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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-F-T-348: The Impact of Model Library Population On RapidPlan Based Dose-Volume Histograms (DVHs) Prediction for Rectal Cancer Patients Treated with Volumetric-Modulated Radiotherapy (VMAT)

Purpose: RapidPlan uses a library consisting of expert plans from different patients to create a model that can predict achievable dose-volume histograms (DVHs) for new patients. The goal of this study is to investigate the impacts of model library population (plan numbers) on the DVH prediction for rectal cancer patients treated with volumetric-modulated radiotherapy (VMAT) Methods: Ninety clinically accepted rectal cancer patients’ VMAT plans were selected to establish 3 models, named as Model30, Model60 and Model90, with 30,60, and 90 plans in the model training. All plans had sufficient target coverage and bladder and femora sparings. Additional 10 patients were enrolled to test the DVH prediction differences with these 3 models. The predicted DVHs from these 3 models were compared and analyzed. Results: Predicted V40 (Vx, percent of volume that received x Gy for the organs at risk) and Dmean (mean dose, cGy) of the bladder were 39.84±13.38 and 2029.4±141.6 for the Model30,37.52±16.00 and 2012.5±152.2 for the Model60, and 36.33±18.35 and 2066.5±174.3 for the Model90. Predicted V30 and Dmean of the left femur were 23.33±9.96 and 1443.3±114.5 for the Model30, 21.83±5.75 and 1436.6±61.9 for the Model60, and 20.31±4.6 and 1415.0±52.4 for the Model90.There were no significant differences among the 3 models for the bladder and left femur predictions. Predicted V40 and Dmean of the right femur were 19.86±10.00 and 1403.6±115.6 (Model30),18.97±6.19 and 1401.9±68.78 (Model60), and 21.08±7.82 and 1424.0±85.3 (Model90). Although a slight lower DVH prediction of the right femur was found on the Model60, the mean differences for V30 and mean dose were less than 2% and 1%, respectively. Conclusion: There were no significant differences among Model30, Model60 and Model90 for predicting DVHs on rectal patients treated with VMAT. The impact of plan numbers for model library might be limited for cancers with similar target shape.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

MatRIS: Multi-level Math Library Abstraction for Heterogeneity and Performance Portability using IRIS Runtime

Vendor libraries are tuned for a specific architecture and are not portable to others. Moreover, they lack support for heterogeneity and multi-device orchestration, which is required for efficient use of contemporary HPC and cloud resources. To address these challenges, we introduce MatRIS—a multilevel math library abstraction for scalable and performance-portable sparse/dense BLAS/LAPACK operations using IRIS runtime. The MatRIS-IRIS co-design introduces three levels of abstraction to make the implementation completely architecture agnostic and provide highly productive programming. We demonstrate that MatRIS is portable without any change in source code and can fully utilize multi-device heterogeneous systems by achieving high performance and scalability on Summit, Frontier, and a CADES cloud node equipped with four NVIDIA A100 GPUs and four AMD MI100 GPUs. A detailed performance study is presented in which MatRIS demonstrates multi-device scalability. When compared, MatRIS provides competitive and even better performance than libraries from vendors and other third parties.

Monil, M. A. H.↗
DOE OSTI2025

The ArborX Library: Version 2.0

This article provides an overview of the 2.0 release of the ArborX library, a performance portable geometric search library based on Kokkos. We describe the major changes in ArborX 2.0 including a new interface for the library to support a wider range of user problems, new search data structures (brute force and distributed), support for user functions to be executed on the results (callbacks), and an expanded set of the supported algorithms (ray tracing and clustering).

GPU↗
DOE OSTI2015

Tensor Algebra Library for NVidia Graphics Processing Units

This is a general purpose math library implementing basic tensor algebra operations on NVidia GPU accelerators. This software is a tensor algebra library that can perform basic tensor algebra operations, including tensor contractions, tensor products, tensor additions, etc., on NVidia GPU accelerators, asynchronously with respect to the CPU host. It supports a simultaneous use of multiple NVidia GPUs. Each asynchronous API function returns a handle which can later be used for querying the completion of the corresponding tensor algebra operation on a specific GPU. The tensors participating in a particular tensor operation are assumed to be stored in local RAM of a node or GPU RAM. The main research area where this library can be utilized is the quantum many-body theory (e.g., in electronic structure theory).

Liakh, Dmitry↗
DOE OSTI2019

Modelica IBPSA MPC Library v0.1

The Modelica IBPSA MPC Library is a free open-source library with basic models that codify best practices for the implementation of models to be used in Nonlinear Model Predictive Control of building and community energy systems. The development of the Modelica IBPSA MPC Library is organized through the IBPSA Project 1 (https://ibpsa.github.io/project1) of the International Building Performance Simulation Association (IBPSA).

