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At least 1,081 records · Page 60

HPDR: High-Performance Portable Scientific Data Reduction Framework

The rapid growth in scientific data generation is outpacing advancements in computing systems necessary for efficient storage, transfer, and analysis, particularly in the context of exascale computing. With the deployment of first-generation exascale computing systems and next-generation experimental facilities, this gap is widening and necessitates effective data reduction techniques to manage enormous data volumes. Over the past decade, various data reduction methods, including lossless compression, error-controlled lossy compression, and data refactoring, have been developed to accelerate I/O in scientific workflows. Despite significant reductions in data volume, these methods introduce considerable computational overhead, which can become the new bottleneck in data processing. To mitigate this, GPU-accelerated data reduction algorithms have been introduced. However, challenges remain in their integration into exascale workflows, including limited portability across different GPU architectures, substantial memory transfer overhead, and reduced scalability on dense multi-GPU systems. To address these challenges, we propose HPDR, a high-performance and portable data reduction framework. HPDR is designed to enable the execution of state-of-the-art reduction algorithms across diverse processor architectures while reducing memory transfer overhead to 2.3 % of the original, resulting in up to 3.5× faster throughput compared to existing solutions. It also achieves up to 96% of the theoretical speedup in multi-GPU settings. In addition, evaluations on accelerating I/O operations at scale up to 1,024 nodes of the Frontier supercomputer demonstrate that HPDR can achieve up to 103 TB/s reduction throughput, providing up to 4× acceleration in parallel I/O performance compared to existing data reduction routines. This work highlights the potential of HPDR to significantly enhance data reduction efficiency in exascale computing environments.

Chen, Jieyang [University of Oregon]↗

Optimizing Performance of Combustion Chemistry Solvers on Intel's Many Integrated Core (MIC) Architectures

This work investigates novel algorithm designs and optimization techniques for restructuring chemistry integrators in zero and multidimensional combustion solvers, which can then be effectively used on the emerging generation of Intel's Many Integrated Core/Xeon Phi processors. These processors offer increased computing performance via large number of lightweight cores at relatively lower clock speeds compared to traditional processors (e.g. Intel Sandybridge/Ivybridge) used in current supercomputers. This style of processor can be productively used for chemistry integrators that form a costly part of computational combustion codes, in spite of their relatively lower clock speeds. Performance commensurate with traditional processors is achieved here through the combination of careful memory layout, exposing multiple levels of fine grain parallelism and through extensive use of vendor supported libraries (Cilk Plus and Math Kernel Libraries). Important optimization techniques for efficient memory usage and vectorization have been identified and quantified. These optimizations resulted in a factor of ~ 3 speed-up using Intel 2013 compiler and ~ 1.5 using Intel 2017 compiler for large chemical mechanisms compared to the unoptimized version on the Intel Xeon Phi. The strategies, especially with respect to memory usage and vectorization, should also be beneficial for general purpose computational fluid dynamics codes.

97 MATHEMATICS AND COMPUTING↗

Mixed Integer Nonlinear Programming Approaches to Enhance Resiliency and Response Strategies in Critical Infrastructure

