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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute

PIConGPU, Particle In Cell on GPUs, is an open source simulations framework for plasma and laser-plasma physics used to develop advanced particle accelerators for radiation therapy of cancer, high energy physics and photon science. While PIConGPU has been optimized for at least 5 years to run well on NVIDIA GPU-based clusters, there has been limited exploration by the development team of potential scalability bottlenecks using recently updated and new tools including NVIDIA’s NVProf tool and the brand-new NVIDIA NSight Suite (Systems and Compute) tools. PIConGPU is a highly optimized application that runs production jobs at scale on a system Oak Ridge Leadership Facility’s (OLCF) Summit supercomputer (using the full machine at 4600 nodes; at 98% of GPU utilization on all ~28000 NVIDIA Volta GPUs). PIConGPU has been selected as one of the the eight applications for OLCF’s coveted Center for Accelerated Application Readiness (CAAR) program aimed at the facility’s Frontier supercomputer (OLCF’s first exascale system to launch in 2021), to partner with our vendors (primary vendors: AMD and Cray/HPE) ensuring that Frontier will be able to perform large-scale science when it opens to users in 2022. To this effect, performance engineers on the PIConGPU team wanted to dive deep into the application to understand at the finest granularity, which portions of the code could be further optimized to exploit the hardware on Summit at it’s maximum potential and also to elucidate which key kernels should be tracked and optimized for the CAAR effort to port this code to Frontier. Any bottlenecks that are observed via performance profiling on Summit are likely to also impact scalability on the Frontier-dev system and the Frontier Early Access (EA) system. Additionally, the engineers wanted to take a closer look at the newest NVIDIA profiling tools which allows us to identify the most useful features on these tools and will provide an opportunity to compare it to new AMD and Cray’s performance analysis tool releases and provide feedback to our vendor partners on what features are most important and mission critical for CAAR efforts. The primary goal of this report is to focus on the evaluation of PIConGPU’s most time-intensive kernels using NVProf and NSight Suite. Three kernels, Current Deposition (also known as Compute Current), Particle Push (Move and Mark), and Shift Particles are known to be some of the most time-consuming kernels in PIConGPU. The Current xi Deposition kernel and Particle Push kernel both set up the particle attributes for running any physics simulation with PIConGPU, so it is crucial to improve the performance of these two kernels. In this report, we measure single GPU metrics for the three kernels, offer high level takeaways from the conducted analysis, and compare the profiling data from NSight Compute to that of NVProf. This analysis was performed using a grid size of 240 x 272 x 224, and 10 time steps with the Mid-November Figure of Merit (FOM) run setup. The Traveling Wave Electron Acceleration (TWEAC) science case used in this run is a representative science case for PIConGPU. This execution can also be used for baseline analysis on AMD MI50/ MI60 systems. As of the time of writing, the PIConGPU application has limited use for features of NSight Systems, so this report will mainly focus on insights garnered from NSight Compute. For this analysis, we run the “full” metric set available in NSight Compute version 2020.1.2 and use NSight Systems version 2020.3.1 to generate the application timeline.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

2019 Argonne Leadership Computing Facility Science Report

The Argonne Leadership Computing Facility (ALCF) is a U.S. Department of Energy (DOE) Office of Science User Facility that enables breakthroughs in science and engineering by providing supercomputing resources and expertise to the research community. ALCF computing resources - available to researchers from academia, industry, and government agencies - support large-scale computing projects aimed at solving some of the world’s most complex and challenging scientific problems. Through awards of supercomputing time and support services, the ALCF enables its users to accelerate the pace of discovery and innovation across disciplines.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A Parallel Computing Infrastructure for Building Energy Simulation

