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DOE OSTI2024

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

TChem 2.0

The TChem toolkit is an object-oriented C++ software library that enables numerical simulations using complex chemistry and facilitates the analysis of detailed kinetic models. The toolkit provides capabilities for thermodynamic properties and gas-phase and surface chemistry. The computations rely on the Kokkos framework for parallel execution on many-core and GPU-based platforms. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. SAND2021-2752 O

Kim, Kyungjoo↗

DOE OSTI2021

Simulations of Quantum Circuits with Approximate Noise using qsim and Cirq

We introduce multinode quantum trajectory simulations with qsim, an open source high performance simulator of quantum circuits. qsim can be used as a backend of Cirq, a Python software library for writing quantum circuits. We present a novel delayed inner product algorithm for quantum trajectories which can result in an order of magnitude speedup for low noise simulation. We also provide tools to use this framework in Google Cloud Platform, with high performance virtual machines in a single mode or multinode setting. Multinode configurations are well suited to simulate noisy quantum circuits with quantum trajectories. Finally, we introduce an approximate noise model for Google's experimental quantum computing platform and compare the results of noisy simulations with experiments for several quantum algorithms on Google's Quantum Computing Service.

Isakov, Sergei V.↗

DOE OSTI2024

Visualization at exascale: Making it all work with VTK-m

The VTK-m software library enables scientific visualization on exascale-class supercomputers. Exascale machines are particularly challenging for software development in part because they use GPU accelerators to provide the vast majority of their computational throughput. Algorithmic designs for GPUs and GPU-centric computing often deviate from those that worked well on previous generations of high-performance computers that relied on traditional CPUs. Fortunately, VTK-m provides scientific visualization algorithms for GPUs and other accelerators. VTK-m also provides a framework that simplifies the implementation of new algorithms and adds a porting layer to work across multiple processor types. This paper describes the main challenges encountered when making scientific visualization available at exascale. Here, we document the surprises and obstacles faced when moving from pre-exascale platforms to the final exascale designs and the performance on those systems including scaling studies on Frontier, an exascale machine with over 37,000 AMD GPUs. We also report on the integration of VTK-m with other exascale software technologies. Finally, we show how VTK-m helps scientific discovery for applications such as fusion and particle acceleration that leverage an exascale supercomputer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

pbd-industrial-limit-of-performance (PBD limit of performance) v1.0.0

Software repository that contains models used for a paper about Platform-Based Design with limit of performance analysis for an industrial pilot study. This repository contains process and control models in Modelica and IDAES and scripts to develop an ML based controller that computes the control function that maximizes the techno-economic performance of cost and energy computed by the model. This software is meant to be released to reproduce the work described in a Journal publication that is now drafted with the working title "Energy System Limit of Performance Analysis using an Online Machine Learning Multi-Resolution Optimization Framework".

Amusat, Oluwamayowa [Lawrence Berkeley National La↗

DOE OSTI2021

Griffin: A Moose-based Reactor Multiphysics Application For Radiation Transport And Depletion Simulations

Griffin is a MOOSE-based reactor multiphysics application that streamlines the analysis of a variety of nuclear multiphysics applications, including steady-state and transient radiation transport, core performance, fuel depletion, criticality and decay heat calculations, reprocessing and post-irradiation examination. This streamlining is accomplished via enhanced flexibility of the tools, uniform syntax in the MOOSE framework, dynamic linking of all relevant physics and a single point of execution. The design for flexible multi-physics, multi-radiation, multi-scheme tasks demands and ultimately makes Griffin a highly extendable code system. A software quality assurance (SQA) procedure is enforced during Griffin development.

