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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

MPMC and MCMD: Free High-Performance Simulation Software for Atomistic Systems

Advancements in parallel computing and hardware have allowed computational exploration of chemical systems of interest with unprecendented accuracy and efficiency. The typical development of molecular simulation software is initially inspired by a particular scientific inquiry. The softwares presented herein, MPMC (Massively Parallel Monte Carlo) and MCMD (Monte Carlo/Molecular Dynamics) were born out of a pursuit to simulate condensed phase physical and chemical interactions in porous materials. MPMC first began in 2005 and has been used for dozens of published results in the literature but has not yet been introduced in a standalone paper. MCMD is a more recent expansion and re-write with some published work, focused on adding molecular dynamics algorithms for transport and other time-dependent properties of chemical systems. Each software functions as a standalone with some unique and other overlapping features. Here, a driving aim of this work is to consider periodic, long-range polarization effects in classical simulation, and both codes are optimized to perform such calculations. Sample results will be presented which highlight methodically that inclusion of explicit polarization produces simulation results with predictive power which in general are in greater agreement with experiment than non-polarizable analogous simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Accelerating x-ray tracing for exascale systems using Kokkos

The upcoming exascale computing systems Frontier and Aurora will draw much of their computing power from GPU accelerators. The hardware for these systems will be provided by AMD and Intel, respectively, each supporting their own GPU programming model. The challenge for applications that harness one of these exascale systems will be to avoid lock-in and to preserve performance portability. We report here on our results of using Kokkos to accelerate a real-world application on NERSC's Perlmutter Phase 1 (using NVIDIA A100 accelerators) and Crusher, the testbed system for OLCF's Frontier (using AMD MI250X). By porting to Kokkos, we successfully ran the same X-ray tracing code on both systems and achieved speed-ups between 13 % and 66 % compared to the original CUDA code. Finally, these results are a highly encouraging demonstration of using Kokkos to accelerate production science code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Integrated State Estimation and Contingency Analysis Software Implementation using High Performance Computing Techniques

Power system simulation tools are traditionally developed in sequential mode and codes are optimized for single core computing only. However, the increasing complexity in the power grid models requires more intensive computation. The traditional simulation tools will soon not be able to meet the grid operation requirements. Therefore, power system simulation tools need to evolve accordingly to provide faster and better results for grid operations. This paper presents an integrated state estimation and contingency analysis software implementation using high performance computing techniques. The software is able to solve large size state estimation problems within one second and achieve a near-linear speedup of 9,800 with 10,000 cores for contingency analysis application. The performance evaluation is presented to show its effectiveness.

Chen, Yousu↗
DOE OSTI2024

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.

Biosensors↗
DOE OSTI2020

Development of uncertainty-aware equation-of-state models: Application to copper

Sophisticated hydrodynamic codes are commonly used to understand and predict events relevant to natural and applied sciences. The degree to which these simulations reflect reality, however, is dependent on how well we understand the materials and underlying physics involved. These research communities need material models that communicate the uncertainty in the physical properties, which at their basest form comes from the uncertainty in the underlying experimental measurements. Additionally, we have constructed a new framework for using both experimental measurements and the associated experimental uncertainties to build equation-of-state models that reflect not only current best measurements but also the accuracy of those measurements. This method had been used to construct an ensemble of equation-of-state models for copper that communicates the experimental uncertainties in the data through the equation-of-state model, which is available for application in any simulation metric of interest.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

A 3D helical filament surrogate model for 3D tokamak equilibria

A novel approach for efficient representation of three-dimensional (3D) tokamak equilibria is investigated, where a set of helical current filaments occupying the plasma region are employed to resolve deviations from the two-dimensional (2D) axi-symmetric state. A discrete set of 3D filaments, located at rational surfaces for a given toroidal mode number n and following the 2D equilibrium field lines (thus forming closed current loops), are found to provide a surrogate model of 3D equilibria with reasonable accuracy. Specifically, application of the filament model to 3D perturbed equilibria, due to the resonant magnetic perturbation (RMP) in DIII-D and MAST-U discharges, reveals that (1) a single helical filament per rational surface is sufficient; (2) 21 such helical filaments are capable of representing the n = 2 3D response field in MAST-U with less than 10% relative error as compared to that computed by a full magnetohydrodynamic code; (3) optimizing currents (both amplitude and phase) flowing in 3D filaments with fixed geometry, the highest accuracy fitting is found to depend on the characteristics of the 3D equilibria such as the coil current phasing of the RMP coils in our case studies. Here, whis filament approach is also applicable for generating surrogate models of other type of 3D tokamak equilibria, including those during the initial phase of the plasma disruption.

