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At least 1,099 records · Page 61

WfBench: Automated Generation of Scientific Workflow Benchmarks

The prevalence of scientific workflows with high computational demands calls for their execution on various distributed computing platforms, including large-scale leadership-class high-performance computing (HPC) clusters. To handle the deployment, monitoring, and optimization of workflow executions, many workflow systems have been developed over the past decade. There is a need for workflow benchmarks that can be used to evaluate the performance of workflow systems on current and future software stacks and hardware platforms.We present a generator of realistic workflow benchmark specifications that can be translated into benchmark code to be executed with current workflow systems. Our approach generates workflow tasks with arbitrary performance characteristics (CPU, memory, and I/O usage) and with realistic task dependency structures based on those seen in production workflows. We present experimental results that show that our approach generates benchmarks that are representative of production workflows, and conduct a case study to demonstrate the use and usefulness of our generated benchmarks to evaluate the performance of workflow systems under different configuration scenarios.

Coleman, Taina↗

Wide-area lustre file system using LNet routers

Scientific and big data computations are increasingly being distributed across wide-area networks, and they often require access to remote files. The file systems that are directly mounted over wide-area networks transparently support such computations, and also obviate the need for special purpose file transfer tools. In typical distributed file systems, the access is limited to local sites, and in particular, the reach of Lustre file system implemented over InfiniBand (IB) is limited to at most tens of miles due to 2.5ms latency bound. We describe LNet router methods that connect IB Lustre file system to remote Ethernet clients over wide-area networks. We collect extensive Lustre throughput measurements over 10Gbps connections with 0-366ms round-trip times. They demonstrate that Gbps throughput can be sustained over connections spanning the globe. We present Lustre throughput profiles over local and wide-area connections, which show the effects of various buffers and credits; in particular, they highlight the throughput limits for large transfers over wide-area connections. Furthermore, the measurements show the positive effects of pipelining in achieving higher throughput for successively file transfers compared to rates indicated by IOzone benchmark rates.

Rao, Nageswara↗

Optimization and Augmentation for Data Parallel Contour Trees

Contour trees are used for topological data analysis in scientific visualization. While originally computed with serial algorithms, recent work has introduced a vector-parallel algorithm. Furthermore, this algorithm is relatively slow for fully augmented contour trees which are needed for many practical data analysis tasks. We therefore introduce a representation called the hyperstructure that enables efficient searches through the contour tree and use it to construct a fully augmented contour tree in data parallel, with performance on average 6 times faster than the state-of-the-art parallel algorithm in the TTK topological toolkit.

97 MATHEMATICS AND COMPUTING↗

ChatMPI: LLM-Driven MPI Code Generation for HPC Workloads

The Message Passing Interface (MPI) standard plays a crucial role in enabling scientific applications for parallel computing and is an essential component in high-performance computing (HPC). However, implementing MPI code manually—especially applying a proper domain decomposition and communication pattern—is a challenging and error-prone task. We present ChatMPI, an AI assistant for MPI parallelization of sequential C codes. In our analysis, we focus on testing six essential HPC workloads, which are based on Basic Linear Algebra Subprograms levels 1, 2, and 3 as well as sparse, stencil, and iterative operations. We analyze the process of creating ChatMPI by using the ChatHPC library. This lightweight large language model (LLM)–based infrastructure enables HPC experts to efficiently create and supervise trustworthy AI capabilities for critical HPC software tasks. We study the data required for training (fine-tuning) ChatMPI to generate parallel codes that not only use MPI syntax correctly but also apply HPC techniques to reduce memory communication and maximize performance by using proper work decomposition. With a relatively small training dataset composed of a few dozen prompts and fewer than 15 minutes of fine-tuning on one node equipped with two NVIDIA H100 GPUs, ChatMPI elevates trustworthiness for MPI code generation of current LLMs (e.g., Code Llama, ChatGPT-4o and ChatGPT 5). Additionally, we evaluate the performance of the MPI codes generated by ChatMPI in comparison with the ones generated by ChatGPT-4o and ChatGPT-5. The codes generated by ChatMPI provide up to a 4 × boost in performance by using better problem decomposition, communication patterns, and HPC techniques (e.g., communication avoiding).

