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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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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A massively-parallel, unstructured overset method for mesh connectivity

Here we present a method that dynamically and efficiently performs connectivity calculations between many O(10 5 ) moving, unstructured overset meshes in parallel. In order to connect overset meshes, elements exterior to the solution domain must be removed from the simulation. In regions with many overlapping meshes, elements must be selectively removed to reduce redundancy while maintaining a solution over the entire domain. Around masked regions interpolation partner pairing is required between meshes to provide boundary conditions. For general unstructured meshes, these steps involve challenging computational geometry calculations which must be efficient and automatic. For many moving meshes each step must be massively parallelized and scalable to large numbers of computational cores. To establish communication patterns a parallelized master/slave algorithm is used which minimizes global communication and storage. To remove elements a parallel ‘Forest Fire’ flood-fill algorithm is used to set a masking variable. For interpolation partner pairing, and other necessary searches, k-dimensional tree data structures (k-d trees) are extensively used. Often in a calculation, the connectivity between overset meshes remains largely the same between time steps. The temporal coherence of the various objects in the connectivity calculation is directly used to only update necessary information with time, resulting in substantial cost savings. Details of the different algorithms are presented. Resulting connectivity and timings are shown for complex geometries. Parallel scaling is demonstrated for 100,000 spherical particles within a channel up to 492,000 processors.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

ParNCL and ParGAL: Data-parallel Tools for Postprocessing of Large-scale Earth Science Data

Earth science high-performance applications often require extensive analysis of their output in order to complete the scien- tific goals or produce a visual image or animation. Often this analysis cannot be done in situ because it requires calculating time-series statistics from state sampled over the entire length of the run or analyzing the relationship between similar time series from previous simulations or observations. Many of the tools used for this postprocessing are not themselves high- performance applications, but the new Parallel Gridded Analysis Library (ParGAL) provides high-performance data-parallel versions of several common analysis algorithms for data from a structured or unstructured grid simulation. The library builds on several scalable systems, including the Mesh Oriented DataBase (MOAB), a library for representing mesh data that sup- ports structured, unstructured finite element, and polyhedral grids; the Parallel-NetCDF (PNetCDF) library; and Intrepid, an extensible library for computing operators (such as gradient, curl, and divergence) acting on discretized fields. We have used ParGAL to implement a parallel version of the NCAR Command Language (NCL) a scripting language widely used in the climate community for analysis and visualization. The data-parallel algorithms in ParGAL/ParNCL are both higher performing and more flexible than their serial counterparts.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Parallel computation safety analysis irradiation targets fission product molybdenum in neutronic aspect using the successive over-relaxation algorithm

One of the research activities in support of commercial radioisotope production program is a safety research on target FPM (Fission Product Molybdenum) irradiation. FPM targets form a tube made of stainless steel which contains nuclear-grade high-enrichment uranium. The FPM irradiation tube is intended to obtain fission products. Fission materials such as Mo{sup 99} used widely the form of kits in the medical world. The neutronics problem is solved using first-order perturbation theory derived from the diffusion equation for four groups. In contrast, Mo isotopes have longer half-lives, about 3 days (66 hours), so the delivery of radioisotopes to consumer centers and storage is possible though still limited. The production of this isotope potentially gives significant economic value. The criticality and flux in multigroup diffusion model was calculated for various irradiation positions and uranium contents. This model involves complex computation, with large and sparse matrix system. Several parallel algorithms have been developed for the sparse and large matrix solution. In this paper, a successive over-relaxation (SOR) algorithm was implemented for the calculation of reactivity coefficients which can be done in parallel. Previous works performed reactivity calculations serially with Gauss-Seidel iteratives. The parallel method can be used to solve multigroup diffusion equation system and calculate the criticality and reactivity coefficients. In this research a computer code was developed to exploit parallel processing to perform reactivity calculations which were to be used in safety analysis. The parallel processing in the multicore computer system allows the calculation to be performed more quickly. This code was applied for the safety limits calculation of irradiated FPM targets containing highly enriched uranium. The results of calculations neutron show that for uranium contents of 1.7676 g and 6.1866 g (× 10{sup 6} cm{sup −1}) in a tube, their delta reactivities are the still within safety limits; however, for 7.9542 g and 8.838 g (× 10{sup 6} cm{sup −1}) the limits were exceeded.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

A Shift Selection Strategy for Parallel Shift-invert Spectrum Slicing in Symmetric Self-consistent Eigenvalue Computation