Blum, David↗
DOE OSTI2018

CSlib, a library to couple codes via Client/Server messaging

The CSlib is a small, portable library which enables two (or more) independent simulation codes to be coupled, by exchanging messages with each other. Both codes link to the library when they are built, and can them communicate with each other as they run. The messages contain data or instructions that the two codes send back-and-forth to each other. The messaging can take place via files, sockets, or MPI. The latter is a standard distributed-memory message-passing library.

Plimpton, Steve↗
DOE OSTI2018

fftMPI, a library for performing 2d and 3d FFTs in parallel

The fftMPI library enables two and three dimensional Fast Fourier Transforms (FFTs) to be performed efficiently in parallel on a variety of platforms from desktop machines to supercomputers. It allows for flexibility in the initial distribution of the FFT grid across processors, as well as the final output. It handles the data communication and reordering necessary to perform multi-dimensional FFTs in parallel. It relies on open-source or vendor-provided libraries to perform one dimensional FFTs on a single processor. It uses MPI for inter-processor communication, which is a standard distributed memory message-passing library.

Plimpton, Steven↗
DOE OSTI2021

Optimization Plugin Library

The Optimization Plugin library ("op") is a lightweight general optimization solver interface. The primary purpose of op is to simplify the process of integrating different optimization solvers (serial or parallel) with scalable parallel physics engines. By design it has several features that help make this a reality. The core abstraction interface was developed to encompass a large class of optimization problems in an optimizer-agnostic way. This enables us to describe the optimization problem once and then use a variety of supported "op" optimizers with ideally no code-changes. The abstraction interface is made up of lightweight wrappers that make it easy to integrate with existing simulation codes. This makes integration less intrusive and should minimize changes to existing physics codes. The "op" interface includes an assortment of utility methods that help specify parallel communication patterns as well as methods to convert from optimization-specific interfaces to the more general "op" interface. Lastly a dynamic library linking interface is provided to allow for use of proprietary optimization engines without explicit reference in the source code, along with standard shared library interfaces for opensource engines.

Jekel, CharlesF↗
DOE OSTI2023

Demand Flexibility Controls Library using Semantics (DFLEXLIBS) v0.1

DFLEXLIBS is a library/repository of HVAC-based demand flexibility control applications developed using Python. The library is based on portable control applications that exclusively contain control logic and are abstract to building details, such as point names and communication protocols. The library leverages semantic models and control platform-oriented interfaces to configure and run the controls in specific buildings. To date, the library contains two applications and two interfaces (for BOPTEST and VOLTTRON) and has been demonstrated in five heterogeneous buildings.

Paul, Lazlo↗
DOE OSTI2024

Polyglot C Library

The C library component of Polyglot. Polyglot utilizes a combination of custom and open source tools and libraries to provide developers with a consistent environment for building tools, etc. for a wide variety of targets with minimal changes to the code being built. It supports a variety of architectures and operating systems/firmware in as target-agnostic way as possible. This allows for developers to minimize the amount of time/effort required to port tools-in particular, forensic tools-to a wide variety of targets. The project is comprised of two main components: a frontend toolchain that understands how to utilize other tools in order to build code for a specific target, and a minimalistic C library specific to Polyglot. These collectively provide the method to build code for a specific target, and the capability for code to interact with the underlying operating system when run on the target. Both components are written in a way to minimize the amount of target-specific knowledge required to both develop and utilize the project.

Huddleston, TimothyA.↗
DOE OSTI2025

Generic Discretization Library

The GenDiL library is a collection of C++ software abstractions designed to discretize and solve partial differential equations (PDEs) for high-performance computing (HPC) applications. Its primary focus is on modern C++ generic programming, which helps ensure portability across various hardware architectures. The central idea behind the library is to provide building blocks for numerical algorithms-such as discretization methods and iteration patterns-so that domain experts can focus on the math, rather than the low-level details of hardware or implementation. By defining abstractions for data types, iteration over computational grids, and scheduling of operations, the library isolates the high-level PDE algorithms from the platform-specific optimizations needed to achieve efficient performance.

Dudouit, Yohann [Lawrence Livermore National Labor↗
DOE OSTI2026

Geophysical Monitoring Program Core Seismic Libraries

The Geophysical Monitoring Program Core Seismic Libraries contain a broad array of seismic and waveform analysis libraries useful for a wide range of seismic analysis processes. These include signal processing, travel time calculation, waveform correlation, array processing, geometry and geodesy, and plotting libraries.

