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All sources NASA NTRS DOE OSTI

DOE OSTI2016

On-demand data analytics in HPC environments at leadership computing facilities: Challenges and experiences

Scaling-up scientific data analysis and machine learning algorithms for data-driven discovery is a grand challenge that we face today. Despite the growing need for analysis from science domains that are generating `Big Data' from instruments and simulations, building high-performance analytical workflows of data-intensive algorithms have been daunting because: (i) the `Big Data' hardware and software architecture landscape is constantly evolving, (ii) newer architectures impose new programming models, and (iii) data-parallel kernels of analysis algorithms and their performance facets on different architectures are poorly understood. To address these problems, we have: (i) identified scalable data-parallel kernels of popular data analysis algorithms, (ii) implemented `Mini-Apps' of those kernels using different programming models (e.g. Map Reduce, MPI, etc.), (iii) benchmarked and validated the performance of the kernels in diverse architectures. In this paper, we discuss two of those Mini-Apps and show the execution of principal component analysis built as a workflow of the Mini-Apps. We show that Mini-Apps enable scientists to (i) write domain-specific data analysis code that scales on most HPC hardware and (ii) and offers the ability (most times with over a 10x speed-up) to analyze data sizes 100 times the size of what off-the-shelf desktop/workstations of today can handle.

Harney, John↗

DOE OSTI2015

Locality Aware Concurrent Start for Stencil Applications

Stencil computations are at the heart of many physical simulations used in scientific codes. Thus, there exists a plethora of optimization efforts for this family of computations. Among these techniques, tiling techniques that allow concurrent start have proven to be very efficient in providing better performance for these critical kernels. Nevertheless, with many core designs being the norm, these optimization techniques might not be able to fully exploit locality (both spatial and temporal) on multiple levels of the memory hierarchy without compromising parallelism. It is no longer true that the machine can be seen as a homogeneous collection of nodes with caches, main memory and an interconnect network. New architectural designs exhibit complex grouping of nodes, cores, threads, caches and memory connected by an ever evolving network-on-chip design. These new designs may benefit greatly from carefully crafted schedules and groupings that encourage parallel actors (i.e. threads, cores or nodes) to be aware of the computational history of other actors in close proximity. In this paper, we provide an efficient tiling technique that allows hierarchical concurrent start for memory hierarchy aware tile groups. Each execution schedule and tile shape exploit the available parallelism, load balance and locality present in the given applications. We demonstrate our technique on the Intel Xeon Phi architecture with selected and representative stencil kernels. We show improvement ranging from 5.58% to 31.17% over existing state-of-the-art techniques.

Locality Aware execution, jagged tiling↗

DOE OSTI2015

OpenACC acceleration of the Nek5000 spectral element code

We present a case study of porting NekBone, a skeleton version of the Nek5000 code, to a parallel GPU-accelerated system. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. The original NekBone Fortran source code has been used as the base and enhanced by OpenACC directives. The profiling of NekBone provided an assessment of the suitability of the code for GPU systems, and indicated possible kernel optimizations. To port NekBone to GPU systems required little effort and a small number of additional lines of code (approximately one OpenACC directive per 1000 lines of code). The naïve implementation using OpenACC leads to little performance improvement: on a single node, from 16 Gflops obtained with the version without OpenACC, we reached 20 Gflops with the naïve OpenACC implementation. An optimized NekBone version leads to a 43 Gflop performance on a single node. In addition, we ported and optimized NekBone to parallel GPU systems, reaching a parallel efficiency of 79.9% on 1024 GPUs of the Titan XK7 supercomputer at the Oak Ridge National Laboratory.

Computer Science↗

NASA NTRS2008

A New Technique for Retrieval of Tropospheric and Stratospheric Ozone Profiles using Sky Radiance Measurements at Multiple View Angles: Application to a Brewer Spectrometer

