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At least 1,351 records · Page 75

Preparing MPICH for exascale

The advent of exascale supercomputers heralds a new era of scientific discovery, yet it introduces significant architectural challenges that must be overcome for MPI applications to fully exploit its potential. Among these challenges is the adoption of heterogeneous architectures, particularly the integration of GPUs to accelerate computation. Additionally, the complexity of multithreaded programming models has also become a critical factor in achieving performance at scale. The efficient utilization of hardware acceleration for communication, provided by modern NICs, is also essential for achieving low latency and high throughput communication in such complex systems. In response to these challenges, the MPICH library, a high-performance and widely used Message Passing Interface (MPI) implementation, has undergone significant enhancements. Here, this paper presents four major contributions that prepare MPICH for the exascale transition. First, we describe a lightweight communication stack that leverages the advanced features of modern NICs to maximize hardware acceleration. Second, our work showcases a highly scalable multithreaded communication model that addresses the complexities of concurrent environments. Third, we introduce GPU-aware communication capabilities that optimize data movement in GPU-integrated systems. Finally, we present a new datatype engine aimed at accelerating the use of MPI derived datatypes on GPUs. These improvements in the MPICH library not only address the immediate needs of exascale computing architectures but also set a foundation for exploiting future innovations in high-performance computing. By embracing these new designs and approaches, MPICH-derived libraries from HPE Cray and Intel were able to achieve real exascale performance on OLCF Frontier and ALCF Aurora respectively.

Guo, Yanfei [Argonne National Laboratory (ANL), Ar↗

International ACM Symposium on High Performance Parallel and Distributed Computing Conference for 2017, 2018, 2019, and 2020

The 28th ACM HPDC Conference was held in Phoenix, Arizona, June 24 and 28, 2019 (hpdc.org/2019), that was colocated with ACM FCRC 2019 (fcrc.acm.org). During the conference, Prof. Geoffrey Fox, Indiana University, was given the HPDC Achievement Award for 2019. Prof gave a keynote speech entitled “Perspectives on High-Performance Computing in a Big Data World. In addition, to the keynote speakers from HPDC and FCRC conferences, the conference organized successfully five workshops and one Ph.D. forum. The ACM FCRC had a total of 2700 attendees, and HPDC had a total of 120 attendees that included 32 students. We have used the DOE sponsorship to support the conference proceedings that acknowledge the DoE support and partially supported the travel to the HPDC PC meeting, Keynote speaker accommodation, best papers, presentation and poster award.

42 ENGINEERING↗

A domain decomposition method of stochastic PDEs: An iterative solution techniques using a two-level scalable preconditioner

Recent advances in high performance computing systems and sensing technologies motivate computational simulations with extremely high resolution models with capabilities to quantify uncertainties for credible numerical predictions. A two-level domain decomposition method is reported in this investigation to devise a linear solver for the large-scale system in the Galerkin spectral stochastic finite element method (SSFEM). In particular, a two-level scalable preconditioner is introduced in order to iteratively solve the large-scale linear system in the intrusive SSFEM using an iterative substructuring based domain decomposition solver. The implementation of the algorithm involves solving a local problem on each subdomain that constructs the local part of the preconditioner and a coarse problem that propagates information globally among the subdomains. The numerical and parallel scalabilities of the two-level preconditioner are contrasted with the previously developed one-level preconditioner for two-dimensional flow through porous media and elasticity problems with spatially varying non-Gaussian material properties. A distributed implementation of the parallel algorithm is carried out using MPI and PETSc parallel libraries. The scalabilities of the algorithm are investigated in a Linux cluster.

42 ENGINEERING↗

Impacts of floating-point non-associativity on reproducibility for HPC and deep learning applications

Run to run variability in parallel programs caused by floating-point non-associativity has been known to significantly affect reproducibility in iterative algorithms, due to accumulating errors. Non-reproducibility can critically affect the efficiency and effectiveness of correctness testing for stochastic programs. Recently, the sensitivity of deep learning training and inference pipelines to floating-point non-associativity has been found to sometimes be extreme. It can prevent certification for commercial applications, accurate assessment of robustness and sensitivity, and bug detection. New approaches in scientific computing applications have coupled deep learning models with high-performance computing, leading to an aggravation of debugging and testing challenges. Here we perform an investigation of the statistical properties of floating-point non-associativity within modern parallel programming models, and analyze performance and productivity impacts of replacing atomic operations with deterministic alternatives on GPUs. We examine the recently-added deterministic options in PyTorch within the context of GPU deployment for deep learning, uncovering and quantifying the impacts of input parameters triggering run to run variability and reporting on the reliability and completeness of the documentation. Finally, we evaluate the strategy of exploiting automatic determinism that could be provided by deterministic hardware, using the Groq LPUTM accelerator for inference portions of the deep learning pipeline. We demonstrate the benefits that a hardware-based strategy can provide within reproducibility and correctness efforts.

