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At least 127 records · Page 7

All sources NASA NTRS DOE OSTI

DOE OSTI2014

Collaborating CPU and GPU for large-scale high-order CFD simulations with complex grids on the TianHe-1A supercomputer

Programming and optimizing complex, real-world CFD codes on current many-core accelerated HPC systems is very challenging, especially when collaborating CPUs and accelerators to fully tap the potential of heterogeneous systems. In this paper, with a tri-level hybrid and heterogeneous programming model using MPI + OpenMP + CUDA, we port and optimize our high-order multi-block structured CFD software HOSTA on the GPU-accelerated TianHe-1A supercomputer. HOSTA adopts two self-developed high-order compact definite difference schemes WCNS and HDCS that can simulate flows with complex geometries. We present a dual-level parallelization scheme for efficient multi-block computation on GPUs and perform particular kernel optimizations for high-order CFD schemes. The GPU-only approach achieves a speedup of about 1.3 when comparing one Tesla M2050 GPU with two Xeon X5670 CPUs. To achieve a greater speedup, we collaborate CPU and GPU for HOSTA instead of using a naive GPU-only approach. We present a novel scheme to balance the loads between the store-poor GPU and the store-rich CPU. Taking CPU and GPU load balance into account, we improve the maximum simulation problem size per TianHe-1A node for HOSTA by 2.3×, meanwhile the collaborative approach can improve the performance by around 45% compared to the GPU-only approach. Further, to scale HOSTA on TianHe-1A, we propose a gather/scatter optimization to minimize PCI-e data transfer times for ghost and singularity data of 3D grid blocks, and overlap the collaborative computation and communication as far as possible using some advanced CUDA and MPI features. Scalability tests show that HOSTA can achieve a parallel efficiency of above 60% on 1024 TianHe-1A nodes. With our method, we have successfully simulated an EET high-lift airfoil configuration containing 800M cells and China's large civil airplane configuration containing 150M cells. To our best knowledge, those are the largest-scale CPU–GPU collaborative simulations that solve realistic CFD problems with both complex configurations and high-order schemes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1996

Parallelization and Algorithmic Enhancements of High Resolution IRAS Image Construction

The Infrared Astronomical Satellite caried out a nearly complete survey of the infrared sky, and the survey data are important for the study of many astrophysical phenomena. However, many data sets at other wavelengths have higher resolutions than that of the co-added IRAS maps, and high resolution IRAS images are strongly desired both for their own information content and their usefulness in correlation. The HIRES program was developed by the Infrared Processing and Analysis Center (IPAC) to produce high resolution (approx. 1') images from IRAS data using the Maximum Correlation Method (MCM). We describe the port of HIRES to the Intel Paragon, a massively parallel supercomputer, other software developments for mass production of HIRES images, and the IRAS Galaxy Atlas, a project to map the Galactic plane at 60 and 100(micro)m.

Satellite infrared IRAS IRAS maps IRAS images↗

DOE OSTI2019

Software-Defined Networking Traffic Engineering Process for Operational Technology Networks

Network design goals are often functional with little consideration for security. Growth and maintenance of critical infrastructure mission-focused networks can be ad hoc and preclude large-scale technology replacements, reconfigurations, or even patching. These restrictions are contributing factors to increased vulnerabilities. Over 90% of all attacks begin with phishing and include lateral movement (Frinke 2019). Adopting a software-defined networking (SDN) approach is an effective mitigation strategy for many existing vulnerabilities. SDNs deny-by-default approach to networking restricts an adversary’s freedom of movement without impacting an organization’s mission. SDN implementations require a process that identifies an organization’s mission-specific network communications. A well-defined traffic engineering process ensures that only known devices communicate with each other on specific ports.

