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At least 145 records · Page 8

Optimizing I/O Performance of HPC Applications with Autotuning

Parallel Input output is an essential component of modern high-performance computing (HPC). Obtaining good I/O performance for a broad range of applications on diverse HPC platforms is a major challenge, in part, because of complex inter dependencies between I/O middleware and hardware. The parallel file system and I/O middleware layers all offer optimization parameters that can, in theory, result in better I/O performance. Unfortunately, the right combination of parameters is highly dependent on the application, HPC platform, problem size, and concurrency. Scientific application developers do not have the time or expertise to take on the substantial burden of identifying good parameters for each problem configuration. They resort to using system defaults, a choice that frequently results in poor I/O performance. We expect this problem to be compounded on exascale-class machines, which will likely have a deeper software stack with hierarchically arranged hardware resources. We present as a solution to this problem an autotuning system for optimizing I/O performance, I/O performance modeling, I/O tuning, and I/O patterns. We demonstrate the value of this framework across several HPC platforms and applications at scale.

Behzad, Babak↗

A Pulsar-Inspired Timing Framework for Power System: Optimization and Performance Evaluation

Due to their excellent stability, neutron pulsar stars are considered promising candidate timing sources for power system applications. However, the complexity of pulsar signals necessitates advanced processing algorithms to provide accurate timing references. This paper presents the foundational framework for pulsar signal processing, serving as the basis for further optimization. To enhance the timing accuracy and computation efficiency in pulsar period searches, three algorithms are proposed as the initial optimization step: wavelet de-noising, fast folding, and cross-correlation for profile evaluation. Wavelet de-noising improves signal-to-noise ratio (SNR) by 36%–70%. Fast folding reduces computation time from hundreds of seconds to mere milliseconds. Cross-correlation works better than traditional SNR-based methods by effectively identifying the optimal period. The performance of the proposed algorithms is evaluated using observation data from telescopes. Together, these algorithms significantly improve pulsar timing performance, reducing the error of the Pulse Per Second (PPS) signal from hundreds to tens of microseconds.

Wu, Ori [ORNL] (ORCID:0000000326723410)↗

The Institute for Sustained Performance, Energy, and Resilience Final Project Report

Over the course of the five years of the Scientific Discovery through Advanced Computation (SciDAC-3) program, computational scientists working on behalf of the Department of Energy's Office of Science (DOE SC) exploited a new generation of petascale computing resources to make previously inaccessible discoveries in a broad range of disciplines including physics, chemistry, and materials science. The computing systems underpinning this work increased in performance potential from tens to hundreds of PFlop/s, but in the process evolving significantly from architectures in 2011, when SciDAC-3 began. Although Moore's law continues unabated, the end of Dennard scaling has necessitated a fundamental shift in computer architecture focused on power efficiency. To that end, processors are increasingly varied as they strive to satisfy performance, productivity, reliability, and energy efficiency in the face of divergent computational requirements. The diversity among these machines presents a number of challenges to merely porting today's scientific applications, much less achieving good performance. Therefore, at the beginning of SciDAC-3, USC and its collaborators anticipated that both vastly increased scale (e.g., more chips, more cores per chip, wider SIMD) and heterogeneity would exacerbate performance optimization challenges while simultaneously promoting the issues of energy and heterogeneity will exacerbate performance optimization challenges while simultaneously promoting the issues of energy consumption and resilience to the forefront. To ensure that DOE's computational scientists could successfully exploit emerging high performance computing (HPC) systems, DOE SC’s Advanced Scientific Computing Research Program (ASCR) funded the SciDAC-3 Institute for Sustained Performance, Energy, and Resilience (SUPER). Led by USC, this was a broadly based project with expertise in compilers and system tools, performance engineering, energy management, and resilience. SUPER followed the successful model developed in the previous SciDAC-2 Performance Engineering Research Institute (PERI) of leveraging the research investments DOE and others have made and integrating the results to create new capabilities beyond the reach of any one group. To accomplish this, SUPER was organized into multi-institution teams conducting the research activities in performance portability, energy efficiency, exascale resilience, and overall optimization. SUPER researchers also collaborated with other SciDAC-3 institutes, 13 of the 19 Scientific Computation Application Partnerships (SAP), as well as the broader DOE computational sciences community. These collaborations both focused our research on the real challenges facing petascale scientific computing as well as ensured the broad and immediate impact of the results of our research.