In order to study grid-interactive efficient buildings, Pacific Northwest National Laboratories (PNNL) needs an infrastructure for urban-scale building energy modeling. Such an infrastructure should be fast, scalable, and easy-to-use. Given a set of data from the Energy Information Administration’s Commercial Building Energy Consumption Survey (CBECS) and tool to translate survey data into simulation inputs, this project aimed to conduct the simulation of the entire dataset in parallel. Before running the simulations, the necessary software was bundled into a container for use on the PNNL supercomputing network. Then, the parallel simulation workflow was designed using GNU Make, a file creation software, and submitted to a supercomputing partition which could run hundreds of simulations simultaneously. The EnergyPlus simulations output hourly electric meter data for each CBECS sample, which represents the electricity consumption of similar commercial buildings across the United States. Analyzing and visualizing the meter data is important to the future of the work, and this project wrote code to make common analysis methods simple, fast, and accessible. Moving forwards, the model will need to be expanded to include data from other sources and its accuracy will need to be improved and eventually validated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations. To make advancements in all the aforementioned scientific areas, many technical aspects need to be more thoroughly studied and deeply understood in parallel discrete event simulation (PDES). The unique dynamics inherent in a discrete event modeling approach, by their very nature, intersect and influence the entire stack of the computing system, including (a) the unique nature of the instruction sets exercised in PDES workloads without a predominance of high-precision floating point operations, (b) virtual time-constrained multi-threaded execution of many logical processes per processor, (c) extremely variable and difficult to predict network traffic characteristics, (d) interfaces and inter-dependencies with machine learning and artificial intelligence codes at higher software layers, and (e) highly challenging load balancing needs, especially in effectively accounting for accelerated/extremely heterogeneous computing in current and future high-performance computing systems. Efficient and accurate parallel execution of PDES workloads is also dominated by challenges in dealing with their asynchronous concurrency fundamentally present at the model level. Conservative synchronization, optimistic/speculative synchronization, and their hybrid schemes open new questions in fundamental computer science with respect to reversibility of computation and prediction (lookahead) of behaviors inherent within model codes. On the implementation front, there are relatively few scalable, general-purpose parallel discrete event simulators in the world, and even fewer have been studied on emerging hardware platforms. To enable scientific advances using PDES, the research needs in computer science must also be pursued and met in the intersection of the algorithmic and hardware-aware aspects of scalable PDES engines. This report is aimed at capturing a computer science-oriented view of this important area of research in PDES, presenting a sample of important applications with their inherent discrete event technology elements. Needs are outlined in core areas of parallel discrete event research as well as cross-cutting directions in computer science research that positively impact scientific advancements across several important application areas. A selection of priority research opportunities in advanced computing for PDES is identified to serve as reference for key research topics and their order of importance for scientific advancements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Early Performance Results on 4th Gen Intel(R) Xeon (R) Scalable Processors with DDR and Intel(R) Xeon(R) processors, codenamed Sapphire Rapids with HBM

The Crossroads supercomputer was designed to simulate some of the most complex physical devices in the world. These simulations routinely require 1/2 petabyte or more of system memory running on thousands of compute nodes for months at a time on the most powerful supercomputers. Improvements in time to solutions for these workloads can have major impact on our mission capabilities. In this paper we present early results of representative application workloads on 4th Gen Intel Xeon and Intel Xeon Processors codenamed Sapphire Rapids with HBM. These results demonstrate an extremely promising 8.57x improvement (node to node) over our prior generation Intel Broadwell (BDW) based HPC systems. No code modifications were required to achieve this speedup, providing a compelling path forward toward major reductions in time to solution and the complexity of physical systems that can be simulated in the future.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Performance Results on CPU/GPU Exascale Architectures for OMEGA: The Ocean Model for E3SM Global Applications

The US Department of Energy (DOE) conducts climate simulations on some of the world’s largest supercomputers. These exascale machines use heterogeneous architectures with both CPUs and GPUs, and scientific codes must adapt to make full use of this computing power. Los Alamos National Lab is developing Omega: The Ocean Model for E3SM Global Applications, which is specifically designed for modern exascale computers. It uses external libraries that have been optimized for a variety of architectures to run on different supercomputers. Omega is an unstructured-mesh ocean model based on TRiSK numerical methods. It will be the new ocean component of the DOE’s Energy Exascale Earth System Model (E3SM). The algorithms in Omega follow those of the current ocean component, MPAS-Ocean, but it will be written in C++ rather than Fortran to take advantage of the Kokkos performance portability library. Omega spatial operators are written as Kokkos kernels to run efficiently on both CPUs and GPUs. Work on Omega began in 2023 with a new C++ framework for unstructured mesh partitioning, halo exchanges, parallel IO, and Kokkos interfaces. The current version, Omega-0, is being developed to solve the shallow water equations and at present includes all of the tendency terms but not time stepping. Here we share the results of Omega-0 verification and performance testing. Verification includes unit tests implemented with CTest as well as convergence tests in Polaris, an in-house python package with a large suite of test problems. Performance tests compare simulations conducted on CPUs versus GPUs and across different architectures: tests are run on Frontier, which has AMD “Optimized 3rd Gen EPYC” CPUs and AMD MI250X GPUs, as well as Perlmutter, which is composed of AMD EPYC 7763 CPUs and NVIDIA A100 GPUs.

