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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗
DOE OSTI2013

SciDAC Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas

During the first year of the SciDAC gyrokinetic particle simulation (GPS) project, the GPS team (Zhihong Lin, Liu Chen, Yasutaro Nishimura, and Igor Holod) at the University of California, Irvine (UCI) studied the tokamak electron transport driven by electron temperature gradient (ETG) turbulence, and by trapped electron mode (TEM) turbulence and ion temperature gradient (ITG) turbulence with kinetic electron effects, extended our studies of ITG turbulence spreading to core-edge coupling. We have developed and optimized an elliptic solver using finite element method (FEM), which enables the implementation of advanced kinetic electron models (split-weight scheme and hybrid model) in the SciDAC GPS production code GTC. The GTC code has been ported and optimized on both scalar and vector parallel computer architectures, and is being transformed into objected-oriented style to facilitate collaborative code development. During this period, the UCI team members presented 11 invited talks at major national and international conferences, published 22 papers in peer-reviewed journals and 10 papers in conference proceedings. The UCI hosted the annual SciDAC Workshop on Plasma Turbulence sponsored by the GPS Center, 2005-2007. The workshop was attended by about fifties US and foreign researchers and financially sponsored several gradual students from MIT, Princeton University, Germany, Switzerland, and Finland. A new SciDAC postdoc, Igor Holod, has arrived at UCI to initiate global particle simulation of magnetohydrodynamics turbulence driven by energetic particle modes. The PI, Z. Lin, has been promoted to the Associate Professor with tenure at UCI.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

RELAP-7 User's Guide

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework, MOOSE (Multi-Physics Object Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s capability and extends the analysis capability for all reactor system simulation scenarios.This document is a user's guide on how to use the RELAP-7 code.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

NEAMS Workbench Status and Capabilities

The mission of the US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program is to develop, apply, deploy, and support state-of-the-art predictive modeling and simulation tools for the design and analysis of current and future nuclear energy systems. This is accomplished by using computing architectures that range from laptops to leadership-class facilities. The NEAMS Workbench is a new initiative that will facilitate the transition from conventional tools to high fidelity tools by providing a common user interface for model creation, review, execution, output review, and visualization for integrated codes. The Workbench can use common user input, including engineering-scale specifications that are expanded into application-specific input requirements through the use of customizable templates. The templating process can enable multifidelity analysis of a system from a common set of input data. Additionally, the common user input processor can provide an enhanced alternative application input that provides additional conveniences over the native input, especially for legacy codes. Expansion of the integrated codes and application templates available in the Workbench will broaden the NEAMS user community and will facilitate system analysis and design. Current and planned capabilities of the NEAMS Workbench are detailed here.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

NEAMS Workbench Status and Capabilities

The mission of the US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program is to develop, apply, deploy, and support state-of-the-art predictive modeling and simulation tools for the design and analysis of current and future nuclear energy systems. This is accomplished by using computing architectures that range from laptops to leadership-class facilities. The NEAMS Workbench is a new initiative that will facilitate the transition from conventional tools to highfidelity tools by providing a common user interface for model creation, review, execution, output review, and visualization for integrated codes. The Workbench can use common user input, including engineering-scale specifications that are expanded into application-specific input requirements through the use of customizable templates. The templating process can enable multifidelity analysis of a system from a common set of input data. Additionally, the common user input processor can provide an enhanced alternative application input that provides additional conveniences compared with native input, especially for legacy codes. Expansion of the integrated codes and application templates available in the Workbench will broaden the NEAMS user community and will facilitate system analysis and design. Current and planned capabilities of the NEAMS Workbench are detailed herein.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Nek5000 developments in support of industry and the NRC