97 MATHEMATICS AND COMPUTING↗

Optimizing High Performance Markov Clustering for Pre-Exascale Architectures

HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations and heavily makes use of the sparse matrix-sparse matrix multiplication kernel (SpGEMM). The existing parallel algorithms in HipMCL are not scalable to Exascale architectures, both due to their communication costs dominating the runtime at large concurrencies and also due to their inability to take advantage of accelerators that are increasingly popular. In this work, we systematically remove scalability and performance bottlenecks of HipMCL. We enable GPUs by performing the expensive expansion phase of the MCL algorithm on GPU. Additionally, we propose a CPU-GPU joint distributed SpGEMM algorithm called pipelined Sparse SUMMA and integrate a probabilistic memory requirement estimator that is fast and accurate. Furthermore, we develop a new merging algorithm for the incremental processing of partial results produced by the GPUs, which improves the overlap efficiency and the peak memory usage. We also integrate a recent and faster algorithm for performing SpGEMM on CPUs. We validate our new algorithms and optimizations with extensive evaluations. With the enabling of the GPUs and integration of new algorithms, HipMCL is up to 12.4x faster, being able to cluster a network with 70 million proteins and 68 billion connections just under 15 minutes using 1024 nodes of ORNL's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

Hybrid Optimization and Performance Platform (HOPP)

As part of NREL's Hybrid Energy Systems Research, this software assesses optimal designs for the deployment of utility-scale hybrid energy plants, particularly considering wind, solar and storage.

Tripp, CharlesEdison [National Renewable Energy La↗

Experiences in autotuning matrix multiplication for energy minimization on GPUs

In this study, we report extensive results and analysis of autotuning the computationally intensive graphics processing units kernel for dense matrix–matrix multiplication in double precision. In contrast to traditional autotuning and/or optimization for runtime performance only, we also take the energy efficiency into account. For kernels achieving equal performance, we show significant differences in their energy balance. We also identify the memory throughput as the most influential metric that trades off performance and energy efficiency. Finally, as a result, the performance optimal case ends up not being the most efficient kernel in overall resource use.

97 MATHEMATICS AND COMPUTING↗

Role of Cr Content in Microstructure, Creep, and Oxidation Resistance of Alumina-Forming Austenitic Alloys at 850–900 °C

Creep-rupture properties and oxidation behavior of a series of alumina-forming austenitic (AFA) alloys with variations of Cr contents, based on Fe-(13.5-18)Cr-25Ni-4Al-1.5Nb-0.1C in weight percent, have been evaluated at 850–900 °C. The study investigates material responses in the properties and microstructure through compositional modifications in AFA alloys, targeting performance optimization of alloys under high-temperature, corrosive industrial environments. The creep-rupture life of the alloys at 850 °C and 30MPa monotonically decreased with increasing Cr content, which was correlated with changes in secondary phase volume fractions, such as the reduction in B2-NiAl + Laves-Fe2Nb and increase in Sigma-FeCr with Cr content. The oxidation test at 900 °C in a water-vapor containing environment revealed a range of Cr content from 13.9 to 15.7 wt.%, enabling the formation of stable, protective external alumina scale as well as preventing internal oxidation/nitridation for up to total 7000 h exposure. On the other hand, the alloys with >16.7 wt.% Cr formed Sigma precipitates, which caused a reduction in not only Cr but also Al in the austenite matrix, resulting in less oxidation resistance than other alloys. The findings will guide the further optimization of material performance in the AFA alloy series.

36 MATERIALS SCIENCE↗

Structural Mass Saving Potential of a 5-MW Direct-Drive Generator Designed for Additive Manufacturing

As wind turbine blade diameters and tower height increase to capture more energy in the wind, higher structural loads results in more structural support material increasing the cost of scaling. Weight reductions in the generator transfer to overall cost savings of the system. Additive manufacturing facilitates a design-for-functionality approach, thereby removing traditional manufacturing constraints and labor costs. The most feasible additive manufacturing technology identified for large, direct-drive generators in this study is powder-binder jetting of a sand cast mold. A parametric finite element analysis optimization study is performed, optimizing for mass and deformation. Also, topology optimization is employed for each parameter-optimized design.The optimized U-beam spoked web design results in a 24 percent reduction in structural mass of the rotor and 60 percent reduction in radial deflection.

17 WIND ENERGY↗

Innovative Joining Method for Hybrid Composites with Tailored Performance

In various industries, such as renewables and aerospace, the demand for carbon fiber is rapidly growing to meet the requirements of high-performance applications with optimized designs. Traditionally, these optimized designs have been limited to single-material composites due to process constraints. However, this study aims to explore the feasibility of transitioning between two different fiber types for pultrusion and filament winding processes, thereby enhancing design flexibility, and optimizing performance. This research introduces a novel method of hybrid reinforcement through splicing techniques. By employing a splicing method, fibers are merged prior to infusion, resulting in a transition of higher strength compared to traditional joints. Moreover, this technique enables the creation of composites with variable compositions, allowing for the selective placement of properties in a process previously characterized by static properties. The objective of this paper is to evaluate the mechanical properties of dry fiber splicing and its impact on the resulting composite material. Through comprehensive analysis, we aim to provide insights into the feasibility and advantages of employing this innovative splicing technique in composite manufacturing processes.