Software Defined Networking, Situational Awareness↗

NASA NTRS1983

Development and evaluation of a Fault-Tolerant Multiprocessor (FTMP) computer. Volume 2: FTMP software

The software developed for the Fault-Tolerant Multiprocessor (FTMP) is described. The FTMP executive is a timer-interrupt driven dispatcher that schedules iterative tasks which run at 3.125, 12.5, and 25 Hz. Major tasks which run under the executive include system configuration control, flight control, and display. The flight control task includes autopilot and autoland functions for a jet transport aircraft. System Displays include status displays of all hardware elements (processors, memories, I/O ports, buses), failure log displays showing transient and hard faults, and an autopilot display. All software is in a higher order language (AED, an ALGOL derivative). The executive is a fully distributed general purpose executive which automatically balances the load among available processor triads. Provisions for graceful performance degradation under processing overload are an integral part of the scheduling algorithms.

Lala, J. H.↗

DOE OSTI2021

High-order algorithmic developments and optimizations for large-scale GPU-accelerated simulations (Milestone CEED-MS36)

The goal of this milestone was to improve the high-order software ecosystem for CEED-enabled ECP applications by making progress on efficient matrix-free kernels targeting forthcoming ECP architectures. These kernels included matrix-free preconditioning and the development of new set of CEED solver bake-off problems. As part of this milestone, we also released the next version of the CEED software stack, CEED-4.0, reported on results from several application collaborations, and documented the efforts of porting to AMD GPUs for Frontier and other modern architectures, such as Fugaku. The specific tasks addressed in this milestone were: (1) Port and run CEED benchmarks/miniapps on Frontier EA systems; (2) Demonstrate performant libCEED integration in MFEM, Nek and applications; (3) Matrix-free preconditioning of high-order operators; (4) Benchmark problems for fast high-order solvers on GPU platforms; and (5) Public release of CEED-4.0. The artifacts delivered include the next version of the CEED software stack, CEED-4.0, the next libCEED release, libCEED-0.8, and a number of developments integrated within applications to improve their GPU and CPU performance and capabilities. See the CEED website, https://ceed.exascaleproject.org and the CEED GitHub organization, https://github.com/ceed for more details.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Web Extensible Display Manager

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a web gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.

Slominski, Ryan↗

NASA NTRS2013

Tool Use Within NASA Software Quality Assurance

As space mission software systems become larger and more complex, it is increasingly important for the software assurance effort to have the ability to effectively assess both the artifacts produced during software system development and the development process itself. Conceptually, assurance is a straightforward idea - it is the result of activities carried out by an organization independent of the software developers to better inform project management of potential technical and programmatic risks, and thus increase management's confidence in the decisions they ultimately make. In practice, effective assurance for large, complex systems often entails assessing large, complex software artifacts (e.g., requirements specifications, architectural descriptions) as well as substantial amounts of unstructured information (e.g., anomaly reports resulting from testing activities during development). In such an environment, assurance engineers can benefit greatly from appropriate tool support. In order to do so, an assurance organization will need accurate and timely information on the tool support available for various types of assurance activities. In this paper, we investigate the current use of tool support for assurance organizations within NASA, and describe on-going work at JPL for providing assurance organizations with the information about tools they need to use them effectively.

software assurance↗

NASA NTRS2017

Novel End-to-End Molecular Biology Approach for Direct Nanopore 1D cDNA Sequencing of Reverse Transcribed mRNAs Purified from Cell Cultures by the NASA ISS WetLab2 SPM

