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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 667 records · Page 37

Applying Machine Learning to Understand Write Performance of Large-scale Parallel Filesystems

In high-performance computing (HPC), I/O performance prediction offers the potential to improve the efficiency of scientific computing. In particular, accurate prediction can make runtime estimates more precise, guide users toward optimal checkpoint strategies, and better inform facility provisioning and scheduling policies. HPC I/O performance is notoriously difficult to predict and model, however, in large part because of inherent variability and a lack of transparency in the behaviors of constituent storage system components. In this work we seek to advance the state of the art in HPC I/O performance prediction by (1) modeling the mean performance to address high variability, (2) deriving model features from write patterns, system architecture and system configurations, and (3) employing Lasso regression model to improve model accuracy. We demonstrate the efficacy of our approach by applying it to a crucial subset of common HPC I/O motifs, namely, file-per-process checkpoint write workloads. We conduct experiments on two distinct production HPC platforms—Titan at the Oak Ridge Leadership Computing Facility and Cetus at the Argonne Leadership Computing Facility—to train and evaluate our models. We find that we can attain ≤ 30% relative error for 92.79% and 99.64% of the samples in our test set on these platforms, respectively.

Xie, Bing↗

Next-Generation Marine Energy Software Needs Assessment

Over the past decade the marine energy industry has continued to grow and evolve, with new concepts and technologies constantly being pursued. Additionally, the field of computing is vastly different today than it was five or ten years ago. By utilizing advanced software and hardware architectures, like graphics processing units as well as parallelization and high-performance computing resources, software can produce higher quality outputs and a higher volume of outputs. These software and hardware resources can enable the marine energy community to exploit computational advancements from other research fields, which can include machine learning, differentiable programming, and controls co-design. Better integration of existing software and development of potential new software is necessary to take advantage of trends in modern computing and respond to the current and future needs of the marine energy community. In order to better understand the existing marine energy software landscape and industry needs, DOE's Water Power Technologies Office (WPTO) tasked Sandia National Laboratories and the National Renewable Energy Laboratory to update the needs assessment by identifying existing software gaps and software needs, and assisting WPTO in planning the next wave of marine energy software development. The proposed effort involved cataloguing and analyzing the available data on existing software related to marine energy. The marine energy software landscape has vastly changed in the last ten years. There are now nearly 230 different software packages utilized by the marine energy sector, compared to a decade ago when the Cardinal Engineering survey identified approximately 40 software packages. In 2012, the marine energy software landscape was captured in two tables, whereas the current marine energy software landscape required development of a software database to collect and categorize software.

16 TIDAL AND WAVE POWER↗

A PIC Bootstrapping Strategy for Exascale CFD-DEM Simulation

The exascale computing era comes with the release of MFIX-Exa, a new code for studying gas-particle fluidization using CFD-DEM and PIC models on massively parallel, heterogeneous high-performance computing architectures. However, as compute resources continue to grow in scale and complexity, so too does the impetus to use them efficiently. Here, we propose a novel bootstrapping method to minimize neglected simulation time and cast the approach more broadly among a growing field of multi-fidelity methods.

Porcu, Roberto↗

Parallel point defect identification in molecular dynamics simulations without post-processing: A compute and dump style for LAMMPS

Two classes for the molecular dynamics program LAMMPS – one compute style and one dump style – are presented that are designed to identify, count, and output point defects in cascade damage and related molecular dynamics simulations. The calculations are done in parallel across multiple MPI processes, and can be done at the same time as the original simulation. This drastically reduces storage requirements by eliminating the need to post-process every atom in the system. Non-cubic lattices, free surfaces, and large voids can be eliminated from the output by suitable choices of the reference lattice. The classes are derived from LAMMPS’s Dump and Compute classes, and pose no additional overhead to LAMMPS if they are not used.

