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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Creating Continuous Integration Infrastructure for Software Development on U.S. Department of Energy High-Performance Computing Systems

The Exascale Computing Project (ECP) software deployment effort developed and advanced DevOps capabilities. One goal was to enable robust continuous integration (CI) workflows that span the protected high performance computing (HPC) environments found within many of the Department of Energy’s (DOE) national laboratories. This article highlights several challenges encountered with enabling automation, such as charging models for CI jobs, and meeting individualized security requirements that revolve around strongly associating running code with a human identity. Here, it also describes how the Jacamar CI tool evolved to meet latter requirements and became a key aspect of the solutions currently offered. Derived from this experience, we offer a conceptual framework for understanding current and future CI challenges at DOE facilities and offer suggestions for long-term solutions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Data analysis and modeling pipelines for controlled networked social science experiments

There is large interest in networked social science experiments for understanding human behavior at-scale. Significant effort is required to perform data analytics on experimental outputs and for computational modeling of custom experiments. Moreover, experiments and modeling are often performed in a cycle, enabling iterative experimental refinement and data modeling to uncover interesting insights and to generate/refute hypotheses about social behaviors. The current practice for social analysts is to develop tailor-made computer programs and analytical scripts for experiments and modeling. This often leads to inefficiencies and duplication of effort. In this work, we propose a pipeline framework to take a significant step towards overcoming these challenges. Our contribution is to describe the design and implementation of a software system to automate many of the steps involved in analyzing social science experimental data, building models to capture the behavior of human subjects, and providing data to test hypotheses. The proposed pipeline framework consists of formal models, formal algorithms, and theoretical models as the basis for the design and implementation. We propose a formal data model, such that if an experiment can be described in terms of this model, then our pipeline software can be used to analyze data efficiently. The merits of the proposed pipeline framework is elaborated by several case studies of networked social science experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Software stewardship and advancement of a high-performance computing scientific application: QMCPACK

Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗
DOE OSTI2020

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamFVT

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs. The testing of the adjoint code is performed in a separate document.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

ExaSGD: 2022 Kernel Thrust Activities

The Kernel Thrust milestone ADSE22-407 covers the development of device-capable optimization algorithms and solvers technologies required by the ExaSGD project’s software stack in order to solve security-constrained alternating current optimal power flow (SC-ACOPF) problems on emerging exascale architectures. To this extent, in FY22 the main objective of the Kernel Thrust was (i) provide sparse optimization solver that runs efficiently on hardware accelerator devices (i.e., NVIDIA and AMD GPUs) to perform intra-node computations, (ii) strengthen the reliability and increase the performance of the mixed-dense sparse (MDS) solver of HiOp for deployment on the FY22 target architectures, Summit and Crusher, and (iii) increase performance by improving the mathematical algorithm and refining the parallel MPI-based implementation of the coarse-grain parallel solver HiOp-PriDec for capabilities deployment on the FY22 target architectures, Summit and Crusher. This document presents the developments and contributions done by the Kernels Thrust Team in FY22 toward completion of the above-mentioned objectives. These contributions progressed along four main development (sub)thrusts: (1) Design and implementation of a sparse optimization solver for use on hardware accelerators; (2) Improvement of the mathematical algorithm and of the parallel implementation of HiOp-PriDec to ensure readiness and efficient coarse-grain parallelism for FY23 target exascale machine; and (3) Support Software and Application Development Thrusts of the exaSGD project in their deployment of the project’s software stack on AMD- and NVIDIA-based architectures. The development of the sparse optimization solver (thrust 1 above) was new in FY22 and resulted in a new sparse solver in HiOp (available as of version 0.6). The second development thrust was a continuation of the efforts from FY21 and improved the mathematical algorithm and the communication strategy of the HiOp-PriDec solver. The last developement thrust is a large collaborative effort. Namely, the project’s teams from multiple labs (LLNL, PNNL, ORNL, and NREL) performed large-scale demonstration of the ExaSGD software stack, namely the optimization solvers of HiOp interfaced with the modeling front-end ExaGO and the stochastic sampler PowerScenarios. These demonstration efforts solved large-scale instances of the SC-ACOPF challenge problem of medium network sizes (10, 000-bus system) and large number of contingencies on Summit (NVIDIA accelerators) and Crusher (AMD accelerators) systems at ORNL.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Insights From the Software Design of a Multiphysics Multicomponent Scientific Code