Guzorek, Steven↗

Institute for Sustained Performance, Energy, and Resilience (SUPER): University of Utah Final Report

Over the course of this project, computational scientists working on behalf of the Department of Energy's Office of Science (DOE SC) were exploiting a new generation of petascale computing resources to make previously inaccessible discoveries in a broad range of disciplines including physics, chemistry and material science. The computational systems underpinning this work increased in performance potential from tens to hundreds of Pflop/s, and evolved significantly from those in use at the beginning of the project in terms of available concurrency; wider use of accelerators such as graphics processing units(GPUs); and changes to the memory hierarchy including the incorporation of a new generation of persistent devices (e.g., phase change memory). To ensure that DOE's computational scientists can successfully exploit this emerging generation of high performance computing (HPC) systems, the University of Southern California (USC) assembled a broad team of computer scientists with the expertise to address the most pressing challenges of DOE's computing systems: (a) end-to-end performance optimization, including single-node performance, interprocessor communication, load balancing and I/O; (b) performance portability for heterogeneous systems, including accelerators; (c) minimizing energy consumption; (d) resilient computation; and, (e) exploiting new memory technology.

97 MATHEMATICS AND COMPUTING↗

Conversion of the LLNL/CAMS 1 MV biomedical AMS system to a semi-automated natural abundance 14C spectrometer: system optimization and performance evaluation

The Lawrence Livermore National Laboratory – Center for Accelerator Mass Spectrometry compact 1 MV biomedical accelerator mass spectrometer was repurposed and optimized for the semi-automated radiocarbon measurement of natural abundance environmental samples. Here we present results from 15 months of routine system operation and evaluate the system performance based on 30 sample wheels measured with consistent operating conditions over 7 months from August 2019 to March 2020. Additionally, the average measurement precision was 2.7 ± 0.7‰. System accuracy was assessed with measurements of 14 C-free materials, standard materials with 14 C-content spanning 0.5 to 1.5 F 14 C, and by comparison to split samples measured with the 10 MV AMS system. Overall, this system can routinely measure samples as small as 300 µgC and less than 33000 years without the need for size-specific correction protocols.

43 PARTICLE ACCELERATORS↗

Design and performance of optimal detectors for guided wave structural health monitoring

Ultrasonic guided wave measurements in a long term structural health monitoring system are affected by measurement noise, environmental conditions, transducer aging and malfunction. This results in measurement variability which affects detection performance, especially in complex structures where baseline data comparison is required. This paper derives the optimal detector structure, within the framework of detection theory, where a guided wave signal at the sensor is represented by a single feature value that can be used for comparison with a threshold. Three different types of detectors are derived depending on the underlying structure’s complexity: (i) Simple structures where defect reflections can be identified without the need for baseline data; (ii) Simple structures that require baseline data due to overlap of defect scatter with scatter from structural features; (iii) Complex structure with dense structural features that require baseline data. The detectors are derived by modeling the effects of variabilities and uncertainties as random processes. Analytical solutions for the performance of detectors in terms of the probability of detection and false alarm are derived. A finite element model is used to generate guided wave signals and the performance results of a Monte-Carlo simulation are compared with the theoretical performance. initial results demonstrate that the problems of signal complexity and environmental variability can in fact be exploited to improve detection performance.

60 APPLIED LIFE SCIENCES↗

BISON fuel performance modeling optimization for experiment X447 and X447A using axial swelling and cladding strain measurements

With the recent need to qualify new reactor designs such as the Versatile Test Reactor (VTR), fuel performance calculations need to be performed to determine safety criteria of the proposed designs. In order to validate the fuel performance results obtained by a fuel performance code, BISON, for new reactor designs, legacy fuel from EBR-II and FFTF MFF with Post -Irradiation Examination (PIE) data need to be used as validation cases to benchmark models. Here in this work, BISON has been paired with the Fuels Irradiation & Physics Database (FIPD) and IFR Materials Information System (IMIS) to supply PIE data for comparison with simulations of EBR-II experiments X447/X447A. X447/X447A were assessed by implementing models for Fuel Cladding Chemical Interaction (FCCI) within BISON and optimizing the friction coefficient between the fuel surface and the cladding, the anisotropic swelling factor, and the HT9 first thermal creep scalar (which scales the first term in the HT9 creep equation) to best match the PIE axial fuel swelling height and cladding profilometry for all pins in X447/X447A. The optimal values were found using a generic algorithm developed to select different values for the three parameters until end criteria was met and error couldn’t be reduced further. The BISON-simulated cladding profilometry was evaluated using Standard Error of the Estimate (SEE) to account for the profile shape of the cladding profilometry. Optimal values for the friction coefficient, anisotropic fuel swelling factor, and HT9 first thermal creep scalar were found to best fit the BISON simulation results to the PIE measurements found in IMIS and FIPD. Improvements to current models are suggested to account for the underprediction of fuel swelling at low burnups and the overprediction of fuel swelling at higher burnups observed for the axial fuel swelling height. Although two pins in EBR-II X447/X447A (DP70 and DP75) were known to fail due to FCCI, none of the pins simulated in BISON reached a cumulative damage fraction (CDF) above 0.008 with FCCI correlations coupled in the BISON simulations. The error estimate generated for all pins in X447/X447A using optimal values was 209 µm, which is deemed acceptable.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Learning concave-convex profiles of data transport over dedicated connections

