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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

OpenSoC Fabric

Recent advancements in technology scaling have shown a trend towards greater integration with large-scale chips containing thousands of processors connected to memories and other I/O devices using non-trivial network topologies. Software simulation proves insufficient to study the tradeoffs in such complex systems due to slow execution time, whereas hardware RTL development is too time-consuming. We present OpenSoC Fabric, an on-chip network generation infrastructure which aims to provide a parameterizable and powerful on-chip network generator for evaluating future high performance computing architectures based on SoC technology. OpenSoC Fabric leverages a new hardware DSL, Chisel, which contains powerful abstractions provided by its base language, Scala, and generates both software (C++) and hardware (Verilog) models from a single code base. The OpenSoC Fabric2 infrastructure is modeled after existing state-of-the-art simulators, offers large and powerful collections of configuration options, and follows object-oriented design and functional programming to make functionality extension as easy as possible.

Source record↗
DOE OSTI2017

DCA_Tools

HPC software for ab-initio, condensed-matter physics, quantum mechanics calculations needs to be built on top of well tested libraries some of which address requirements unique to the programming domain. During the development of the DCA++ code, that we use in our research, we have developed a collection of libraries that may be of use to other computational scientists working in the same or similar domains. The libraries include: a) a pythonic input-language system, b) tensors whose shape is constructed from generalized dimension objects such at time domains. frequency domains, momentum domains, vertex domains et. al. and c) linear algebra operations that resolve to BLA/LAPACK operations when possible. This supports the implementation of Greens functions and operations on them such as are used in condensed matter physics.

Summers, Michael S↗
DOE OSTI2023

A Fine-grained Asynchronous Bulk Synchronous parallelism model for PGAS applications

The Partitioned Global Address Space (PGAS) model is well suited for executing irregular applications on cluster-based systems, due to its efficient support for short, one-sided messages. Separately, the actor model has been gaining popularity as a productive asynchronous message-passing approach for distributed objects in enterprise and cloud computing platforms, typically implemented in languages such as Erlang, Scala or Rust. To the best of our knowledge, there has been no past work on using the actor model to deliver both productivity and scalability to irregular PGAS applications with large number of small messages. In this paper, we introduce a new programming system for PGAS applications, in which point-to-point remote operations can be expressed as fine-grained asynchronous actor messages. In our approach, the programmer does not need to worry about programming complexities related to message aggregation and termination detection. Our approach can be viewed as extending the classical Bulk Synchronous Parallelism model with fine-grained asynchronous communications within a phase or superstep. Here, we believe that our approach offers a desirable point in the productivity-performance space for PGAS applications, with more scalable performance and higher productivity relative to past approaches. Specifically, for seven irregular mini-applications from the Bale Kernels and three graph kernels executed using 2048 cores in the NERSC Cori system, our approach shows geometric mean performance improvements of ≥ 20X relative to standard PGAS versions (UPC and OpenSHMEM) while maintaining comparable productivity to those versions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

A high performance cost-effective digital complex correlator for an X-band polarimetry survey

The detailed knowledge of the Milky Way radio emission is important to characterize galactic foregrounds masking extragalactic and cosmological signals. The update of the global sky models describing radio emissions over a very large spectral band requires high sensitivity experiments capable of observing large sky areas with long integration times. Here, we present the design of a new 10 GHz (X-band) polarimeter digital backend to map the polarization components of the galactic synchrotron radiation field of the Northern Hemisphere sky. The design follows the digital processing trends in radio astronomy and implements a large bandwidth (1 GHz) digital complex cross-correlator to extract the Stokes parameters of the incoming synchrotron radiation field. The hardware constraints cover the implemented VLSI hardware description language code and the preliminary results. The implementation is based on the simultaneous digitized acquisition of the Cartesian components of the two linear receiver polarization channels. The design strategy involves a double data rate acquisition of the ADC interleaved parallel bus, and field programmable gate array device programming at the register transfer mode. The digital core of the back-end is capable of processing 32 Gbps and is built around an Altera field programmable gate array clocked at 250 MHz, 1 GSps analog to digital converters and a clock generator. The control of the field programmable gate array internal signal delays and a convenient use of its phase locked loops provide the timing requirements to achieve the target bandwidths and sensitivity. This solution is convenient for radio astronomy experiments requiring large bandwidth, high functionality, high volume availability and low cost. Of particular interest, this correlator was developed for the Galactic Emission Mapping project and is suitable for large sky area polarization continuum surveys. The solutions may also be adapted to be used at signal processing subsystem levels for large projects like the square kilometer array testbeds.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A RESTful API for accessing microbial community data for MG-RAST