Using simulations for scientific discovery requires that the software used in the simulations undergoes a rigorous design and development process similar to that of the lab instruments in the experimental sciences. To devise a good design methodology, it is critical to understand the requirements, constraints, and challenges. Furthermore, this article describes insights from the long-term stewardship of a multiphysics multicomponent software, FLASH, that was designed more than 20 years ago for astrophysics, now serves multiple communities, and has been successful in adapting to the changing world of high-performance computing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

PUFFIn Software Modeling for Quality Management

PUFFIn (PENELOPE User Friendly Fast Interface) was designed as a fast and simple Monte Carlo simulation tool for the transport of photons and electrons, with a primary purpose as a learning and education tool for a broad range of static configurations in the radiation processing industry. Development of the PUFFIn software is funded by the Office of Radiological Security (ORS) within the United States National Nuclear Security Administration (NNSA). PUFFIn helps fill the education and knowledge gaps in the industry, as identified in reports by Fermilab (2017) and the IAEA (2020). PUFFIn uses the PENELOPE (NEA-2023) physics engine to perform simulations on static configurations. PUFFIn has support for multiple geometry types from simple, single material simulations to full 3D configurations created from CAD input files or images from X-Ray Tomography scans. PUFFin was designed to be easy for the novice user, it will generate the input and geometry files required by PENLOPE and will display the output plots within the PUFFIn interface. PUFFin is distributed for free but requires a free workshop so users can be adequately trained in its use. Workshops have been presented in the past at Texas A&M university, the Aerial-CRT facility in Strasbourg France and Jakarta Indonesia. PUFFIn simulations have been validated by 10 MeV ebeam experiments done at Aerial-CRT in France (Radiation Physics and Chemistry 222 (2024) 111774). Further user experimental comparisons were made at the medical product hands on workshop at Texas A&M in October 2024.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Experiences with Porting the FLASH Code to Ookami, an HPE Apollo 80 A64FX Platform

We present initial experiences with running the community simulation code FLASH, developed at the University of Chicago for multi-scale multi-physics applications, on Ookami, a technology testbed featuring the A64FX processor developed by Fujitsu. Our effort focused largely on running FLASH “right out of the box” to see which combinations of compilers and software implementations (e.g. MPI) allowed the code to run with minimal modification. FLASH was one application in a larger effort to deploy Ookami; it served as a test for different versions of newly installed software, and as a cornerstone for the FAQ page of the Ookami website. Here, we report on our results with different compilers and other software, along with our initial scaling results and attempts to utilize the A64FX’s SVE instructions and NUMA architecture. We found that FLASH readily ran with different compilers and MPI implementations, and showed the expected good scaling with no turning. However, more work must be done to fully take advantage of the A64FX’s architectural features and produce a significant speedup for FLASH on Ookami.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Giving Research Software Engineers a Larger Stage Through the Better Scientific Software Fellowship

The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. The BSSwF’s vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). Furthermore, case studies from several of the program’s participants illustrate the diverse ways the BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as the BSSwF can help recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations, and ideas for a larger audience.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Overcoming Challenges to Continuous Integration in HPC

Continuous integration (CI) has become a ubiquitous practice in modern software development, with major code hosting services offering free automation on popular platforms. CI offers major benefits, as it enables detecting bugs in code prior to committing changes. While high-performance computing (HPC) research relies heavily on software, HPC machines are not considered “common” platforms. This presents several challenges that hinder the adoption of CI in HPC environments, making it difficult to maintain bug-free HPC projects, and resulting in adverse effects on the research community. Here we explore the challenges that impede HPC CI, such as hardware diversity, security, isolation, administrative policies, and non-standard authentication, environments, and job submission mechanisms. We propose several solutions that could enhance the quality of HPC software and the experience of developers. Implementing these solutions would require significant changes at HPC centers, but if these changes are made, it would ultimately enable faster and better science.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Compressive sensing optical design and simulation tool

A system or method for designing optical systems includes generating a mathematical model of an imaging system; tracing a plurality of light rays from a source through the model of the imaging system in a forward direction and a backward direction incident upon an arbitrarily defined detector location; calculating the total light rays incident upon the arbitrarily defined detector location in response to the plurality of light rays; tracing a series of calibration images first through the computational or compressive imager mathematical model; measuring an output set of parameters based on a plurality of detected rays calibration images at the defined detector location; storing the output set of parameters in software, and determining an estimated system transfer function.

42 ENGINEERING↗
DOE OSTI2025

Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.

97 MATHEMATICS AND COMPUTING↗