The central importance of large-scale eigenvalue problems in scientific computation necessitates the development of massively parallel algorithms for their solution. Recent advances in dense numerical linear algebra have enabled the routine treatment of eigenvalue problems with dimensions on the order of hundreds of thousands on the world’s largest supercomputers. In cases where dense treatments are not feasible, Krylov subspace methods offer an attractive alternative due to the fact that they do not require storage of the problem matrices. However, demonstration of scalability of either of these classes of eigenvalue algorithms on computing architectures capable of expressing massive parallelism is non-trivial due to communication requirements and serial bottlenecks, respectively. In this work, we introduce the SISLICE method: a parallel shift-invert algorithm for the solution of the symmetric self-consistent field (SCF) eigenvalue problem. The SISLICE method drastically reduces the communication requirement of current parallel shift-invert eigenvalue algorithms through various shift selection and migration techniques based on density of states estimation and k-means clustering, respectively. This work demonstrates the robustness and parallel performance of the SISLICE method on a representative set of SCF eigenvalue problems and outlines research directions that will be explored in future work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Parallel FETI‐DP algorithm for efficient simulation of large‐scale EM problems

Summary An efficient parallelization of the dual‐primal finite‐element tearing and interconnecting (FETI‐DP) algorithm is presented for large‐scale electromagnetic simulations. As a nonoverlapping domain decomposition method, the FETI‐DP algorithm formulates a global interface problem, whose iterative solution is accelerated with a solution of a global corner problem. To achieve a good load balance for parallel computation, the original computational domain is decomposed into subdomains with similar sizes and shapes. The subdomains are then distributed to processors based on their close proximity to minimize inter‐processor communication. The parallel generalized minimal residual method, enhanced with the iterative classical Gram‐Schmidt orthogonalization scheme to reduce global communication, is adopted to solve the global interface problem with a fast convergence rate. The global corner‐related coarse problem is solved iteratively with a parallel communication‐avoiding biconjugate gradient stabilized method to minimize global communication, and its convergence is accelerated by a diagonal preconditioner constructed from the coarse system matrix. To alleviate neighboring communication overhead, the non‐blocking communication approach is employed in both generalized minimal residual and communication‐avoiding biconjugate gradient stabilized iterative solutions. Three numerical examples are presented to demonstrate the accuracy, scalability, and capability of the proposed parallel FETI‐DP algorithm for electromagnetic modeling of general objects and antenna arrays. Copyright © 2016 John Wiley & Sons, Ltd.

Zhang, Kedi↗
DOE OSTI2018

On the adequacy of lightweight thread approaches for high-level parallel programming models

High-level parallel programming models (PMs) are becoming crucial in order to extract the computational power of current on-node multi-threaded parallelism. The most popular PMs, such as OpenMP or OmpSs, are directive-based: the complexity of the hardware is hidden by the underlying runtime system, improving coding productivity. The implementations of OpenMP usually rely on POSIX threads (pthreads), offering excellent performance for coarse-grained parallelism and a perfect match with the current hardware. OmpSs is a task oriented PM based on an ad hoc runtime solution called Nanos++; it is the precursor of the tasking parallelism in the OpenMP tasking specification. A recent trend in runtimes and applications points to leveraging massive on-node parallelism in conjunction with fine-grained and dynamic scheduling paradigms. In this paper we analyze the behavior of the OpenMP and OmpSs PMs on top of the recently emerged Generic Lightweight Threads (GLT) API. GLT exposses a common API for lightweight thread (LWT) libraries that offers the possibility of running the same application over different native LWT solutions. We describe the design details of those high-level PMs implemented on top of GLT and analyze different scenarios in order to assess where the use of LWTs may benefit application performance. Our work reveals those scenarios where LWTs overperform pthread-based solutions and compares the performance between an ad hoc solution and a generic implementation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

MOOSE ProbML: Parallelized probabilistic machine learning and uncertainty quantification for computational energy applications

Here, this paper presents the development and demonstration of massively parallel probabilistic machine learning (ML) and uncertainty quantification (UQ) capabilities within the Multiphysics Object-Oriented Simulation Environment (MOOSE), an open-source computational platform for parallel finite element and finite volume analyses. In addressing the computational expense and uncertainties inherent in complex multiphysics simulations, this paper integrates Gaussian process (GP) variants, active learning, Bayesian inverse UQ, adaptive forward UQ, Bayesian optimization, evolutionary optimization, and Markov chain Monte Carlo (MCMC) within MOOSE. It also elaborates on the interaction among key MOOSE systems — Sampler, MultiApp, Reporter, and Surrogate — in enabling these capabilities. The modularity offered by these systems enables development of a multitude of probabilistic ML and UQ algorithms in MOOSE. Example code demonstrations include parallel active learning and parallel Bayesian inference via active learning. The impact of these developments is illustrated through five applications relevant to computational energy applications: UQ of nuclear fuel fission product release, using parallel active learning Bayesian inference; very rare events analysis in nuclear microreactors using active learning; advanced manufacturing process modeling using multi-output GPs (MOGPs) and dimensionality reduction; fluid flow using deep GPs (DGPs); and tritium transport model parameter optimization for fusion energy, using batch Bayesian optimization. These capabilities are part of the MOOSE framework.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Performance and Accuracy Implications of Parallel Split Physics-Dynamics Coupling in the Energy Exascale Earth System Atmosphere Model