Dedicated data transport infrastructures are increasingly being deployed to support distributed big-data and high-performance computing scenarios. These infrastructures employ data transfer nodes that use sophisticated software stacks to support network transport among sites, which often house distributed file and storage systems. Throughput measurements collected over such infrastructures for a range of round trip times (RTTs) reflect the underlying complex end-to-end connections, and have revealed dichotomous throughput profiles as functions of RTT. In particular, concave regions of throughput profiles at lower RTTs indicate near-optimal performance, and convex regions at higher RTTs indicate bottlenecks due to factors such as buffer or credit limits. We present a machine learning method that explicitly infers these concave and convex regions and transitions between them using sigmoid functions. We also provide distribution-free confidence estimates for the generalization error of these concave-convex profile estimates. Throughput profiles for data transfers over 10 Gbps connections with 0–366 ms RTT provide important performance insights, including the near optimality of transfers performed with the XDD tool between XFS filesystems, and the performance limits of wide-area Lustre extensions using LNet routers. A direct application of generic machine learning packages does not adequately highlight these critical performance regions or provide as precise confidence estimates.

Rao, Nageswara↗

The influence of non-idealities on the thermoelectric power factor of nanostructured superlattices

Cross-plane superlattices composed of nanoscale layers of alternating potential wells and barriers have attracted great attention for their potential to provide thermoelectric power factor improvements and higher ZT figure of merit. Previous theoretical works have shown that the presence of optimized potential barriers could provide improvements to the Seebeck coefficient through carrier energy filtering, which improves the power factor by up to 40%. However, experimental corroboration of this prediction has been extremely scant. In this work, we employ quantum mechanical electronic transport simulations to outline the detrimental effects of random variation, imperfections, and non-optimal barrier shapes in a superlattice geometry on these predicted power factor improvements. Thus, we aim to assess either the robustness or the fragility of these theoretical gains in the face of the types of variation one would find in real material systems. We show that these power factor improvements are relatively robust against: overly thick barriers, diffusion of barriers into the body of the wells, and random fluctuations in barrier spacing and width. However, notably, we discover that extremely thin barriers and random fluctuation in barrier heights by as little as 10% is sufficient to entirely destroy any power factor benefits of the optimized geometry. Our results could provide performance optimization routes for nanostructured thermoelectrics and elucidate the reasons why significant power factor improvements are not commonly realized in superlattices, despite theoretical predictions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Gas Gun Model and Comparison to Experimental Performance of Pipe Guns Operating with Light Propellant Gases and Large Cryogenic Pellets

Injection of multiple large (~10 to 30 mm diameter) shattered pellets into ITER plasmas is presently part of the scheme planned to mitigate the deleterious effects of disruptions on the vessel components. To help in the design and optimize performance of the pellet injectors for this application, a model referred to as “the gas gun simulator” has been developed and benchmarked against experimental data. The computer code simulator is a Java program that models the gas-dynamics characteristics of a single-stage gas gun. Following a stepwise approach, the code utilizes a variety of input parameters to incrementally simulate and analyze the dynamics of the gun as the projectile is launched down the barrel. Using input data, the model can calculate gun performance based on physical characteristics, such as propellant-gas and fast-valve properties, barrel geometry, and pellet mass. Although the model is fundamentally generic, the present version is configured to accommodate cryogenic pellets composed of H2, D2, Ne, Ar, and mixtures of them and light propellant gases (H2, D2, and He). The pellets are solidified in situ in pipe guns that consist of stainless steel tubes and fast-acting valves that provide the propellant gas for pellet acceleration (to speeds ~200 to 700 m/s). The pellet speed is the key parameter in determining the response time of a shattered pellet system to a plasma disruption event. The calculated speeds from the code simulations of experiments were typically in excellent agreement with the measured values. With the gas gun simulator validated for many test shots and over a wide range of physical and operating parameters, it is a valuable tool for optimization of the injector design, including the fast valve design (orifice size and volume) for any operating pressure (~40 bar expected for the ITER application) and barrel length for any pellet size (mass, diameter, and length). Key design parameters and proposed values for the pellet injectors for the ITER disruption mitigation systems are discussed.

Combs, Stephen Kirk↗

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