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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 127 records · Page 7

Production Level CFD Code Acceleration for Hybrid Many-Core Architectures

In this work, a novel graphics processing unit (GPU) distributed sharing model for hybrid many-core architectures is introduced and employed in the acceleration of a production-level computational fluid dynamics (CFD) code. The latest generation graphics hardware allows multiple processor cores to simultaneously share a single GPU through concurrent kernel execution. This feature has allowed the NASA FUN3D code to be accelerated in parallel with up to four processor cores sharing a single GPU. For codes to scale and fully use resources on these and the next generation machines, codes will need to employ some type of GPU sharing model, as presented in this work. Findings include the effects of GPU sharing on overall performance. A discussion of the inherent challenges that parallel unstructured CFD codes face in accelerator-based computing environments is included, with considerations for future generation architectures. This work was completed by the author in August 2010, and reflects the analysis and results of the time.

Duffy, Austen C.↗

Residual entanglement of accelerated fermions is useful

The non-vanishing residual entanglement, between the fermionic modes in the infinite acceleration limit, does not violate CHSH inequality, therefore it is not non-local. In this paper, we study the usefulness of the residual fermionic entanglement in single mode approximation and beyond single mode approximation. It is shown that there are some cases where the CHSH inequality is not violated by the residual entanglement, but the state is useful for quantum teleportation. Conditions for the violation of the CHSH inequality in terms of the “presence probability” of the particle in different Rindler regions are given for the state to be useful for teleportation and superdense coding. - Highlights: • Werner state is shared between an inertial observer and a uniformly accelerated one. • Single mode and beyond single mode approximation are considered. • Usefulness of residual entanglement in the infinite acceleration limit is studied. • The CHSH inequality and the quantum teleportation are used as a criterion. • Useful states for quantum information processing are found in the infinite acceleration.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Reproducibility in materials informatics: lessons from ‘A general-purpose machine learning framework for predicting properties of inorganic materials’

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open data and open-source tools to propel the field. Despite the increasing usefulness and capabilities of these tools, developers neglecting to follow reproducible practices presents a significant barrier for other researchers looking to use or build upon their work. In this study, we investigate the challenges encountered while attempting to reproduce a section of the results presented in “A general-purpose machine learning framework for predicting properties of inorganic materials.” Our analysis identifies four major categories of challenges: (1) reporting software dependencies, (2) recording and sharing version logs, (3) sequential code organization, and (4) clarifying code references within the manuscript. The result is a proposed set of tangible action items for those aiming to make material informatics tools accessible to, and useful for the community.

36 MATERIALS SCIENCE↗

SU-F-P-10: A Web-Based Radiation Safety Relational Database Module for Regulatory Compliance

Purpose: Maintaining compliance with Radioactive Materials Licenses is inherently a time-consuming task requiring focus and attention to detail. Staff tasked with these responsibilities, such as the Radiation Safety Officer and associated personnel must retain disparate records for eventual placement into one or more annual reports. Entering results and records in a relational database using a web browser as the interface, and storing that data in a cloud-based storage site, removes procedural barriers. The data becomes more adaptable for mining and sharing. Methods: Web-based code was written utilizing the web framework Django, written in Python. Additionally, the application utilizes JavaScript for front-end interaction, SQL, HTML and CSS. Quality assurance code testing is performed in a sequential style, and new code is only added after the successful testing of the previous goals. Separate sections of the module include data entry and analysis for audits, surveys, quality management, and continuous quality improvement. Data elements can be adapted for quarterly and annual reporting, and for immediate notification of user determined alarm settings. Results: Current advances are focusing on user interface issues, and determining the simplest manner by which to teach the user to build query forms. One solution has been to prepare library documents that a user can select or edit in place of creation a new document. Forms are being developed based upon Nuclear Regulatory Commission federal code, and will be expanded to include State Regulations. Conclusion: Establishing a secure website to act as the portal for data entry, storage and manipulation can lead to added efficiencies for a Radiation Safety Program. Access to multiple databases can lead to mining for big data programs, and for determining safety issues before they occur. Overcoming web programming challenges, a category that includes mathematical handling, is providing challenges that are being overcome.

61 RADIATION PROTECTION AND DOSIMETRY↗

SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis

Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. This cooperative binding establishes a shared SOX2-VSX2 transcriptional code that promotes the expression of crucial regulators of neurogenesis while repressing the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural identity.