This paper describes and applies a new technique for retrieving diurnal variability in tropospheric ozone vertical distribution using ground-based measurements of ultraviolet sky radiances. The measured radiances are obtained by a polarization-insensitive modified Brewer double spectrometer located at Goddard Space Flight Center, in Greenbelt, Maryland, USA. Results demonstrate that the Brewer angular (0-72deg viewing zenith angle) and spectral (303-320 nm) measurements of sky radiance in the solar principal plane provide sufficient information to derive tropospheric ozone diurnal variability. In addition, the Brewer measurements provide stratospheric ozone vertical distributions at least twice per day near sunrise and sunset. Frequent measurements of total column ozone amounts from direct-sun observations are used as constraints in the retrieval. The vertical ozone profile resolution is shown in terms of averaging kernels to yield at least four points in the troposphere-low stratosphere, including good information in Umkehr layer 0 (0-5 km). The focus of this paper is on the derivation of stratospheric and tropospheric ozone profiles using both simulated and measured radiances. We briefly discuss the necessary modifications of the Brewer spectrometer that were used to eliminate instrumental polarization sensitivity so that accurate sky radiances can be obtained in the presence of strong Rayleigh scattering and aerosols. The results demonstrate that including a site-specific and time-dependent aerosol correction, based on Brewer direct-sun observations of aerosol optical thickness, is critical to minimize the sky radiance residuals as a function of observing angle in the optimal estimation inversion algorithm and improve the accuracy of the retrieved ozone profile.

Tzortziou, Maria↗

NASA NTRSDate not supplied

NASA and Blue Origin Collaborative Assessment of Precision Landing Algorithms and Computing

NASA’s Safe and Precise Landing Integrated Capabilities Evolution (SPLICE) project is developing sensor, algorithm, and compute technologies for precision landing and hazard avoidance. These technologies are being tested as an integrated Precision Landing and Hazard Avoidance (PL&HA) system on Blue Origin’s New Shephard suborbital vehicle. A key goal for the computing element of this technology development is to characterize the performance of the SPLICE software workloads on the project’s Descent and Landing Computer (DLC). The DLC is a multi-core processor designed as a surrogate for NASA’s High-Performance Space Computer (HPSC). Measurements of the SPLICE workload performance on the DLC provides NASA insight on how PL&HA capabilities will perform on the HPSC, and guidance on how the SPLICE algorithms can be implemented to best utilize the DLC platform. This insight can also be used to derive requirements to guide trade studies on candidate computing architectures, for use on platforms like Blue Moon. NASA and Blue Origin are collaborating under an agreement to pursue this mutual benefit. Performance metrics collected are based on measurement of common compute resources such as percentage used of memory bandwidth, I/O utilization, interrupt latency, and kernel vs. user space code residency. Where possible existing performance counters and metrics that are part of the operating system kernel are used. As the design has a significant FPGA component, performance counters are identified and instantiated in the fabric to measure DMA performance and interface metrics. Collection of metrics is performed on the DLC with a representative workload that simulates a full landing cycle of the Blue Origin New Shepard vehicle. Consideration is given to the other compute implementations and whether they can run SPLICE algorithms at the same rate and with the same latency as the DLC. One option being considered is the use of a RISC-V soft core instantiated in a radiation resilient FPGA fabric such as the Xilinx KU60. Select algorithms from the SPLICE code will be run for comparison with the DLC. This paper describes how the DLC is instrumented to collect performance measurements of the SPLICE workloads, preliminary results from these measurements, and their implications on SPLICE algorithm implementation. The results of experimentation to derive candidate requirements for architecture trades on a PL&HA computing system are also presented.

computer performance↗

DOE OSTI2026

ENDF/B-VIII.1: Updated Nuclear Reaction Data Library for Science and Applications

The ENDF/B-VIII.1 library is the newest recommended evaluated nuclear data file by the Cross Section Evaluation Working Group (CSEWG) for use in nuclear science and technology applications, and incorporates advances made in the six years since the release of ENDF/B-VIII.0. Among key advances made are that the 239 Pu file was reevaluated by a joint international effort and that updated 16,18 O, 19 F, 28–30 Si, 50–54 Cr, 55 Mn, 54,56,57 Fe, 63,65 Cu, 139 La, 233,235,238 U, and 240,241 Pu neutron nuclear data from the IAEA coordinated INDEN collaboration were adopted. Over 60 neutron dosimetry cross sections were adopted from the IAEA's IRDFF-II library. In addition, the new library includes significant changes for 3 He, 6 Li, 9 Be, 51 V, 88 Sr, 103 Rh, 140,142 Ce, Dy, 181 Ta, Pt, 206–208 Pb, and 234,236 U neutron data, and new nuclear data for the photonuclear, charged-particle and atomic sublibraries. Numerous thermal neutron scattering kernels were reevaluated or provided for the very first time. On the covariance side, work was undertaken to introduce better uncertainty quantification standards and testing for nuclear data covariances. The significant effort to reevaluate important nuclides has reduced bias in the simulations of many integral experiments with particular progress noted for fluorine, copper, and stainless steel containing benchmarks. Data issues hindered the successful deployment of the previous ENDF/B-VIII.0 for commercial nuclear power applications in high burnup situations. These issues were addressed by improving the 238 U and 239,240,241 Pu evaluated data in the resonance region. The new library performance as a function of burnup is similar to the reference ENDF/B-VII.1 library.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Geostatistical Mapping of Salinity Conditioned on Borehole Logs, Montebello Oil Field, California