Barno, JustinG [Lawrence Livermore National Labora↗
DOE OSTI2016

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods

Background: 3’ RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and the 3' method is needed to determine their relative merits. To this end, we used two commercially available library preparation kits, the KAPA Stranded mRNA-Seq kit (traditional method) and the Lexogen QuantSeq 3’ mRNASeq kit (3' method), to prepare libraries from mouse liver RNA. We then sequenced and analyzed the libraries to determine the advantages and disadvantages of these two approaches. Results: We found that the traditional whole transcript method and the 3’ RNA-Seq method had similar levels of reproducibility. As expected, the whole transcript method assigned more reads to longer transcripts, while the 3' method assigned roughly equal numbers of reads to transcripts regardless of their lengths. We found that the 3’ RNA-Seq method detected more short transcripts than the whole transcript method. With regard to differential expression analysis, we found that the whole transcript method detected more differentially expressed genes, regardless of the level of sequencing depth. Conclusions: The 3’ RNA-Seq method was better able to detect short transcripts, while the whole transcript RNA-Seq was able to detect more differentially expressed.

3’ RNA-Seq↗
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

FY2012 Status Report on Subgroup Library Development

The goal of SHARP is to develop a suite of modern simulation tools for use on all reactor types of interest. Part of that desire is to build a heterogeneous neutron transport capability which gives accurate, detailed power distributions throughout the entire reactor core, of which we have focused our efforts on deterministic methodologies. The existing SHARP neutronics tool has demonstrated good accuracy when using conventional homogeneous modeling, but when applied on fully heterogeneous problems such as the Advanced Test Reactor (ATR) and Zero Power Reactors (ZPR), the results were not acceptable. These errors are primary attributable to the use of a three step cross section generation procedure (unit cell, lattice, and whole core). Given the success of the DeCART tool on thermal spectrum systems such as PWR, BWR, and VHTR, the subgroup methodology was identified as a potential means by which to resolve the cross section related problems in the NEAMS tools. The subgroup project in NEAMS is thus focused on creating a general purpose cross section methodology that is usable on both thermal and fast spectrum systems. The subgroup methodology is a well studied scheme appearing very early in the nuclear engineering literature. We investigated using the subgroup methodology as a potential means to handle fast reactor problems. A considerable amount of work was performed on the subgroup library software for NEAMS where several subgroup formulations were investigated. Further, while the subgroup method has been demonstrated to be accurate enough on several problems via our own experiences with DeCART, it is not clear what its accuracy will be on more complicated problems such as the ATR. In any case, one must have a capability to generate a library in which subgroup parameters can cover neutron spectrum characteristics of the reactor of interest. For better accuracy, we propose to use MCNP as an alternative pin-cell calculation means of generating the subgroup data and have developed a prototype code package to demonstrate the capability. With regard to fast spectrum systems, there are numerous concerns with the subgroup methodology in which the conventional Bondarenko iteration approach often used would not accurately handle the resonance interference effect that becomes more complex and important in a fast reactor. An alternative methodology involving the local escape cross section looks promising, but substantial research needs to be completed and a basic algorithm tested before success can be confirmed. Overall, the creation of a subgroup library application was not finished, primarily due to the fact that a bulk of the funding was moved into the next fiscal year. A better understanding of the underlying methodology was gained and a means by which to generate subgroup data was created. The work on the subgroup method for an

Smith, M. A.↗
DOE OSTI2012

Guidance on Selection of Cross Section Libraries and Elemental Isotopic Percentages for use with MCNP5 in Criticality Safety Calculations

This memo is a guide for the use of cross section libraries, isotopic percentages and densities with MCNP5 in criticality safety calculations. Because there are numerous libraries to choose from, a subset of libraries is recommended for use by the criticality safety group. Likewise, the selection of isotopic percentages and densities for each element are suggested. The National Nuclear Data Center is the source of information contained in this document unless otherwise specified.

General & Miscellaneous(99)↗
DOE OSTI2012

Analysis of differences in the ENDL99 and ENDL2009 nuclear data libraries pertaining to 238 U

A careful analysis is performed on the differences exhibited in the evaluated elastic and inelastic channels between the ENDL99 and ENDL2009 libraries for neutrons incident on 238 U. The two libraries are compared with experimental data as well as results obtained from calculations utilizing a new Hauser-Feshbach reaction code and two modern, high-quality optical potentials. Overall, the ENDL2009 evaluation is found to be more physical, and a better representation of experimental data. The only exception is that the angular distributions for the elastic channel in the ENDL99 library are in better agreement at backward angles for incident neutron energies in the range 0.7-1.3 MeV. Other issues with the inelastic scattering data in ENDL2009 are pointed out.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