This year, the Nuclear Energy Advanced Modeling Simulation program (NEAMS) thermal-hydraulics verification and validation (V&V) work has focused in three areas of Nek5000 V&V-driven development. First, in a close collaborative effort with the U. S. Nuclear Regulatory Commission (NRC) staff, we have continued V&V efforts for the HYMERES-2 project using the OECD/NEA sponsored testing in the PSI PANDA facility. This year’s focus of ANL-NRC collaboration involves Nek5000 setups and validation for a range of problems relevant to and including the HYMERES-2 benchmark from PSI. The primary outcome of this year efforts is a more efficient geometry and inlet modeling simplification after a careful sensitivity study of the inlet profiles and pipe geometries. The resulting modeling choice of a short recycling/fully-developed turbulent inlet is within the experimental uncertainty estimate. This finding simplifies the next step of the cross-V&V HYMERES-2 project. In addition, the ANL team continue to provide assistance to the NRC staff in the form of Nek5000 application support in general and on the use of the HPC platforms of ALCF and INL in particular. This supports the NRC’s assessment of Nek5000 for use with the NRC Blue CRAB code suite. Second, we have implemented and tested more robust model of URANS, namely the k – τ model, a variant of the k-ω model, along with other improvements to RANS Nek5000 modeling in general. Because of its demonstrated robustness and stability, the k – τ model is the only RANS model that has been implemented in the new GPU version of the Nek5000 code, nekRS. Lastly, we report the initial implementation of Jacobian-free Newton Krylov approach to the direct Newton method for steady fluid solvers aimed at acceleration of RANS modeling and at IC improvement for LES campaigns. Also leveraging the Exascale Computing Project (ECP) ANL/CEED & SMR team’s software development effort to support NEAMS problems at large scale of the advanced computing architectures, NekRS, a GPU variant of Nek5000, built on top of kernels from libParanumal using OCCA for portability, has been successfully run on the full system of Summit (4608 nodes, 27648 GPUs).

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

5G Enabled Transformative Co-design and Co-simulation Framework for Grid Decarbonization and Modernization

5G is a breakthrough technology to enable a fully mobile and connected society, and a 5G-enabled digital continuum will be one of the critical foundations for clean energy economy and grid modernization. The clean energy transformation not only requires innovative manufacturing, algorithm, application, and cross-domain co-simulation, but also a systematic evaluation and comprehensive support on the microelectronic and architectural computing customization to enable and maximize the high renewable penetration in the future power grid. The co-design of decarbonized grid, reliable yet efficient communication, and affordable yet ubiquitous computing will unlock the potential of almost any available tools for the undergoing clean energy transformation. 5G is also an opportunity to rethink the paradigm of infrastructure planning, as computing will be one of the core services for society alongside electricity and communication services.

5G↗
DOE OSTI2023

Mu2e - Extinction Monitor Research & Development

Current efforts are being conducted at Fermi National Laboratory to study potential violations in accepted theory that would otherwise suggest a restructuring of our fundamental understanding of the universe. Mu2e is one of these frontier projects that studies charged lepton flavor violation (CLFV) which if observed, would suggest physics beyond the Standard Model. Therefore, this note encompasses several projects that contribute to the fruition of Mu2e investigations. Due to the broad range of disciplinary inconsistencies that each project requires, all the work is being presented as a means of justifying contribution to Mu2e. The projects are comprised of a G4Beamline simulation analyzing 8GeV proton beam interaction with a titanium window of Recycler ring extinction rates using three Cherenkov radiation-based detectors and supplemental work for the implementation of a micro–Telecommunications Computing Architecture (MicroTCA) crate to establish a peak finding algorithm to ensure that the out-of-time beam is less than 10^-10 fractional level along with inefficiency analysis on scintillation counters for the Cosmic-Ray Veto (CRV) analysis. Preliminary results have been achieved for extinction rate simulation by achieving coincidence rates for 2/3-fold and 3/3-fold on the detectors in the order of 10^-9 and 10^-10, respectively. Only preliminary results of a triangular counter and four rectangular di-counters for the CRV have been realized but other non-experimental contributions were made to the development of the MicroTCA crate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Demonstrating the Potential of Adaptive LMS Filtering on FPGA-Based Qubit Control Platforms for Improved Qubit Readout in 2D and 3D Quantum Processing Units

Advancements in quantum computing underscore the critical need for sophisticated qubit readout techniques to accurately discern quantum states. This abstract presents our research intended for optimizing readout pulse fidelity for 2D and 3D Quantum Processing Units (QPUs), the latter coupled with Superconducting Radio Frequency (SRF) cavities. Focusing specifically on the application of the Least Mean Squares (LMS) adaptive filtering algorithm, we explore its integration into the FPGA-based control systems to enhance the accuracy and efficiency of qubit state detection by improving Signal-to-Noise Ratio (SNR). Implementing the LMS algorithm on the Zynq UltraScale+ RFSoC Gen 3 devices (RFSoC 4x2 FPGA and ZCU216 FPGA) using the Quantum Instrumentation Control Kit (QICK) open-source platform, we aim to dynamically test and adjust the filtering parameters in real-time to characterize and adapt to the noise profile presented in quantum computing readout signals. Our preliminary results demonstrate the LMS filter's capability to maintain high readout accuracy while efficiently managing FPGA resources. These findings are expected to contribute to developing more reliable and scalable quantum computing architectures, highlighting the pivotal role of adaptive signal processing in quantum technology advancements.

