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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Algorithmic Patterns for $$\mathcal {H}$$-Matrices on Many-Core Processors

In this work, we consider the reformulation of hierarchical ( \(\mathcal {H}\) ) matrix algorithms for many-core processors with a model implementation on graphics processing units (GPUs). \(\mathcal {H}\) matrices approximate specific dense matrices, e.g., from discretized integral equations or kernel ridge regression, leading to log-linear time complexity in dense matrix–vector products. The parallelization of \(\mathcal {H}\) matrix operations on many-core processors is difficult due to the complex nature of the underlying algorithms. While previous algorithmic advances for many-core hardware focused on accelerating existing \(\mathcal {H}\) matrix CPU implementations by many-core processors, we here aim at totally relying on that processor type. As main contribution, we introduce the necessary parallel algorithmic patterns allowing to map the full \(\mathcal {H}\) matrix construction and the fast matrix–vector product to many-core hardware. In this work, crucial ingredients are space filling curves, parallel tree traversal and batching of linear algebra operations. The resulting model GPU implementation hmglib is the, to the best of the authors knowledge, first entirely GPU-based Open Source \(\mathcal {H}\) matrix library of this kind. We investigate application examples as present in kernel ridge regression, Gaussian Process Regression and kernel-based interpolation. In this context, an in-depth performance analysis and a comparative performance study against a standard multi-core CPU \(\mathcal {H}\) matrix library highlights profound speedups of our many-core parallel approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Performance optimization, modeling and analysis of sparse matrix-matrix products on multi-core and many-core processors

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. In this work, we firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We examine their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. We build the performance model for hash-table and heap-based algorithms, which supports the recipe. A critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix. Finally, we integrate our implementations into a large-scale protein clustering code named HipMCL, accelerating its SpGEMM kernel by up to 10X and achieving an overall performance boost for the whole HipMCL application by 2.6X.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

High-Performance Sparse Matrix-Matrix Products on Intel KNL and Multicore Architectures

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is vastly used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. While many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We investigate their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. In conclusion, a critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Accelerating a fluvial incision and landscape evolution model with parallelism

Solving inverse problems, performing sensitivity analyses, and achieving statistical rigour in landscape evolution models require running many model realizations. Parallel computation is necessary to achieve this in a reasonable time. However, no previous landscape evolution algorithm is able to leverage modern parallelism. In this report, I describe an algorithm that can utilize the parallel potential of GPUs and many-core processors, in addition to working well in serial. The new algorithm runs 43× faster (70 s vs. 3000 s on a 10,000×10,000 input) than the previous state-of-the-art and exhibits sublinear scaling with input size. I also identify key techniques for multiple flow direction routing and quickly eliminating landscape depressions and local minima. Complete, well-commented, easily adaptable source code for all versions of the algorithm is available on Github and Zenodo.

58 GEOSCIENCES↗
DOE OSTI2018

Notified access in coarray-based hydrodynamics applications on many-core architectures: Design and performance

With the increasing availability of the Remote Direct Memory Access (RDMA) support in computer networks, the so called Partitioned Global Address Space (PGAS) model has evolved in the last few years. Although there are several cases where a PGAS approach can easily solve difficult message passing situations, like in particle tracking and adaptive mesh refinement applications, the producer-consumer pattern, usually adopted in task-based parallelism, can only be implemented inefficiently because of the separation between data transfer and synchronization (which is usually unified in message passing programming models). Here, in this paper, we provide two contributions: (1) we propose an extension for the Fortran language that provides the concept of Notified Access by associating regular coarray variables with event variables. (2) We demonstrate that the MPI extension proposed by foMPI for Notified Access can be used effectively to implement the same concept in a PGAS run-time library like OpenCoarrays. Moreover, for a hydrodynamics mini-application, we found that Fortran 2018 events perform always better than Fortran 2008 sync statements on many-core processors. We finally show how the proposed Notified Access can improve the performance even more.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

MAGIC: M arching Cubes Isosurface Uncertainty Visualization for G auss i an Uncertain Data With Spatial C orrelation

Here, in this paper, we study the propagation of data uncertainty through the marching cubes algorithm for isosurface visualization for correlated uncertain data. Consideration of correlation has been shown paramount for avoiding errors in uncertainty quantification and visualization in multiple prior studies. Although the problem of isosurface uncertainty with spatial data correlation has been previously addressed, there are two major limitations to prior treatments. First, there are no analytical formulations for uncertainty quantification of isosurfaces when the data uncertainty is characterized by a Gaussian distribution with spatial correlation. Second, as a consequence of the lack of analytical formulations,existing techniques resort to a Monte Carlo sampling approach, which is expensive and difficult to integrate into visualization tools. To address these limitations, we present a closed-form framework to efficiently derive uncertainty in marching cubes level-sets for Gaussian uncertain data with spatial correlation (MAGIC). To derive closed-form solutions, we leverage the Hinkley's derivation on the ratio of Gaussian distributions. With our analytical framework, we achieve a significant speed-up and enhanced accuracy of uncertainty quantification over classical Monte Carlo methods. We further accelerate our analytical solutions using many-core processors to achieve speed-ups up to 585× and integrability with production visualization tools for broader impact. We demonstrate the effectiveness of our correlation-aware uncertainty framework through experiments on meteorology, urban flow, and astrophysics simulation datasets.