Continued space bioscience research onboard the International Space Station (ISS) and future long-duration flight missions to the Moon or Mars will require the ability to conduct on-orbit molecular analysis of biological samples independently from Earth. In the last year two new molecular analytic technologies have been installed and the technologies demonstrated onboard the ISS: The Sample Prep Module (SPM) WetLab-2 (WL2) qRT-PCR toolbox and the Oxford Nanopore MinIon Biomolecule Sequencer. Here we describe protocol development and integration into existing ISS technology for end-to-end on-orbit biological sample processing and molecular analysis with real time results generated utilizing only field offline analytic software. For this experiment we isolated primary cells from bone marrow flushes of wild type B6129SF2 mice (Jackson Labs) long bones. The cell isolate was then processed using the SPM to produce total 147nanograms of RNA. The total RNA was purified to only messenger RNA (mRNA) and transferred to Smartcycler Thermocycle ISS kit consumable tube using Eppendorf gel loading pipette tips for further processing. Complementary first strand cDNA was synthesized using OLIGO dT priming followed by addition of SuperScript II Reverse Transcriptase and thermal cycling as per manufacturers instruction. All thermal cycling was conducted using the ISS WetLab-2 Cephid Smarcycler real time thermal cycler. Our protocol takes advantage of mRNAs native poly(A) tail, synthesized in vivo to protect the mRNA from degradation by endonucleases, to eliminate end-prep for adapter ligation. The adapted library is purified using MyOne C1 Streptavidin beads before elution in buffer. The pre-sequencing library is diluted in the loading buffer and injected into the MinIon sample port, drawn into the nanopore window by capillary action, and sequenced using the MinKnown software with local basecalling. The sequencing read produced 34.5 million events and local basecalling produced 117,301 successful reads. NCBI Blast of the data for the mouse genome resulted in 2,462 successful nucleotide collection matches (gene sequences) exceeding 70 homology. These results demonstrate the viability of this novel flight ready end-to-end sample analytic methodology and provide a real time homolog for flight experimentation utilizing supply kits and technologies that have already been demonstrated on ISS.

MinIon↗

DOE OSTI2019

Quantum Associative Memory in Hep Track Pattern Recognition

We have entered the Noisy Intermediate-Scale Quantum Era. A plethora of quantum processor prototypes allow evaluation of potential of the Quantum Computing paradigm in applications to pressing computational problems of the future. Growing data input rates and detector resolution foreseen in High-Energy LHC (2030s) experiments expose the often high time and/or space complexity of classical algorithms. Quantum algorithms can potentially become the lower-complexity alternatives in such cases. In this work we discuss the potential of Quantum Associative Memory (QuAM) in the context of LHC data triggering. We examine the practical limits of storage capacity, as well as store and recall errorless efficiency, from the viewpoints of the state-of-the-art IBM quantum processors and LHC real-time charged track pattern recognition requirements. We present a software prototype implementation of the QuAM protocols and analyze the topological limitations for porting the simplest QuAM instances to the public IBM 5Q and 14Q cloud-based superconducting chips.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Evaluating Performance Portability with the CMS Heterogeneous Pixel Reconstruction code

In the past years the landscape of tools for expressing parallel algorithms in a portable way across various compute accelerators has continued to evolve significantly. There are many technologies on the market that provide portability between CPU, GPUs from several vendors, and in some cases even FPGAs. These technologies include C++ libraries such as Alpaka and Kokkos, compiler directives such as OpenMP, the SYCL open specification that can be implemented as a library or in a compiler, and standard C++ where the compiler is solely responsible for the offloading. Given this developing landscape, users have to choose the technology that best fits their applications and constraints. For example, in the CMS experiment the experience so far in heterogeneous reconstruction algorithms suggests that the full application contains a large number of relatively short computational kernels and memory transfer operations. In this work we use a stand-alone version of the CMS heterogeneous pixel reconstruction code as a realistic use case of HEP reconstruction software that is capable of leveraging GPUs effectively. We summarize the experience of porting this code base from CUDA to Alpaka, Kokkos, SYCL, std::par, and OpenMP offloading. We compare the event processing throughput achieved by each version on NVIDIA and AMD GPUs as well as on a CPU, and compare those to what a native version of the code achieves on each platform.