DeHart, MarkD.↗

DOE OSTI2022

MPACT Software Management Plan (V.4.3)

The MPACT code solves a discretized form of the Boltzmann transport equation on a wide variety of geometries and is distributed with a multigroup neutron cross section library. MPACT provides an advanced geometrically resolved neutral-particle transport capability to solve the flux distribution throughout the entire problem geometry, and it can model the isotopic depletion, decay, and activation of materials. The flux solution in MPACT is provided using a 2D/1D synthesis method within the framework of the 3D coarse mesh finite difference (CMFD) method for which axial and radial correction factors are obtained from 2D method of characteristics (MOC) and 1D nodal expansion method (NEM), PN, or SN. Other key characteristics of the MPACT code include the subgroup method and the embedded self-shielding method (ESSM) for resonance treatment, depletion capability based on the ORIGEN exponential matrix method, and a simplified thermal-hydraulics method for temperature/fluid feedback. The sole purpose of the simplified feedback model is to provide a mechanism for testing during code development and to provide a limited capability for educational applications. Work performed at the code level supports the VERA-QA-001, quality assurance program plan (QAPP) and VERA-QA-002, VERA Software Quality Assurance Plan.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications

Developing software for scientific applications that require the integration of diverse types of computing, instruments, and data present challenges that are distinct from commercial software. These applications require scale, and the need to integrate various programming and computational models with evolving and heterogeneous infrastructure. Pervasive and effective abstractions for distributed infrastructures are thus critical; however, the process of developing abstractions for scientific applications and infrastructures is not well understood. While theory-based approaches for system development are suited for well-defined, closed environments, they have severe limitations for designing abstractions for scientific systems and applications. The design science research (DSR) method provides the basis for designing practical systems that can handle real-world complexities at all levels. In contrast to theory-centric approaches, DSR emphasizes both practical relevance and knowledge creation by building and rigorously evaluating all artifacts. In this work, we show how DSR provides a well-defined framework for developing abstractions and middleware systems for distributed systems. Specifically, we address the critical problem of distributed resource management on heterogeneous infrastructure over a dynamic range of scales, a challenge that currently limits many scientific applications. We use the pilot-abstraction, a widely used resource management abstraction for high-performance, high throughput, big data, and streaming applications, as a case study for evaluating the DSR activities. For this purpose, we analyze the research process and artifacts produced during the design and evaluation of the pilot-abstraction. We find DSR provides a concise framework for iteratively designing and evaluating systems. Finally, we capture our experiences and formulate different lessons learned.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

hPIC2: A hardware-accelerated, hybrid particle-in-cell code for dynamic plasma-material interactions

The exascale era of high performance computing promises to bring the field of computational plasma physics ever closer to the goal of accurate multiscale modeling. Such computers will rely on hardware acceleration to offload work to dedicated components, notably general-purpose graphics processing units (GPUs). However, devices from different manufacturers require software to be written with different parallel programming models, greatly increasing the code maintenance burden of applications designed to perform on more than one such device. hPIC2 is a hybrid plasma simulation code developed with the Kokkos performance portability framework to target the architectures that will drive exascale computing for the foreseeable future. As a hybrid simulation code, hPIC2 investigates the simultaneous use of various plasma models on the same domain, at the same time. hPIC2 also optionally couples to RustBCA, which accurately models ion-material interactions using the binary collision approximation (BCA) method. In conclusion, hPIC2 therefore achieves scalable performance on a variety of computing architectures when simulating complex and diverse plasmas, particularly near plasma-material interfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗

DOE OSTI2022

Caldera_Grid

Caldera Grid is part of Caldera software platform, a suite of collective, open-source tools that was developed to improve the state of the art in modeling the impacts of Electric Vehicle (EV) charging on the grid. Caldera Grid is a co-simulation framework implemented using Hierarchical Engine for Large scale Infrastructure Co-Simulation (HELICS). The framework facilitates the co-simulation of EV charging and Smart Charge Management (SCM) strategies in Caldera Infrastructure Charge Model (ICM) with distribution level grid models in OpenDSS. Vehicle energy needs and charge session requirements generated using Caldera Charge Decision Module (CDM) are fed in as input to Caldera Grid. The EV charging models in Caldera ICM simulates both the uncontrolled charging loads as well as loads modified by the SCM strategies to develop distributed load profiles for each grid node hosting an Electric Vehicle Supply Equipment (EVSE) – also known as chargers. These loads were simulated in OpenDSS alongside existing distribution feeder loads. Each of these models are co-simulated in a HELICS federate. The HELICS co-simulation framework facilitates communication and synchronization between the federates. By co-simulating EV loads and distribution feeder loads, Caldera Grid can assess the potential grid impacts of EV charging on distribution feeders under various grid conditions. A control strategy federate is implemented with an interface where control strategies based on feedback from EV charging status and grid conditions can be developed and implemented. The platform can also support multiple control strategies in a single co-simulation.