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MPI nuts and bolts and more [Slides]

MPI (Message-Passing Interface) is a message-passing library interface specification. All parts of this definition are significant. MPI addresses primarily the message-passing parallel programming model, in which data is moved from the address space of one process to that of another process through cooperative operations on each process. . . MPI is a specification, not an implementation; there are multiple implementations of MPI. This specification is for a library interface; MPI is not a language, and all MPI operations are expressed as functions, subroutines, or methods, according to the appropriate language bindings that, for C and Fortran, are part of the MPI standard. MPI Forum is the organization which is responsible for the MPI Specification.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

ECP SOLLVE: Validation and Verification Testsuite Status Update and Compiler Insight for OpenMP

The OpenMP language continues to evolve with every new specification release, as does the need to validate and verify the new features that have been implemented by the different vendors. With the release of OpenMP 5.0 and OpenMP 5.1, new target offload and host-based features have been introduced to the programming model. While OpenMP continues to grow in maturity, there is an observable growth in the number of compiler and hardware vendors that support OpenMP. In this manuscript, the main focus is on evaluating the conformity and OpenMP implementation progress of various compiler vendors such as Cray, IBM, GNU, Clang/LLVM, NVIDIA, and Intel. More specifically, the 4.5, 5.0, and 5.1 versions of the OpenMP specification are analyzed. For our experimental setup, the Crusher and Summit computing systems hosted by Oak Ridge National Lab’s Computing Facilities are utilized. The effort of vendor agnostic analysis of these implementations is especially valuable for application developers who are using new OpenMP features to accelerate their scientific codes. Insights are presented into the current implementation status of various vendors, the progression of specific compiler’s support for OpenMP overtime, the subset of OpenMP 4.5, 5.0, and 5.1 that is supported by all compilers, and examples of how our test suite has influenced discussion regarding the correct interpretation of the OpenMP specification. By evaluating OpenMP conformity of pre-Exascale computing systems, the aim is to detail progress and status of AMD + Cray ecosystem before the system and their OpenMP implementation is used for mission critical applications when the first Exascale Computer Frontier is made available to applications.

Huber, Thomas↗
DOE OSTI2012

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. We have developed a semi-automatic, web-based platform (MicrobesFlux) for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites) of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes) and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language). Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions) for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG database. Our system facilitates users to reconstruct metabolic networks of organisms based on experimental information. Through human-computer interaction, MicrobesFlux provides users with reasonable predictions of microbial metabolism via flux balance analysis. This prototype platform can be a springboard for advanced and broad-scope modeling of complex biological systems by integrating other “omics” data or 13 C- metabolic flux analysis results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Communicating with future generations - Major obstacles to overcome - 15009

The Department of Energy (DOE) Carlsbad Field Office (CBFO) is responsible for managing activities related to the disposal of transuranic (TRU) and TRU-mixed waste in the geologic repository at the Waste Isolation Pilot Plant (WIPP), 2150 feet (655 meters) below the land surface, at the WIPP, near Carlsbad, New Mexico. The Environmental Protection Agency (EPA) regulations Title 40 Code of Federal Regulations Part 191.14(c) [1] and Title 40 Code of Federal Regulations Part 194.43 [2] require a Passive Institutional Controls program be developed for the WIPP. The primary purpose of the Passive Institutional Controls program is to indicate the location of the repository and the risk it presents to an intruder, thus reducing the likelihood of inadvertent human intrusion into the repository. A plan was put into place during the 1990's with records management and storage, awareness triggers, permanent marker design concepts, including languages, graphics and engineered drawings, plus testing schedules for materials and structures. This work included the thoughts of expert panels and individuals. The plan held up under peer review and met the regulatory requirements. But will it really work? Will future generations a thousand years, two thousand years, or seven thousand years from now really be able to decipher and understand the message? This is the challenge international constructors, operators, and regulators of repositories for the disposal of any hazardous materials must face. It is important to explore the history of language, both written words and graphics; and what we can learn from the past to assist us in communicating with the future. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2013

SIPMaP: A Tool for Modeling Irregular Parallel Computations in the Super Instruction Architecture

Performance modeling is becoming an increasingly important part of the parallel application development process, particularly for expensive computations that will be run on very high-end systems where resources are scarce. We describe a performance modeling tool SIPMaP (Super Instruction Processor Modeling and Prediction) developed for the Super-Instruction Architecture (SIA). The SIA is designed for applications where the dominant data structures are large multi-dimensional arrays and it comprises a DSL, the Super-Instruction Assembly Language (SIAL) that supports expressing algorithms in terms of blocks (tiles), and its runtime system Super Instruction Processor (SIP) that manages distribution and disk storage of the arrays. SIPMaP generates performance models from the SIAL source code. In comparison with many applications where useful performance models have been developed and reported, these programs are irregular and have other difficult to model characteristics such as extensive overlapping of communication and computation.

