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At least 811 records · Page 45

Devastator Parallel Discrete Event Simulation Runtime (Devastator) v1.0

The Devastator runtime is a modern C++ implementation of optimistic parallel discrete event simulation methods. Devastator allows simulation application code to productively specify their component and event functionality with C++14 constructs. It utilizes GASNet-EX for distributed memory communication and includes parallel performance optimizations such as light-weight thread message queues and asynchronous GVT. Furthermore, it supports efficient event broadcasts and pause-rewind-resume functionality to support periodic load balancing and outer loop optimization algorithms.

Chan, Cy↗

Parallel Infrastructure Modeling and Inversion Module for E4D

Electrical resistivity tomography ERT is a method of imaging the electrical conductivity of the subsurface. Electrical conductivity is a useful metric for understanding the subsurface because it is governed by geomechanical and geochemical properties that drive subsurface systems. ERT works by injecting current into the subsurface across a pair of electrodes, and measuring the corresponding electrical potential response across another pair of electrodes. Many such measurements are strategically taken across an array of electrodes to produce an ERT data set. These data are then processed through a computationally demanding process known as inversion to produce an image of the subsurface conductivity structure that gave rise to the measurements. Data can be inverted to provide 2D images, 3D images, or in the case of time-lapse 3D imaging, 4D images. ERT is generally not well suited for environments with buried electrically conductive infrastructure such as pipes, tanks, or well casings, because these features tend to dominate and degrade ERT images. This reduces or eliminates the utility of ERT imaging where it would otherwise be highly useful for, for example, imaging fluid migration from leaking pipes, imaging soil contamination beneath leaking subsurface tanks, and monitoring contaminant migration in locations with dense network of metal cased monitoring wells. The location and dimension of buried metallic infrastructure is often known. If so, then the effects of the infrastructure can be explicitly modeled within the ERT imaging algorithm, and thereby removed from the corresponding ERT image. However, there are a number of obstacles limiting this application. 1) Metallic infrastructure cannot be accurately modeled with standard codes because of the large contrast in conductivity between the metal and host material. 2) Modeling infrastructure in true dimension requires the computational mesh to be highly refined near the metal inclusions, which increases computational demands. 3) The ERT imaging algorithm requires specialized modifications to accommodate high conductivity inclusions within the computational mesh. The solution to each of these challenges was implemented within E4D (formerly FERM3D), which is a parallel ERT imaging code developed at PNNL (IPID #30249). The infrastructure modeling module implement in E4D uses a method of decoupling the model at the metallic interface(s) boundaries, into several well posed sub-problems (one for each distinct metallic inclusion) that are subsequently solved and recombined to form the global solution. The approach is based on the immersed interface method, with has been applied for similar problems in other fields (e.g. semiconductor industry). Comparisons to analytic solutions have shown the results to be very accurate, addressing item 1 above. The solution is implemented about an unstructured mesh, which enables arbitrary shapes to be efficiently modelled, thereby addressing item 2 above. In addition, the algorithm is written in parallel and shows excellent scalability, which also addresses equation 2 above. Finally, because only the boundaries of metallic inclusions are modeled, there are no high conductivity cells within the modeling mesh, and the problem described by item 3 above is no longer applicable.

Johnson, TimC.↗

DaCe - Data Centric Parallel Programming

DaCe is a parallel programming framework that takes code in Python/NumPy and other programming languages, and maps it to high-performance CPU, GPU, and FPGA programs, which can be optimized to achieve state-of-the-art. Internally, DaCe uses the Stateful DataFlow multiGraph (SDFG) data-centric intermediate representation: A transformable, interactive representation of code based on data movement. Since the input code and the SDFG are separate, it is possible to optimize a program without changing its source, so that it stays readable. On the other hand, transformations are customizable and user-extensible, so they can be written once and reused in many applications. With data-centric parallel programming, we enable direct knowledge transfer of performance optimization, regardless of the application or the target processor.

