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At least 289 records · Page 16

DSN Beowulf Cluster-Based VLBI Correlator

The NASA Deep Space Network (DSN) requires a broadband VLBI (very long baseline interferometry) correlator to process data routinely taken as part of the VLBI source Catalogue Maintenance and Enhancement task (CAT M&E) and the Time and Earth Motion Precision Observations task (TEMPO). The data provided by these measurements are a crucial ingredient in the formation of precision deep-space navigation models. In addition, a VLBI correlator is needed to provide support for other VLBI related activities for both internal and external customers. The JPL VLBI Correlator (JVC) was designed, developed, and delivered to the DSN as a successor to the legacy Block II Correlator. The JVC is a full-capability VLBI correlator that uses software processes running on multiple computers to cross-correlate two-antenna broadband noise data. Components of this new system (see Figure 1) consist of Linux PCs integrated into a Beowulf Cluster, an existing Mark5 data storage system, a RAID array, an existing software correlator package (SoftC) originally developed for Delta DOR Navigation processing, and various custom- developed software processes and scripts. Parallel processing on the JVC is achieved by assigning slave nodes of the Beowulf cluster to process separate scans in parallel until all scans have been processed. Due to the single stream sequential playback of the Mark5 data, some ramp-up time is required before all nodes can have access to required scan data. Core functions of each processing step are accomplished using optimized C programs. The coordination and execution of these programs across the cluster is accomplished using Pearl scripts, PostgreSQL commands, and a handful of miscellaneous system utilities. Mark5 data modules are loaded on Mark5 Data systems playback units, one per station. Data processing is started when the operator scans the Mark5 systems and runs a script that reads various configuration files and then creates an experiment-dependent status database used to delegate parallel tasks between nodes and storage areas (see Figure 2). This script forks into three processes: extract, translate, and correlate. Each of these processes iterates on available scan data and updates the status database as the work for each scan is completed. The extract process coordinates and monitors the transfer of data from each of the Mark5s to the Beowulf RAID storage systems. The translate process monitors and executes the data conversion processes on available scan files, and writes the translated files to the slave nodes. The correlate process monitors the execution of SoftC correlation processes on the slave nodes for scans that have completed translation. A comparison of the JVC and the legacy Block II correlator outputs reveals they are well within a formal error, and that the data are comparable with respect to their use in flight navigation. The processing speed of the JVC is improved over the Block II correlator by a factor of 4, largely due to the elimination of the reel-to-reel tape drives used in the Block II correlator.

Rogstad, Stephen P.↗

Massively parallel implementation of the multi-reference Brillouin-Wigner CCSD method

This paper reports the parallel implementation of the Brillouin Wigner MultiReference Coupled Cluster method with Single and Double excitations (BW-MRCCSD). Preliminary tests for systems composed of 304 and 440 correlated obritals demonstrate the performance of our implementation across 1000 cores and clearly indicate the advantages of using improved task scheduling. Possible ways for further improvements of the parallel performance are also delineated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Final Report: Super Instruction Architecture for Scalable Parallel Computations

The most advanced methods for reliable and accurate computation of the electronic structure of molecular and nano systems are the coupled-cluster techniques. These high-accuracy methods help us to understand, for example, how biological enzymes operate and contribute to the design of new organic explosives. The ACES III software provides a modern, high-performance implementation of these methods optimized for high performance parallel computer systems, ranging from small clusters typical in individual research groups, through larger clusters available in campus and regional computer centers, all the way to high-end petascale systems at national labs, including exploiting GPUs if available. This project enhanced the ACESIII software package and used it to study interesting scientific problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

2011 Status of the Automatic Alignment System for the National Ignition Facility

Automated alignment for the National Ignition Facility (NIF) is accomplished using a large-scale parallel control system that directs 192 laser beams along the 300-m optical path. The beams are then focused down to a 50-micron spot in the middle of the target chamber. The entire process is completed in less than 50 minutes. The alignment system commands 9,000 stepping motors for highly accurate adjustment of mirrors and other optics. 41 control loops per beamline perform parallel processing services running on a LINUX cluster to analyze high-resolution images of the beams and their references. This paper describes the status the NIF automatic alignment system and the challenges encountered as NIF development has transitioned from building the laser, to becoming a research project supporting a 24 hour, 7 day laser facility. NIF is now a continuously operated system where performance monitoring is increasingly more critical for operation, maintenance, and commissioning tasks. Equipment wear and the effects of high energy neutrons from fusion experiments are issues which alter alignment efficiency and accuracy. New sensors needing automatic alignment assistance are common. System modifications to improve efficiency and accuracy are prevalent. Handling these evolving alignment and maintenance needs while minimizing the impact on NIF experiment schedule is expected to be an on-going challenge for the planned 30 year operational life of NIF.