Chromatin↗

Level-2 Milestone 5588: Deliver Strategic Plan and Initial Scalability Assessment by Advanced Architecture and Portability Specialists Team

This report documents the fact that the work in creating a strategic plan and beginning customer engagements has been completed. The description of milestone is: The newly formed advanced architecture and portability specialists (AAPS) team will develop a strategic plan to meet the goals of 1) sharing knowledge and experience with code teams to ensure that ASC codes run well on new architectures, and 2) supplying skilled computational scientists to put the strategy into practice. The plan will be delivered to ASC management in the first quarter. By the fourth quarter, the team will identify their first customers within PEM and IC, perform an initial assessment and scalability and performance bottleneck for next-generation architectures, and embed AAPS team members with customer code teams to assist with initial portability development within standalone kernels or proxy applications.

97 MATHEMATICS AND COMPUTING↗

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗

DTS: Building custom, intelligent schedulers

DTS is a decision-theoretic scheduler, built on top of a flexible toolkit -- this paper focuses on how the toolkit might be reused in future NASA mission schedulers. The toolkit includes a user-customizable scheduling interface, and a 'Just-For-You' optimization engine. The customizable interface is built on two metaphors: objects and dynamic graphs. Objects help to structure problem specifications and related data, while dynamic graphs simplify the specification of graphical schedule editors (such as Gantt charts). The interface can be used with any 'back-end' scheduler, through dynamically-loaded code, interprocess communication, or a shared database. The 'Just-For-You' optimization engine includes user-specific utility functions, automatically compiled heuristic evaluations, and a postprocessing facility for enforcing scheduling policies. The optimization engine is based on BPS, the Bayesian Problem-Solver (1,2), which introduced a similar approach to solving single-agent and adversarial graph search problems.

Hansson, Othar↗

Comparison of 250 MHz R10K Origin 2000 and 400 MHz Origin 2000 Using NAS Parallel Benchmarks

This report describes results of benchmark tests on Steger, a 250 MHz Origin 2000 system with R10K processors, currently installed at the NASA Ames National Advanced Supercomputing (NAS) facility. For comparison purposes, the tests were also run on Lomax, a 400 MHz Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to measure system performance. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versions used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Turney, Raymond D.↗

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Turney, Raymond D.↗

Large-Eddy Simulation Code Developed for Propulsion Applications

A large-eddy simulation (LES) code was developed at the NASA Glenn Research Center to provide more accurate and detailed computational analyses of propulsion flow fields. The accuracy of current computational fluid dynamics (CFD) methods is limited primarily by their inability to properly account for the turbulent motion present in virtually all propulsion flows. Because the efficiency and performance of a propulsion system are highly dependent on the details of this turbulent motion, it is critical for CFD to accurately model it. The LES code promises to give new CFD simulations an advantage over older methods by directly computing the large turbulent eddies, to correctly predict their effect on a propulsion system. Turbulent motion is a random, unsteady process whose behavior is difficult to predict through computer simulations. Current methods are based on Reynolds-Averaged Navier- Stokes (RANS) analyses that rely on models to represent the effect of turbulence within a flow field. The quality of the results depends on the quality of the model and its applicability to the type of flow field being studied. LES promises to be more accurate because it drastically reduces the amount of modeling necessary. It is the logical step toward improving turbulent flow predictions. In LES, the large-scale dominant turbulent motion is computed directly, leaving only the less significant small turbulent scales to be modeled. As part of the prediction, the LES method generates detailed information on the turbulence itself, providing important information for other applications, such as aeroacoustics. The LES code developed at Glenn for propulsion flow fields is being used to both analyze propulsion system components and test improved LES algorithms (subgrid-scale models, filters, and numerical schemes). The code solves the compressible Favre-filtered Navier- Stokes equations using an explicit fourth-order accurate numerical scheme, it incorporates a compressible form of Smagorinsky s model for the subgrid-scale turbulence, and it uses generalized curvilinear coordinates to allow analysis of a wide range of geometries. The code runs in parallel on shared memory multiprocessor computers and is written in Fortran 90 with dynamic memory allocation. A sample result for a Mach-1.4 round jet is presented in the figure. Instantaneous Mach number contours in several cross-planes downstream of the nozzle exit are shown, illustrating how an LES captures the large unsteady three-dimensional turbulent structures present in the jet.