Sundarrajan, ManojKumar Cebol↗

DOE OSTI2026

SEED: Semantic Energy Exploration and Discovery

The Bioenergy Knowledge Discovery Framework (KDF) hosts a vast repository of specialized data, yet traditional keyword-based search methods often struggle to provide direct answers, requiring significant domain expertise and manual effort to filter through raw documents. To overcome these barriers, this software introduces a semantic search engine that enables both specialists and non-specialists to query the KDF using natural language. By shifting from rigid keyword matching to intent-based retrieval, the tool automatically identifies and ranks the most relevant sources within the database. The system functions by processing natural language queries to extract the most pertinent information, delivering an AI-generated plain-language summary alongside exact supporting quotes from retrieved documents. This integrated approach provides users with immediate, evidence-based answers while eliminating the need for exhaustive manual review. By surfacing direct insights and contextual evidence, the software enhances the usability of existing KDF resources and democratizes access to complex bioenergy data. Ultimately, this semantic search solution accelerates the discovery process and supports faster, more informed decision-making across the bioenergy sector.

Pan, Meiyu (Melrose) [Oak Ridge National Laborator↗

DOE OSTI2022

Verification and validation testing and tools: comparison between MCNP code versions and nuclear data libraries [Slides]

This presentation discusses the primary goal of software testing which is to test the code for correctness. It also discusses the results for individual suites and the role of validation and verification also referred to in the presentation as V&V. In summation, the V&V framework enables easy comparison between calculations performed with different code versions and/or nuclear data libraries. This entire framework will be distributed with the upcoming MCNP6.3 release. V&V test suites shown and several that were not (Criticality, LAQGSM, Lockwood) will be distributed in the new framework.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Exascale models of stellar explosions: Quintessential multi-physics simulation

The ExaStar project aims to deliver an efficient, versatile, and portable software ecosystem for multi-physics astrophysics simulations run on exascale machines. The code suite is a component-based multi-physics toolkit, built on the capabilities of current simulation codes (in particular Flash-X and Castro), and based on the massively parallel adaptive mesh refinement framework AMReX. It includes modules for hydrodynamics, advanced radiation transport, thermonuclear kinetics, and nuclear microphysics. The code will reach exascale efficiency by building upon current multi- and many-core packages integrated into an orchestration system that uses a combination of configuration tools, code translators, and a domain-specific asynchronous runtime to manage performance across a range of platform architectures. The target science includes multi-physics simulations of astrophysical explosions (such as supernovae and neutron star mergers) to understand the cosmic origin of the elements and the fundamental physics of matter and neutrinos under extreme conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Coso Geothermal Spectral Library for Rocks and Minerals