Ben-Nun, Tal↗

Parallel Variable Population Multi-Objective Optimizer (pvpmoo) v1.0

This is a parallel variable population multi-objective optimizer with an adaptive unified differential evolution algorithm or a genetic algorithm. It can also be used for single objective optimization. Some features of this code include: 1) The population size varies from generation to generation to save the total # of objective function evaluations. 2) The population is uniformly distributed to a number of parallel processors for simultaneous objective function evaluation. 3) The objective function evaluation can be attained from an external simulation program with control variables in its input file and objectives calculated from its output files. 4) The optimizer includes an adaptive unified differential evolution algorithm and a real value genetic algorithm. The parameters in the unified differential evolution algorithm can be chosen to attain any mutation schemes in the published literature.

Qiang, Ji↗

Matrix-based Parallel Redistribution

MatRed is a parallel redistribution tool for HPC applications. It provides a simple approach that only requires a few relation matrices between entities to build redistribution matrices in parallel simulation codes. In particular, MatRed is well-suited for simulation codes based on finite element/volume methods.

Kalchev, DelyanZ [Lawrence Livermore National Labo↗

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiple states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.

97 MATHEMATICS AND COMPUTING↗

Scaling soft matter physics to thousands of graphics processing units in parallel

We describe a multi-graphics processing unit (GPU) implementation of the Ludwig application, which specialises in simulating a variety of complex fluids via lattice Boltzmann fluid dynamics coupled to additional physics describing complex fluid constituents. We describe our methodology in augmenting the original central processing unit (CPU) version with GPU functionality in a maintainable fashion. We present several optimisations that maximise performance on the GPU architecture through tuning for the GPU memory hierarchy. We describe how we implement particles within the fluid in such a way to avoid a major diversion of the CPU and GPU codebases, whilst minimising data transfer at each time step. We detail our halo-exchange communication phase for the code, which exploits overlapping to allow efficient parallel scaling to many GPUs. We present results showing that the application demonstrates excellent scaling to at least 8192 GPUs in parallel, the largest system tested at the time of writing. The GPU version (on NVIDIA K20X GPUs) is around 3.5–5 times faster that the CPU version (on fully utilised AMD Opteron 6274 16-core CPUs), comparing equal numbers of CPUs and GPUs.

Computer Science↗

A massively parallel and memory-efficient FEM toolbox with a hybrid total FETI solver with accelerator support

In this article, we present the ExaScale PaRallel finite element tearing and interconnecting SOlver (ESPRESO) finite element method (FEM) library, which includes an FEM toolbox with interfaces to professional and open-source simulation tools, and a massively parallel hybrid total finite element tearing and interconnecting (HTFETI) solver which can fully utilize the Oak Ridge Leadership Computing Facility Titan supercomputer and achieve superlinear scaling. This article presents several new techniques for finite element tearing and interconnecting (FETI) solvers designed for efficient utilization of supercomputers with a focus on (i) performance—we present a fivefold reduction of solver runtime for the Laplace equation by redesigning the FETI solver and offloading the key workload to the accelerator. We compare Intel Xeon Phi 7120p and Tesla K80 and P100 accelerators to Intel Xeon E5-2680v3 and Xeon Phi 7210 central processing units; and (ii) memory efficiency—we present two techniques which increase the efficiency of the HTFETI solver 1.8 times and push the limits of the largest possible problem ESPRESO that can solve from 124 to 223 billion unknowns for problems with unstructured meshes. Finally, we show that by dynamically tuning hardware parameters, we can reduce energy consumption by up to 33%.

Computer Science↗

Statistical and machine learning models for optimizing energy in parallel applications

Rising power costs and constraints are driving a growing focus on the energy efficiency of high performance computing systems. The unique characteristics of a particular system and workload and their effect on performance and energy efficiency are typically difficult for application users to assess and to control. Settings for optimum performance and energy efficiency can also diverge, so we need to identify trade-off options that guide a suitable balance between energy use and performance. We present statistical and machine learning models that only require a small number of runs to make accurate Pareto-optimal trade-off predictions using parameters that users can control. We study model training and validation using several parallel kernels and more complex workloads, including Algebraic Multigrid (AMG), Large-scale Atomic Molecular Massively Parallel Simulator, and Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics. Here, we demonstrate that we can train the models using as few as 12 runs, with prediction error of less than 10%. Our AMG results identify trade-off options that provide up to 45% improvement in energy efficiency for around 10% performance loss. We reduce the sample measurement time required for AMG by 90%, from 13 h to 74 min.