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗

Hybrid Parallel Contour Trees, Version 1.0

A common operation in scientific visualization is to compute and render a contour of a data set. Given a function of the form f : R^d -> R, a level set is defined as an inverse image f^-1(h) for an isovalue h, and a contour is a single connected component of a level set. The Reeb graph can then be defined to be the result of contracting each contour to a single point, and is well defined for Euclidean spaces or for general manifolds. For simple domains, the graph is guaranteed to be a tree, and is called the contour tree. Analysis can then be performed on the contour tree in order to identify isovalues of particular interest, based on various metrics, and render the corresponding contours, without having to know such isovalues a priori. This code is intended to be the first data-parallel algorithm for computing contour trees. Our implementation will use the portable data-parallel primitives provided by Nvidia’s Thrust library, allowing us to compile our same code for both GPUs and multi-core CPUs. Native OpenMP and purely serial versions of the code will likely also be included. It will also be extended to provide a hybrid data-parallel / distributed algorithm, allowing scaling beyond a single GPU or CPU.

Sewell, Christopher↗

ARES v1.x - Performance Portable Tool to Simulate Supernovae based on Parthenon Framework

Historically, codes for simulating supernovae (such as Arepo, FLASH or LEAFS) have been at the forefront of scientific high-performance computing to the immense computational resources required for full 3D simulations. However, given the shift towards heterogenous HPC architectures, many current-generation codes are at the risk of losing their competitiveness as they are only designed to run on homogeneous CPU-only systems. There exist several efforts to enable these codes for GPU’s, however, these efforts only consider specific architectures or vendors (e.g., implement only CUDA or HIP), limiting themselves to a small range of exascale computing systems. Frameworks such as Kokkos aim to provide a framework which is agnostic of the targeted architecture, enabling the development of performant and portable code. In the Ares code, we develop a performance portable tool to simulate supernovae based on the Parthenon Framework, which in turn uses Kokkos in the background. Here, the Parthenon Framework provides an interface to the underlying mesh-refinement routines, which form the backbone of our code. In addition, we incorporate the already existing Singularity-EOS toolkit to provide us with various equations of state, primarily the Helmholtz equation of state. We also include the JINA Reaclib as a basis for our nuclear network solver. Finally, we implement a gravity solver to complete the required physics. This setup will provide us with a minimal code base to simulate supernova in a similar style to the tried-and-tested Arepo code, but in a futureproof performance portable framework.

Lim, Hyun↗

Accelerated Climate Modeling for Energy (ACME) Final Scientific/Technical Report

Seven Department of Energy (DOE) national laboratories, Universities, and Kitware, undertook a coordinated effort to build an Earth system modeling capability tailored to meet the climate change research strategic objectives of the DOE Office of Science, as well as the broader climate change application needs of other DOE programs.

97 MATHEMATICS AND COMPUTING↗

Final Report: Optimal Model Complexity in Geological Carbon Sequestration: A Response Surface Uncertainty Analysis