Shanmugavelu, Sanjif↗

Parallelization and checkpointing of GPU applications through program transformation

GPUs have emerged as a powerful tool for accelerating general-purpose applications. The availability of programming languages that makes writing general-purpose applications for running on GPUs tractable have consolidated GPUs as an alternative for accelerating general purpose applications. Among the areas that have benefited from GPU acceleration are: signal and image processing, computational fluid dynamics, quantum chemistry, and, in general, the High Performance Computing (HPC) Industry. In order to continue to exploit higher levels of parallelism with GPUs, multi-GPU systems are gaining popularity. In this context, single-GPU applications are parallelized for running in multi-GPU systems. Furthermore, multi-GPU systems help to solve the GPU memory limitation for applications with large application memory footprint. Parallelizing single-GPU applications has been approached by libraries that distribute the workload at runtime, however, they impose execution overhead and are not portable. On the other hand, on traditional CPU systems, parallelization has been approached through application transformation at pre-compile time, which enhances the application to distribute the workload at application level and does not have the issues of library-based approaches. Hence, a parallelization scheme for GPU systems based on application transformation is needed. Like any computing engine of today, reliability is also a concern in GPUs. GPUs are vulnerable to transient and permanent failures. Current checkpoint/restart techniques are not suitable for systems with GPUs. Checkpointing for GPU systems present new and interesting challenges, primarily due to the natural differences imposed by the hardware design, the memory subsystem architecture, the massive number of threads, and the limited amount of synchronization among threads. Therefore, a checkpoint/restart technique suitable for GPU systems is needed. The goal of this work is to exploit higher levels of parallelism and to develop support for application-level fault tolerance in applications using multiple GPUs. Our techniques reduce the burden of enhancing single-GPU applications to support these features. To achieve our goal, this work designs and implements a framework for enhancing a single-GPU OpenCL application through application transformation.

97 MATHEMATICS AND COMPUTING↗

ASCR@40: Highlights and Impacts of ASCR’s Programs

A report compiled by the ASCAC Subcommittee on the 40-year history of ASCR for the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The Office of Advanced Scientific Computing Research (ASCR) sits within the Office of Science in the Department of Energy (DOE). Per their web pages, “the mission of the ASCR program is to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” This succinct statement encompasses a wide range of responsibilities for computing and networking facilities; for procuring, deploying, and operating high performance computing, networking, and storage resources; for basic research in mathematics and computer science; for developing and sustaining a large body of software; and for partnering with organizations across the Office of Science and beyond. While its mission statement may seem very contemporary, the roots of ASCR are quite deep—long predating the creation of DOE. Applied mathematics and advanced computing were both elements of the Theoretical Division of the Manhattan Project. In the early 1950s, the Manhattan Project scientist and mathematician John von Neumann, then a commissioner for the AEC (Atomic Energy Commission), advocated for the creation of a Mathematics program to support the continued development and applications of digital computing. Los Alamos National Laboratory (LANL) scientist John Pasta created such a program to fund researchers at universities and AEC laboratories. Under several organizational name changes, this program has persisted ever since, and would eventually grow to become ASCR.

97 MATHEMATICS AND COMPUTING↗

An Early Investigation of the HHL Quantum Linear Solver for Scientific Applications

In this paper, we explore using the Harrow–Hassidim–Lloyd (HHL) algorithm to address scientific and engineering problems through quantum computing, utilizing the NWQSim simulation package on a high-performance computing platform. Focusing on domains such as power-grid management and climate projection, we demonstrate the correlations of the accuracy of quantum phase estimation, along with various properties of coefficient matrices, on the final solution and quantum resource cost in iterative and non-iterative numerical methods such as the Newton–Raphson method and finite difference method, as well as their impacts on quantum error correction costs using the Microsoft Azure Quantum resource estimator. We summarize the exponential resource cost from quantum phase estimation before and after quantum error correction and illustrate a potential way to reduce the demands on physical qubits. This work lays down a preliminary step for future investigations, urging a closer examination of quantum algorithms’ scalability and efficiency in domain applications.

