Results for “code sharing” — Page 9

NASA NTRS2005

Parallelization of Lower-Upper Symmetric Gauss-Seidel Method for Chemically Reacting Flow

Development of technologies for exploration of the solar system has revived an interest in computational simulation of chemically reacting flows since planetary probe vehicles exhibit non-equilibrium phenomena during the atmospheric entry of a planet or a moon as well as the reentry to the Earth. Stability in combustion is essential for new propulsion systems. Numerical solution of real-gas flows often increases computational work by an order-of-magnitude compared to perfect gas flow partly because of the increased complexity of equations to solve. Recently, as part of Project Columbia, NASA has integrated a cluster of interconnected SGI Altix systems to provide a ten-fold increase in current supercomputing capacity that includes an SGI Origin system. Both the new and existing machines are based on cache coherent non-uniform memory access architecture. Lower-Upper Symmetric Gauss-Seidel (LU-SGS) relaxation method has been implemented into both perfect and real gas flow codes including Real-Gas Aerodynamic Simulator (RGAS). However, the vectorized RGAS code runs inefficiently on cache-based shared-memory machines such as SGI system. Parallelization of a Gauss-Seidel method is nontrivial due to its sequential nature. The LU-SGS method has been vectorized on an oblique plane in INS3D-LU code that has been one of the base codes for NAS Parallel benchmarks. The oblique plane has been called a hyperplane by computer scientists. It is straightforward to parallelize a Gauss-Seidel method by partitioning the hyperplanes once they are formed. Another way of parallelization is to schedule processors like a pipeline using software. Both hyperplane and pipeline methods have been implemented using openMP directives. The present paper reports the performance of the parallelized RGAS code on SGI Origin and Altix systems.

Yoon, Seokkwan↗

DOE OSTI2016

SMT-Aware Instantaneous Footprint Optimization

Modern architectures employ simultaneous multithreading (SMT) to increase thread-level parallelism. SMT threads share many functional units and the whole memory hierarchy of a physical core. Without a careful code design, SMT threads can easily contend with each other for these shared resources, causing severe performance degradation. Minimizing SMT thread contention for HPC applications running on dedicated platforms is very challenging, because they usually spawn threads within Single Program Multiple Data (SPMD) models. To address this important issue, we introduce a simple scheme for SMT-aware code optimization, which aims to reduce the memory contention across SMT threads.

Instantaneous Footprint↗

DOE OSTI2021

Enhancements supporting IC usage of PEM libraries on next-gen platforms

This milestone reports on the culmination of several years of effort by multiple PEM support software development teams to provide capabilities for use in LLNL-developed integrated codes on next-gen ASC platforms, including GPU support. We will provide a survey of relevant Application Program Interfaces (API) that are required to support LLNL IC code capability on relevant architectures, with a focus on Sierra and El Capitan. We will identify and summarize all dependencies between PEM supported libraries and IC supported physics codes. We will provide an assessment of algorithmic improvements that have been deployed, as well as future developments that are required to complete the GPU porting efforts. This assessment will include a description of programming models adopted by each of the PEM projects, distinct algorithmic challenges for each of the capabilities, and information about sharing GPU memory between the APIs and host codes. We will develop targeted test problems to assess computational performance. Finally, this milestone will result in identification of gaps in our effort to assist the LLNL ASC program in prioritization of effort for porting software to El Capitan.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Two NHX‐type transporters from Helianthus tuberosus improve the tolerance of rice to salinity and nutrient deficiency stress

Summary The NHX‐type cation/H + transporters in plants have been shown to mediate Na + (K + )/H + exchange for salinity tolerance and K + homoeostasis. In this study, we identified and characterized two NHX homologues, HtNHX1 and HtNHX2 from an infertile and salinity tolerant species Helianthus tuberosus (cv. Nanyu No. 1). HtNHX1 and HtNHX2 share identical 5′‐ and 3′‐UTR and coding regions, except for a 342‐bp segment encoding 114 amino acids (L 272 to Q 385 ) which is absent in HtNHX2 . Both hydroponics and soil culture experiments showed that the expression of HtNHX1 or HtNHX2 improved the rice tolerance to salinity. Expression of HtNHX2 , but not HtNHX1 , increased rice grain yield, harvest index, total nutrient uptake under K + ‐limited salt‐stress or general nutrient deficiency conditions. The results provide a novel insight into NHX function in plant mineral nutrition.