The critical component of a risk assessment study in evaluating GCS is an analysis of uncertainty in CO2 modeling. In such analyses, direct numerical simulation of CO2 flow and leakage requires many time-consuming model runs. Alternatively, analytical methods have been developed which allow fast and efficient estimation of CO2 storage and leakage, although restrictive assumptions on formation rock and fluid properties are employed. In this study, an intermediate approach is proposed based on the Design of Experiment and Response Surface methodology, which consists of using a limited number of numerical simulations to estimate a prediction outcome as a combination of the most influential uncertain site properties. The methodology can be implemented within a Monte Carlo framework to efficiently assess parameter and prediction uncertainty while honoring the accuracy of numerical simulations. The choice of the uncertain properties is flexible and can include geologic parameters that influence reservoir heterogeneity, engineering parameters that influence gas trapping and migration, and reactive parameters that influence the extent of fluid/rock reactions. The method was tested and verified on modeling long-term CO2 flow, non-isothermal heat transport, and CO2 dissolution storage by coupling two-phase flow with explicit miscibility calculation using an accurate equation of state that gives rise to convective mixing of formation brine variably saturated with CO2. All simulations were performed using three-dimensional high-resolution models including a target deep saline aquifer, overlying caprock, and a shallow aquifer. To evaluate the uncertainty in representing reservoir permeability, sediment hierarchy of a heterogeneous digital stratigraphy was mapped to create multiple irregularly shape stratigraphic models of decreasing geologic resolutions: heterogeneous (reference), lithofacies, depositional environment, and a (homogeneous) geologic formation. To ensure model equivalency, all the stratigraphic models were successfully upscaled from the reference heterogeneous model for bulk flow and transport predictions (Zhang & Zhang, 2015). GCS simulation was then simulated with all models, yielding insights into the level of parameterization complexity that is needed for the accurate simulation of reservoir pore pressure, CO2 storage, leakage, footprint, and dissolution over both short (i.e., injection) and longer (monitoring) time scales. Important uncertainty parameters that impact these key performance metrics were identified for the stratigraphic models as well as for the heterogeneous model, leading to the development of reduced/simplified models at lower characterization cost that can be used for the reservoir uncertainty analysis. All the CO2 modeling was conducted using PFLOTRAN – a massively parallel, multiphase, multi-component, and reactive transport simulator developed by a multi-laboratory DOE/SciDAC (Scientific Discovery through Advanced Computing) project (Zhang et al., 2017, in review). Within the uncertainty analysis framework, increasing reservoir depth were investigated to explore its effect on the uncertainty outcomes and the potential for developing gravity-stable injection with increased storage security (Dai et al., 20126; Dai et al., 2017, in review). Finally, to accurately model CO2 fluid-rock reactions and resulting long-term storage as secondary carbonate minerals, a modified kinetic rate law for general mineral dissolution and precipitation was proposed and verified that is invariant to a scale transformation of the mineral formula weight. This new formulation will lead to more accurate assessment of mineral storage over geologic time scales (Lichtner, 2016).

58 GEOSCIENCES↗

Compiler and Runtime Approaches to Enable Large-Scale Irregular Programs. Final report, July 2013 - July 2019

While regular algorithms, characterized by operations on dense matrices and arrays, have long been the mainstay of scientific, high-performance computing, irregular algorithms, which feature unpredictable accesses to pointer-based data structures, are becoming increasingly common in high performance computing, arising in graph analysis, data mining and visualization, among other domains. Unfortunately, the defining characteristics of irregular applications, their dynamic, unpredictable, data-dependent access patterns and data layouts, make achieving high performance on large scale systems difficult. Scaling applications to peta- and exa-scale requires carefully controlling communication and data movement and placement, an inherently difficult task when access patterns and data layouts are unpredictable! Most irregular applications that attain high performance must be painstakingly hand-written and hand-tuned, with few common principles or paradigms uniting various implementations and easing future development. Despite the increasing importance of irregular applications, there is little programmer knowledge, and even less compiler ability, devoted to optimizing them. This project aims to solve these problems. By allowing programmers to write irregular applications in high level forms, with at most a few annotations highlighting key structural properties, programmers can focus on developing their algorithms and methods. The compiler and run-time system can take on the tedious task of optimizing the application for execution at large scales, and can automatically provide efficient implementations. This will provide portability and ease maintenance for existing irregular applications, but, more importantly, open up whole new domains of computational science to large-scale, high-performance simulation codes.

97 MATHEMATICS AND COMPUTING↗

The SciDAC QuantOm Framework: A composable Workflow

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Jefferson Lab and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event-level by leveraging nuclear theory models and accounting for experimental conditions. In order to efficiently run multiple analyses under varying conditions, a composable workflow was designed where each section (theory, experiment, objective minimization, etc.) has its own dedicated module. The optimization, i.e. the fit of theory to experimental data is carried out by deep learning techniques, such as Generative Adversarial Networks (GANs) or Reinforcement Learning (RL). This presentation gives an overview of the current status of the workflow, highlights present and future challenges, and highlights possible extensions to other projects with similar requirements.