MARS-F↗
DOE OSTI2020

Speeding up particle track reconstruction using a parallel Kalman filter algorithm

One of the most computationally difficult problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is determining the trajectory of charged particles during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material effects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filter-based methods for highly parallel, many-core SIMD architectures that are now prevalent in high-performance hardware. In this paper, we discuss the design and performance of the improved tracking algorithm, referred to as mkFit. A key piece of the algorithm is the Matriplex library, containing dedicated code to optimally vectorize operations on small matrices. The physics performance of the mkFit algorithm is comparable to the nominal CMS tracking algorithm when reconstructing tracks from simulated proton-proton collisions within the CMS detector. We study the scaling of the algorithm as a function of the parallel resources utilized and find large speedups both from vectorization and multi-threading. mkFit achieves a speedup of a factor of 6 compared to the nominal algorithm when run in a single-threaded application within the CMS software framework.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

A Unit Testing Framework for Scientific Legacy Code

Large-scale scientific applications play important roles in supporting research. However, it is often very expensive and time-consuming to make changes to, maintain and evolve the scientific code due to its complexity and poor programming skills of researchers. Therefore, in order to visualize scientific code architecture to optimize software design, understand undocumented source code, and analyze software flow and functionality, we first introduce a unit testing framework (UTF). Then, because such infrastructure's performance is very crucial in practical use since the scientific legacy applications simulate instances in a long period of time, we improve the UTF by applying Message Passing based Parallelization and parallel I/O operations. Furthermore, due to the scientific code has enormous state data and the I/O capacity on the server is limited, we apply in situ data analysis method to encounter fewer resource limitations, and adopt signal processing to greatly reduce data transfer. Last, we demonstrated the correctness and high-efficiency of our framework for legacy Earth model on Titan supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Scaling Irregular Applications through Data Aggregation and Software Multithreading

Bioinformatics, data analytics, semantic databases, knowledge discovery are emerging high performance application areas that exploit dynamic, linked data structures such as graphs, unbalanced trees or unstructured grids. These data structures usually are very large, requiring significantly more memory than available on single shared memory systems. Additionally, these data structures are difficult to partition on distributed memory systems. They also present poor spatial and temporal locality, thus generating unpredictable memory and network accesses. The Partitioned Global Address Space (PGAS) programming model seems suitable for these applications, because it allows using a shared memory abstraction across distributed-memory clusters. However, current PGAS languages and libraries are built to target regular remote data accesses and block transfers. Furthermore, they usually rely on the Single Program Multiple Data (SPMD) parallel control model, which is not well suited to the fine grained, dynamic and unbalanced parallelism of irregular applications. In this paper we present {\bf GMT} (Global Memory and Threading library), a custom runtime library that enables efficient execution of irregular applications on commodity clusters. GMT integrates a PGAS data substrate with simple fork/join parallelism and provides automatic load balancing on a per node basis. It implements multi-level aggregation and lightweight multithreading to maximize memory and network bandwidth with fine-grained data accesses and tolerate long data access latencies. A key innovation in the GMT runtime is its thread specialization (workers, helpers and communication threads) that realize the overall functionality. We compare our approach with other PGAS models, such as UPC running using GASNet, and hand-optimized MPI code on a set of typical large-scale irregular applications, demonstrating speedups of an order of magnitude.

Aggregation↗
DOE OSTI2018

International Neuroscience Initiatives through the Lens of High-Performance Computing

Neuroscience initiatives aim to develop new technologies and tools to measure and manipulate neuronal circuits. In this paper, to deal with the massive amounts of data generated by these tools, the authors envision the co-location of open data repositories in standardized formats together with high-performance computing hardware utilizing open source optimized analysis codes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-523: Investigation of Various MR-Compatible Shielding Materials for Direction Modulated Brachytherapy (DMBT) Tandem Applicator for Cervical Cancer Treatment