Motivation. Critical infrastructures are large, complex engineered systems that must be operated robustly under abnormal conditions resulting from natural hazards or intentional acts. For example, electric power systems must be robust to line faults, water utilities must rapidly mitigate contamination incidents, and computing networks must adapt to adversarial intrusions to protect critical information. Problem. It is difficult for decision-makers within resiliency analysis in critical infrastructure to optimize designs and develop effective response strategies that can account for uncertainties. Facing incomplete information and the sheer scope that a natural hazard or attack vector may incorporate, response can be ineffective without reliable, scalable decision support tools. These problems are intrinsically nonlinear and involve discrete decisions, and unfortunately, existing off-the-shelf mathematical programming methods cannot support optimization-based decision-making of these nonlinear at scale. Method/Approach and Results. This project emphasized development of fundamental optimization strategies that supported real- time mitigation and response for critical infrastructures. In particular, the project developed multi- tree approaches based on piecewise outer-approximations for solution of mixed-integer nonlinear programming (MINLP) problems. These techniques alternate between an MILP or MISOCP relaxation to obtain a lower bound and candidate discrete solutions and an NLP subproblem to obtain upper bounds. Using tailored relaxations based on problem structure, these methods were used to solve several key applications in resilience and response of critical infrastructure. This work resulted in two open-source, copyrighted software packages: CORAMIN (https://github.com/Coramin/Coramin) -- an object-oriented mathematical programming framework that supports tailored multi-tree algorithms for solution of large- scale mixed-integer nonlinear programming; and EGRET (Electrical Grid Research and Engineering Toolkit) (https://github.com/grid- parity-exchange/Egret) -- a declarative mathematical programming framework built upon CORAMIN and Pyomo for formulation and solution of resilience and operations problems in power grid systems. Furthermore, these tools resulted in several important published results, including the following: The first known global optimization approach that could solve the unit-commitment problem with nonlinear power flow constraints on medium-sized test problems; Improved parallel optimization-based bounds tightening and strengthening of relaxations of AC power flow constraints; and, Optimization-based approaches for improved grid resilience and use of demand response to improve grid resilience with reduction in capital requirements. Result Implications. This project developed first-of-a-kind algorithms for decision-making in critical infrastructure resilience operations and planning, as well as a next-generation toolkit for MINLP researchers. These approaches leveraged high-performance computing architectures to solve some of the largest, most challenging nonlinear discrete optimization problems to global optimality, and these successes were captured in open-source software to enable optimization-based decision-making, and efficient solution of MINLP formulations for electric power transmission grids.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Optimizing inference of segmentation on high-resolution images in MLExchange

MLExchange is a machine learning (ML) operations platform providing web user-interfaces (UIs) for data visualization and analysis pipelines at synchrotron facilities. Among these UIs is the segmentation app which helps synchrotron users utilize ML algorithms to automatically segment high-resolution scientific images with minimal manual annotation effort. In this work, we share code optimizations that significantly speed up the segmentation inference workflow of large data in short time. By optimizing the sequence of CPU-GPU data transfers and introducing CPU parallelization to key operations, we improve the per-device, per-image frame computational efficiency and observe close to 3×$$\times$$ speedup over the original segmentation inference workflow run time when utilizing a single GPU. Further adaptations enabling multi-GPU inference yield more than 40×$$\times$$ speedup with 100 GPUs compared to the optimized single GPU inference workflow. This acceleration of the segmentation inference workflow will provide MLExchange users with easy access to segmentation results with little wait time.

Lu, Shizhao↗

Towards improved speed and accuracy of laser powder bed fusion simulations via multiscale spatial representations

Due to the growing popularity of laser powder bed fusion (LPBF) as a metal additive manufacturing technique, there is a strong need to be able to accurately predict build outcomes. Full fidelity simulations of this process are not feasible due to the vast range of length and time scales inherent to it. While part-scale codes for simulating residual stress and distortion have shown reasonable predictive capability, they often neglect many aspects of the process occurring over smaller length/time scales, and thus are unable to capture effects of process parameter adjustments or the behavior of fine features. One way of capturing aspects at more refined length scales is through the use of adaptive mesh refinement (AMR). AMR allows for the process to be simulated at scales approaching the physical spatial dimensions without drastically increasing the total degrees of freedom in the simulation. This manuscript describes the implementation of an AMR algorithm within a multiphysics, parallelized finite element code, and its application to the LPBF problem. In this work, part-scale examples are provided where the use of AMR has allowed for higher fidelity thermal and thermomechanical simulations, as compared to experimental measurements. Results from these higher resolution simulations show that while AMR is a necessary component for increased accuracy in a computationally efficient manner, other improvements are also necessary, including handling of the multiple time scales inherent to the problem and the need for improved AM-specific material models.

42 ENGINEERING↗

ExaMPM

ExaMPM is a mini-application for the Material Point Method (MPM) for studying the application of MPM to future exascale computing systems. MPM is a general method for computational mechanics and fluids and is used in a wide variety of science and engineering disciplines to study problems with large deformations, phase change, fracture, and other phenomena. ExaMPM provides a reference implementation of MPM as described in the 1994 work of Sulsky et.al. (Sulsky, Deborah, Zhen Chen, and Howard L. Schreyer. "A particle method for history-dependent materials." Computer methods in applied mechanics and engineering 118.1-2 (1994): 179-196.). The software can solve basic MPM problems in solid mechanics using the original algorithm of Sulsky with explicit time integration, basic geometries, and free-slip and no-slip boundary conditions as described in the reference. ExaMPM is intended to be used as a starting point to design new parallel algorithms for the next generation of DOE supercomputers.