Johnson, Hans↗
DOE OSTI2025

GPU Acceleration in SRW: Design and Considerations

Synchrotron Radiation Workshop (SRW) is a powerful tool for simulation synchrotron radiation emission and propagation through beamline elements, enabling advanced beamline design and experimental optimization. Recently, GPU acceleration has been developed for SRW to support highly detailed end-to-end simulations of experiments at synchrotron light sources. This work documents the design and implementation of this GPU acceleration support, addressing the complexities of adapting CPU-based components to heterogeneous computing architectures.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

External Radiation and Magnetic-Field Effects on the Coherence and Stability of Transmon Qubits

Superconducting transmon qubits are a central building block of modern quantum computing architectures, yet their coherence properties remain sensitive to external influences that can limit performance or introduce temporal instabilities. In this talk, I will discuss two experimental studies aimed at quantifying these effects. First, I will examine how ionizing radiation impacts qubit relaxation. Using the same transmon device operated at two locations with dramatically different radiation backgrounds—the above-ground SQMS facility at Fermilab (USA) and the deep-underground Gran Sasso Laboratory (Italy)—we observe a higher rate of radiation-induced decay events above ground, even though intrinsic noise remains the dominant source of single-shot errors. I will also discuss the detection efficiency of a radiation detector made using such a device. Second, I will present results on how small magnetic fields, applied either during cooldown or at millikelvin temperatures, influence device stability. We find that fixed-frequency transmons maintain robust coherence up to approximately 600 mG of trapped out-of-plane field, and that controlled application of magnetic field can reduce temporal fluctuations in T1. Together, these studies provide insight into how external environments shape transmon coherence and offer potential pathways for improving qubit stability in scalable quantum processors.

Roy, Tanay [Fermilab]↗
DOE OSTI2025

LAROMance Grade 91 Model Integration in NEML2

New reactor designs are targeting higher operating temperatures for increased thermal efficiency when compared to the current fleet of light water reactors. Designing structural components for these high temperature environments with reliable long-term operations requires material models that can accurately capture the deformation mechanisms active in these environments. The LAROMance surrogate material models are based on a database of mechanistic crystal plasticity simulations for high-temperature conditions. Inputs to the LAROMance models reflect the microstructural pedigree of the material, like dislocation densities and precipitate contents. Based on the evolution of these microstructural features, the LAROMance model provides the engineering scale constitutive model response. The LAROMance model was recently parameterized for Grade 91, a high temperature alloy. In the present work, the Grade 91 LAROMance model is implemented in the New Material Model Library, version 2 (NEML2). NEML2 provides a modular way to build material models from smaller blocks and was developed to vectorize the material update to efficiently run on modern computational architectures with graphics processing unit accelerators. NEML2 constitutive models can be used in simulations based on the multiphysics object-oriented simulation environment (MOOSE). This report provides details on the implementation of the Grade 91 LAROMance model in NEML2 and its verification of engineering scale finite element simulations in MOOSE.

42 - ENGINEERING↗
DOE OSTI2026

Enhancing Coherence Limits in Superconducting Quantum Systems for Computing and Sensing

This talk will highlight recent efforts at the SQMS Center to develop qudit-based quantum computing architectures using superconducting three-dimensional (3D) cavities, as well as the use of these ultra-coherent cavities for quantum sensing. I will present systematic studies of materials and devices aimed at identifying and mitigating the dominant sources of decoherence—including two-level systems (TLS), quasiparticles, and other noise mechanisms—in both transmons and 3D cavities. These investigations include microwave loss characterization of niobium, tantalum, aluminum, their native oxides, and substrate materials such as silicon and sapphire. By combining measurements on qubits and cavities, we disentangle subsystem-specific loss mechanisms and establish a hierarchy of mitigation strategies, leading to transmon coherence times exceeding one millisecond. I will also discuss studies of quasiparticle dynamics, including quasiparticle bursts observed in qubits operated both above ground and at the Gran Sasso underground laboratory, and the observation that applied magnetic fields can suppress temporal T₁ fluctuations. Building on these advances, we demonstrate a record-coherence two-cell cavity-qudit system with coherence times exceeding 20 milliseconds. Leveraging tunable sideband interactions together with error-resilient protocols, including measurement-based error correction and post-selection, we achieve high-fidelity quantum state control, including the preparation of Fock states up to N=20 with fidelities above 95% and the generation of high-fidelity two-mode entangled states. Finally, I will discuss how these ultra-coherent quantum systems are enabling emerging quantum sensing applications, including searches for dark matter and gravitational waves.