Purpose: To evaluate various shielding materials such as Gold (Au), Osmium (Os), Tantalum (Ta), and Tungsten (W) based alloys for use with a novel intensity modulation capable direction modulated brachytherapy (DMBT) tandem applicator for image guided cervical cancer HDR brachytherapy. Methods: The novel MRI-compatible DMBT tandem, made from nonmagnetic tungsten-alloy rod with diameter of 5.4 mm, has 6 symmetric peripheral holes of 1.3 mm diameter with 2.05 mm distance from the center for a high degree intensity modulation capacity. The 0.3 mm thickness of bio-compatible plastic tubing wraps the tandem. MCNPX was used for Monte Carlo simulations of the shields and the mHDR Ir-192 V2 source. MC-generated 3D dose matrices of different shielding materials of Au, Os, Ta, and W with 1 mm3 resolution were imported into an in-house-coded inverse optimization planning system to evaluate 19 clinical patient plans. Prescription dose was 15Gy. All plans were normalized to receive the same HRCTV D90. Results: In general, the plan qualities for various shielding materials were similar. The OAR D2cc for bladder was very similar for Au, Os, and Ta with 11.64±2.30Gy. For W, it was very close 11.65±2.30Gy. The sigmoid D2cc was 9.82±2.46Gy for Au and Os while it was 9.84±2.48Gy for Ta and W. The rectum D2cc was 7.44±3.06Gy for Au, 7.43±3.07Gy for Os, 7.48±3.05Gy for Ta, and 7.47±3.05Gy for W. The HRCTV D98 and V100 were very close with 16.37±1.87 Gy and 97.37±1.93 Gy, on average, respectively. Conclusion: Various MRI-compatible shielding alloys were investigated for the DMBT tandem applicator. The clinical plan qualities were not significantly different among these various alloys, however. Therefore, the candidate metals (or in combination) can be used to select best alloys for MRI image guided cervical cancer brachytherapy using the novel DMBT applicator that is capable of unprecedented level of intensity modulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-787: Utility of the Two Candidate 192-Ir and 169-Yb HDR Sources for Use with a Novel Direction Modulated Brachytherapy Tandem Applicator for Cervical Cancer Treatment

Purpose: A novel tungsten alloy shielded, MRI-compatible, direction modulated brachytherapy (DMBT) concept tandem applicator, which enables unprecedented intensity modulation, was used to evaluate treatment plan quality improvement over a conventional tandem. The utility of the 192-Ir and 169-Yb HDR sources, for use with the DMBT applicator, was evaluated. Methods: The total diameter of the DMBT tandem applicator is 6.0 mm, which consists of 5.4-mm diameter tungsten alloy and 0.3 mm thick plastic sheath. The tandem has 6 symmetric peripheral 1.3-mm diameter grooves for the source to travel. MCNPX v.2.6 was used to simulate the 192-Ir and 169-Yb sources inside the DMBT applicator. First, TG-43 source parameters were evaluated. Second, 3D dose matrix with 1 mm3 resolution were imported into an in-house-coded inverse optimization treatment planning program to obtain optimal plans for 19 clinical cases. All plans were compared with the standard tandem and ring plans. Prescription dose was 15.0 Gy. All plans were normalized to receive the same HRCTV D90. Results: Generally, the DMBT tandem (and ring) plans were better than the conventional tandem and ring plans for 192-Ir and 169-Yb HDR sources. The mean data of D2cc for bladder, rectum, and sigmoid were 11.65±2.30 Gy, 7.47±3.05 Gy, and 9.84±2.48 Gy for Ir-192 DMBT tandem, respectively. These data for Yb-169 were 11.67±2.26 Gy, 7.44±3.02 Gy, and 9.83±2.38 Gy, respectively. The HR-CTV D98 and V100 were 16.37±1.86 Gy and 97.37 ± 1.92 Gy for Ir-192 DMBT, respectively. The corresponding values for Yb-169 were 16.43±1.86 Gy, and 97.51 ± 1.91 Gy. Plans with the 169-Yb source generally produced more favorable results where V100 increased by 13.65% while D2cc across all OARs reduced by 0.54% compared with the 192-Ir plans. Conclusion: For the DMBT tandem applicator, 169-Yb source seems to produce more directional beams resulting in increased intensity modulation capacity, thus resulting in more conformal plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-F-BRA-05: Utility of the Combined Use of Two Types of HDR Sources with the Direction Modulation Brachytherapy (DMBT) Tandem Applicator for Cervical Cancer Treatment

