Search NASA⌕ Search

SEARCH · Search NASA

Results for “Parallel Applications”

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.

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

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Abstract Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.

Chemistry↗
DOE OSTI2024

From minimum-viable-products to full models: a step-wise development of diagnostic forward models in support of design, analysis and modelling on the ST40 tokamak

Like most magnetic confined fusion experiments, the ST40 tokamak started off with a small subset of diagnostics and gradually increased the diagnostic set to include more complex and comprehensive systems. To make the most of each operational phase, forward models of various diagnostics are used and developed to aid design, provide consistency-checks during commissioning, test analysis methods, and build workflows to constrain high-level parameters to inform interpretation, theory and modelling. For new models and new analysis workflows, minimum-viable-products are released early, and their complexity is increased in a step-wise manner, facilitating the support of all programme phases on multiple parallel applications, while enabling learning opportunities and feedback loops. In this contribution we review the philosophy, scope and architecture of the framework under development. We discuss the details of some forward models, with examples on how they are used to aid diagnostic design, to investigate analysis methodologies through synthetic data, and how they are embedded in experimental analysis workflows. We compare previously published experimental results with new, more advanced analysis workflows employing more recent, detailed models and new diagnostic data, providing confirmation of the published material from the 2021–22 experimental campaign.

integrated data analysis↗
DOE OSTI2021

Deterministic Fast Scrambling with Neutral Atom Arrays

Fast scramblers are dynamical quantum systems that produce many-body entanglement on a timescale that grows logarithmically with the system size N. Here, we propose and investigate a family of deterministic, fast scrambling quantum circuits realizable in near-term experiments with arrays of neutral atoms. We show that three experimental tools—nearest-neighbor Rydberg interactions, global single-qubit rotations, and shuffling operations facilitated by an auxiliary tweezer array—are sufficient to generate nonlocal interaction graphs capable of scrambling quantum information using only O(logN) parallel applications of nearest-neighbor gates. These tools enable direct experimental access to fast scrambling dynamics in a highly controlled and programmable way and can be harnessed to produce highly entangled states with varied applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Performance Assessment of Emerging Memories Through FPGA Emulation

Emerging memory technologies offer the prospect of large capacity, high bandwidth, and a range of access latencies ranging from DRAM-like to SSD-like. In this paper, we evaluate the performance of parallel applications on CPUs whose main memories sweep a wide range of latencies within a bandwidth cap. We use an FPGA emulator, the logic in memory emulator (LiME) to accelerate evaluation. The LiME framework uses a multiprocessor system on chip (MPSoC) combining multicore CPU, integrated memory controller, and FPGA fabric, and enables emulation orders of magnitude faster than software simulation. This work highlights the performance impact of higher latency on concurrent applications and identifies conditions under which future high latency memories can effectively be used as main memory.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks

We present a new method for reducing parallel applications' communication time by mapping their MPI tasks to processors in a way that lowers the distance messages travel and the amount of congestion in the network. Assuming geometric proximity among the tasks is a good approximation of their communication interdependence, we use a geometric partitioning algorithm to order both the tasks and the processors, assigning task parts to the corresponding processor parts. In this way, interdependent tasks are assigned to “nearby” cores in the network. We also present a number of algorithmic optimizations that exploit specific features of the network or application to further improve the quality of the mapping. We specifically address the case of sparse node allocation, where the nodes assigned to a job are not necessarily located in a contiguous block nor within close proximity to each other in the network. Furthermore, our methods generalize to contiguous allocations as well, and results are shown for both contiguous and non-contiguous allocations. We show that, for the structured finite difference mini-application MiniGhost, our mapping methods reduced communication time up to 75% relative to MiniGhost's default mapping on 128K cores of a Cray XK7 with sparse allocation. For the atmospheric modeling code E3SM/HOMME, our methods reduced communication time up to 31% on 16K cores of an IBM BlueGene/Q with contiguous allocation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Addressing Global Data Dependencies in Heterogeneous Asynchronous Runtime Systems on GPUs