42 ENGINEERING↗

Studies with Cluster upstream and downstream of the bow shock: An experimenter's perspective

Some open questions in the physics of bow shock formation, the evolution of the particle distributions from solar wind into the magnetosheath, and the acceleration of ions at the moment of the shock are summarized. A layout of the current situation is presented in view of recent theoretical developments and the new diagnostic tools provided by the Cluster mission. The transition of ions across the quasi-perpendicular bow shock and their downstream thermalization are discussed. The processes and spatial scales are found to be species dependent and are discussed for H(+), He(2+), and He(+). The theory of particle acceleration at quasi-parallel shocks are reviewed. It is shown how Cluster can study the time variable structures of the shock as predicted by hybrid simulation. It is emphasized that high time resolution measurement with simultaneous species separation is necessary for the study of the ion acceleration. Suggestions for the spacecraft separations at the bow shock are suggested.

Moebius, E.↗

Modeling mesoscale fission gas behavior in UO2 by directly coupling the phase field method to spatially resolved cluster dynamics

Abstract Fission gas release within uranium dioxide nuclear fuel occurs as gas atoms diffuse through grains and arrive at grain boundary (GB) bubbles; these GB bubbles grow and interconnect with grain edge bubbles; and grain edge tunnels grow and connect to free surfaces. In this study, a hybrid multi-scale/multi-physics simulation approach is presented to investigate these mechanisms of fission gas release at the mesoscale. In this approach, fission gas production, diffusion, clustering to form intragranular bubbles, and re-solution within grains are included using spatially resolved cluster dynamics in the Xolotl code. GB migration and intergranular bubble growth and coalescence are included using the phase field method in the MARMOT code. This hybrid model couples Xolotl to MARMOT using the MultiApp and Transfer systems in the MOOSE framework, with Xolotl passing the arrival rate of gas atoms at GBs and intergranular bubble surfaces to MARMOT and MARMOT passing evolved GBs and bubble surface positions to Xolotl. The coupled approach performs well on the two-dimensional simulations performed in this work, producing similar results to the standard phase field model when Xolotl does not include fission gas clustering or re-solution. The hybrid model performs well computationally, with a negligible cost of coupling Xolotl and MARMOT and good parallel scalability. The hybrid model predicts that intragranular fission gas clustering and bubble formation results in up to 70% of the fission gas being trapped within grains, causing the increase in the intergranular bubble fraction to slow by a factor of six. Re-solution has a small impact on the fission gas behavior at 1800 K but it has a much larger impact at 1000 K, resulting in a twenty-times increase in the concentration of single gas atoms within grains. Due to the low diffusion rate, this increase in mobile gas atoms only results in a small acceleration in the growth of the intergranular bubble fraction. Finally, the hybrid model accounts for migrating GBs sweeping up gas atoms. This results in faster intergranular bubble growth with smaller initial grain sizes, since the additional GB migration results in more immobile gas clusters reaching GBs.

Kim, Dong-Uk↗

A Formal Model for Real-Time Parallel Computation

The imposition of real-time constraints on a parallel computing environment--- specifically high-performance, cluster-computing systems--- introduces a variety of challenges with respect to the formal verification of the system's timing properties. In this paper, we briefly motivate the need for such a system, and we introduce an automaton-based method for performing such formal verification. We define the concept of a consistent parallel timing system: a hybrid system consisting of a set of timed automata (specifically, timed Buechi automata as well as a timed variant of standard finite automata), intended to model the timing properties of a well-behaved real-time parallel system. Finally, we give a brief case study to demonstrate the concepts in the paper: a parallel matrix multiplication kernel which operates within provable upper time bounds. We give the algorithm used, a corresponding consistent parallel timing system, and empirical results showing that the system operates under the specified timing constraints.