Zeng, Yang↗

DOE OSTI2015

A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Texas A&M University in the JET Collaboration - Final Report

This final report summarizes the work done by PIs at Texas A&M University within the JET Topical Collaboration. The main focus of the group at Texas A&M has been the development and implementation of a hadronization model suitable to calculate hadronization of jet showers in heavy ion collisions event by event. The group successfully developed a hybrid model of parton recombination and remnant string fragmentation including recombination with thermal partons. A code realizing this model was developed and shared with other JET members. In addition, the group at Texas A&M worked on both open and hidden heavy flavor probes. In particular, they developed a description of heavy flavor hadronization based on recombination, and consistent with in-medium scattering rates of heavy quarks, and suggested the D s meson as a precise probe of the hadronization mechanism. Another noteworthy focus of their work was electromagnetic probes, in particular, dileptons and photons from interactions of jets with the medium. In the soft sector the group has made several contributions to modern topics, e.g. the splitting of elliptic flow between isospin partners and the role of the initial strong gluon fields.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

SIERRA Multimechanics Module: Aria Thermal Theory Manual - Version 4.50.

This document describes the theoretical foundation of thermal analysis in Sierra Mechanics. The SIERRA Multimechanics Module: Aria, henceforth referred to as Aria for brevity, was developed at Sandia National Laboratories under the ASC program, and approximates linear and nonlinear continuum models of heat transfer. Aria uses the SIERRA Framework, which provides data management services commonly required by computational mechanics software, and facilitates the development of coupled, multi-mechanics applications for massively parallel computers. The mathematical models in Aria are based heavily on those of COYOTE, a well-established thermal analysis program that was also developed at Sandia and its ASC code predecessor, Calore. Aria, Calore and COYOTE share a significant body of numerical methods, which are described in detail by Reddy and Gartling. Throughout this document, the terms software and implementation are synonymous with the Aria thermal-fluid analysis computer program. Whether one uses Aria to perform heat transfer analysis, or in developing a new capability for the Aria application, this document provides the information needed understand the existing numerical algorithm implementations. Justification for the fundamental assumptions of heat transfer, nor derivation of the energy conservation equations are included in this document. For a more thorough theoretical background, one is referred to one of the many available textbooks, e.g. Another reference, which is freely available in downloadable electronic form, is Lienhard and Lienhard.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

SIERRA Multimechanics Module: Aria Thermal Theory Manual - Version 4.48

This document describes the theoretical foundation of thermal analysis in Sierra Mechanics. The SIERRA Multimechanics Module: Aria, henceforth referred to as Aria for brevity, was developed at Sandia National Laboratories under the ASC program, and approximates linear and nonlinear continuum models of heat transfer. Aria uses the SIERRA Framework, which provides data management services commonly required by computational mechanics software, and facilitates the development of coupled, multi-mechanics applications for massively parallel computers. The mathematical models in Aria are based heavily on those of COYOTE, a well-established thermal analysis program that was also developed at Sandia and its ASC code predecessor, Calore. Aria, Calore and COYOTE share a significant body of numerical methods, which are described in detail by Reddy and Gartling. Throughout this document, the terms software and implementation are syn onymous with the Aria thermal-fluid analysis computer program. Whether one uses Aria to perform heat transfer analysis, or in developing a new capability for the Aria application, this document provides the information needed understand the existing numerical algorithm implementations. Justification for the fundamental assumptions of heat transfer, nor derivation of the energy conservation equations are included in this document. For a more thorough theoretical background, one is referred to one of the many available textbooks, e.g. Another reference, which is freely available in downloadable electronic form, is Lienhard and Lienhard.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

SIERRA Multimechanics Module: Aria Thermal Theory Manual (Version 4.46)

This document describes the theoretical foundation of thermal analysis in Sierra Mechanics. The SIERRA Multimechanics Module: Aria, henceforth referred to as Aria for brevity, was developed at Sandia National Laboratories under the ASC program, and approximates linear and nonlinear continuum models of heat transfer. Aria uses the SIERRA Framework, which provides data management services commonly required by computational mechanics software, and facilitates the development of coupled, multi-mechanics applications for massively parallel computers. The mathematical models in Aria are based heavily on those of COYOTE, a well-established thermal analysis program that was also developed at Sandia and its ASC code predecessor, Calore. Aria, Calore and COYOTE share a significant body of numerical methods, which are described in detail by Reddy and Gartling. Throughout this document, the terms software and implementation are synonymous with the Aria thermal-fluid analysis computer program.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

SIERRA Multimechanics Module: Aria Thermal Theory Manual (Version 4.44)

