functional expression of disease (Section 8.2).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A Shift Selection Strategy for Parallel Shift-invert Spectrum Slicing in Symmetric Self-consistent Eigenvalue Computation

The central importance of large-scale eigenvalue problems in scientific computation necessitates the development of massively parallel algorithms for their solution. Recent advances in dense numerical linear algebra have enabled the routine treatment of eigenvalue problems with dimensions on the order of hundreds of thousands on the world’s largest supercomputers. In cases where dense treatments are not feasible, Krylov subspace methods offer an attractive alternative due to the fact that they do not require storage of the problem matrices. However, demonstration of scalability of either of these classes of eigenvalue algorithms on computing architectures capable of expressing massive parallelism is non-trivial due to communication requirements and serial bottlenecks, respectively. In this work, we introduce the SISLICE method: a parallel shift-invert algorithm for the solution of the symmetric self-consistent field (SCF) eigenvalue problem. The SISLICE method drastically reduces the communication requirement of current parallel shift-invert eigenvalue algorithms through various shift selection and migration techniques based on density of states estimation and k-means clustering, respectively. This work demonstrates the robustness and parallel performance of the SISLICE method on a representative set of SCF eigenvalue problems and outlines research directions that will be explored in future work.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Envisioning Science in 2050

To explore future-focused questions that could impact the future of DOE, a Community of Interest (COI) on Future Scientific Methodologies, sponsored by the Office of Advanced Scientific Computing Research (ASCR), was held over three non-consecutive days in November 2020. The COI’s charge was to create a vision for how future computational fabrics might shape, and be shaped by, scientific and technological advances over the next 10 to 30 years.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2017

FEM-BEM coupling methods for Tokamak plasma axisymmetric free-boundary equilibrium computations in unbounded domains

Incorporating boundary conditions at infinity into simulations on bounded computational domains is a repeatedly occurring problem in scientific computing. The combination of finite element methods (FEM) and boundary element methods (BEM) is the obvious instrument, and we adapt here for the first time the two standard FEM-BEM coupling approaches to the free-boundary equilibrium problem: the Johnson–Nédélec coupling and the Bielak–MacCamy coupling. We recall also the classical approach for fusion applications, dubbed according to its first appearance von-Hagenow–Lackner coupling and present the less used alternative introduced by Albanese, Blum and de Barbieri in . We show that the von-Hagenow–Lackner coupling suffers from undesirable non-optimal convergence properties, that suggest that other coupling schemes, in particular Johnson–Nédélec or Albanese–Blum–de Barbieri are more appropriate for non-linear equilibrium problems. Moreover, we show that any of such coupling methods requires Newton-like iteration schemes for solving the corresponding non-linear discrete algebraic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

High Performance Computing Facility Operational Assessment 2016 - Oak Ridge Leadership Computing Facility

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Randomized algorithms for accelerating linear algebraic computations

The project supported the development of new methodologies for performing matrix computations that form key building blocks in modern scientific computing, such as low rank approximation of matrices, and efficient representations of global operators that arise in simulations of physical phenomena.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1988

Parallel algorithms for mapping pipelined and parallel computations

Many computational problems in image processing, signal processing, and scientific computing are naturally structured for either pipelined or parallel computation. When mapping such problems onto a parallel architecture it is often necessary to aggregate an obvious problem decomposition. Even in this context the general mapping problem is known to be computationally intractable, but recent advances have been made in identifying classes of problems and architectures for which optimal solutions can be found in polynomial time. Among these, the mapping of pipelined or parallel computations onto linear array, shared memory, and host-satellite systems figures prominently. This paper extends that work first by showing how to improve existing serial mapping algorithms. These improvements have significantly lower time and space complexities: in one case a published O(nm sup 3) time algorithm for mapping m modules onto n processors is reduced to an O(nm log m) time complexity, and its space requirements reduced from O(nm sup 2) to O(m). Run time complexity is further reduced with parallel mapping algorithms based on these improvements, which run on the architecture for which they create the mappings.

Nicol, David M.↗

NASA NTRS2002

1999 NCCS Highlights

The NASA Center for Computational Sciences (NCCS) is a high-performance scientific computing facility operated, maintained and managed by the Earth and Space Data Computing Division (ESDCD) of NASA Goddard Space Flight Center's (GSFC) Earth Sciences Directorate. The mission of the NCCS is to advance leading-edge science by providing the best people, computers, and data storage systems to NASA's Earth and space sciences programs and those of other U.S. Government agencies, universities, and private institutions. Among the many computationally demanding Earth science research efforts supported by the NCCS in Fiscal Year 1999 (FY99) are the NASA Seasonal-to-Interannual Prediction Project, the NASA Search and Rescue Mission, Earth gravitational model development efforts, the National Weather Service's North American Observing System program, Data Assimilation Office studies, a NASA-sponsored project at the Center for Ocean-Land-Atmosphere Studies, a NASA-sponsored microgravity project conducted by researchers at the City University of New York and the University of Pennsylvania, the completion of a satellite-derived global climate data set, simulations of a new geodynamo model, and studies of Earth's torque. This document presents highlights of these research efforts and an overview of the NCCS, its facilities, and its people.