Gaussian↗
DOE OSTI2018

Parallelized and Vectorized Tracking Using Kalman Filters with CMS Detector Geometry and Events

The High-Luminosity Large Hadron Collider at CERN will be characterized by greater pileup of events and higher occupancy, making the track reconstruction even more computationally demanding. Existing algorithms at the LHC are based on Kalman filter techniques with proven excellent physics performance under a variety of conditions. Starting in 2014, we have been developing Kalman-filter-based methods for track finding and fitting adapted for many-core SIMD processors that are becoming dominant in high-performance systems. This paper summarizes the latest extensions to our software that allow it to run on the realistic CMS-2017 tracker geometry using CMSSW-generated events, including pileup. The reconstructed tracks can be validated against either the CMSSW simulation that generated the hits, or the CMSSW reconstruction of the tracks. In general, the code's computational performance has continued to improve while the above capabilities were being added. We demonstrate that the present Kalman filter implementation is able to reconstruct events with comparable physics performance to CMSSW, while providing generally better computational performance. Further plans for advancing the software are discussed.

Cerati, Giuseppe↗
DOE OSTI2018

Job Management with mpi_jm

About this book: This book constitutes the refereed post-conference proceedings of 13 workshops held at the 33rd International ISC High Performance 2018 Conference, in Frankfurt, Germany, in June 2018: HPC I/O in the Data Center, HPC-IODC 2018; Workshop on Performance and Scalability of Storage Systems, WOPSSS 2018; 13th Workshop on Virtualization in High­-Performance Cloud Computing, VHPC 2018; Third International Workshop on In Situ Visualization, WOIV 2018; 4th International Workshop on Communication Architectures for HPC, Big Data, Deep Learning and Clouds at Extreme Scale, ExaComm 2018; International Workshop on OpenPOWER for HPC, IWOPH 2018; IXPUG Workshop: Many-Core Computing on Intel Processors; Workshop on Sustainable Ultrascale Computing Systems; Approximate and Transprecision Computing on Emerging Technologies, ATCET 2018; First Workshop on the Convergence of Large-Scale Simulation and Artificial Intelligence; Third Workshop for Open Source Supercomputing, OpenSuCo 2018; First Workshop on Interactive High-Performance Computing; Workshop on Performance Portable Programming Models for Accelerators, P^3MA 2018. The 53 full papers included in this volume were carefully reviewed and selected from 80 submissions. They cover all aspects of research, development, and application of large-scale, high performance experimental and commercial systems. Topics include HPC computer architecture and hardware; programming models, system software, and applications; solutions for heterogeneity, reliability, power efficiency of systems; virtualization and containerized environments; big data and cloud computing; and artificial intelligence.

Berkowitz, Evan↗
DOE OSTI2019

Parallelized Kalman-Filter-Based Reconstruction of Particle Tracks on Many-Core Architectures with the CMS Detector

In the High-Luminosity Large Hadron Collider (HL-LHC), one of the most challenging computational problems is expected to be finding and fitting charged-particle tracks during event reconstruction. The methods currently in use at the LHC are based on the Kalman filter. Such methods have shown to be robust and to provide good physics performance, both in the trigger and offline. In order to improve computational performance, we explored Kalman-filter-based methods for track finding and fitting, adapted for many-core SIMD and SIMT architectures. Our adapted Kalman-filter-based software has obtained significant parallel speedups using such processors, e.g., Intel Xeon Phi, Intel Xeon SP (Scalable Processors) and (to a limited degree) NVIDIA GPUs. Recently, an effort has started towards the integration of our software into the CMS software framework, in view of its exploitation for the Run III of the LHC. Prior reports have shown that our software allows in fact for some significant improvements over the existing framework in terms of computational performance with comparable physics performance, even when applied to realistic detector configurations and event complexity. Here, we demonstrate that in such conditions physics performance can be further improved with respect to our prior reports, while retaining the improvements in computational performance, by making use of the knowledge of the detector and its geometry.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Solving a trillion unknowns per second with HPGMG on Sunway TaihuLight

Benchmarks for supercomputers are important tools, not only for evaluating and ranking modern supercomputers, but also for providing hints for future architecture design. As a new benchmark, HPGMG (high performance geometric multigrid) solves a linear equation set with a full geometric multi-grid algorithm. It involves computation on different scales, data movement with various volumes, global communication and neighbor communication with both large and small messages, etc., and is more correlated to real world applications than traditional benchmarks such as LINPACK. Therefore, it is desirable to examine how well HPGMG can perform on leadership supercomputers such as Sunway Taihulight. Sunway Taihulight, the No. 1 supercomputer in the Top 500 list from June 2016 to June 2018, which uses a specially designed many-core architecture SW26010, is of great interest to the community of high performance computing. With careful analysis and code design, we came up with an efficient implementation of HPGMG on SW26010 processors. We not only employed traditional optimization techniques such as 2.5D partitioning, double buffering, and collective data load, but also introduced a micro-benchmark to help with the choice of optimization direction and parameter tuning. Another contribution is that we proposed a new procedure for the major operations, by granulating and reordering the smooth function and the ghost exchange operation, leading to reduced memory copy and accelerated communication process. Our optimized implementation of HPGMG on Sunway TaihuLight achieved a ground-breaking performance of 1.036 × 10 12 Degrees of Freedom per second at the finest level, which is No. 1 on the HPGMG list of Nov 2017.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