Slattery, StuartR↗

HIPPO – A Software Platform for Electricity Market Research and Development

The goal of this project is to provide Regional transmission organizations (RTOs) and independent system operators (ISOs) a market design and prototyping software, High-Performance Power-Grid Optimization (HIPPO), that they can evaluate electricity market design options, calculate market planning strategies and operational performance. With the high standards and strict reliability requirements for operating power systems, impacts of new technologies need to be fully investigated prior to any consideration for adoption. A market design and prototyping software tool which can be used to prototype electricity market design options, to calculate market planning strategies and operational performance with high precision, and to investigate the impacts for integrating future power grid technologies will be valuable to RTOs/ISOs who operate power systems, to vendors like GE and ABB who provide the market solvers, and to market participants and researchers who are actively doing market research. HIPPO is a such tool that can be used to improve the current market operations and provide capabilities for rigorous forward-looking design and prototyping of next-generation energy markets. HIPPO has a high-resolution model for the day-ahead SCUC, which was validated with MISO and GE-Grid Solutions. HIPPO is built with parallel and distributed computing capabilities and can be executed in both multi-thread and high-performance computing (HPC) settings. This capability provides fast solution speed necessary to handle the larger and more complex SCUC problems of real-world cases and the potentially growing size and complexity of future scenarios. In addition, HIPPO has a concurrent optimizer (CO) which manages multiple algorithm executions simultaneously and leverages the advantages from different algorithms. This structure provides flexibility to better benchmark competing approaches. Highly accurate market model, fast solution technologies and flexible model and algorithm control are the features which will make HIPPO an extensible platform for developing and testing multiple approaches to meet a wide range of future market needs.

24 POWER TRANSMISSION AND DISTRIBUTION↗

ExaMPM

ExaMPM is a mini-application for the Material Point Method (MPM) for studying the application of MPM to future exascale computing systems. MPM is a general method for computational mechanics and fluids and is used in a wide variety of science and engineering disciplines to study problems with large deformations, phase change, fracture, and other phenomena. ExaMPM provides a reference implementation of MPM as described in the 1994 work of Sulsky et.al. (Sulsky, Deborah, Zhen Chen, and Howard L. Schreyer. "A particle method for history-dependent materials." Computer methods in applied mechanics and engineering 118.1-2 (1994): 179-196.). The software can solve basic MPM problems in solid mechanics using the original algorithm of Sulsky with explicit time integration, basic geometries, and free-slip and no-slip boundary conditions as described in the reference. ExaMPM is intended to be used as a starting point to design new parallel algorithms for the next generation of DOE supercomputers.

Slattery, Stuart R↗

Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important features of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.

97 MATHEMATICS AND COMPUTING↗

Nonconforming Mesh Refinement for High-Order Finite Elements

In this study, we propose a general algorithm for nonconforming adaptive mesh refinement (AMR) of unstructured meshes in high-order finite element codes. Our focus is on $h$-refinement with a fixed polynomial order. The algorithm handles triangular, quadrilateral, hexahedral, and prismatic meshes of arbitrarily high-order curvature, for any order finite element space in the de Rham sequence. We present a flexible data structure for meshes with hanging nodes and a general procedure to construct the conforming interpolation operator, both in serial and in parallel. The algorithm and data structure allow anisotropic refinement of tensor product elements in two and three dimensions and support unlimited refinement ratios of adjacent elements. We report numerical experiments verifying the correctness of the algorithms and perform a parallel scaling study to show that we can adapt meshes containing billions of elements and run efficiently on 393,000 parallel tasks. Finally, we illustrate the integration of dynamic AMR into a high-order Lagrangian hydrodynamics solver.

