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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 sources NASA NTRS DOE OSTI

DOE OSTI2013

Tools for Simulation and Benchmark Generation at Exascale

The path to exascale high-performance computing (HPC) poses several challenges related to power, performance, resilience, productivity, programmability, data movement, and data management. Investigating the performance of parallel applications at scale on future architectures and the performance impact of different architecture choices is an important component of HPC hardware/software co-design. Simulations using models of future HPC systems and communication traces from applications running on existing HPC systems can offer an insight into the performance of future architectures. This work targets technology developed for scalable application tracing of communication events and memory profiles, but can be extended to other areas, such as I/O, control flow, and data flow. It further focuses on extreme-scale simulation of millions of Message Passing Interface (MPI) ranks using a lightweight parallel discrete event simulation (PDES) toolkit for performance evaluation. Instead of simply replaying a trace within a simulation, the approach is to generate a benchmark from it and to run this benchmark within a simulation using models to reflect the performance characteristics of future-generation HPC systems. This provides a number of benefits, such as eliminating the data intensive trace replay and enabling simulations at different scales. The presented work utilizes the ScalaTrace tool to generate scalable trace files, the ScalaBenchGen tool to generate the benchmark, and the xSim tool to run the benchmark within a simulation.

Lagadapati, Mahesh↗

DOE OSTI2014

Improving the Performance of the Extreme-scale Simulator

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation-based toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1) a new deadlock resolution protocol to reduce the parallel discrete event simulation management overhead and (2) a new simulated MPI message matching algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement, such as by reducing the simulation overhead for running the NAS Parallel Benchmark suite inside the simulator from 1,020\% to 238% for the conjugate gradient (CG) benchmark and from 102% to 0% for the embarrassingly parallel (EP) and benchmark, as well as, from 37,511% to 13,808% for CG and from 3,332% to 204% for EP with accurate process failure simulation.

Engelmann, Christian↗

DOE OSTI2017

Roofline Analysis in the Intel® Advisor to Deliver Optimized Performance for applications on Intel® Xeon Phi™ Processor

In this session we show, in two case studies, how the roofline feature of Intel Advisor has been utilized to optimize the performance of kernels of the XGC1 and PICSAR codes in preparation for Intel Knights Landing architecture. The impact of the implemented optimizations and the benefits of using the automatic roofline feature of Intel Advisor to study performance of large applications will be presented. This demonstrates an effective optimization strategy that has enabled these science applications to achieve up to 4.6 times speed-up and prepare for future exascale architectures. # Goal/Relevance of Session The roofline model [1,2] is a powerful tool for analyzing the performance of applications with respect to the theoretical peak achievable on a given computer architecture. It allows one to graphically represent the performance of an application in terms of operational intensity, i.e. the ratio of flops performed and bytes moved from memory in order to guide optimization efforts. Given the scale and complexity of modern science applications, it can often be a tedious task for the user to perform the analysis on the level of functions or loops to identify where performance gains can be made. With new Intel tools, it is now possible to automate this task, as well as base the estimates of peak performance on measurements rather than vendor specifications. The goal of this session is to demonstrate how the roofline feature of Intel Advisor can be used to balance memory vs. computation related optimization efforts and effectively identify performance bottlenecks. A series of typical optimization techniques: cache blocking, structure refactoring, data alignment, and vectorization illustrated by the kernel cases will be addressed. # Description of the codes ## XGC1 The XGC1 code [3] is a magnetic fusion Particle-In-Cell code that uses an unstructured mesh for its Poisson solver that allows it to accurately resolve the edge plasma of a magnetic fusion device. After recent optimizations to its collision kernel [4], most of the computing time is spent in the electron push (pushe) kernel, where these optimization efforts have been focused. The kernel code scaled well with MPI+OpenMP but had almost no automatic compiler vectorization, in part due to indirect memory addresses and in part due to low trip counts of low-level loops that would be candidates for vectorization. Particle blocking and sorting have been implemented to increase trip counts of low-level loops and improve memory locality, and OpenMP directives have been added to vectorize compute-intensive loops that were identified by Advisor. The optimizations have improved the performance of the pushe kernel 2x on Haswell processors and 1.7x on KNL. The KNL node-for-node performance has been brought to within 30% of a NERSC Cori phase I Haswell node and we expect to bridge this gap by reducing the memory footprint of compute intensive routines to improve cache reuse. ## PICSAR is a Fortran/Python high-performance Particle-In-Cell library targeting at MIC architectures first designed to be coupled with the PIC code WARP for the simulation of laser-matter interaction and particle accelerators. PICSAR also contains a FORTRAN stand-alone kernel for performance studies and benchmarks. A MPI domain decomposition is used between NUMA domains and a tile decomposition (cache-blocking) handled by OpenMP has been added for shared-memory parallelism and better cache management. The so-called current deposition and field gathering steps that compose the PIC time loop constitute major hotspots that have been rewritten to enable more efficient vectorization. Particle communications between tiles and MPI domain has been merged and parallelized. All considered, these improvements provide speedups of 3.1 for order 1 and 4.6 for order 3 interpolation shape factors on KNL configured in SNC4 quadrant flat mode. Performance is similar between a node of cori phase 1 and KNL at order 1 and better on KNL by a factor 1.6 at order 3 with the considered test case (homogeneous thermal plasma).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗

DOE OSTI2023

An Open-Source Parallel EMT Simulation Framework: Preprint

As the integration level of inverter-based resources (IBR) increases, ensuring the reliable operation of the bulk power systems requires the use of electromagnetic transient (EMT) simulation tools to identify and mitigate system-wide stability risks. Conducting EMT studies for large-scale, IBR-rich grids, however, is challenging due to the inherent computational bottleneck caused by the underlying high-fidelity models and required small time steps. This paper introduces ParaEMT: an open-source, generic EMT simulation framework designed to accelerate simulations by leveraging advanced parallel computational technologies, such as high-performance computers. This paper presents a comprehensive exposition of ParaEMT, covering its modeling library, simulation strategy, framework structure, operational procedures, and auxiliary features, alongside its extensible parallel computational architecture. Notably, ParaEMT is a publicly accessible and modularized framework written in Python, thereby facilitating future development and the integration of new models and algorithms. The accuracy and efficiency of ParaEMT are demonstrated by rigorous validations via multiple case studies.

electromagnetic transient simulation↗

DOE OSTI2018

Simulating the Effect of Fracture Connectivity on Repository Performance with GDSA Framework - 18589

This work examines the possible migration of radionuclides from a deep geologic nuclear waste repository sited in fractured crystalline host rock. The key safety concern is the potential effect on waste isolation of the inter-connectivity of the fracture network, which is primarily established by the temporal evolution of the temperature and stress fields at the time of original rock intrusion and cooling. Two end members are considered in these simulations, one with a high degree of connectivity to the biosphere, such that advective transport through the fracture and fault network controls radionuclide migration, and the other with a low degree of connectivity, such that slow diffusive transport through the crystalline rock matrix is the controlling process for radionuclide migration to the biosphere. Both end members have several areally extensive, high-transmissivity deformation zones, whose distance to the repository is an important factor for waste isolation capability. Uncertainties in fracture properties (transmissivity, orientation, radius) and fracture distribution also give rise to uncertainty in waste isolation capability (i.e., the overall connectivity of the repository with the surface biosphere). These types of natural system uncertainties are generally present in any geologic site-characterization program and thus represent an important factor in assessing repository performance in hard rock environments. The waste considered in these simulations are spent fuel rod assemblies from the U.S. commercial nuclear reactor fleet. Thermal output of the waste must be considered in the simulations and can influence the rate and timing of waste package failure, waste form degradation, and fluid flux due to thermal expansion around the repository horizon. To achieve a high-fidelity representation of radionuclide transport in fractures and rock matrix, combined with thermal energy transport and fluid flow in fractures and matrix, the mathematical model is solved numerically in a parallel high-performance computing (HPC) environment on a finite volume unstructured grid consisting of approximately 5 million cells, using Geologic Disposal Safety Assessment (GDSA) Framework (https://pa.sandia.gov), an open-source performance assessment tool for deep underground disposal of nuclear waste. GDSA Framework uses PFLOTRAN to solve the balance equations on a three-dimensional grid with heterogeneous properties, using multiple processors in a parallel configuration based on domain decomposition. The fracture networks in these simulations are originally generated as discrete fracture networks (DFNs), which are sets of two-dimensional planes distributed in a three-dimensional domain. The method used in GDSA Framework maps the stochastically generated DFN to an equivalent continuous porous medium (ECPM) domain that allows for the simulation of coupled heat flow, fluid flow, and radionuclide transport, including heat conduction through the matrix of the fractured rock, which is a process not easily modeled in a DFN representation. Computational efficiency is also greatly enhanced using the ECPM method, allowing for a realistic representation and analysis of uncertainties in a multi-realization performance assessment of a deep geologic repository. The effect of fracture connectivity on the waste isolation safety function, as brought to light by these GDSA Framework simulations, points to the importance of including a realistic representation of uncertainties in fracture properties and distribution (effectively, uncertainty in spatial heterogeneity) in repository safety assessment simulations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