We present a geostatistics-based stochastic salinity estimation framework for the Montebello Oil Field that capitalizes on available total dissolved solids (TDS) data from groundwater samples as well as electrical resistivity (ER) data from borehole logging. Data from TDS samples (n = 4924) was coded into an indicator framework based on falling below four selected thresholds (500, 1000, 3000, and 10,000 mg/L). Collocated TDS-ER data from the surrounding groundwater basin were then employed to produce a kernel density estimator to establish conditional probabilities for ER data (n = 8 boreholes) falling below the selected TDS thresholds within the Montebello Oil Field area. Directional variograms were estimated from these indicator coded data, and 500 TDS realizations from conditional indicator simulation were generated for the subsurface region above the Montebello Oil Field reservoir. Simulations were summarized as 3D maps of median TDS, most likely salinity class, and probability for exceeding each of the specified TDS thresholds. Results suggested TDS was below 500 mg/L in most of the study area, with a trend toward higher values (500 to 1000 mg/L) to the southwest; consistent with the average regional groundwater flow direction. Discrete localized zones of TDS greater than 1000 mg/L were observed, with one of these zones in the greater than 10,000 mg/L range; however, these areas were not prevalent. The probabilistic approach used here is adaptable and is readily modified to include additional data and types and can be employed in time-lapse salinity modeling through Bayesian updating.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Using Rollback Avoidance to Mitigate Failures in Next-Generation Extreme-Scale Systems

High-performance computing (HPC) systems enable scientists to numerically model complex phenomena in many important physical systems. The next major milestone in the development of HPC systems is the construction of the rst supercomputer capable executing more than an exa op, 10 18 oating point operations per second. On systems of this scale, failures will occur much more frequently than on current systems. As a result, resilience is a key obstacle to building next-generation extremescale systems. Coordinated checkpointing is currently the most widely-used mechanism for handling failures on HPC systems. Although coordinated checkpointing remains e ective on current systems, increasing the scale of today's systems to build next-generation systems will increase the cost of fault tolerance as more and more time is taken away from the application to protect against or recover from failure. Rollback avoidance techniques seek to mitigate the cost of checkpoint/restart by allowing an application to continue its execution rather than rolling back to an earlier checkpoint when failures occur. These techniqes include failure prediction and preventive migration, replicated computation, fault-tolerant algorithms, and softwarebased memory fault correction. In this thesis, we examine how rollback avoidance techniques can be used to address failures on extreme-scale systems. Using a combination of analytic modeling and simulation, we evaluate the potential impact of rollback avoidance on these systems. We then present a novel rollback avoidance technique that exploits similarities in application memory. Finally, we examine the feasibility of using this technique to protect against memory faults in kernel memory.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Test Plan for the Second Reirradiation Heating Test of Fuel Particles from AGR 2 Compact 6-4-1

Post irradiation examination (PIE) and high-temperature heating tests of tristructural isotropic (TRISO)-coated fuel particles and compacts from the second Advanced Gas Reactor (AGR) irradiation experiment, AGR 2, are in progress. This test plan describes the reirradiation and subsequent high-temperature testing of loose fuel particles obtained from AGR 2 compact 6-4-1. Four of these particles will have been cracked, gamma counted, and re-irradiated in the Neutron Radiography (NRAD) reactor prior to the heating test. The heating test will involve heating the particles in the Fuel Accident Condition Simulator (FACS) furnace to a peak temperature of approximately 1600°C while collecting fission products released from the particles for post-heating test analysis. The intention of the test is to assess the retention of fission products in the fuel kernel. Reirradiation of the particles will allow a determination of the retention of short-lived fission products I-131 (t1/2 = 8.02 days) and Xe-133 (t1/2 = 5.2 days) in the kernel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2019