58 GEOSCIENCES↗
DOE OSTI2024

Nuclear Computational Resource Center Progress and Status Report

The Nuclear Computational Resource Center (NCRC) at Idaho National Laboratory (INL), supported by the United States Department of Energy Office of Nuclear Energy (DOE-NE), provides access to supercomputer systems and protected software in support of nuclear energy research and development. The NCRC vision recognizes the central role modeling and simulation plays in nuclear energy innovation as well as ensuring the safe, secure, and efficient operations of existing nuclear energy systems. To accomplish this vision, the NCRC supports processes and systems which provide access to computational tools, supercomputing systems, and training in support of nuclear energy innovation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Workflows for Science: A comprehensive guide for ensemble workflow tools usage with applications on OLCF systems

The growing demand for robust computational and workflow environments for scientific applications and user communities at the Oak Ridge Leadership Computing Facility (OLCF) has prompted collaboration with ensemble tools development teams and facility users to produce this technical paper. We connect science applications to the RADICAL-Pilot (RP) workflow tool to execute ensemble instantiations using the Frontier supercomputer. The documented installation, usage, and execution demonstrates how RP streamlines scientific workflows at OLCF. We outline the specific steps OLCF users can follow to integrate this tool with their applications and advance their research. This document stands as a comprehensive guide to OLCF users of ensemble workflow tools with examples on real applications using the Frontier supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Experiences with SYCL on AMD GPUs with Kokkos

With the recent diversification of the hardware landscape in the high-performance computing (HPC) community, performance-portability solutions are becoming more and more important. One of the most popular choices is Kokkos, which recently became a Linux Foundation project. Most of its development is supported by the US Department of Energy and the French Alternative Energies and Atomic Energy Commission. Kokkos is implemented as a C++ library with multiple backends to support CPUs as well as various GPU architectures. These backends include OpenMP, CUDA, HIP, and also SCYL. This approach enables users to leverage the preferred vendor toolchain for the respective platform (e.g. CUDA, ROCm, OneAPI). The SYCL backend is used to target Intel GPUs, in particular to support the Aurora exascale supercomputer. However, SYCL itself also offers a large degree of portability, and in fact Kokkos’ CI for SYCL has been running on NVIDIA hardware due to a lack of access to Intel GPUs. In this report, we describe our experience with using Kokkos SYCL backend on AMD GPUs targeting the Frontier supercomputer at Oak Ridge National Laboratory. The two major SYCL implementations are DPC++ and AdaptiveCpp. While the Kokkos SYCL backend has been implemented using the former, the latter was the first implementation to target AMD GPUs. We will discuss the experience with both of these SYCL implementations in terms of functionality and performance. Using Kokkos to evaluate SYCL toolchains has a number of benefits. Kokkos’ use of SYCL is fairly complex, exercising features such as graphs, relocatable device functions, atomics – including for non-arithmetic types, as well as pinned and page migratable memory allocations. Kokkos also needs to implement capabilities such as Kokkos’ hierarchical parallelism that are not a straight-forward mapping to SYCL capabilities. Furthermore, a large number of libraries and applications that represent diverse use cases are implemented in Kokkos, providing readily available test cases for a toolchain evaluation. Preliminary results show that support for AMD GPUs in DPC++ is much less mature than for NVIDIA GPUs or Intel GPUs. While the situation has improved significantly over the last year, we still encounter many runtime failures, dispatching problems, and code generation issues. With AdaptiveCpp the challenges arise even earlier in the evaluation process. Since Kokkos’ SYCL implementation is largely focused on supporting Intel GPUs, we opted to leverage SYCL extensions which are available in DPC++ but not in AdaptiveCpp. Furthermore, AdaptiveCpp appears to be less conformant with the SYCL2020 standard which Kokkos relies on. In some cases, we are able to work around the lack of feature support, in other cases we have to disable certain Kokkos capabilities to evaluate the toolchain. Our evaluation will leverage Kokkos’ unit tests to establish basic functionality and feature completeness. We then use simple benchmarks for components of a CG implementation as a measure of usability and performance of the SYCL toolchains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

nbodykit: An Open-source, Massively Parallel Toolkit for Large-scale Structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface, we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, two- and three-point correlation functions, a friends-of-friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enables nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high-performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1982