Andriotis, Nikolaos↗

DOE OSTI2025

Assessing VQLS for Fluid Dynamics on a Hybrid Quantum-HPC Stack

Recent advances in quantum linear solvers offer a promising direction for accelerating extreme scientific computations such as fluid dynamics. However, the deep and complex circuits required by many quantum algorithms limit their practical use on current quantum hardware. The Variational Quantum Linear Solver (VQLS) presents a viable alternative for near-term quantum devices (NISQ), and initial efforts have explored its application to select fluid dynamics problems. In this work, we evaluate the use of VQLS for canonical fluid dynamics problems, aiming to identify pathways for generalizing its implementation across a broader class of systems. We analyze the impact of various circuit ansatz and classical optimizers on solution quality and convergence behavior. Furthermore, we assess the algorithm's feasibility within a hybrid quantum–high-performance computing (HPC) framework by porting it to QFw, a state-of-the-art quantum-HPC software stack. 11This manuscript has been authored by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the US DOE under Contract No. DE-AC05-00OR22725.

Gopalakrishnan Meena, Murali [ORNL] (ORCID:0000000↗

DOE OSTI2019

Regression for Assessing Contaminant Plume Trends

The Department of Energy’s (DOE) Hanford site has significant dissolved-phase groundwater contaminant plumes, for which remediation activities are ongoing. Assessing concentration trends is critical for making decisions regarding remedy implementation or performance. The SOCRATES single-page web application provides a quality-assured framework for data access and consistent data analytics using standard methods. To provide trend information for remedial decisions, statistical analyses based on ordinary least squares (OLS) are already supported by SOCRATES. The presence of censored data, however, can skew the result of an OLS regression. Other methods, such as the Akritas-Theil-Sen (ATS) or Tobit regressions can be more powerful. These two regression methods are used by Hanford site personnel to analyze groundwater contaminant concentration data, which often include nondetects (censored data). The ATS method uses comparisons of observation-pair ranks and the Tobit method uses a maximum likelihood estimation method. The Tobit method can also accommodate covariates, such as river stage or groundwater level fluctuations. Both ATS and Tobit regressions can be performed with the statistics software R, but to incorporate these methods into SOCRATES, their R code was ported into JavaScript. For quality assurance verification, the new code was tested with hexavalent chromium concentration data from the Hanford 100-K West Area and compared to regression analyses that were previously conducted on this data using R.

100-K Area↗

NASA NTRS1991

Lunar rovers and local positioning system

Telerobotic rovers equipped with adequate actuators and sensors are clearly necessary for extraterrestrial construction. They will be employed as substitutes for humans, to perform jobs like surveying, sensing, signaling, manipulating, and the handling of small materials. Important design criteria for these rovers include versatility and robustness. They must be easily programmed and reprogrammed to perform a wide variety of different functions, and they must be robust so that construction work will not be jeopardized by parts failures. The key qualities and functions necessary for these rovers to achieve the required versatility and robustness are modularity, redundancy, and coordination. Three robotic rovers are being built by CSC as a test bed to implement the concepts of modularity and coordination. The specific goal of the design and construction of these robots is to demonstrate the software modularity and multirobot control algorithms required for the physical manipulation of constructible elements. Each rover consists of a transporter platform, bus manager, simple manipulator, and positioning receivers. These robots will be controlled from a central control console via a radio-frequency local area network (LAN). To date, one prototype transporter platform frame was built with batteries, motors, a prototype single-motor controller, and two prototype internal LAN boards. Software modules were developed in C language for monitor functions, i/o, and parallel port usage in each computer board. Also completed are the fabrication of half of the required number of computer boards, the procurement of 19.2 Kbaud RF modems for inter-robot communications, and the simulation of processing requirements for positioning receivers. In addition to the robotic platform, the fabrication of a local positioning system based on infrared signals is nearly completed. This positioning system will make the rovers into a moving reference system capable of performing site surveys. In addition, a four degree mechanical manipulator especially suited for coordinated teleoperation was conceptually designed and is currently being analyzed. This manipulator will be integrated into the rovers as their end effector. Twenty internal LAN cards fabricated by a commercial firm are being used, a prototype manipulator and a range finder for a positioning system were built, a prototype two-motor controller was designed, and one of the robots is performing its first telerobotic motion. In addition, the robots' internal LAN's were coordinated and tested, hardware design upgrades based on fabrication and fit experience were completed, and the positioning system is running. The rover system is able to perform simple tasks such as sensing and signaling; coordination systems which allow construction tasks to begin were established, and soon coordinated teams of robots in the laboratory will be able to manipulate common objects.