formal methods↗

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

OKeefe, Matthew↗

Editorial to the special issue on the 2015 TOUGH Symposium

This Special Issue of Transport in Porous Media features selected papers from the 2015 TOUGH Symposium, which took place on September 28–30, 2015, in Berkeley, California, USA. Such symposia are held every 3 years and are a forum where users of the TOUGH family of numerical simulators meet for an open exchange on the code applications and recent enhancements. The TOUGH codes (TOUGH is an acronym for Transport of Unsaturated Groundwater and Heat) were originally developed in the early 1980s for geothermal reservoir simulation by a team of researchers at the Lawrence Berkeley National Laboratory (LBNL) headed by Karsten Pruess (see http://esd.lbl.gov/TOUGH). The TOUGH codes have a modular structure in which different fluid components can be incorporated into the code by means of a replaceable equation of state (EOS) package. Since its first release, a variety of important EOS modules have been developed, enabling the modeling of volatile organic compounds, decay chains of multiple radionuclides, gas hydrates, tight and shale gas behavior, enhanced oil recovery, and supercritical water and CO 2 . Derivatives and descendants of the basic TOUGH code include coupled multi-phase flow and reactive chemical transport; coupled thermo-hydrologic-mechanical processes; inverse modeling for parameter estimation, sensitivity analysis, and uncertainty quantification; and parallelization for multi-core PCs, workstation clusters, and supercomputers. The TOUGH codes have been applied to a large variety of problems, including geothermal and petroleum reservoir engineering, nuclear waste and CO 2 geologic sequestration, subsurface environmental remediation, methane gas hydrate production, compressed air energy storage, and many other energy and environmental applications. Finally, the international TOUGH user community currently numbers almost 400 organizations (research laboratories, government agencies, private companies, universities, etc.) in over 60 countries.

99 GENERAL AND MISCELLANEOUS↗

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗

Solving global optimization problems on GPU cluster

The paper contains the results of investigation of a parallel global optimization algorithm combined with a dimension reduction scheme. This allows solving multidimensional problems by means of reducing to data-independent subproblems with smaller dimension solved in parallel. The new element implemented in the research consists in using several graphic accelerators at different computing nodes. The paper also includes results of solving problems of well-known multiextremal test class GKLS on Lobachevsky supercomputer using tens of thousands of GPU cores.

97 MATHEMATICS AND COMPUTING↗

Combining Tensor Decompositions and Graph Analytics to Provide Cyber Situational Awareness at HPC Scale

This paper describes MADHAT (Multidimensional Anomaly Detection fusing HPC, Analytics, and Tensors), an integrated workflow that demonstrates the applicability of HPC resources to the problem of maintaining cyber situational awareness. MADHAT combines two high-performance packages: ENSIGN for large-scale sparse tensor decompositions and HAGGLE for graph analytics. Tensor decompositions isolate coherent patterns of network behavior in ways that common clustering methods based on distance metrics cannot. Parallelized graph analysis then uses directed queries on a representation that combines the elements of identified patterns with other available information (such as additional log fields, domain knowledge, network topology, whitelists and blacklists, prior feedback, and published alerts) to confirm or reject a threat hypothesis, collect context, and raise alerts. MADHAT was developed using the collaborative HPC Architecture for Cyber Situational Awareness (HACSAW) research environment and evaluated on structured network sensor logs collected from Defense Research and Engineering Network (DREN) sites using HPC resources at the U.S. Army Engineer Research and Development Center DoD Supercomputing Resource Center (ERDC DSRC). To date, MADHAT has analyzed logs with over 650 million entries.

Cyber security, Tensor decomposition, graph analyt↗

PV Hosting Capacity Estimation: Experiences with Scalable Framework

Hosting capacity is an indication of the amount of solar photovoltaics (PV) that can be hosted in a distribution system without additional changes to infrastructure or oper-ations. This paper presents a framework for estimating the PV hosting capacity at scale. First, we analyze computational, modeling and other key challenges of performing relevant, large-scale simulations, provided along with the experiences and lessons learned. Then, we develop two open-source Python-based software tools to conduct repeatable distribution analyses: the Distribution Integration Solution Cost Options (DISCO) for configuring and analyzing simulations and the Job Automation and Deployment Engine (JADE) for parallelizing jobs on high-performance computing clusters. A case study of hosting capacity estimation for the SMART-DS San Francisco (SFO) 2000+ synthetic feeders, is used to demonstrate the capability of the developed DISCO+JADE framework and tools. The framework and tools can help utilities assess the overall hosting capacity of their service territory, which can help them better plan for the overall upgrade costs to integrate more PV in the future. The experiences are shared to aid the tool users and researchers to conduct relevant studies and research.