Lersch, Daniel↗

Scaling the SciDAC QuantOm Workflow

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Jefferson Lab and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event-level by combining the input from theoretical and experimental nuclear physics into a single, composable workflow. The optimization itself (I.e. fitting the experimental data with theoretical predictions) is carried out by a machine / deep learning algorithm. The size of the acquired DIS data as well as the complexity of the workflow itself require that the analysis is performed across multiple GPUs on high performance computing systems, such as Polaris at Argonne National Laboratory. This presentation discusses the novelties and challenges that came along with parallelizing this workflow. Recent results are compared to common distributed training techniques.

Lersch, Daniel↗

Tokamak Disruption Simulation (Final Technical Report)

The Tokamak Disruption Simulation collaboration was a SciDAC (Scientific Discovery through Advanced Computing) program led by Xianzhu Tang of the Los Alamos National Laboratory but with separate grants to each institution. I was the PI for Columbia University and the only person at Columbia directly funded by this SciDAC. Disruptions are a sudden loss of confinement in tokamaks, and a reliable method of preventing disruptions must be developed before tokamak fusion power plants become feasible. A related plasma confinement concept, the stellarator, is the only way known way of preventing disruptions with the required reliability. The largest devices, both existing and under construction, for confining plasmas for fusion using magnetic fields are tokamaks, so it is important to solve their disruption issues. The sudden loss of confinement in tokamaks can be from a bit of material falling into the plasma, which causes the plasma energy to be quickly lost by radiation, or by an instability causing a breakup of the confining surfaces formed by the magnetic field. This breakup can occur more than a million times faster than one would naively think possible. The sudden breakup of surfaces is called a fast magnetic reconnection and also results in a sudden cooling of the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SAGIPS: A scalable Framework for scidac quantom

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Thomas Jefferson National Accelerator Facility and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event level by taking into leveraging nuclear theory models and accounting for experimental conditions. In order to efficiently run multiple analyses under varying conditions, a composable workflow was designed where each section (theory, experiment, objective minimization, etc.) has its own dedicated module. This presentation gives an overview over of the current status of this workflow, highlights present and future challenges, and highlights possible extensions to other projects with similar requirements.

Lersch, Daniel [Thomas Jefferson National Accelera↗

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗

Monolithic parallel processor, phase 1A

A four-bit parallel processor LSI array was designed and fabricated using COS/MOS integrated-circuit technology. The design features include the provision for interconnecting groups of parallel-processor chips to form an expanded processor of any desired word length. This 800-transistor "computer on a chip' circuit has the logic capability of a medium-size, medium-speed, general-purpose computer suitable for sophisticated scientific data processing. The ability to fabricate this device repetitively was demonstrated.

Source record↗

A computer program for the calculation of laminar and turbulent boundary layer flows

The results are presented of a study to produce a computer program to calculate laminar and turbulent boundary layer flows. The program is capable of calculating the following types of flow: (1) incompressible or compressible, (2) two dimensional or axisymmetric, and (3) flows with significant transverse curvature. Also, the program can handle a large variety of boundary conditions, such as blowing or suction, arbitrary temperature distributions and arbitrary wall heat fluxes. The program has been specialized to the calculation of equilibrium air flows and all of the thermodynamic and transport properties used are for air. For the turbulent transport properties, the eddy viscosity approach has been used. Although the eddy viscosity models are semi-empirical, the model employed in the program has corrections for pressure gradients, suction and blowing and compressibility. The basic method of approach is to put the equations of motion into a finite difference form and then solve them by use of a digital computer. The program is written in FORTRAN 4 and requires small amounts of computer time on most scientific machines. For example, most laminar flows can be calculated in less than one minute of machine time, while turbulent flows usually require three or four minutes.

Dwyer, H. A.↗