Avery, James↗

NASA NTRS1996

Petabyte Class Storage at Jefferson Lab (CEBAF)

By 1997, the Thomas Jefferson National Accelerator Facility will collect over one Terabyte of raw information per day of Accelerator operation from three concurrently operating Experimental Halls. When post-processing is included, roughly 250 TB of raw and formatted experimental data will be generated each year. By the year 2000, a total of one Petabyte will be stored on-line. Critical to the experimental program at Jefferson Lab (JLab) is the networking and computational capability to collect, store, retrieve, and reconstruct data on this scale. The design criteria include support of a raw data stream of 10-12 MB/second from Experimental Hall B, which will operate the CEBAF (Continuous Electron Beam Accelerator Facility) Large Acceptance Spectrometer (CLAS). Keeping up with this data stream implies design strategies that provide storage guarantees during accelerator operation, minimize the number of times data is buffered allow seamless access to specific data sets for the researcher, synchronize data retrievals with the scheduling of postprocessing calculations on the data reconstruction CPU farms, as well as support the site capability to perform data reconstruction and reduction at the same overall rate at which new data is being collected. The current implementation employs state-of-the-art StorageTek Redwood tape drives and robotics library integrated with the Open Storage Manager (OSM) Hierarchical Storage Management software (Computer Associates, International), the use of Fibre Channel RAID disks dual-ported between Sun Microsystems SMP servers, and a network-based interface to a 10,000 SPECint92 data processing CPU farm. Issues of efficiency, scalability, and manageability will become critical to meet the year 2000 requirements for a Petabyte of near-line storage interfaced to over 30,000 SPECint92 of data processing power.

Chambers, Rita↗

NASA NTRS2002

Repair and Utilization of the Kratos XSAM 800 X-Ray Photoelectron Spectrometer (XPS)

The objectives for this summer faculty fellowship were first to repair the Kratos XSAM 800 X-ray Photoelectron Spectrometer (XPS) and then to utilize the instrument to participate in ongoing research projects at KSC and in the researcher's own laboratory at UCF. The first 6 weeks were used in repairing the instrument. Working both alone and with the Kratos service engineer, a number of hardware problems, largely associated with the sample stage control system, were corrected. Defective parts were identified and fixed in the computer driver boards, the stage power supply, and the driver interface. The power supply was completely replaced. After four weeks of work, the instrument was functional. This occurred on a Wednesday. The following Friday the instrument had to be completely shut down because the power to the O & C Building was to be turned off. The instrument was properly secured. On Monday, the instrument was powered up and the original problems returned. After another 2 weeks of work, a software problem was identified. This problem caused the computer to use a defective port for the sample stage control. It was circumvented by rewriting the startup routine. The final 3 weeks of the fellowship were spent using the XPS to analyze samples being studied in the Langley materials project (Martha Williams) and a catalyst project (Dr. Orlando Melendez). During this time, several sample analysis requests from other groups at KSC also came in and those samples were run as well. The summer faculty fellowship also allowed many contacts to be made. After meeting with the sensors group, two projects were identified for collaboration and white papers are being prepared. One project aims to develop small, very sensitive hydrogen detectors and the other to develop a broad area, easily monitored, zero power consumption hydrogen detector. In addition to the work mentioned above, the XPS was utilized in a study underway in Dr. Hampton's laboratory at UCF.