DeBonis, James R.↗

Implementation of Krylov acceleration method for 3D S{sub N} transport code AETIUS with unstructured tetrahedral mesh - 25557

We have been developing an in-house deterministic neutron and gamma transport solver, AETIUS (An Easy modeling Transport code using Unstructured tetrahedral mesh, Shared memory parallel). To achieve fast results, BiCGStab (one of the Krylov acceleration methods) was implemented as a within-group iteration solver. In this paper, two test problems (simple double cube problem and helical tube in the outer cube problem) were used to verify the acceleration performance. The number of iterations and the calculation time were demonstrated and compared with the source iteration. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

Current Status of Problem 2 in the HTGR T/H Benchmark

Problem 2 of the HTGR T/H Benchmark is for modeling the depressurized conduction cooldown (DCC) transient. This presentation shares the status of code-to-code and code-to-date comparisons (Exercises 1 and 2) of Problem 2 with results from several participants. A key factor in the discrepancy between results and data in Exercise 2 is the assumed power distribution that is used to model PG-29. This talk highlights both the similarities and differences in solutions and discusses areas where further investigation is merited.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Modernization efforts for the R -Matrix code SAMMY [Abstract]

The R-Matrix code SAMMY is a widely used nuclear data evaluation code focused on the resolved range, which includes corrections for experimental effects. The code is still mostly written in Fortran 77, and uses a memory management system suitable for the time of its initial writing (1984). A modernization effort is under way to bring the code in-line with modern software development practices. A continuous-integration testing framework was added, automating the large existing set of test cases. It is run on every commit. The memory management was updated to current standard practices suitable for modern software analysis tools. The code can be obtained from https://code.ornl.gov/RNSD/SAMMY. The resonance parameters and covariance information are now stored in C++ objects shared by SAMMY and AMPX, the processing code that generates nuclear data libraries for SCALE. This allows for easier maintenance and access to the resonance parameters inside and outside of SAMMY. This feature is already used by accessing and changing parameters in memory in the Bayesian Monte Carlo Evaluation Framework for Cross Sections Nuclear Data and Integral Benchmark Experiments project, Further plans include the switch to the ENDF reading and writing routines in AMPX, as these routines are more robust, easier to maintain, and support more features. Of note here is support for the new GNDS format. Previously it wasn’t easy to share the full covariance matrix for evaluations containing more than one isotope due to limitations on the ENDF format; this is now supported in GNDS. The data are currently available in a binary SAMMY format and can be exported to GNDS to make them more widely available and sharable. The next step will be to use the same resonance processing code at 0K in AMPX and SAMMY as one of the available Reich-Moore R-Matrix formalism. The first step toward this goal is to isolate the reconstruction into a module that takes resonance parameters as its input and does not depend on SAMMY global parameters. This goal has been achieved and it should now be possible to more easily change the resonance formalism and add enhancements as the Phenomenological R-Matrix parameterization of direct, doorway, and compound nuclear reactions discussed elsewhere on this conference. This concerted modernization and enhancement effort provides multiple advantages to the nuclear data community. It will allow parameter optimization using enhanced formalisms, including experimental effects, that better match complex experimental data. Then those evaluated parameters can immediately be passed off to AMPX to be reconstructed with the exact same cross section model and be put into a data library for subsequent testing using SCALE and the Valid Benchmark suite or other suitable benchmark suites.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Multi-node and Multi-core Performance Studies of a Monte Carlo code RMC