Simultaneous calculation of atmospheric processes is faster than calculating processes one at a time. This type of parallelism is beneficial or perhaps even necessary to provide good performance on modern supercomputers, which achieve faster performance through increased processor count rather than improved clock speed. The scalability of the Energy Exascale Earth System Model (E3SM) Atmosphere Model (EAM) is limited by the fluid dynamics which scales up to the number of mesh cells in the global mesh. In contrast, the suite of physics parameterizations in EAM is scalable up to the total number of physics columns, which is an order of magnitude greater than the number of mesh cells. A proposed solution to unlocking the greater potential performance from the physics suite is to solve the physics and dynamics in parallel. This work represents a first attempt at parallel splitting of the grid-scale fluid dynamics model and the subgrid-scale physics parameterizations in a global atmosphere model. We will demonstrate that switching to parallel physics-dynamics coupling extends the scalability of the EAM to up to 3 times the previous peak scalability limit and is up to 20% faster than the sequentially split coupling at the highest core counts and the same time step. Decadal simulations of both coupling approaches show very little impact to the model climate. This improved performance does not come without drawbacks, however. Parallel splitting requires a shorter time step and other modifications which largely offset performance gains. A mass fixer is required for conservation. Techniques for mitigating these issues are also discussed.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-time scale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to stochastic MD time steps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a nonequilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

Rosa-Raíces, Jorge L.↗
DOE OSTI2023

Multi-level parallelization of quantum-chemical calculations

Here, strategies for multiple-level parallelizations of quantum-mechanical calculations are discussed, with an emphasis on using groups of workers for performing parallel tasks. These parallel programming models can be used for a variety ab initio quantum chemistry approaches, including the fragment molecular orbital method and replica-exchange molecular dynamics. Strategies for efficient load balancing on problems of increasing granularity are introduced and discussed. A four-level parallelization is developed based on a multi-level hierarchical grouping, and a high parallel efficiency is achieved on the Theta supercomputer using 131 072 OpenMP threads.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

YAPPA: a Compiler-Based Parallelization Framework for Irregular Applications on MPSoCs

Modern embedded systems include hundreds of cores. Because of the difficulty in providing a fast, coherent memory architecture, these systems usually rely on non-coherent, non-uniform memory architectures with private memories for each core. However, programming these systems poses significant challenges. The developer must extract large amounts of parallelism, while orchestrating communication among cores to optimize application performance. These issues become even more significant with irregular applications, which present data sets difficult to partition, unpredictable memory accesses, unbalanced control flow and fine grained communication. Hand-optimizing every single aspect is hard and time-consuming, and it often does not lead to the expected performance. There is a growing gap between such complex and highly-parallel architectures and the high level languages used to describe the specification, which were designed for simpler systems and do not consider these new issues. In this paper we introduce YAPPA (Yet Another Parallel Programming Approach), a compilation framework for the automatic parallelization of irregular applications on modern MPSoCs based on LLVM. We start by considering an efficient parallel programming approach for irregular applications on distributed memory systems. We then propose a set of transformations that can reduce the development and optimization effort. The results of our initial prototype confirm the correctness of the proposed approach.

Irregular applications↗
DOE OSTI2021

Logically Parallel Communication for Fast MPI+Threads Applications

Supercomputing applications are increasingly adopting the MPI+threads programming model over the traditional "MPI everywhere" approach to better handle the disproportionate increase in the number of cores compared with other on-node resources. In practice, however, most applications observe a slower performance with MPI+threads primarily because of poor communication performance. Recent research efforts on MPI libraries address this bottleneck by mapping logically parallel communication, that is, operations that are not subject to MPI's ordering constraints to the underlying network parallelism. Domain scientists, however, typically do not expose such communication independence information because the existing MPI-3.1 standard's semantics can be limiting. Researchers had initially proposed user-visible endpoints to combat this issue, but such a solution requires intrusive changes to the standard (new APIs). The upcoming MPI-4.0 standard, on the other hand, allows applications to relax unneeded semantics and provides them with many opportunities to express logical communication parallelism. Here in this article, we show how MPI+threads applications can achieve high performance with logically parallel communication. Through application case studies, we compare the capabilities of the new MPI-4.0 standard with those of the existing one and user-visible endpoints (upper bound). Logical communication parallelism can boost the overall performance of an application by over 2x.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