97 MATHEMATICS AND COMPUTING↗

Massively Parallel, Three-Dimensional Transport Solutions for the k-Eigenvalue Problem

We have implemented a new multilevel parallel decomposition in the Denovo dis- crete ordinates radiation transport code. In concert with Krylov subspace iterative solvers, the multilevel decomposition allows concurrency over energy in addition to space-angle, enabling scalability beyond the limits imposed by the traditional KBA space-angle partitioning. Furthermore, a new Arnoldi-based k-eigenvalue solver has been implemented. The added phase-space concurrency combined with the high- performance Krylov and Arnoldi solvers has enabled weak scaling to O(100K) cores on the Jaguar XK6 supercomputer. The multilevel decomposition provides sucient parallelism to scale to exascale computing and beyond.

Arnoldi↗

Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography

Parallel-beam tomography systems at synchrotron facilities have limited field of view (FOV) determined by the available beam size and detector system coverage. Scanning the full size of samples bigger than the FOV requires various data acquisition schemes such as grid scan, 360-degree scan with offset center-of-rotation (COR), helical scan, or combinations of these schemes. Though straightforward to implement, these scanning techniques have not often been used due to the lack of software and methods to process such types of data in an easy and automated fashion. The ease of use and automation is critical at synchrotron facilities where using visual inspection in data processing steps such as image stitching, COR determination, or helical data conversion is impractical due to the large size of datasets. Here, we provide methods and their implementations in a Python package, named Algotom, for not only processing such data types but also with the highest quality possible. The efficiency and ease of use of these tools can help to extend applications of parallel-beam tomography systems.

36 MATERIALS SCIENCE↗

Point-by-point inscribed sapphire parallel fiber Bragg gratings in a fully multimode system for multiplexed high-temperature sensing

In this work, we study the point-by-point inscription of sapphire parallel fiber Bragg gratings (sapphire pFBGs) in a fully multimode system. A parallel FBG is shown to be critical in enabling detectable and reliable high-order grating signals. The impacts of modal volume, spatial coherence, and grating location on reflectivity are examined. Three cascaded seventh-order pFBGs are fabricated in one sapphire fiber for wavelength multiplexed temperature sensing. Using a low-cost, fully multimode 850-nm interrogator, reliable measurement up to 1500°C is demonstrated.

42 ENGINEERING↗

COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients

Background: The COVID-19 pandemic remains a significant global threat. However, despite urgent need, there remains uncertainty surrounding best practices for pharmaceutical interventions to treat COVID-19. In particular, conflicting evidence has emerged surrounding the use of hydroxychloroquine and azithromycin, alone or in combination, for COVID-19. The COVID-19 Evidence Accelerator convened by the Reagan-Udall Foundation for the FDA, in collaboration with Friends of Cancer Research, assembled experts from the health systems research, regulatory science, data science, and epidemiology to participate in a large parallel analysis of different data sets to further explore the effectiveness of these treatments. Methods: Electronic health record (EHR) and claims data were extracted from seven separate databases. Parallel analyses were undertaken on data extracted from each source. Each analysis examined time to mortality in hospitalized patients treated with hydroxychloroquine, azithromycin, and the two in combination as compared to patients not treated with either drug. Cox proportional hazards models were used, and propensity score methods were undertaken to adjust for confounding. Frequencies of adverse events in each treatment group were also examined. Results: Neither hydroxychloroquine nor azithromycin, alone or in combination, were significantly associated with time to mortality among hospitalized COVID-19 patients. No treatment groups appeared to have an elevated risk of adverse events. Conclusion: Administration of hydroxychloroquine, azithromycin, and their combination appeared to have no effect on time to mortality in hospitalized COVID-19 patients. Continued research is needed to clarify best practices surrounding treatment of COVID-19.