Computer Science↗
DOE OSTI2015

Helium: lifting high-performance stencil kernels from stripped x86 binaries to halide DSL code

Highly optimized programs are prone to bit rot, where performance quickly becomes suboptimal in the face of new hardware and compiler techniques. In this paper we show how to automatically lift performance-critical stencil kernels from a stripped x86 binary and generate the corresponding code in the high-level domain-specific language Halide. Using Halide's state-of-the-art optimizations targeting current hardware, we show that new optimized versions of these kernels can replace the originals to rejuvenate the application for newer hardware. The original optimized code for kernels in stripped binaries is nearly impossible to analyze statically. Instead, we rely on dynamic traces to regenerate the kernels. We perform buffer structure reconstruction to identify input, intermediate and output buffer shapes. Here, we abstract from a forest of concrete dependency trees which contain absolute memory addresses to symbolic trees suitable for high-level code generation. This is done by canonicalizing trees, clustering them based on structure, inferring higher-dimensional buffer accesses and finally by solving a set of linear equations based on buffer accesses to lift them up to simple, high-level expressions. Helium can handle highly optimized, complex stencil kernels with input-dependent conditionals. We lift seven kernels from Adobe Photoshop giving a 75 % performance improvement, four kernels from Irfan View, leading to 4.97 x performance, and one stencil from the mini GMG multigrid benchmark netting a 4.25 x improvement in performance. We manually rejuvenated Photoshop by replacing eleven of Photoshop's filters with our lifted implementations, giving 1.12 x speedup without affecting the user experience.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

AI Benchmark Democratization and Carpentry

Benchmarks are a cornerstone of modern machine learning, enabling reproducibility, comparison, and scientific progress. However, AI benchmarks are increasingly complex, requiring dynamic, AI-focused workflows. Rapid evolution in model architectures, scale, datasets, and deployment contexts makes evaluation a moving target. Large language models often memorize static benchmarks, causing a gap between benchmark results and real-world performance. Beyond traditional static benchmarks, continuous adaptive benchmarking frameworks are needed to align scientific assessment with deployment risks. This calls for skills and education in AI Benchmark Carpentry. From our experience with MLCommons, educational initiatives, and programs like the DOE's Trillion Parameter Consortium, key barriers include high resource demands, limited access to specialized hardware, lack of benchmark design expertise, and uncertainty in relating results to application domains. Current benchmarks often emphasize peak performance on top-tier hardware, offering limited guidance for diverse, real-world scenarios. Benchmarking must become dynamic, incorporating evolving models, updated data, and heterogeneous platforms while maintaining transparency, reproducibility, and interpretability. Democratization requires both technical innovation and systematic education across levels, building sustained expertise in benchmark design and use. Benchmarks should support application-relevant comparisons, enabling informed, context-sensitive decisions. Dynamic, inclusive benchmarking will ensure evaluation keeps pace with AI evolution and supports responsible, reproducible, and accessible AI deployment. Community efforts can provide a foundation for AI Benchmark Carpentry.

von Laszewski, Gregor [Virginia U.]↗
DOE OSTI2011

iotbx.cif : a comprehensive CIF toolbox

iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Ompparser

ompparser is a standalone and unified OpenMP parser, which is motivated by the facts that: 1) The differences in terms of syntax and semantics of OpenMP constructs between C/C++ and Fortran are minor. 2) Current OpenMP compilers often develop their own parsers, which represent redundant work. The features of ompparser include: 1) ompparser can be used standalone for static source code analysis, e.g. tools for semantics checking or similarity analysis between C/C++ and Fortran programs 2) omppaser can be integrated into an OpenMP compiler implementation can reduce the development efforts, and there is no need to create and maintain two separate parsers for C/C++ and Fortran. 3) ompparser provides a complete reference OpenMP grammar in the Backus-Naur Form that formally describes all the latest OpenMP language constructs. This will help users understand the rules and restriction of the OpenMP standard, which no longer contains a reference grammar in its recent versions.