97 MATHEMATICS AND COMPUTING↗

Optimization of convergent collimators for pixelated SPECT systems

Purpose: The optimization of the collimator design is essential to obtain the best possible sensitivity in single photon emission computed tomography imaging. The aim of this work is to present a methodology for maximizing the sensitivity of convergent collimators, specifically designed to match the pitch of pixelated detectors, for a fixed spatial resolution value and to present some initial results using this approach. Methods: Given the matched constraint, the optimal collimator design cannot be simply found by allowing the highest level of septal penetration and spatial resolution consistent with the imposed restrictions, as it is done for the optimization of conventional collimators. Therefore, an algorithm that interactively calculates the collimator dimensions, with the maximum sensitivity, which respect the imposed restrictions was developed and used to optimize cone and fan beam collimators with tapered square-shaped holes for low (60-300 keV) and high energy radiation (300-511 keV). The optimal collimator dimensions were locally calculated based on the premise that each hole and septa of the convergent collimator should locally resemble an appropriate optimal matched parallel collimator. Results: The optimal collimator dimensions, calculated for subcentimeter resolutions (3 and 7.5 mm), common pixel sizes (1.6, 2.1, and 2.5 mm), and acceptable septal penetration at 140 keV, were approximately constant throughout the collimator, despite their different hole incidence angles. By using these input parameters and a less strict septal penetration value of 5%, the optimal collimator dimensions and the corresponding mass per detector area were calculated for 511 keV. It is shown that a low value of focal distance leads to improvements in the average sensitivity at a fixed source-collimator distance and resolution. The optimal cone beam performance outperformed that of other optimal collimation geometries (fan and parallel beam) in imaging objects close to the collimator surface. Conclusions: These results demonstrate the potential of this kind of optimal convergent collimators for the use in small field of view imaging applications.

43 PARTICLE ACCELERATORS↗

Exploring Memory Hierarchy to Improve Scientific Data Read Performance, In: 2015 IEEE International Conference on Cluster Computing

Improving read performance is one of the major challenges with speeding up scientific data analytic applications. Utilizing the memory hierarchy is one major line of researches to address the read performance bottleneck. Related methods usually combine solide-state-drives(SSDs) with dynamic random-access memory(DRAM) and/or parallel file system(PFS) to mitigate the speed and space gap between DRAM and PFS. However, these methods are unable to handle key performance issues plaguing SSDs, namely read contention that may cause up to 50% performance reduction. In this paper, we propose a framework that exploits the memory hierarchy resource to address the read contention issues involved with SSDs. The framework employs a general purpose online read algorithm that able to detect and utilize memory hierarchy resource to relieve the problem. To maintain a near optimal operating environment for SSDs, the framework is able to orchastrate data chunks across different memory layers to facilitate the read algorithm. Compared to existing tools, our framework achieves up to 50% read performance improvement when tested on datasets from real-world scientific simulations.

Computer Science↗

Development of mpi_EPIC model for global agroecosystem modeling

Models that address policy-maker concerns about multi-scale effects of food and bioenergy production systems are computationally demanding. We integrated the message passing interface algorithm into the process-based EPIC model to accelerate computation of ecosystem effects. Simulation performance was further enhanced by applying the Vampir framework. When this enhanced mpi_EPIC model was tested, total execution time for a global 30-year simulation of a switchgrass cropping system was shortened to less than 0.5 hours on a supercomputer. The results illustrate that mpi_EPIC using parallel design can balance simulation workloads and facilitate large-scale, high-resolution analysis of agricultural production systems, management alternatives and environmental effects.

54 ENVIRONMENTAL SCIENCES↗

An accurate and efficient fragmentation approach via the generalized many-body expansion for density matrices

With relevant chemical space growing larger and larger by the day, the ability to extend computational tractability over that larger space is of paramount importance in virtually all fields of science. The solution we aim to provide here for this issue is in the form of the generalized many-body expansion for building density matrices (GMBE-DM) based on the set-theoretical derivation with overlapping fragments, through which the energy can be obtained by a single Fock build. In combination with the purification scheme and the truncation at the one-body level, the DM-based GMBE(1)-DM-P approach shows both highly accurate absolute and relative energies for medium-to-large size water clusters with about an order of magnitude better than the corresponding energy-based GMBE(1) scheme. Simultaneously, GMBE(1)-DM-P is about an order of magnitude faster than the previously proposed MBE-DM scheme [F. Ballesteros and K. U. Lao, J. Chem. Theory Comput. 18, 179 (2022)] and is even faster than a supersystem calculation without significant parallelization to rescue the fragmentation method. For even more challenging systems including ion–water and ion–pair clusters, GMBE(1)-DM-P also performs about 3 and 30 times better than the energy-based GMBE(1) approach, respectively. In addition, this work provides the first overlapping fragmentation algorithm with a robust and effective binning scheme implemented internally in a popular quantum chemistry software package. Thus, GMBE(1)-DM-P opens a new door to accurately and efficiently describe noncovalent clusters using quantum mechanics.