Survey of new vector computers: The CRAY 1S from CRAY research; the CYBER 205 from CDC and the parallel computer from ICL - architecture and programming

Problems which can arise with vector and parallel computers are discussed in a user oriented context. Emphasis is placed on the algorithms used and the programming techniques adopted. Three recently developed supercomputers are examined and typical application examples are given in CRAY FORTRAN, CYBER 205 FORTRAN and DAP (distributed array processor) FORTRAN. The systems performance is compared. The addition of parts of two N x N arrays is considered. The influence of the architecture on the algorithms and programming language is demonstrated. Numerical analysis of magnetohydrodynamic differential equations by an explicit difference method is illustrated, showing very good results for all three systems. The prognosis for supercomputer development is assessed.

Gentzsch, W.↗
NASA NTRS1983

The impact of CFD on development test facilities - A National Research Council projection

The results of a National Research Council study on the effect that advances in computational fluid dynamics (CFD) will have on conventional aeronautical ground testing are reported. Current CFD capabilities include the depiction of linearized inviscid flows and a boundary layer, initial use of Euler coordinates using supercomputers to automatically generate a grid, research and development on Reynolds-averaged Navier-Stokes (N-S) equations, and preliminary research on solutions to the full N-S equations. Improvements in the range of CFD usage is dependent on the development of more powerful supercomputers, exceeding even the projected abilities of the NASA Numerical Aerodynamic Simulator (1 BFLOP/sec). Full representation of the Re-averaged N-S equations will require over one million grid points, a computing level predicted to be available in 15 yr. Present capabilities allow identification of data anomalies, confirmation of data accuracy, and adequateness of model design in wind tunnel trials. Account can be taken of the wall effects and the Re in any flight regime during simulation. CFD can actually be more accurate than instrumented tests, since all points in a flow can be modeled with CFD, while they cannot all be monitored with instrumentation in a wind tunnel.

Korkegi, R. H.↗
NASA NTRS1985

Vector computer memory bank contention

A number of vector supercomputers feature very large memories. Unfortunately the large capacity memory chips that are used in these computers are much slower than the fast central processing unit (CPU) circuitry. As a result, memory bank reservation times (in CPU ticks) are much longer than on previous generations of computers. A consequence of these long reservation times is that memory bank contention is sharply increased, resulting in significantly lowered performance rates. The phenomenon of memory bank contention in vector computers is analyzed using both a Markov chain model and a Monte Carlo simulation program. The results of this analysis indicate that future generations of supercomputers must either employ much faster memory chips or else feature very large numbers of independent memory banks.

Bailey, D. H.↗
NASA NTRS1985

Integrated risk/cost planning models for the US Air Traffic system

A prototype network planning model for the U.S. Air Traffic control system is described. The model encompasses the dual objectives of managing collision risks and transportation costs where traffic flows can be related to these objectives. The underlying structure is a network graph with nonseparable convex costs; the model is solved efficiently by capitalizing on its intrinsic characteristics. Two specialized algorithms for solving the resulting problems are described: (1) truncated Newton, and (2) simplicial decomposition. The feasibility of the approach is demonstrated using data collected from a control center in the Midwest. Computational results with different computer systems are presented, including a vector supercomputer (CRAY-XMP). The risk/cost model has two primary uses: (1) as a strategic planning tool using aggregate flight information, and (2) as an integrated operational system for forecasting congestion and monitoring (controlling) flow throughout the U.S. In the latter case, access to a supercomputer is required due to the model's enormous size.

Mulvey, J. M.↗
NASA NTRS1985

Optical disks and superconductors

Supercomputers whose anticipated operational capability in the 1990s is of the order of 1 teraoperation/sec require a new generation of peripheral storage devices. The solution presented for this peripheral device problem encompasses hardware, data base software, and special expert systems to manage the operational environment of the supercomputer complex; attention, however, is given to the application of optical disk storage methods.

Wallgren, K. R.↗
NASA NTRS1985

Visualizing flow in the Space Shuttle Main Engine

Ongoing work is described aimed at applying advanced post-processing techniques to interpret and understand the complex flow behavior of the Space Shuttle Main Engine. The use of color graphics and powerful new engineering work stations to effectively present massive amounts of numerical data is emphasized. This combination of tools can result in better designs, faster turnaround, and more complete understanding of complex engineering systems like the Shuttle. Furthermore, it allows engineers access to the massive amounts of data generated by supercomputers and provides a more efficient coupling of man and supercomputer.

Belie, R. G.↗