Wang, Anjia↗
DOE OSTI2025

Spectral Bounds on Hyperbolic 3-Manifolds: Associativity and the Trace Formula

We constrain the low-energy spectra of Laplace operators on closed hyperbolic manifolds and orbifolds in three dimensions, including the standard Laplace--Beltrami operator on functions and the Laplacian on powers of the cotangent bundle. Our approach employs linear programming techniques to derive rigorous bounds by leveraging two types of spectral identities. The first type, inspired by the conformal bootstrap, arises from the consistency of the spectral decomposition of the product of Laplace eigensections, and involves the Laplacian spectra as well as integrals of triple products of eigensections. We formulate these conditions in the language of representation theory of PSL 2 (C) and use them to prove upper bounds on the first and second Laplacian eigenvalues. The second type of spectral identities follows from the Selberg trace formula. We use them to find upper bounds on the spectral gap of the Laplace--Beltrami operator on hyperbolic 3-orbifolds, as well as on the systole length of hyperbolic 3-manifolds, as a function of the volume. Further, we prove that the spectral gap λ 1 of the Laplace--Beltrami operator on all closed hyperbolic 3-manifolds satisfies λ 1 < 47.32. Along the way, we use the trace formula to estimate the low-energy spectra of a large set of example orbifolds and compare them with our general bounds, finding that the bounds are nearly sharp in several cases.

Bonifacio, James [University of Mississippi, MS (U↗
DOE OSTI2015

Automated Design Space Exploration with Aspen

Architects and applications scientists often use performance models to explore a multidimensional design space of architectural characteristics, algorithm designs, and application parameters. With traditional performance modeling tools, these explorations forced users to first develop a performance model and then repeatedly evaluate and analyze the model manually. These manual investigations proved laborious and error prone. More importantly, the complexity of this traditional process often forced users to simplify their investigations. To address this challenge of design space exploration, we extend our Aspen (Abstract Scalable Performance Engineering Notation) language with three new language constructs: user-defined resources, parameter ranges, and a collection of costs in the abstract machine model. Then, we use these constructs to enable automated design space exploration via a nonlinear optimization solver. We show how four interesting classes of design space exploration scenarios can be derived from Aspen models and formulated as pure nonlinear programs. The analysis tools are demonstrated using examples based on Aspen models for a three-dimensional Fast Fourier Transform, the CoMD molecular dynamics proxy application, and the DARPA Streaming Sensor Challenge Problem. Our results show that this approach can compose and solve arbitrary performance modeling questions quickly and rigorously when compared to the traditional manual approach.

Spafford, Kyle L.↗
DOE OSTI2023

Precursor Analysis Report: SQL Slammer Worm Infection of Davis-Besse Nuclear Power Plant 2003

The SQL Slammer Worm Infection of Davis-Besse Nuclear Power Plant 2003 Precursor Analysis Report leverages publicly available information about Davis-Besse’s 2003 cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. On 25 January 2003, the SQL Slammer worm infected more than 90% of vulnerable hosts and crashed the internet in 10 to 15 minutes, making it one of the fastest spreading worms in history. SQL Slammer is a fileless, memory-resident worm that remotely exploits a stack-based buffer overflow vulnerability on local hosts to intensively scan and rapidly self-propagate across the internet. The worm infected approximately 300,000 unpatched hosts running Microsoft Structured Query Language (SQL) Server 2000 or Microsoft Desktop Engine (MSDE) 2000 with SQL Server Resolution Service. The SQL Slammer worm indirectly infected FirstEnergy’s Davis-Besse nuclear power plant by first infecting a consultant’s company network server and then propagating through an external misconfigured connection into Davis-Besse’s site network. The infection caused major network congestion, slow performance, data overloads, and the inability of local hosts to communicate with each other, which eventually caused a loss of availability and a loss of view when the Safety Parameter Display System (SPDS) and Plant Process Computer (PPC) crashed. At the time of the infection, the plant was already offline, the digital monitoring systems had redundant analog backups, and the plant control and safety functions were not affected, so there were no concerns of a safety breach. However, this incident resulted in many lessons learned and spawned important discussions about cybersecurity’s role in nuclear safety and electric power reliability regulation, policy, and guidance. Researchers and analysts identified 10 unique techniques utilized during the attack with a total of 640 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Eight of the identified techniques used during Davis-Besse cyber attack were precursors to the triggering event. Analysis identified 596 observables associated with these precursor techniques, 428 of which were assessed to have an increased likelihood of being perceived in the 331 days preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2022

GNDS v2.0 release and future developments [Slides]

This presentation begins by discussing the major changes in v2.0 of GNDS and that the GNDS-2.0 formatted libraries are now available. It also examines how code support for GNDS is growing with processing codes, APIs and transport codes, and evaluation/testing codes. The presentation states that while migrating to GNDS can be a major effort it worthwhile, especially for anyone who is just getting started as nuclear data creator or user. Additionally, this presentation outlines the established milestones that the EG-GNDS (the group in charge of GNDS specs) has for the next GNDS release and elaborates on the first goal, which is to migrate GNDS specifications to the new JSON schema language.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