This document describes the theoretical foundation of thermal analysis in Sierra Mechanics. The SIERRA Multimechanics Module: Aria, henceforth referred to as Aria for brevity, was developed at Sandia National Laboratories under the ASC program, and approximates linear and nonlinear continuum models of heat transfer. Aria uses the SIERRA Framework, which provides data management services commonly required by computational mechanics software, and facilitates the development of coupled, multi-mechanics applications for massively parallel computers. The mathematical models in Aria are based heavily on those of COYOTE, a well-established thermal analysis program that was also developed at Sandia and its ASC code predecessor, Calore. Aria, Calore and COYOTE share a significant body of numerical methods, which are described in detail by Reddy and Gartling. Throughout this document, the terms software and implementation are synonymous with the Aria thermal-fluid analysis computer program.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

SIERRA Multimechanics Module: Aria Thermal Theory Manual (Version 4.42)

This document describes the theoretical foundation of thermal analysis in Sierra Mechanics. The SIERRA Multimechanics Module: Aria, henceforth referred to as Aria for brevity, was developed at Sandia National Laboratories under the ASC program, and approximates linear and nonlinear continuum models of heat transfer. Aria uses the SIERRA Framework, which provides data management services commonly required by computational mechanics software, and facilitates the development of coupled, multi-mechanics applications for massively parallel computers. The mathematical models in Aria are based heavily on those of COYOTE, a well-established thermal analysis program that was also developed at Sandia and its ASC code predecessor, Calore. Aria, Calore and COYOTE share a significant body of numerical methods, which are described in detail by Reddy and Gartling. Throughout this document, the terms software and implementation are synonymous with the Aria thermal-fluid analysis computer program.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

2025 TEM Workshop

The TEM Data Management Workshop will take place on August 26 from 9 a.m. to 12 p.m. MT, and will be held virtually on TEAMS. The primary goal of this workshop is to engage NSUF users and stakeholders in discussions about the data needs for the utilization of AI and ML in the analysis of TEM data. Key topics to be covered include data storage, data sharing, data tagging, metadata inclusion, standardized data formats, data augmentation, and annotated training datasets. Additionally, the workshop will provide valuable insights into resources such as the Nuclear Research Data System (NRDS) for data storage and sharing, as well as open-source codes for data analysis.

Bachhav, Mukesh↗

NASA NTRS1985

Parallel computation with the force

A methodology, called the force, supports the construction of programs to be executed in parallel by a force of processes. The number of processes in the force is unspecified, but potentially very large. The force idea is embodied in a set of macros which produce multiproceossor FORTRAN code and has been studied on two shared memory multiprocessors of fairly different character. The method has simplified the writing of highly parallel programs within a limited class of parallel algorithms and is being extended to cover a broader class. The individual parallel constructs which comprise the force methodology are discussed. Of central concern are their semantics, implementation on different architectures and performance implications.

Jordan, H. F.↗

DOE OSTI2022

Review of the U.S. Policies, Codes, and Standards of Zero-Carbon Buildings

The global issue of climate change has accelerated the international commitment to net-zero carbon emission development. Decarbonizing the building sector has been put on several governments’ sustainable development agendas. To provide a reference for decarbonizing the building sector, this paper summarizes the U.S. experience in zero-carbon buildings (ZCBs) from the aspects of policies, codes, and standards at the federal and local levels and those of professional societies. Based on the definition and boundaries of ZCBs, this paper introduces policies on building energy efficiency, electrification, on-site renewable energy deployment, and “buy clean”, illustrating highlights in building phases, energy systems, materials production, and fiscal incentives. The synergic efforts and coordination between federal and local levels and with professional societies are also introduced. Successful experiences in policy and standard implementation are summarized, including the systemic work of multilevel governance, clearly defined goals and stringent policies, constant upgrades of codes and standards, transparency in reporting and information sharing, and increased financial and investment opportunities. This paper provides concrete recommendations for developing zero-carbon building policies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NASA NTRS2000

Message Passing vs. Shared Address Space on a Cluster of SMPs

The convergence of scalable computer architectures using clusters of PCs (or PC-SMPs) with commodity networking has become an attractive platform for high end scientific computing. Currently, message-passing and shared address space (SAS) are the two leading programming paradigms for these systems. Message-passing has been standardized with MPI, and is the most common and mature programming approach. However message-passing code development can be extremely difficult, especially for irregular structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality, and high protocol overhead. In this paper, we compare the performance of and programming effort, required for six applications under both programming models on a 32 CPU PC-SMP cluster. Our application suite consists of codes that typically do not exhibit high efficiency under shared memory programming. due to their high communication to computation ratios and complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications: however, on certain classes of problems SAS performance is competitive with MPI. We also present new algorithms for improving the PC cluster performance of MPI collective operations.