Large-scale parallel applications with complex global data dependencies beyond those of reductions pose significant scalability challenges in an asynchronous runtime system. Internodal challenges include identifying the all-to-all communication of data dependencies among the nodes. Intranodal challenges include gathering together these data dependencies into usable data objects while avoiding data duplication. This paper addresses these challenges within the context of a large-scale, industrial coal boiler simulation using the Uintah asynchronous many-task runtime system on GPU architectures. We show significant reduction in time spent analyzing data dependencies through refinements in our dependency search algorithm. Multiple task graphs are used to eliminate subsequent analysis when task graphs change in predictable and repeatable ways. Using a combined data store and task scheduler redesign reduces data dependency duplication ensuring that problems fit within host and GPU memory. Furthermore, these modifications did not require any changes to application code or sweeping changes to the Uintah runtime system. We report results running on the DOE Titan system on 119K CPU cores and 7.5K GPUs simultaneously. Our solutions can be generalized to other task dependency problems with global dependencies among thousands of nodes which must be processed efficiently at large scale.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

BCL: A Cross-Platform Distributed Data Structures Library

One-sided communication is a useful paradigm for irregular parallel applications, but most one-sided programming environments, including MPI's one-sided interface and PGAS programming languages, lack application-level libraries to support these applications. We present the Berkeley Container Library, a set of generic, cross-platform, high-performance data structures for irregular applications, including queues, hash tables, Bloom filters and more. BCL is written in C++ using an internal DSL called the BCL Core that provides one-sided communication primitives such as remote get and remote put operations. The BCL Core has backends for MPI, OpenSHMEM, GASNet-EX, and UPC++, allowing BCL data structures to be used natively in programs written using any of these programming environments. Along with our internal DSL, we present the BCL ObjectContainer abstraction, which allows BCL data structures to transparently serialize complex data types while maintaining efficiency for primitive types. We also introduce the set of BCL data structures and evaluate their performance across a number of high-performance computing systems, demonstrating that BCL programs are competitive with hand-optimized code, even while hiding many of the underlying details of message aggregation, serialization, and synchronization.

Brock, Benjamin↗
DOE OSTI2018

Stack Trace Analysis Tool (STAT)

STAT is a light weight debugging tool that gathers and merges stack traces from all of the processes in a parallel application. STAT uses the MRNet tree based overlay network to broadcast commands from the tool front-end to the STAT daemons and for the front-end to gather the traces from the STAT daemons. As the traces propagate through the MRNet network tree, they are merged across all tasks to fonn a single call prefix tree. The call prefix tree can be examined to identify tuks with similar function call patterns and to delineate a small set of equivalence classes. A representative task from each of these classes can then be fed into a full feature debugger like TotalView for root cause analysis.

ECP↗
DOE OSTI2017

MPI Profiler

loupe is a PMPl-based library to profile MPI routines in a parallel application.

Castillo, Emilio↗
DOE OSTI2019

Software Defined Networking for HPC Interconnects and its Extension across Domains (Final Technical Report for DE-SC0016039)

This project seeks to incorporate OpenFlow-style Software Defined Networking capability into existing High Performance Computing (HPC) interconnect technology, InfiniBand, and to extend such capability beyond one domain. We develop SDN-enhanced InfiniBand that supports OpenFlow functionality for HPC interconnects, investigate the required techniques and the potential benefits for applying SDN on different types of HPC interconnects, and develop software to control the network and expose SDN capability to external networks through the OpenFlow interface. We have also developed techniques to evaluate communication characteristics of parallel applications, which determines the workload on interconnects, investigated newly proposed Interconnection network technologies including new network topologies and routing schemes, and designed novel interconnect routing and modeling techniques. Major activities and findings are summarized as follows.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

symPACK: A GPU-Capable Fan-Out Sparse Cholesky Solver

Sparse symmetric positive definite systems of equations are ubiquitous in scientific workloads and applications. Parallel sparse Cholesky factorization is the method of choice for solving such linear systems. Therefore, the development of parallel sparse Cholesky codes that can efficiently run on today’s large-scale heterogeneous distributed-memory platforms is of vital importance. Modern supercomputers offer nodes that contain a mix of CPUs and GPUs. To fully utilize the computing power of these nodes, scientific codes must be adapted to offload expensive computations to GPUs. We present symPACK, a GPU-capable parallel sparse Cholesky solver that uses one-sided communication primitives and remote procedure calls provided by the UPC++ library. We also utilize the UPC++ "memory kinds" feature to enable efficient communication of GPU-resident data. We show that on a number of large problems, symPACK outperforms comparable state-of-the-art GPU-capable Cholesky factorization codes by up to 14x on the NERSC Perlmutter supercomputer.