SU-E-J-38: Comparison of 6MV Photon Dose in a Perpendicular and Parallel Magnetic Field

Purpose: Integrating a linac with an MRI system would allow for real time tumour tracking however the patient will be irradiated in the presence of a magnetic field. The present study experimentally investigates the magnetic field effects on entrance, exit, and interface dose for both transverse and parallel magnetic fields. Methods: Polystyrene was used to construct a set of phantoms for Gafchromic film measurements. One phantom had an adjustable air gap and four other phantoms had one surface at various angles. The linac-MR prototype consisting of a biplanar permanent magnet coupled to a linac was used for the transverse magnetic field measurements. A couple of solenoid electromagnets, stacked on top of each other and irradiated along their bore, were used for the parallel field measurements. Results: All doses are relative to no magnetic field. The transverse magnetic field reduced the entrance dose for all surface angles by strongly deflecting the contaminant electrons. The exit dose in a transverse magnetic field was found to be significantly higher. The entrance dose with a parallel magnetic field present is higher due to the contaminant electrons being concentrated within the beam area. The air gap phantom measurements, done in a transverse magnetic field, show a significant increase of the dose at the proximal side of the air gap and a decrease at the distal side. The measurements, done in the parallel magnetic field, show the concentration of secondary electrons in the air gap. Conclusion: The radiation dose measurements of a 6MV beam in a parallel and transverse magnetic field presented here are currently being replicated using Monte Carlo simulations. This verified Monte Carlo system could provide the dose calculation basis for future linac-MR systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

SU-F-J-146: Experimental Validation of 6 MV Photon PDD in Parallel Magnetic Field Calculated by EGSnrc

Purpose: Integrated linac-MR systems are uniquely suited for real time tumor tracking during radiation treatment. Understanding the magnetic field dose effects and incorporating them in treatment planning is paramount for linac-MR clinical implementation. We experimentally validated the EGSnrc dose calculations in the presence of a magnetic field parallel to the radiation beam travel. Methods: Two cylindrical bore electromagnets produced a 0.21 T magnetic field parallel to the central axis of a 6 MV photon beam. A parallel plate ion chamber was used to measure the PDD in a polystyrene phantom, placed inside the bore in two setups: phantom top surface coinciding with the magnet bore center (183 cm SSD), and with the magnet bore’s top surface (170 cm SSD). We measured the field of the magnet at several points and included the exact dimensions of the coils to generate a 3D magnetic field map in a finite element model. BEAMnrc and DOSXYZnrc simulated the PDD experiments in parallel magnetic field (i.e. 3D magnetic field included) and with no magnetic field. Results: With the phantom surface at the top of the electromagnet, the surface dose increased by 10% (compared to no-magnetic field), due to electrons being focused by the smaller fringe fields of the electromagnet. With the phantom surface at the bore center, the surface dose increased by 30% since extra 13 cm of air column was in relatively higher magnetic field (>0.13T) in the magnet bore. EGSnrc Monte Carlo code correctly calculated the radiation dose with and without the magnetic field, and all points passed the 2%, 2 mm Gamma criterion when the ion chamber’s entrance window and air cavity were included in the simulated phantom. Conclusion: A parallel magnetic field increases the surface and buildup dose during irradiation. The EGSnrc package can model these magnetic field dose effects accurately. Dr. Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters to create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.

Jin, Ye↗
DOE OSTI2021

Design Considerations for GPU-based Mixed Integer Programming on Parallel Computing Platforms

Mixed Integer Programming (MIP) is a powerful abstraction in combinatorial optimization that finds real-life application across many significant sectors. The recent proliferation of graphical processing unit (GPU)-based accelerated computing architectures in large-scale parallel computing or supercomputing presents new opportunities as well as challenges in the advancement of MIP solver technology to effectively use the new accelerated computing platforms and scale to large parallel systems. Here, we recount the conventional processor-based strategies and focus on configurations where the most promising intersection lies between parallel MIP solver approaches and the specific strengths of accelerated parallel platforms. We note that the best potential lies in solving problems whose individual matrix sizes (of the linear program relaxation) fit entirely within one accelerator's memory and whose branch-and-bound (or branch-and-cut) trees cannot be fully contained within a small number of computational nodes. Additionally, we identify ideal features of computational linear algebra support on GPU accelerators that would help advance this direction of scalable parallel solution of MIP problems on GPU-based accelerated computing architectures.

Perumalla, Kalyan↗
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↗