42 ENGINEERING↗

Flexible User-Defined Domain Decomposition in Kilometer-Scale E3SM Land Model Simulation

The Energy Exascale Earth System Model (E3SM) Land Model (ELM) has been extended to kilometer-scale (km-ELM) resolutions, enabling high-fidelity simulations of terrestrial processes at 1 km x 1 km grid spacing. In ELM, domain decomposition partitions the computational domain across processors, ensuring efficient parallel execution. Currently, round-robin decomposition is applied, providing a straightforward way to distribute computational workload. As ELM continues evolving at the kilometer-scale (km-scale), particularly with integrating lateral flow modeling, decomposition strategies must also account for the increased workload and data movement. This paper introduces a flexible user-defined domain decomposition framework, allowing users to customize domain partitioning based on application requirements. The impact of different decomposition strategies is evaluated across various applications concerning computation, communication, and I/O. Results demonstrate that while 1D partitioning yields superior I/O performance, k-nearest neighbors (KNN) clustering effectively reduces inter-process communication overhead. This study lays the groundwork for scalable partitioning in large-scale land surface simulations, enhancing next-generation Earth system modeling.

Wang, Dali [ORNL] (ORCID:0000000168065108)↗

Dynamic load balancing with enhanced shared-memory parallelism for particle-in-cell codes

Furthering our understanding of many of today’s interesting problems in plasma physics – including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects – requires large-scale kinetic simulations using particle-in-cell (PIC) codes. However, these simulations are extremely demanding, requiring that contemporary PIC codes be designed to efficiently use a new fleet of exascale computing architectures. To this end, the key issue of parallel load balance across computational nodes must be addressed. We discuss the implementation of dynamic load balancing by dividing the simulation space into many small, self-contained regions or ‘‘tiles,’’ along with shared-memory (e.g., OpenMP) parallelism both over many tiles and within single tiles. The load balancing algorithm can be used with three different topologies, including two space-filling curves. Here, we tested this implementation in the code Osiris and show low overhead and improved scalability with OpenMP thread number on simulations with both uniform load and severe load imbalance. Compared to other load-balancing techniques, our algorithm gives order-of-magnitude improvement in parallel scalability for simulations with severe load imbalance issues.

97 MATHEMATICS AND COMPUTING↗

Multigrid Reduction in Time for Chaotic Dynamical Systems

As CPU clock speeds have stagnated and high performance computers continue to have ever higher core counts, increased parallelism is needed to take advantage of these new architectures. Traditional serial time-marching schemes can be a significant bottleneck, as many types of simulations require large numbers of time-steps which must be computed sequentially. Parallel-in-time schemes, such as the Multigrid Reduction in Time (MGRIT) method, remedy this by parallelizing across time-steps and have shown promising results for parabolic problems. However, chaotic problems have proved more difficult, since chaotic initial value problems (IVPs) are inherently ill-conditioned. MGRIT relies on a hierarchy of successively coarser time-grids to iteratively correct the solution on the finest time-grid, but due to the nature of chaotic systems, small inaccuracies on the coarser levels can be greatly magnified and lead to poor coarse-grid corrections. Here we introduce a modified MGRIT algorithm based on an existing quadratically converging nonlinear extension to the multigrid Full Approximation Scheme (FAS), as well as a novel time-coarsening scheme. Together, these approaches better capture long-term chaotic behavior on coarse-grids and greatly improve convergence of MGRIT for chaotic IVPs. Further, we introduce a novel low-memory variant of the algorithm for solving chaotic PDEs with MGRIT which not only solves the IVP, but also provides estimates for the unstable Lyapunov vectors of the system. Finally, we provide supporting numerical results for the Lorenz system and demonstrate parallel speedup for the chaotic Kuramoto–Sivashinsky PDE over a significantly longer time-domain than in previous works.