60 APPLIED LIFE SCIENCES↗

High Performance Computing Productivity Study - Evaluation of Parallel Tools Platform (PTP) Eclipse Plug-In

This report is a DARPA funded Work For Others (WFO) evaluation of the Parallel Tools Platform (PTP) version 5.0.3 (Released October 18, 2011). PTP is currently being developed and supported as an open source product managed by Project Lead Greg Watson and team at IBM plus several other contributors. The tool has been in development since 2005 with a goal of providing an infrastructure for the integration of high performance computing tools. Basic functionality such as source code editing, compiling, launching, and debugging, plus more advanced features including performance monitoring and deployment have been bundled into an Eclipse Integrated Development Environment (IDE) plug-in to give parallel application programmers the features and improved productivity gained from using a common, well established development platform. The evaluation encompasses the basic aspects of using PTP, beginning with the installation and configuration of the plug-in, followed by code development and debugging. Each aspect is evaluated based on the expectations of my experience as an Eclipse user and is presented in the following format: • Feature description • User Experience • Evaluation The feature description is based on the provided documentation for PTP and the ‘generic’ expectations of what the feature should provide. The user experience reveals the actual use and exercise of the feature – specifically in the context and perspective of the evaluation platform provided by Lawrence Livermore National Laboratory. The evaluation of each feature includes the overall outcome of the user experience, along with the expectations that were not met, met, or exceeded along with any issues that were encountered.

97 MATHEMATICS AND COMPUTING↗

Multiscale Molecular Simulations at the Petascale: Parallelization of Reactive Force Field Model for Blue Gene/Q (ALCF-2 Early Science Program Technical Report)

Our efforts in developing a highly parallel implementation of the reactive force field model, the Multi-state Empirical Valence Bond (MS-EVB) method, are discussed. We have introduced multi-threading, a state decomposition parallelism, and replica exchange capabilities. Example calculations are presented to demonstrate the improved productivity and scalability of the new code on the Blue Gene/Q supercomputer, Mira. We show that we are now able to successfully scale to half of Mira and have the potential to scale even further.

Lange, Adiran W.↗

A Comparative Critical Analysis of Modern Task-Parallel Runtimes

The rise in node-level parallelism has increased interest in task-based parallel runtimes for a wide array of application areas. Applications have a wide variety of task spawning patterns which frequently change during the course of application execution, based on the algorithm or solver kernel in use. Task scheduling and load balance regimes, however, are often highly optimized for specific patterns. This paper uses four basic task spawning patterns to quantify the impact of specific scheduling policy decisions on execution time. We compare the behavior of six publicly available tasking runtimes: Intel Cilk, Intel Threading Building Blocks (TBB), Intel OpenMP, GCC OpenMP, Qthreads, and High Performance ParalleX (HPX). With the exception of Qthreads, the runtimes prove to have schedulers that are highly sensitive to application structure. No runtime is able to provide the best performance in all cases, and those that do provide the best performance in some cases, unfortunately, provide extremely poor performance when application structure does not match the scheduler's assumptions.

Wheeler, Kyle Bruce↗

Methodology for Augmenting Existing Paths with Additional Parallel Transects: Visual Sample Plan

Visual Sample Plan (VSP) is sample planning software that is used, among other purposes, to plan transect sampling paths to detect areas that were potentially used for munition training. This module was developed for application on a large site where existing roads and trails were to be used as primary sampling paths. Gap areas between these primary paths needed to found and covered with parallel transect paths. These gap areas represent areas on the site that are more than a specified distance from a primary path. These added parallel paths needed to optionally be connected together into a single path—the shortest path possible. The paths also needed to optionally be attached to existing primary paths, again with the shortest possible path. Finally, the process must be repeatable and predictable so that the same inputs (primary paths, specified distance, and path options) will result in the same set of new paths every time. This methodology was developed to meet those specifications.

54 ENVIRONMENTAL SCIENCES↗

Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture

In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments. In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in tt native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant effort was required to safely and efficiently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI OpenMP hybrid implementations attain up to 65x better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6x better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.

97 MATHEMATICS AND COMPUTING↗