Roy, Tanay [Fermilab] (ORCID:000000019442862X)↗
DOE OSTI2026

Entity—Hardware-agnostic Particle-in-cell Code for Plasma Astrophysics. II. General Relativistic Module

Black hole (BH) environments often host plasmas that are fully collisionless or contain intrinsically collisionless regions, including relativistic jets and coronae, where particle energization is ubiquitous. Capturing the physics of these systems requires numerical methods capable of modeling relativistic, magnetized, collisionless plasmas in strong gravitational fields. In this work, we introduce the general relativistic module for Entity—the first open-source, coordinate-agnostic, performance-portable, particle-in-cell code. The code enables fast axisymmetric simulations of collisionless plasmas around BHs on any modern high-performance computing architecture (both GPUs and CPUs).

Galishnikova, Alisa [Flatiron Institute, New York,↗
DOE OSTI2026

Enhanced climate reproducibility testing with false discovery rate correction

Simulating the Earth's climate is an important and complex problem, thus climate models are similarly complex, comprised of millions of lines of code. In order to appropriately utilize the latest computational and software infrastructure advancements in Earth system models running on modern hybrid computing architectures to improve their performance, precision, accuracy, or all three; it is important to ensure that model simulations are repeatable and robust. This introduces the need for establishing statistical or non-bit-for-bit reproducibility, since bit-for-bit reproducibility may not always be achievable. Here, we propose a short-simulation ensemble-based test for an atmosphere model to evaluate the null hypothesis that modified model results are statistically equivalent to that of the original model. We implement this test in version 2 of the US Department of Energy's Energy Exascale Earth System Model (E3SM). The test evaluates a standard set of output variables across the two simulation ensembles and uses a false discovery rate correction to account for multiple testing. The false positive rates of the test are examined using re-sampling techniques on large simulation ensembles and are found to be lower than the currently implemented bootstrapping-based testing approach in E3SM. We also evaluate the statistical power of the test using perturbed simulation ensemble suites, each with a progressively larger magnitude of change to a tuning parameter. The new test is generally found to exhibit more statistical power than the current approach, being able to detect smaller changes in parameter values with higher confidence.

Kelleher, Michael E. [Oak Ridge National Laborator↗
DOE OSTI2026

TChem-atm (v2.0.0): scalable performance-portable multiphase atmospheric chemistry

We present TChem-atm, a performance-portable approach that enables efficient simulation of chemically detailed and multiphase atmospheric chemistry on modern heterogeneous computing architectures. Unlike previous efforts that rely on architecture-specific code or focus exclusively on gas-phase chemistry, TChem-atm supports fully coupled gas–aerosol systems with execution across CPUs, NVIDIA GPUs, and AMD GPUs through the Kokkos programming model. It integrates the flexible multiphase capabilities of the Community Atmospheric Model Chemistry Package (CAMP) with the high-performance kinetic routines of TChem, and includes automatic Jacobian construction with support for a range of stiff ODE solvers. In a proof-of-concept integration with the particle-resolved model PartMC, TChem-atm reproduces the existing PartMC–CAMP implementation within solver tolerances and delivers substantial GPU speedups, especially for large particle populations. Performance benchmarks reveal substantial speedups on GPU platforms, particularly for large particle populations, with consistent results across hardware backends. TChem-atm enables performance-portable execution across CPUs and GPUs, though optimal efficiency may require modest architecture-specific tuning (e.g., team and vector sizes), with up to a twofold improvement on the NVIDIA H100. It directly supports sectional and particle-resolved host models, while modal aerosol schemes require minor adaptation to provide particle-scale quantities such as representative diameters. By enabling chemically detailed, multiphase simulations with performance portability and host-model flexibility, TChem-atm facilitates the incorporation of advanced chemistry into atmospheric models.

Díaz-Ibarra, Oscar Homero [Sandia National Laborat↗
NASA NTRS1972

Space Ultrareliable Modular Computer (SUMC) instruction simulator

The design principles, description, functional operation, and recommended expansion and enhancements are presented for the Space Ultrareliable Modular Computer interpretive simulator. Included as appendices are the user's manual, program module descriptions, target instruction descriptions, simulator source program listing, and a sample program printout. In discussing the design and operation of the simulator, the key problems involving host computer independence and target computer architectural scope are brought into focus.

Curran, R. T.↗
NASA NTRS1977

Highly reliable multiprocessors

Highly reliable fault-tolerant computer systems are discussed for use in flight-critical avionic and control systems of future commercial transport aircraft. Such aircraft are envisioned to have integrated systems, to be terminally configured, and to be equipped with fly-by-wire flight control systems, all of which require highly reliable, fault-tolerant computers. Two candidate computer architectures are identified as having the potential of satisfying the commercial transport aircraft requirements.

Murray, N. D.↗