PAGANI: a parallel adaptive GPU algorithm for numerical integration

We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core utilization is difficult to achieve because the adaptive work-load can vary greatly across the integration space and is impossible to predict a priori. Existing parallel algorithms utilize sequential computations on independent processors, which results in bottlenecks due to the need for data redistribution and processor synchronization. Our algorithm employs a high-throughput approach in which all existing sub-regions are processed and sub-divided in parallel. Repeated sub-region classification and filtering improves upon a brute-force approach and allows the algorithm to make efficient use of computation and memory resources. A CUDA implementation shows orders of magnitude speedup over the fastest open-source CPU method and extends the achievable accuracy for difficult integrands. Our algorithm typically outperforms other existing deterministic parallel methods.

Sakiotis, Ioannis↗
DOE OSTI2022

m-CUBES An efficient and portable implementation of multi-dimensional integration for gpus

The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation. Multi-dimensional integration is often time-prohibitive on CPUs. Efficient implementation on many-core architectures is challenging as the workload across the integration space cannot be predicted a priori. We propose m-Cubes, a novel implementation of the well-known Vegas algorithm for execution on GPUs. Vegas transforms integration variables followed by calculation of a Monte Carlo integral estimate using adaptive partitioning of the resulting space. m-Cubes improves performance on GPUs by maintaining relatively uniform workload across the processors. As a result, our optimized Cuda implementation for Nvidia GPUs outperforms parallelization approaches proposed in past literature. We further demonstrate the efficiency of m-Cubes by evaluating a six-dimensional integral from a cosmology application, achieving significant speedup and greater precision than the CUBA library's CPU implementation of VEGAS. We also evaluate m-Cubes on a standard integrand test suite. m-Cubes outperforms the serial implementations of the Cuba and GSL libraries by orders of magnitude speedup while maintaining comparable accuracy. Our approach yields a speedup of at least 10 when compared against publicly available Monte Carlo based GPU implementations. In summary, m-Cubes can solve integrals that are prohibitively expensive using standard libraries and custom implementations. A modern C++ interface header-only implementation makes m-Cubes portable, allowing its utilization in complicated pipelines with easy to define stateful integrals. Compatibility with non-Nvidia GPUs is achieved with our initial implementation of m-Cubes using the Kokkos framework.

Sakiotis, Ioannis↗
DOE OSTI2019

XVis: Visualization for the Extreme-Scale Scientific Computation Ecosystem (Final Report)

Scientific computing is no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. The XVis project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressing four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis. This report reviews the accomplishments of the XVis project to prepare scientific visualization for Exascale computing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5-4.5x. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. Finally, the in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

CMSSW Scaling Limits on Many-Core Machines

Today the LHC offline computing relies heavily on CPU resources, despite the interest in compute accelerators, such as GPUs, for the longer term future. The number of cores per CPU socket has continued to increase steadily, reaching the levels of 64 cores (128 threads) with recent AMD EPYC processors, and 128 cores on Ampere Altra Max ARM processors. Over the course of the past decade, the CMS data processing framework, CMSSW, has been transformed from a single-threaded framework into a highly concurrent one. The first multithreaded version was brought into production by the start of the LHC Run 2 in 2015. Since then, the framework's threading efficiency has gradually been improved by adding more levels of concurrency and reducing the amount of serial code paths. The latest addition was support for concurrent Runs. In this work we review the concurrency model of the CMSSW, and measure its scalability with real CMS applications, such as simulation and reconstruction, on mode rn many-core machines. We show metrics such as event processing throughput and application memory usage with and without the contribution of I/O, as I/O has been the major scaling limitation for the CMS applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Performance evaluation of the three-point angular correlation function

In recent years, we have observed an increase in the diversity of the processors ecosystem. Different designs and architectures are being studied based on their performance and power characteristics. While using benchmarks for this purpose allows for reproducibility and easy understanding of the results, using real scientific applications allows researchers to realize the actual implications of each design on the overall performance of their codes. This paper analyzes the performance of different implementations of a three-point angular correlation function. This function is used in the study of Large-Scale Distribution of galaxies in a variety of computational platforms. The function is based on histogram construction and presents a large computational cost. This cost dramatically increases with the size of the datasets. We have considered two different GPUs, a set of x86 Intel machines (multi- and many-core), ARM chipsets, as well as an FPGA. We first study the best possible implementation for each platform in terms of time to solution. We then compare the power used by those platforms for a predefined number of datasets. Energy is one of the main constraints that computer architects are facing nowadays. The results will be used to evaluate the performance of this function considering those two targets – time and energy – for those platforms and to analyze the suitability of each of those platforms for this specific problem.

Computer Science↗