Test Plan for Cyclic Heating of AGR-3/4 Compact 8-1

Post irradiation examination (PIE) and heating tests of tristructural isotropic (TRISO)-coated fuel particles, fuel compacts, and graphite from Advanced Gas Reactor (AGR) irradiation experiment AGR 3/4 are in progress. The AGR-3/4 test train consisted of twelve separate capsules irradiated in the northeast flux trap of the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) from December 14, 2011, to April 12, 2014 (Collin 2015). The plan for the reirradiation in the Neutron Radiography Reactor (NRAD) and subsequent 1200°C heating test of AGR-3/4 Compact 8-1 in the Fuel Accident Condition Simulator (FACS) furnace was described previously in (Stempien 2019). One of the main goals of that test was to assess the retention of short-lived fission products I-131 (t1/2 = 8.02 d) and Xe-133 (t1/2 = 5.2 d) in fuel kernels. Xe-133 release had ostensibly leveled off after approximately 80 hours. An issue with the condensation plate exchanges forced this test to be stopped after approximately 96 hours. The issue was resolved, and the test was restarted by heating FACS back up to 1200°C. During this reheating phase, an additional release of Xe-133, approximately equal in size to the release during the initial heating to 1200°C, was detected in the fission gas monitoring system (FGMS). To test whether this release is related to temperature transients (i.e. from heating and reheating), this new plan will describe three additional temperature cycles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Nekbone performance on GPUs with OpenACC and CUDA Fortran implementations

We present a hybrid GPU implementation and performance analysis of Nekbone, which represents one of the core kernels of the incompressible Navier–Stokes solver Nek5000. The implementation is based on OpenACC and CUDA Fortran for local parallelization of the compute-intensive matrix–matrix multiplication part, which significantly minimizes the modification of the existing CPU code while extending the simulation capability of the code to GPU architectures. Our discussion includes the GPU results of OpenACC interoperating with CUDA Fortran and the gather–scatter operations with GPUDirect communication. We demonstrate performance of up to 552 Tflops on 16, 384 GPUs of the OLCF Cray XK7 Titan.

Computer Science↗

DOE OSTI2019

Detecting baryon acoustic oscillations in dark matter from kinematic weak lensing surveys

Abstract We investigate the feasibility of extracting baryon acoustic oscillations (BAO) from cosmic shear tomography. We particularly focus on the BAO scale precision that can be achieved by future spectroscopy-based, kinematic weak lensing (KWL) surveys in comparison to the traditional photometry-based weak lensing surveys. We simulate cosmic shear tomography data of such surveys with a few simple assumptions to focus on the BAO information, extract the spatial power spectrum, and constrain the recovered BAO feature. Due to the small shape noise and the shape of the lensing kernel, we find that a Dark Energy Task Force Stage IV version of such KWL survey can detect the BAO feature in dark matter by 3σ and measure the BAO scale at the precision level of 4 per cent, while it will be difficult to detect the feature in photometry-based weak lensing surveys. With a more optimistic assumption, a KWL-Stage IV could achieve a ${\sim } 2{{\ \rm per\ cent}}$ BAO scale measurement with 4.9σ confidence. A built-in spectroscopic galaxy survey within such KWL survey will allow cross-correlation between galaxies and cosmic shear, which will tighten the constraint beyond the lower limit we present in this paper and therefore possibly allow a detection of the BAO scale bias between galaxies and dark matter.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Extracting the spectrum of a flow by spatial filtering

We show that the spectrum of a flow field can be extracted within a local region by straightforward filtering in physical space. We find that for a flow with a certain level regularity, the filtering kernel must have a sufficient number of vanishing moments in order for the "filtering spectrum" to be meaningful. Our derivation follows a similar analysis by [1] for the wavelet spectrum, where we show that the filtering kernel has to have at least p vanishing moments in order to correctly extract a spectrum k (-alpha) with (alpha) less/equal to p + 2. For example, any ow with a spectrum shallower than k (-3) can be extracted by a straightforward average on grid-cells of a stencil. We construct two new "simple stencil" kernels, MI and MII, with only two and three fixed stencil weight coefficients, respectively, and that have sufficient vanishing moments to allow for extracting spectra steeper than k(-3). We demonstrate our results using synthetic fields, 2D turbulence from a Direct Numerical Simulation, and 3D turbulence from the JHU Database. Our method guarantees energy conservation and can be useful in both simulations and experiments when a straightforward Fourier analysis is not justified, such as within coherent flow structures covering non-rectangular regions or in geophysical flows on Earth's curved surface.