hybrid software for QC-HPC↗

THEMIS: A Parameter Estimation Framework for the Event Horizon Telescope

The Event Horizon Telescope (EHT) provides the unprecedented ability to directly resolve the structure and dynamics of black hole emission regions on scales smaller than their horizons. This has the potential to critically probe the mechanisms by which black holes accrete and launch outflows, and the structure of supermassive black hole spacetimes. However, accessing this information is a formidable analysis challenge for two reasons. First, the EHT natively produces a variety of data types that encode information about the image structure in nontrivial ways; these are subject to a variety of systematic effects associated with very long baseline interferometry and are supplemented by a wide variety of auxiliary data on the primary EHT targets from decades of other observations. Second, models of the emission regions and their interaction with the black hole are complex, highly uncertain, and computationally expensive to construct. As a result, the scientific utilization of EHT observations requires a flexible, extensible, and powerful analysis framework. We present such a framework, Themis, which defines a set of interfaces between models, data, and sampling algorithms that facilitates future development. We describe the design and currently existing components of Themis, how Themis has been validated thus far, and present additional analyses made possible by Themis that illustrate its capabilities. Importantly, we demonstrate that Themis is able to reproduce prior EHT analyses, extend these, and do so in a computationally efficient manner that can efficiently exploit modern high-performance computing facilities. Themis has already been used extensively in the scientific analysis and interpretation of the first EHT observations of M87.

79 ASTRONOMY AND ASTROPHYSICS↗

Cloud identification using genetic algorithms and massively parallel computation

As a Guest Computational Investigator under the NASA administered component of the High Performance Computing and Communication Program, we implemented a massively parallel genetic algorithm on the MasPar SIMD computer. Experiments were conducted using Earth Science data in the domains of meteorology and oceanography. Results obtained in these domains are competitive with, and in most cases better than, similar problems solved using other methods. In the meteorological domain, we chose to identify clouds using AVHRR spectral data. Four cloud speciations were used although most researchers settle for three. Results were remarkedly consistent across all tests (91% accuracy). Refinements of this method may lead to more timely and complete information for Global Circulation Models (GCMS) that are prevalent in weather forecasting and global environment studies. In the oceanographic domain, we chose to identify ocean currents from a spectrometer having similar characteristics to AVHRR. Here the results were mixed (60% to 80% accuracy). Given that one is willing to run the experiment several times (say 10), then it is acceptable to claim the higher accuracy rating. This problem has never been successfully automated. Therefore, these results are encouraging even though less impressive than the cloud experiment. Successful conclusion of an automated ocean current detection system would impact coastal fishing, naval tactics, and the study of micro-climates. Finally we contributed to the basic knowledge of GA (genetic algorithm) behavior in parallel environments. We developed better knowledge of the use of subpopulations in the context of shared breeding pools and the migration of individuals. Rigorous experiments were conducted based on quantifiable performance criteria. While much of the work confirmed current wisdom, for the first time we were able to submit conclusive evidence. The software developed under this grant was placed in the public domain. An extensive user's manual was written and distributed nationwide to scientists whose work might benefit from its availability. Several papers, including two journal articles, were produced.

Buckles, Bill P.↗

Research Institute for Advanced Computer Science: Annual Report October 1998 through September 1999

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. RIACS is located at the NASA Ames Research Center (ARC). It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in the year 2002. ARC has been designated NASA's Center of Excellence in Information Technology. In this capacity, ARC is charged with the responsibility to build an Information Technology Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA ARC and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of information technology research necessary to meet the future challenges of NASA missions: (1) Automated Reasoning for Autonomous Systems. Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. (2) Human-Centered Computing. Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities; (3) High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to data analysis of large datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply information technology research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, and visiting scientist programs, designed to encourage and facilitate collaboration between the university and NASA information technology research communities.

Leiner, Barry M.↗

Research Institute for Advanced Computer Science

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. RIACS is located at the NASA Ames Research Center. It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in the year 2002. Ames has been designated NASA's Center of Excellence in Information Technology. In this capacity, Ames is charged with the responsibility to build an Information Technology Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA Ames and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of information technology research necessary to meet the future challenges of NASA missions: (1) Automated Reasoning for Autonomous Systems. Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth; (2) Human-Centered Computing. Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities; (3) High Performance Computing and Networking. Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to data analysis of large datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply information technology research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, and visiting scientist programs, designed to encourage and facilitate collaboration between the university and NASA information technology research communities.

Gross, Anthony R.↗

[Activities of Research Institute for Advanced Computer Science]

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administrations missions. RIACS is located at the NASA Ames Research Center, Moffett Field, California. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1. Automated Reasoning for Autonomous Systems Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. 2. Human-Centered Computing Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities. 3. High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to analysis of large scientific datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

Gross, Anthony R.↗

SPARClite v. 8/17/16

SPARClite is a compressible CFD code useful for analysis of problems involving high speed flows of fluids around solid structures. It is being built for efficient use on next-generation high performance computers, and is intended to be developed at a high level of software quality to meet the rigors of Sandia’s production software needs.