Bellavita, Julian↗
DOE OSTI2023

Massively-parallel Lagrangian particle code and applications

Massively-parallel, distributed-memory algorithms for the Lagrangian particle hydrodynamic method (Samulyak et al., 2018) have been developed, verified, and implemented. The key component of parallel algorithms is a particle management module that includes a parallel construction of octree databases, dynamic adaptation and refinement of octrees, and particle migration between parallel subdomains. The particle management module is based on the p4est (parallel forest of k-trees) library. The massively-parallel Lagrangian particle code has been applied to a variety of fundamental science and applied problems. A summary of Lagrangian particle code applications to the injection of impurities into thermonuclear fusion devices and to the simulation of supersonic hydrogen jets in support of laser-plasma wakefield acceleration research has also been presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)↗
DOE OSTI2019

SAFIRE : Scalable and Accurate Fault Injection for Parallel Multi-threaded Applications

The software SAFIRE implements a fault injection tool to evaluate the impact of soft errors on parallel, multi-threaded applications. It implements instruction-level fault models that emulate soft errors by flipping bits in the register operands of executed machine instructions. SAFIRE is based on the LLVM compiler and utilizes novel techniques to optimize instruction instrumentation and fault injection. By detailed measurements, SAFIRE is multiple times faster than other state-of-the-art fault injection techniques, while having the same accuracy.

Georgakoudis, Giorgis↗
DOE OSTI2019

Performance portability study for massively parallel computational fluid dynamics application on scalable heterogeneous architectures

Patient-specific hemodynamic simulations have the possibility to greatly improve both the diagnosis and treatment of a variety of vascular diseases. Portability will enable wider adoption of computational fluid dynamics (CFD) applications in the biomedical research community and targeting to platforms ideally suited to different vascular regions. Here, we introduce a case study in performance portability that assesses (1) the ease of porting an MPI application optimized for one specific architecture to new platforms using variants of hybrid MPI+X programming models; (2) performance portability seen when simulating blood flow in three different vascular regions on diverse heterogeneous architectures; (3) model-based performance prediction for future architectures; and (4) performance scaling of the hybrid MPI+X programming on parallel heterogeneous systems. We report on the lessons learned in porting HARVEY, a massively parallel CFD application, from traditional multicore CPUs to diverse heterogeneous architectures ranging from NVIDIA/AMD GPUs to Intel MICs and Altera FPGAs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

HDF5 in the exascale era: Delivering efficient and scalable parallel I/O for exascale applications

Accurately modeling real-world systems requires scientific applications at exascale to generate massive amounts of data and manage data storage efficiently. However, parallel input and output (I/O) faces challenges due to new application workflows and the state-of-the-art memory, interconnect, and storage architectures considered in exascale designs. The storage hierarchy has expanded with node-local persistent memory, solid-state storage, and traditional disk and tape-based storage, thus requiring efficiency at each layer and much more efficient data movement among these layers. This paper discusses how the ExaHDF5 project improved the I/O performance and data management for exascale architectures by enhancing HDF5, a widely used parallel I/O library. The team developed an Asynchronous I/O Virtual Object Layer (VOL) connector that allowed overlapping I/O with computation. They also created a Cache VOL to complement asynchronous I/O by incorporating fast storage layers, such as burst buffer and node-local storage, into the parallel I/O workflow through caching and staging data. Additionally, the team enabled data aggregation and I/O at the node level by using a Subfiling Virtual File Driver (VFD). To demonstrate superior I/O performance with HDF5 at exascale, the ExaHDF5 team collaborated with several exascale applications. In this paper, we show I/O performance improvements for three applications: Cabana (a particle-based simulation library), EQSIM (a regional earthquake simulation software), and E3SM (a climate system modeling library).

Asynchronous I/Ol↗