97 MATHEMATICS AND COMPUTING↗

Energy-Screened Many-Body Expansion: A Practical Yet Accurate Fragmentation Method for Quantum Chemistry

We introduce an implementation of the truncated many-body expansion, MBE(n), in which the n-body corrections are screened using the effective fragment potential force field, and only those that exceed a specified energy threshold are computed at a quantum-mechanical level of theory. This energy-screened MBE(n) approach is tested at the n = 3 level for a sequence of water clusters, (H2O) N=6–34 . A threshold of 0.25 kJ/mol eliminates more than 80% of the subsystem electronic structure calculations and is even more efficacious in that respect than is distance-based screening. Even so, the energy-screened MBE(3) method is faithful to a full-system quantum chemistry calculation to within 1–2 kJ/mol/monomer, even in good quality basis sets such as aug-cc-pVTZ. These errors can be reduced by means of a two-layer approach that involves a Hartree–Fock calculation for the entire cluster. Such a correction proves to be necessary in order to obtain accurate relative energies for conformational isomers of (H2O)20, but the cost of a full-system Hartree–Fock calculation remains smaller than the cost of three-body subsystem calculations at correlated levels of theory. At the level of second-order Møller–Plesset perturbation theory (MP2), a screened MBE(3) calculation plus a full-system Hartree–Fock calculation is less expensive than a full-system MP2 calculation starting at N = 12 water molecules. This is true even if all MBE(3) subsystem calculations are performed on a single 40-core compute node, i.e., without significant parallelization. Energy-screened MBE(n) thus provides a fragment-based method that is accurate, stable in large basis sets, and low in cost, even when the latter is measured in aggregate computer time.

74 ATOMIC AND MOLECULAR PHYSICS↗

Parallel Nonnegative CP Decomposition of Dense Tensors

The CP tensor decomposition is a low-rank approximation of a tensor. We present a distributed-memory parallel algorithm and implementation of an alternating optimization method for computing a CP decomposition of dense tensors that can enforce nonnegativity of the computed low-rank factors. The principal task is to parallelize the Matricized-Tensor Times Khatri-Rao Product (MTTKRP) bottleneck subcomputation. The algorithm is computation efficient, using dimension trees to avoid redundant computation across MTTKRPs within the alternating method. Our approach is also communication efficient, using a data distribution and parallel algorithm across a multidimensional processor grid that can be tuned to minimize communication. We benchmark our software on synthetic as well as hyperspectral image and neuroscience dynamic functional connectivity data, demonstrating that our algorithm scales well to 100s of nodes (up to 4096 cores) and is faster and more general than the currently available parallel software.

Ballard, Grey↗

Oineus v1.0

A library for multi-threaded computation of persistence diagrams. The algorithm for computing persistence diagrams in a lock-free manner was published in the 'Towards Lock-free Persistent Homology' (D. Morozov, A. Nigmetov, Brief Announcement: SPAA 2020); it scales better than the only other shared-memory parallel implementation of persistent homology computation PHAT. Library includes python bindings to compute persistence diagrams and their vectorizations for lower-star filtrations on grid data. It is intended to be used by scientists working on Topological Data Analysis and its applications in different areas.

Nigmetov, Arnur↗

Modeling performance of data collection systems for high-energy physics

Exponential increases in scientific experimental data are outpacing silicon technology progress, necessitating heterogeneous computing systems—particularly those utilizing machine learning (ML)—to meet future scientific computing demands. The growing importance and complexity of heterogeneous computing systems require systematic modeling to understand and predict the effective roles for ML. We present a model that addresses this need by framing the key aspects of data collection pipelines and constraints and combining them with the important vectors of technology that shape alternatives, computing metrics that allow complex alternatives to be compared. For instance, a data collection pipeline may be characterized by parameters such as sensor sampling rates and the overall relevancy of retrieved samples. Alternatives to this pipeline are enabled by development vectors including ML, parallelization, advancing CMOS, and neuromorphic computing. By calculating metrics for each alternative such as overall F1 score, power, hardware cost, and energy expended per relevant sample, our model allows alternative data collection systems to be rigorously compared. We apply this model to the Compact Muon Solenoid experiment and its planned high luminosity-large hadron collider upgrade, evaluating novel technologies for the data acquisition system (DAQ), including ML-based filtering and parallelized software. The results demonstrate that improvements to early DAQ stages significantly reduce resources required later, with a power reduction of 60% and increased relevant data retrieval per unit power (from 0.065 to 0.31 samples/kJ). However, we predict that further advances will be required in order to meet overall power and cost constraints for the DAQ.