Shan, Hongzhang↗

DOE OSTI2016

The Effects of Different Lattice Codes on Results of Sensitivity and Uncertainty Analysis

According to the UAM ('Uncertainty Analysis in Modeling') benchmark, uncertainties in the LWR system calculations at all stages should be determined and quantified. As the neutronics calculations are prerequisite for the predictions of the reactor system, and the uncertainties introduced by the neutronics calculations would be propagated to the subsequent calculations, hence uncertainty analysis has been firstly focused on the neutronics phase to quantify the uncertainties of the reactor-physics predictions in UAM. For the lattice physics, the objective of uncertainty analysis is focused on uncertainty quantifications of the few-group constants; for the core physics, uncertainties of the core steady-state stand-alone neutronics calculations are focused on. Based on the previous researches, the nuclear-data uncertainty has been treated as one of the most significant source of uncertainty and received the most focus. In the previous works, the domestic code UNICORN has the capability of performing sensitivity analysis and uncertainty analysis using the direct numerical perturbation (DNP) method and statistical sampling (SS) method. In this paper, the capability of the UNICORN code has been improved. The domestic lattice code NECP-CACTI has been added in UNICORN to perform the lattice calculations, with DRAGON5.0 and NECP-CACTI available for lattice calculations. For DRAGON5.0 and NECP-CACTI, all the methods and technologies are shared in UNICORN. Therefore, the effects of different lattice codes on the results of sensitivity and uncertainty analysis have been researched and determined in this paper. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

NASA NTRS2002

Message Passing and Shared Address Space Parallelism on an SMP Cluster

Currently, message passing (MP) and shared address space (SAS) are the two leading parallel programming paradigms. MP has been standardized with MPI, and is the more common and mature approach; however, code development can be extremely difficult, especially for irregularly structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality and high protocol overhead. In this paper, we compare the performance of and the programming effort required for six applications under both programming models on a 32-processor PC-SMP cluster, a platform that is becoming increasingly attractive for high-end scientific computing. Our application suite consists of codes that typically do not exhibit scalable performance under shared-memory programming due to their high communication-to-computation ratios and/or complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications, while being competitive for the others. A hybrid MPI+SAS strategy shows only a small performance advantage over pure MPI in some cases. Finally, improved implementations of two MPI collective operations on PC-SMP clusters are presented.

Shan, Hongzhang↗

NASA NTRS1999

Field Encapsulation Library The FEL 2.2 User Guide

This document describes version 2.2 of the Field Encapsulation Library (FEL), a library of mesh and field classes. FEL is a library for programmers - it is a "building block" enabling the rapid development of applications by a user. Since FEL is a library intended for code development, it is essential that enough technical detail be provided so that one can make full use of the code. Providing such detail requires some assumptions with respect to the reader's familiarity with the library implementation language, C++, particularly C++ with templates. We have done our best to make the explanations accessible to those who may not be completely C++ literate. Nevertheless, familiarity with the language will certainly help one's understanding of how and why things work the way they do. One consolation is that the level of understanding essential for using the library is significantly less than the level that one should have in order to modify or extend the library. One more remark on C++ templates: Templates have been a source of both joy and frustration for us. The frustration stems from the lack of mature or complete implementations that one has to work with. Template problems rear their ugly head particularly when porting. When porting C code, successfully compiling to a set of object files typically means that one is almost done. With templated C++ and the current state of the compilers and linkers, generating the object files is often only the beginning of the fun. On the other hand, templates are quite powerful. Used judiciously, templates enable more succinct designs and more efficient code. Templates also help with code maintenance. Designers can avoid creating objects that are the same in many respects, but not exactly the same. For example, FEL fields are templated by node type, thus the code for scalar fields and vector fields is shared. Furthermore, node type templating allows the library user to instantiate fields with data types not provided by the FEL authors. This type of flexibility would be difficult to offer without the support of the language. For users who may be having template-related problems, we offer the consolation that support for C++ templates is destined to improve with time. Efforts such as the Standard Template Library (STL) will inevitably drive vendors to provide more thorough, optimized tools for template code development. Furthermore, the benefits will become harder to resist for those who currently subscribe to the least-common-denominator "code it all in C" strategy. May FEL bring you both increased productivity and aesthetic satisfaction.

Moran, Patrick J.↗