Howard, Micah↗

SPARC v. 8/17/2016

SPARC is a compressible CFD code useful for analysis of problems involving high speed flows of fluids around solid structures. It is being built for efficient use on next-generation high performance computers, and is intended to be developed at a high level of software quality to meet the rigors of Sandia’s production software needs.

Howard, Micah↗

Towards an HPC Complementary Computing Facility

This Letter considers the design for computing facilities that are complementary to the leadership class High Performance Computing (HPC) facilities. This design envisions a future where funding agencies are allocating greater resources for leadership class facilities and these facilities will provide a significant part of the total compute cycles for HEP Experiments. While a leadership class facility (LCF) may provide cycles and advanced architectures, the facility does not necessarily provide all of the services needed to help HEP users make the best use of the HPC facility, as well as the services needed to provide computing for workflows that are not a good fit for the HPC facilities. This Letter outlines some of the necessary components of a facility designed to provide those services and capabilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Exascale Multiphysics Nuclear Reactor Simulations for Advanced Designs

ENRICO is a coupled application developed under the U.S. Department of Energy's Exascale Computing Project (ECP) targeting the modeling of advanced nuclear reactors. It couples radiation transport with heat and fluid simulation, including the high-fidelity, highresolution Monte-Carlo code Shift and the Computational fluid dynamics code NekRS. NekRS is a highly-performant open-source code for simulation of incompressible and low-Mach fluid flow, heat transfer, and combustion with a particular focus on turbulent flows in complex domains. It is based on rapidly convergent high-order spectral element discretizations that feature minimal numerical dissipation and dispersion. State-of-the-art multilevel preconditioners, efficient high-order time-splitting methods, and runtime-adaptive communication strategies are built on a fast OCCA-based kernel library, libParanumal, to provide scalability and portability across the spectrum of current and future high-performance computing platforms. On Frontier, Nek5000/RS has recently achieved an unprecedented milestone in breaching over 1 billion spectral elements and 350 billion degrees of freedom. Shift has demonstrated the capability to transport upwards of 1 billion particles per second in full core nuclear reactor simulations featuring complete temperature-dependent, continuous-energy physics on Frontier. Shift achieved a weak-scaling efficiency of 97.8% on 8192 nodes of Frontier and calculated 6 reactions in 214,896 fuel pin regions below 1% statistical error yielding first-of-a-kind resolution for a Monte Carlo transport application.

Hamilton, Steven P.↗

A performance comparison of current HPC systems: Blue Gene/Q, Cray XE6 and InfiniBand systems

We present here a performance analysis of three of current architectures that have become commonplace in the High Performance Computing world. Blue Gene/Q is the third generation of systems from IBM that use modestly performing cores but at large-scale in order to achieve high performance. The XE6 is the latest in a long line of Cray systems that use a 3-D topology but the first to use its Gemini interconnection network. InfiniBand provides the flexibility of using compute nodes from many vendors that can be connected in many possible topologies. The performance characteristics of each vary vastly, and the way in which nodes are allocated in each type of system can significantly impact on achieved performance. In this work we compare these three systems using a combination of micro-benchmarks and a set of production applications. In addition we also examine the differences in performance variability observed on each system and quantify the lost performance using a combination of both empirical measurements and performance models. Our results show that significant performance can be lost in normal production operation of the Cray XE6 and InfiniBand Clusters in comparison to Blue Gene/Q.

Application analysis↗

Effects of Spatial Resolution on Retropropulsion Aerodynamics in an Atmospheric Environment

Development of a powered descent capability for atmospheric environments is heavily reliant on computational simulation. The prohibitive computational cost of such simulations motivates an improvement in the understanding of the minimum computational fidelity re-quired to accurately characterize aerodynamic-propulsive interference for such applications. This work examines the applicability of detached eddy simulation methods for retropropulsion in atmospheric environments through utilization of a GPU-accelerated computational framework, yielding data that are largely unachievable with conventional high-performance computing resources. This effort was specifically designed to quantitatively assess the effects of spatial resolution on vehicle aerodynamics for nominal operation of a low lift-to-drag ratio, human-scale Mars lander concept. The test matrix and scaling approach span relevant nozzle expansion conditions as well as mid-supersonic to high-subsonic operating conditions. Solutions were generated using computational grids ranging from 143 million to 1.14 billion grid points (degrees of freedom). This paper will provide an overview of the computational campaign, approach, and discussion of preliminary results focused on a range of operating conditions for a conceptual low lift-to-drag, human-scale Mars lander.

Ashley M Korzun↗