Chemistry↗

TGE: Machine Learning Based Task Graph Embedding for Large-Scale Topology Mapping

Task mapping is an important problem in parallel and distributed computing. The goal in task mapping is to find an optimal layout of the processes of an application (or a task) onto a given network topology. We target this problem in the context of staging applications. A staging application consists of two or more parallel applications (also referred to as staging tasks) which run concurrently and exchange data over the course of computation. Task mapping becomes a more challenging problem in staging applications, because not only data is exchanged between the staging tasks, but also the processes of a staging task may exchange data with each other. We propose a novel method, called Task Graph Embedding (TGE), that harnesses the observable graph structures of parallel applications and network topologies. TGE employs a machine learning based algorithm to find the best representation of a graph, called an embedding, onto a space in which the task-to-processor mapping problem can be solved. We evaluate and demonstrate the effectiveness of TGE experimentally with the communication patterns extracted from runs of XGC, a large-scale fusion simulation code, on Titan.

Choi, Jong Youl↗

TU-AB-201-04: Optimizing the Number of Catheter Implants and Their Tracks for Prostate HDR Brachytherapy

Purpose: In prostate HDR brachytherapy, interstitial implants are placed manually on the fly. The aim for this research is to develop a computer algorithm to find optimal and reliable implant trajectories using minimal number of implants. Methods: Our new algorithm mainly uses these key ideas: (1) positive charged static particles are uniformly placed on the surface of prostate and critical structures such as urethra, bladder, and rectum. (2) Positive charged kinetic particles are placed at a cross-section of the prostate with an initial velocity parallel to the principal implant direction. (3) The kinetic particles move through the prostate, interacting with each other, spreading out, while staying away from the prostate surface and critical structures. The initial velocity ensures that the trajectories observe the curvature constraints of typical implant procedures. (4) The finial trajectories of kinetic particles are smoothed using a third-degree polynomial regression, which become the implant trajectories. (5) The dwelling times and final dose distribution are calculated using least-distance programming. Results: (1) We experimented with previously treated cases. Our plan achieves all prescription goals while reducing the number of implants by 41%! Our plan also has less uniform target dose, which implies a higher dose is delivered to the prostate. (2) We expect future implant procedures will be performed under the guidance of such pre-calculated trajectories. To assess the applicability, we randomly perturb the tracks to mimic the manual implant errors. Our studies showed the impact of these perturbations are negligible, which is compensated by the least distance programming. Conclusions: We developed a new inverse planning system for prostate HDR therapy that can find optimal implant trajectories while minimizing the number of implants. For future work, we plan to integrate our new inverse planning system with an existing needle tracking system.

60 APPLIED LIFE SCIENCES↗

Implementation of the Waveform Correlation Event Detection System (WCEDS) Method for Regional Seismic Event Detection in Utah

Backprojection techniques are a class of methods for detecting and locating events that have been successfully implemented at local scales for dense networks. This paper develops the framework for applying a backprojection method to detect and locate a range of event sizes across a heteorogeneous regional network. This article extends previous work on the development of a backprojection method for local and regional seismic event detection, the Waveform Correlation Event Detection System (WCEDS). The improvements outlined here make the technique much more flexible for regional earthquake or explosion monitoring. We first explore how the backprojection operator can be formulated using either a travel-time model or a stack of full waveforms, showing that the former approach is much more flexible and can lead to the detection of smaller events, and to significant improvements in the resolution of event parameters. Second, we discuss the factors that influence the grid of event hypotheses used for backprojection, and develop an algorithm for generating suitable grids for networks with variable density. Third, we explore the effect of including different phases in the backprojection operator, showing that the best results for the study region can be obtained using only the Pg phase, and by including terms for penalizing early arrivals when evaluating the fit for a given event hypothesis. Fourth, we incorporate two parallel backprojection computations with different distance thresholds to enable the robust detection of both network-wide and small (sub-network-only) events. Finally, the set of improvements are outlined by applying WCEDS to four example events on the University of Utah Seismograph Stations (UUSS) network.

58 GEOSCIENCES↗