An integrated open mineral spectral library designed to enhance the utility and precision of mineral spectral data for geothermal exploration, developed from a reliable and comprehensive digital dataset for seamless sharing by integrating field data, the USGS spectral library, and pertinent information obtained from Coso geothermal field (Coso) in California. The ASD FieldSpec portable spectrometer was utilized for collecting spectral data, which was subsequently analyzed using the THOR Material Identification tool in ENVI, The Spectral Geologist (TSG) software by CSIRO, and the Fully Constrained Linear Spectral Unmixing algorithm (FCLSU) in MATLAB. Scanning Electron Microscopy (SEM) with a mineralogy-analyzing function was employed to assess the mineral composition of samples, ensuring precise mineralogical analysis. A portable X-ray fluorescence (pXRF) spectrometer was also utilized to gather information on elemental enrichment. A framework for developing spectra data and establishing spectral libraries for various geological cases was proposed within this study. The characteristic spectra of six alteration minerals - alunite, chalcedony, epidote, hematite, kaolinite, and opal - were acquired from Coso samples. The spectral library for the Coso alteration minerals was introduced for further application in academic study or industrial exploration. To browse the Coso Geothermal Spectral data and related figures from spreadsheets: #1 Unzip and store the following items in the same folder. 'Contact Probe Data.zip', 'Sample Photos.zip', and 'Coso spectra of higher-certainity minerals.xlsx'. #2 Open 'Coso spectra of higher-certainity minerals.xlsx'. The hyperlinks in the spreadsheet lead to the folders or figures of: spectra .asd file, spectra ASC II file, spectra plots, and sample photos. The spectra data is raw data without splice correction. Spectra .asd files require particular software to open. (These cannot be opened in GIS software such as ArcGIS.) Spectra ASC II files can be opened in a text editor or spread sheet program.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

Coupled Monte Carlo Transport and Conjugate Heat Transfer for Wire-Wrapped Bundles Within the MOOSE Framework

Cardinal is an open-source application that couples OpenMC Monte Carlo transport and NekRS computational fluid dynamics (CFD) to the Multiphysics Object-Oriented Simulation Environment (MOOSE), closing neutronics and thermal-fluid gaps in conducting high-resolution multiscale and multiphysics analyses of nuclear systems. We first provide a brief introduction to Cardinal's software design, data mapping, and coupling strategy to highlight our approach to overcoming common challenges in high-fidelity multiphysics simulations. Here we then present two Cardinal simulations for hexagonal pin bundles. The first is a validation of Cardinal's conjugate heat transfer coupling of NekRS's Reynolds-Averaged Navier Stokes model with MOOSE's heat conduction physics for a bare seven-pin Freon-12 bundle flow experiment. Predictions for pin surface temperatures under three different heating modes agree reasonably well with experimental data and similar CFD modeling from the literature. The second simulation is a multiphysics coupling of OpenMC, NekRS, and BISON for a reduced-scale, seven-pin wire-wrapped version of an Advanced Burner Reactor bundle. Wire wraps are approximated using a momentum source model, and coupled predictions are provided for velocity, temperature, and power distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

SYMBIOSYS: A Methodology for Performance Analysis of Composable HPC Data Services

Microservices are a powerful new way of building, customizing, and deploying distributed services owing to their flexibility and maintainability. Several large-scale distributed platforms have emerged to serve the growing needs of data-centric workloads and services in commercial computing. Concurrently, high-performance computing (HPC) systems and software are rapidly evolving to meet the demands of diversified applications and heterogeneity. The interplay of hardware factors, software configuration parameters, and the flexibility offered with a microservice architecture makes it nontrivial to estimate the optimal service instantiation for a given application workload. Further, this problem is exacerbated when considering that these services operate in a dynamic and heterogeneous HPC environment. An optimally integrated service can be vastly more performant than a haphazardly integrated one. Existing performance tools for HPC either fail to understand the request-response model of communication inherent to microservices or they operate within a narrow scope, limiting the insight that can be gleaned from employing them in isolation. We propose a methodology for integrated performance analysis of HPC microservices frameworks and applications called SYMBIOSYS. We describe its design and implementation within the context of the Mochi framework. This integration is achieved by combining distributed callpath profiling and tracing with a performance data exchange strategy that collects fine-grained, low-level metrics from the RPC communication library and network layers. The result is a portable, low-overhead performance analysis setup that provides a holistic profile of the dependencies among microservices and how they interact with the Mochi RPC software stack. Using HEPnOS, a production-quality Mochi data service, we demonstrate the low-overhead operation of SYMBIOSYS at scale and use it to identify the root causes of poorly performing service configurations.

microservices↗