Over the past 15 years the architecture of high-performance computing systems has become increasingly heterogeneous with individual computing cores being subdivided into nodes and even auxiliary co-processing units such as graphics processing units or the Intel many integrated core co-processors. In fact, future computer platforms is moving toward a larger number of nodes and cores with lower memory available per node. Today, several production Monte Carlo codes use some types of hybrid parallelism strategy that makes use of shared-memory parallelism within a computing node and message-passing parallelism between nodes, which enables the codes to utilize available computing resources as much as possible, both among and within computing nodes on a cluster. The so-called hybrid parallelization is also possible with Reactor Monte Carlo Code RMC by activating both MPI and OpenMP parallel algorithms together. On HPC' which typically consists of several or several-ten thousand nodes equipping 16-32 computing intra-cores per node, simulation of RMC can be carried out in the hybrid parallelization with the MPI inter-node parallelization and the OpenMP intra-node parallelization. RMC has adopted a hybrid message-passing and shared-memory approach to parallelism, which enables the code to utilize available computing resources, both among and within computing nodes on a cluster. Shared-memory parallelism is especially valuable for large-model simulations because it enables multiple compute cores within a node to share common model information such as the geometry description, material, cross section and tally data, thus reducing the memory usage per processor. The calculation on the Tianhe-2 supercomputer took 6144 cores, resulting in a rate of 173,314,000 neutrons/minute for BEAVRS benchmark. While pin-wise full core H-M benchmark burnup calculations with millions of depletion regions was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 1,843,200 burnable regions per minute. Keeping up with the continuing trend for increases in the number of computing resources within modern HPC systems is a significant challenge for teams that develop and maintain high-performance MC radiation transport solvers. order to address this challenge, RMC has adopted a hybrid message-passing and shared-memory approach to parallelism, which enables the code to utilize available computing resources, both among and within computing nodes on a cluster. Shared-memory parallelism is especially valuable for large-model simulations because it enables multiple compute cores within a node to share common model information such as the geometry description, material and composition definitions, and cross section data, thus reducing the memory usage per processor. The parallel performance has been studied by using two complex and representative benchmarks, H-M and BEAVRS benchmark. All simulations were run on Intel Xeon E5-2692 12 core, 2.2 GHz processors at MilkyWay-2 Super Computer with up to 12,288 available computing cores. While employing MPI parallelism, excellent parallel efficiency is achieved even above 12,000 processors and RMC reaches the parallel efficiency of 96% on 12,288 cores for the pin-by-pin computation of the BEAVRS benchmark. While BEAVRS criticality benchmark was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 173,314,000 particles per minute. While pin-wise full core H-M benchmark burnup calculations with millions of depletion regions was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 1,843,200 burnable regions per minute. Results from these studies demonstrate that RMC, using the hybrid parallel model described in this paper, is able to handle pin-wise full core burnup calculations with millions of depletion regions and scales well through thousands of processors. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Compact, low power, high resolution ADC per pixel for large area pixel detectors

A compact ADC circuit can include one or more comparators, and a serial DAC (Digital-to-Analog) circuit that provides a signal to the comparator (or comparators). In addition, the ADC circuit can include a serial DAC redistribution sequencer that can provide a plurality of signals as input to the serial DAC circuit and is subject to a redistribution cycle and which receives as input a signal from a data multiplexer whose input connects electronically to an output of the comparator. The circuit can further include an ADC code register that provides an ADC output that connects electronically to the output of the comparator and the input to the data multiplexer. Shared logic circuitry for sharing common logic between pixels can be included, wherein the shared logic circuitry connects electronically to the data multiplexer and the ADC code register, wherein the shared logic circuitry promotes area and power savings for the pixel detector circuit.

Zimmerman, Tom↗

Compact, low power, high resolution ADC per pixel for large area pixel detectors

A compact ADC circuit can include one or more comparators, and a serial DAC (Digital-to-Analog) circuit that provides a signal to the comparator (or comparators). In addition, the ADC circuit can include a serial DAC redistribution sequencer that can provide a plurality of signals as input to the serial DAC circuit and is subject to a redistribution cycle and which receives as input a signal from a data multiplexer whose input connects electronically to an output of the comparator. The circuit can further include an ADC code register that provides an ADC output that connects electronically to the output of the comparator and the input to the data multiplexer. Shared logic circuitry for sharing common logic between pixels can be included, wherein the shared logic circuitry connects electronically to the data multiplexer and the ADC code register, wherein the shared logic circuitry promotes area and power savings for the pixel detector circuit.

Fahim, Farah↗

ecode - Electron Transport Algorithm Testing v. 1.0

ecode is a Monte Carlo code used for testing algorithms related to electron transport. The code can read basic physics parameters, such as energy-dependent stopping powers and screening parameters. The code permits simple planar geometries of slabs or cubes. Parallelization consists of domain replication, with work distributed at the start of the calculation and statistical results gathered at the end of the calculation. Some basic routines (such as input parsing, random number generation, and statistics processing) are shared with the Integrated Tiger Series codes. A variety of algorithms for uncertainty propagation are incorporated based on the stochastic collocation and stochastic Galerkin methods. These permit uncertainty only in the total and angular scattering cross sections. The code contains algorithms for simulating stochastic mixtures of two materials. The physics is approximate, ranging from mono-energetic and isotropic scattering to screened Rutherford angular scattering and Rutherford energy-loss scattering (simple electron transport models). No production of secondary particles is implemented, and no photon physics is implemented.

Franke, Brian C.↗