Purpose: To maximize the dose to HRCTV while minimizing dose to the OARs, the combination of two HDR brachytherapy sources, 192-Ir and 169-Yb, used in combination with the recently-proposed novel direction modulated brachytherapy (DMBT) tandem applicator were examined. Methods: The DMBT tandem, made from nonmagnetic tungsten-alloy rod, with diameter of 5.4mm, has 6 symmetric peripheral holes of 1.3mm diameter. The 0.3mm thick bio-compatible plastic tubing wraps the tandem. MCNPX v.2.6 was used to simulate the mHDR 192-Ir V2 and 4140 HDR 169-Yb sources inside the DMBT applicator. Thought was by combining the higher energy 192-Ir (380keV) and lower energy 169-Yb (92.7keV) sources could create unprecedented level of dose conformality when combined with the high-degree intensity modulation capable DMBT tandem applicator. 3D dose matrices, with 1 mm3 resolution, were imported into an in-house-coded inverse optimization planning system to evaluate plan quality of 19 clinical patient cases. Prescription dose was 15Gy. All plans were normalized to receive the same HRCTV D90. Results: Generally, the use of dual sources produced better plans than using either of the sources alone, with significantly better performance in some patients. The mean D2cc for bladder, rectum, and sigmoid were 11.65±2.30Gy, 7.47±3.05Gy, and 9.84±2.48Gy for 192-Ir-only, respectively. For 169 -Yb-only, they were 11.67±2.26Gy, 7.44±3.02Gy, and 9.83±2.38Gy, respectively. The corresponding data for the dual sources were 11.51±2.24Gy, 7.30±3.00Gy, and 9.68 ±2.39Gy, respectively. The HRCTV D98 and V100 were 16.37±1.86Gy and 97.37±1.92Gy for Ir-192-only, respectively. For 169-Yb-only, they were 16.43±1.86Gy, and 97.51±1.91Gy, respectively. For the dual source, they were 16.42±1.87Gy and 97.47±1.93Gy, respectively. Conclusion: The plan quality improves, in some cases quite significantly, for when dual 192-Ir and 169-Yb sources are used in combination with highly intensity modulation capable DMBT tandem applicator for image guided cervical cancer brachytherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

A local-view array library for partitioned global address space C++programs

Multidimensional arrays are an important data structure in many scientific applications. Unfortunately, built-in support for such arrays is inadequate in C++, particularly in the distributed setting where bulk communication operations are required for good performance. In this paper, we present a multidimensional library for partitioned global address space (PGAS) programs, supporting the one-sided remote access and bulk operations of the PGAS model. The library is based on Titanium arrays, which have proven to provide good productivity and performance. These arrays provide a local view of data, where each rank constructs its own portion of a global data structure, matching the local view of execution common to PGAS programs and providing maximum flexibility in structuring global data. Unlike Titanium, which has its own compiler with array-specific analyses, optimizations, and code generation, we implement multidimensional arrays solely through a C++library. The main goal of this effort is to provide a library-based implementation that can match the productivity and performance of a compiler-based approach. We implement the array library as an extension to UPC++, a C++library for PGAS programs, and we extend Titanium arrays with specializations to improve performance. We evaluate the array library by porting four Titanium benchmarks to UPC++, demonstrating that it can achieve up to 25% better performance than Titanium without a significant increase in programmer effort..

Kamil, A↗
DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

co2amp: A software program for modeling the dynamics of ultrashort pulses in optical systems with CO 2 amplifiers

We describe a computer code for simulating the amplification of ultrashort mid-infrared laser pulses in CO 2 amplifiers and their propagation through arbitrary optical systems. This code is based on a comprehensive model that includes an accurate consideration of the CO 2 active medium and a physical optics propagation algorithm, and takes into account the interaction of the laser pulse with the material of the optical elements. Finally, the application of the code for optimizing an isotopic regenerative amplifier is described.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

HPC4Energy Final Report : GE Energy

Power System planning tools are being used today to simulate systems that are far larger and more complex than just a few years ago. Advances in renewable technologies and more pervasive control technology are driving planning engineers to analyze an increasing number of scenarios and system models with much more detailed network representations. Although the speed of individual CPU’s has increased roughly according to Moore’s Law, the requirements for advanced models, increased system sizes, and larger sensitivities have outstripped CPU performance. This computational dilemma has reached a critical point and the industry needs to develop the technology to accurately model the power system of the future. The hpc4energy incubator program provided a unique opportunity to leverage the HPC resources available to LLNL and the power systems domain expertise of GE Energy to enhance the GE Concorda PSLF software. Well over 500 users worldwide, including all of the major California electric utilities, rely on Concorda PSLF software for their power flow and dynamics. This pilot project demonstrated that the GE Concorda PSLF software can perform contingency analysis in a massively parallel environment to significantly reduce the time to results. An analysis with 4,127 contingencies that would take 24 days on a single core was reduced to 24 minutes when run on 4,217 cores. A secondary goal of this project was to develop and test modeling techniques that will expand the computational capability of PSLF to efficiently deal with systems sizes greater than 150,000 buses. Toward this goal the matrix reordering implementation time was sped up 9.5 times by optimizing the code and introducing threading.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