42 ENGINEERING↗

DOE OSTI2016

On the performance and energy efficiency of sparse linear algebra on GPUs

In this paper we unveil some performance and energy efficiency frontiers for sparse computations on GPU-based supercomputers. We compare the resource efficiency of different sparse matrix–vector products (SpMV) taken from libraries such as cuSPARSE and MAGMA for GPU and Intel’s MKL for multicore CPUs, and develop a GPU sparse matrix–matrix product (SpMM) implementation that handles the simultaneous multiplication of a sparse matrix with a set of vectors in block-wise fashion. While a typical sparse computation such as the SpMV reaches only a fraction of the peak of current GPUs, we show that the SpMM succeeds in exceeding the memory-bound limitations of the SpMV. We integrate this kernel into a GPU-accelerated Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) eigensolver. LOBPCG is chosen as a benchmark algorithm for this study as it combines an interesting mix of sparse and dense linear algebra operations that is typical for complex simulation applications, and allows for hardware-aware optimizations. In a detailed analysis we compare the performance and energy efficiency against a multi-threaded CPU counterpart. The reported performance and energy efficiency results are indicative of sparse computations on supercomputers.

Anzt, Hartwig↗

DOE OSTI2017

Discovery of a Protocluster Associated with a Lyα Blob Pair at z = 2.3

Bright Lyα blobs (LABs)—extended nebulae with sizes of ∼100 kpc and Lyα luminosities of ∼10{sup 44} erg s{sup −1}—often reside in overdensities of compact Lyα emitters (LAEs) that may be galaxy protoclusters. The number density, variance, and internal kinematics of LABs suggest that they themselves trace group-like halos. Here, we test this hierarchical picture, presenting deep, wide-field Lyα narrowband imaging of a 1° × 0.°5 region around a LAB pair at z = 2.3 discovered previously by a blind survey. We find 183 Lyα emitters, including the original LAB pair and three new LABs with Lyα luminosities of (0.9--1.3)×10{sup 43} erg s{sup −1} and isophotal areas of 16–24 arcsec{sup 2}. Using the LAEs as tracers and a new kernel density estimation method, we discover a large-scale overdensity (Boötes J1430+3522) with a surface density contrast of δ{sub Σ}=2.7, a volume density contrast of δ ∼10.4, and a projected diameter of ≈20 comoving Mpc. Comparing with cosmological simulations, we conclude that this LAE overdensity will evolve into a present-day Coma-like cluster with log(M/M{sub ⊙}) ∼ 15.1 ± 0.2. In this and three other wide-field LAE surveys re-analyzed here, the extents and peak amplitudes of the largest LAE overdensities are similar, not increasing with survey size, and implying that they were indeed the largest structures then and today evolve into rich clusters. Intriguingly, LABs favor the outskirts of the densest LAE concentrations, i.e., intermediate LAE overdensities of δ{sub Σ}=1--2. We speculate that these LABs mark infalling protogroups being accreted by the more massive protocluster.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

Physics Integration KErnels (PIKE)

Pike is a software library for coupling and solving multiphysics applications. It provides basic interfaces and utilities for performing code-to-code coupling. It provides simple "black-box" Picard iteration methods for solving the coupled system of equations including Jacobi and Gauss-Seidel solvers. Pike was developed originally to couple neutronics and thermal fluids codes to simulate a light water nuclear reactor for the Consortium for Simulation of Light-water Reactors (CASL) DOE Energy Innovation Hub. The Pike library contains no physics and just provides interfaces and utilities for coupling codes. It will be released open source under a BSD license as part of the Trilinos solver framework (trilinos.org) which is also BSD. This code provides capabilities similar to other open source multiphysics coupling libraries such as LIME, AMP, and MOOSE.

Pawlowski, Roger↗

DOE OSTI2014

Physics Integration KErnels (PIKE)

Pawlowski, Roger↗

DOE OSTI2016

Towards Real-Time Detection and Tracking of Spatio-Temporal Features: Blob-Filaments in Fusion Plasma [Spatio-Temporal Features in Large Irregular Data: Blob-Filaments in Fusion Plasma]

This work was originally motivated the need to identify and track blob filaments, a feature often associated with instability in magnetically confined fusion plasma. Understanding and mitigating such instability would improve fusion reactors and make fusion a truly inexhaustible source of clean energy. Similar spatio-temporal features are important in many other applications, for example, ignition kernels in combustion and tumor cells in a medical image. This work presents an approach for extracting these features by dividing the overall task into three steps: local identification of feature cells, grouping feature cells into extended feature, and tracking movement of feature through overlapping in space. Through our extensive work in parallelization, we demonstrate that this approach can effectively make use of a large number of compute nodes to detect and track blobs in fusion plasma. On a set of 4.3TB data, we observed linear speedup on 1024 processes and completed blob detection in less than three milliseconds using Edison, a Cray XC30 system at NERSC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