Hampton, Michael D.↗

NASA NTRS2017

Implementation of (O-)CGR in The ONE

Routing in Delay-/Disruption-Tolerant Networking (DTN) requires specific solutions as link impairments prevent the use of ordinary Internet algorithms, based on a timely dissemination of network topology information. Among DTN routing algorithms there is a dichotomy between opportunistic and deterministic (scheduled) solutions. The former are numerous and apply to terrestrial environments; CGR is the most widely supported algorithm designed for scheduled connectivity, and it is usually applied to space networks. However, in an attempt to provide a unified approach, an opportunistic variant of CGR, Opportunistic CGR (OCGR) has been recently proposed by some of the authors. Performance evaluations are normally carried out for opportunistic solutions by means of simulators, such as The ONE considered in this paper. CGR by contrast is more often studied by means of small testbeds. As the simulation approach could be complementary for CGR, and essential for OCGR, the authors have recently ported both of them into The ONE, by developing and releasing as free software a specific additional package. The aim of this paper is to show the rationale of this choice and discuss the many challenges that needed to be tackled to achieve this primary goal.

Tempesta, G.↗

DOE OSTI2022

Evaluation of Portable Programming Models to Accelerate LArTPC Detector Simulations

The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential for analysis algorithm development and physics model interpretations. Accurate LArTPC detector response simulations are computationally demanding, and can become a bottleneck in the analysis workflow. Compute devices such as General-Purpose Graphics Processing Units (GPGPUs) have the potential to substantially accelerate simulations compared to traditional CPU-only processing. The software development that requires often carries the cost of specialized code refactorization and porting to match the target hardware architecture. With the rapid evolution and increased diversity of the computer architecture landscape, it is highly desirable to have a portable solution that also maintains reasonable performance. We report our ongoing effort in evaluating Kokkos as a basis for this portable programming model using LArTPC simulations in the context of the Wire-Cell Toolkit, a C++ library for LArTPC simulations, data analysis, reconstruction and visualization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2011

MicroShell Minimalist Shell for Xilinx Microprocessors

MicroShell is a lightweight shell environment for engineers and software developers working with embedded microprocessors in Xilinx FPGAs. (MicroShell has also been successfully ported to run on ARM Cortex-M1 microprocessors in Actel ProASIC3 FPGAs, but without project-integration support.) Micro Shell decreases the time spent performing initial tests of field-programmable gate array (FPGA) designs, simplifies running customizable one-time-only experiments, and provides a familiar-feeling command-line interface. The program comes with a collection of useful functions and enables the designer to add an unlimited number of custom commands, which are callable from the command-line. The commands are parameterizable (using the C-based command-line parameter idiom), so the designer can use one function to exercise hardware with different values. Also, since many hardware peripherals instantiated in FPGAs have reasonably simple register-mapped I/O interfaces, the engineer can edit and view hardware parameter settings at any time without stopping the processor. MicroShell comes with a set of support scripts that interface seamlessly with Xilinx's EDK tool. Adding an instance of MicroShell to a project is as simple as marking a check box in a library configuration dialog box and specifying a software project directory. The support scripts then examine the hardware design, build design-specific functions, conditionally include processor-specific functions, and complete the compilation process. For code-size constrained designs, most of the stock functionality can be excluded from the compiled library. When all of the configurable options are removed from the binary, MicroShell has an unoptimized memory footprint of about 4.8 kB and a size-optimized footprint of about 2.3 kB. Since MicroShell allows unfettered access to all processor-accessible memory locations, it is possible to perform live patching on a running system. This can be useful, for instance, if a bug is discovered in a routine but the system cannot be rebooted: Shell allows a skilled operator to directly edit the binary executable in memory. With some forethought, MicroShell code can be located in a different memory location from custom code, permitting the custom functionality to be overwritten at any time without stopping the controlling shell.

Werne, Thomas A.↗