Olin-Ammentorp, Wilkie (ORCID:0000000224729862)↗

Simulation of unsteady blood flows in a patient-specific compliant pulmonary artery with a highly parallel monolithically coupled fluid-structure interaction algorithm

Computational fluid dynamics (CFD) is increasingly used to study blood flows in patient-specific arteries for understanding certain cardiovascular diseases. The techniques work quite well for relatively simple problems, but need improvements when the problems become harder in the case when (1) the geometry becomes complex (from a few branches to a full pulmonary artery), (2) the model becomes more complex (from fluid-only calculation to coupled fluid-structure interaction calculation), (3) both the fluid and wall models become highly nonlinear, and (4) the computer on which we run the simulation is a supercomputer with tens of thousands of processor cores. To push the limit of CFD in all four fronts, in this paper, we develop and study a highly parallel algorithm for solving a monolithically coupled fluid-structure system for the modeling of the interaction of the blood flow and the arterial wall. As a case study, we consider a patient-specific, full size pulmonary artery obtained from CT (Computed Tomography) images, with an artificially added layer of wall with a fixed thickness. The fluid is modeled with a system of incompressible Navier-Stokes equations and the wall is modeled by a geometrically nonlinear elasticity equation. As far as we know this is the first time the unsteady blood flow in a full pulmonary artery is simulated without assuming a rigid wall. We report the proposed numerical algorithm and software scale well beyond 10,000 processor cores on a supercomputer for solving the fluid-structure interaction problem discretized with a stabilized finite element method in space and an implicit scheme in time involving hundreds of millions of unknowns.

97 MATHEMATICS AND COMPUTING↗

Compressing unstructured mesh data from simulations using machine learning

The amount of data output from a computer simulation has grown to terabytes and petabytes as increasingly complex simulations are being run on massively parallel systems. As we approach exaflop computing in the next decade, it is expected that the I/O subsystem will not be able to write out these large volumes of data. In this paper, we explore the use of machine learning to compress the data before it is written out. Despite the computational constraints that limit us to using very simple learning algorithms, our results show that machine learning is a viable option for compressing unstructured data. Furthermore, we demonstrate that by simply using a better sampling algorithm to generate the training set, we can obtain more accurate results compared to random sampling, but at no extra cost. Further, by carefully selecting and incorporating points with high prediction error, we can improve reconstruction accuracy without sacrificing the compression rate.

97 MATHEMATICS AND COMPUTING↗

A New Class of AMG Interpolation Methods Based on Matrix-Matrix Multiplications

A new class of distance-two interpolation methods for algebraic multigrid (AMG) that can be formulated in terms of sparse matrix-matrix multiplications is presented and analyzed. Compared with similar distance-two prolongation operators, the proposed algorithms exhibit improved efficiency and portability to various computing platforms, since they allow one to easily exploit existing high-performance sparse matrix kernels. The new interpolation methods have been implemented in hypre, a widely used parallel multigrid solver library. With the proposed interpolations, the overall time of hypre's BoomerAMG setup can be considerably reduced, while sustaining equivalent, sometimes improved, convergence rates. Numerical results for a variety of test problems on parallel machines are presented that support the superiority of the proposed interpolation operators over the existing ones in hypre.

97 MATHEMATICS AND COMPUTING↗

A Generic Advanced Computing Framework for Executing Windows-based Dynamic Contingency Analysis Tool in Parallel on Cluster Machines

Dynamic contingency analysis tool (DCAT) has been developed to assess the impact and likelihood of extreme contingencies and potential cascading events across their systems and interconnections. By including more customized protection models and corrective actions into the Windows-based commercial tools, DCAT can help operators understand the cascading behavior and find mitigation approaches to reduce the risk of cascading outages in a more realistic manner. In order to further enhance the capability of DCAT, this paper presents a design of an advanced computing framework that enables DCAT to run on a cluster machine to improve its computational performance. This framework is generic and can be applied to other Windows-based simulation tools to fill the technical gap of applying advanced computing technology to vendors' Windows-based tools. The preliminary tests using medium to large power systems have shown the effectiveness of this framework and its potential for accelerating the adoption of advanced computing in utilities.

Advanced computing, dynamic contingency analysis, ↗

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