Bennett, Jerome↗

DOE OSTI2019

Nuclear Physics Network Requirements Review Report

The Energy Sciences Network (ESnet) is the Office of Science’s high-performance network user facility, delivering highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the U.S. Department of Energy (DOE) science mission by connecting each and every DOE lab and its user facilities. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) Program, and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet connects DOE national laboratories, user facilities, and major experiments so scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large data sets, and access distributed data repositories. While ESnet provides network connectivity, it cannot be characterized as an internet service provider as it is specifically built to provide a range of network services that are tailored to meet the unique requirements of DOE’s data-intensive science. In short, ESnet’s mission is to enable and accelerate scientific discovery by delivering unparalleled network infrastructure, capabilities, and tools. ESnet’s vision is summarized by these three points. 1. Scientific progress will be completely unconstrained by the physical location of instruments, people, computational resources, or data. 2. Collaborations at every scale, in every domain, will have the information and tools they need to achieve maximum benefit from scientific facilities, global networks, and emerging network capabilities. 3. ESnet will foster the partnerships and pioneer the technologies necessary to ensure that these transformations occur. In May 2019, ESnet and the Office of Nuclear Physics (NP) of the DOE Office of Science organized an ESnet requirements review of NP-supported activities. Preparation for this event included identification of key stakeholders to the process: program and facility management, research groups, technology providers, and a number of external observers. These individuals were asked to prepare formal case study documents about their relationship to the NP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task and facilitated a smooth transition to the in-person review.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Argonne Leadership Computing Facility (2020 Operational Assessment Report)

In 2004, the U.S. Department of Energy’s (DOE’s) Advanced Scientific Computing Research (ASCR) program founded the Leadership Computing Facility (LCF) with a mission to provide the world’s most advanced computational resources to the open science community. The LCF is a huge investment in the nation’s scientific and technological future, inspired by a growing demand for capability computing and its impact on science and engineering.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Asynchronous in situ connected-components analysis for complex fluid flows

Fluid flow in porous media is at the heart of problems such as groundwater contamination and carbon sequestration, and presents an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. We present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. A task management framework is constructed to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and hide the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent averaging over fluid subregions using connected components analysis. Simulations performed on Oak Ridge National Lab s Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis for typical production simulation of two-fluid flow.

Mcclure, James↗

DOE OSTI2016

Asynchronous In Situ Connected-Components Analysis for Complex Fluid flows, In: ISAV '16 Proceedings of the 2nd Workshop on In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization

The simulation of multiscale physics is an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. To address this, we present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. All analyses are performed in parallel using distributed memory and use the same domain decomposition as the simulation. A task management framework is constructed to leverage available parallelism within a node for analysis. The capabilities of the framework are to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and minimize the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid-phase flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent analysis over fluid sub-regions determined from connected components analysis. Simulations performed on Oak Ridge National Lab's Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis approach for typical production simulation of two-fluid-phase flow.

Computer Science↗

DOE OSTI2017

Python in the NERSC Exascale Science Applications Program for Data

We describe a new effort at the National Energy Re- search Scientific Computing Center (NERSC) in performance analysis and optimization of scientific Python applications targeting the Intel Xeon Phi (Knights Landing, KNL) many- core architecture. The Python-centered work outlined here is part of a larger effort called the NERSC Exascale Science Applications Program (NESAP) for Data. NESAP for Data focuses on applications that process and analyze high-volume, high-velocity data sets from experimental/observational science (EOS) facilities supported by the US Department of Energy Office of Science. We present three case study applications from NESAP for Data that use Python. These codes vary in terms of “Python purity” from applications developed in pure Python to ones that use Python mainly as a convenience layer for scientists without expertise in lower level programming lan- guages like C, C++ or Fortran. The science case, requirements, constraints, algorithms, and initial performance optimizations for each code are discussed. Our goal with this paper is to contribute to the larger conversation around the role of Python in high-performance computing today and tomorrow, highlighting areas for future work and emerging best practices

Ronaghi, Zahra↗

DOE OSTI2024

HPC and Cloud Convergence Beyond Technical Boundaries: Strategies for Economic Sustainability, Standardization, and Data Accessibility

At the IEEE/ACM International Conference for High-Performance Computing, Networking, Storage, and Analysis (SC23), held in Denver, experts discussed the convergence of high-performance computing and cloud computing. Experts explored how this integration could address current scientific computing limitations, enhance computational capabilities, and foster global collaboration while focusing on economic, security, technical, and community challenges and opportunities.

97 MATHEMATICS AND COMPUTING↗