distributed energy resources↗

iTOUGH2 v7.1

iTOUGH2 (inverse TOUGH2) provides inverse modeling capabilities for TOUGH2, a simulator for multi-dimensional, multi-phase, multi-component, non-isothermal flow and transport in fractured porous media. iTOUGH2 performs sensitivity analyses, data-worth analyses, parameter estimation, and uncertainty propagation analyses in geosciences and reservoir engineering and other application areas. iTOUGH2 supports a number of different combinations of fluids and components (equation-of-state (EOS) modules). In addition, the optimization routines implemented in iTOUGH2 can also be used for sensitivity analysis, automatic model calibration, and uncertainty quantification of any external code that uses text-based input and output files using the PEST protocol. iTOUGH2 solves the inverse problem by minimizing a non-linear objective function of the weighted differences between model output and the corresponding observations. Multiple minimization algorithms (derivative-free, gradient-based, and second-order; local and global) are available. iTOUGH2 also performs Latin Hypercube Monte Carlo simulations for uncertainty propagation analyses. A detailed residual and error analysis is provided. This upgrade includes (a) global sensitivity analysis methods, (b) dynamic memory allocation (c) additional input features and output analyses, (d) increased forward simulation capabilities, (e) parallel execution on multicore PCs and Linux clusters, and (f) bug fixes.

Finsterle, Stefan↗

Status on the Development of a Modeling and Simulation Framework for the Economic Assessment of Nuclear Hybrid Energy Systems

An effort to design and build a modeling and simulation framework to assess the economic viability of Nuclear Hybrid Energy Systems (NHES) was undertaken in fiscal year 2015 (FY15). The purpose of this report is to document the various tasks associated with the development of such a framework and to provide a status on its progress. Several tasks have been accomplished. First, starting from a simulation strategy, a rigorous mathematical formulation has been achieved in which the economic optimization of a Nuclear Hybrid Energy System is presented as a constrained robust (under uncertainty) optimization problem. Some possible algorithms for the solution of the optimization problem are presented. A variation of the Simultaneous Perturbation Stochastic Approximation algorithm has been implemented in RAVEN and preliminary tests have been performed. The development of the software infrastructure to support the simulation of the whole NHES has also moved forward. The coupling between RAVEN and an implementation of the Modelica language (OpenModelica) has been implemented, migrated under several operating systems and tested using an adapted model of a desalination plant. In particular, this exercise was focused on testing the coupling of the different code systems; testing parallel, computationally expensive simulations on the INL cluster; and providing a proof of concept for the possibility of using surrogate models to represent the different NHES subsystems. Another important step was the porting of the RAVEN code under the Windows™ operating system. This accomplishment makes RAVEN compatible with the development environment that is being used for dynamic simulation of NHES components. A very simplified model of a NHES on the electric market has been built in RAVEN to confirm expectations on the analysis capability of RAVEN to provide insight into system economics and to test the capability of RAVEN to identify limit surfaces even for stochastic constraints. This capability will be needed in the future to enforce the stochastic constraints on the electric demand coverage from the NHES. The development team gained experience with many of the tools that are currently envisioned for use in the economic analysis of NHES and completed several important steps. Given the complexity of the project, preference has been given to a structural approach in which several independent efforts have been used to build the cornerstone of the simulation framework. While this is good approach in establishing such a complex framework, it may delay reaching more complete results on the performance of analyzed system configurations. The integration of the previously reported exergy analysis approach was initially proposed as part of this milestone. However, in reality, the exergy-based apportioning of cost will take place only in a second stage of the implementation since it will be used to properly allocate cost among the different NHES subsystems. Therefore, exergy does not appear at the level of the main drivers in the analysis framework; the latter development of the base framework is the focus of this report.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Computing the Properties of Matter with Leadership Computing Resources (Closeout Report for DE-SC0018121)

In order to add more capabilities to Halide, we have designed a new framework called Tiramisu and integrated this framework into Halide. Since Tiramisu enables Halide to target heterogeneous architectures, our development efforts have been refocused on Tiramisu. Most high-performance computer systems today are complex and increasingly heterogeneous; they may have CPUs, GPUs and FPGAs. Achieving best performance requires taking full advantage of all these different architectures. To address this issue, we have designed Tiramisu, an optimization framework that enables Halide (and other DSLs) to target heterogeneous architectures. Tiramisu is an optimization framework that takes as input a high level, architecture-independent representation of code and a set of scheduling and data mapping commands that guide code transformation. The input can either be generated by a domain-specific language (DSL) compiler such as Halide or directly written by a programmer. Tiramisu then applies the user-specified code and data-layout transformations and generates an architecture-specific, low-level intermediate representation (IR) that takes advantage of modern architectural features such as multicore parallelism, non-uniform memory (NUMA) hierarchies, clusters, and accelerators like GPUs and FPGAs. We integrated Tiramisu within Halide and implemented a representative set of benchmarks to evaluate this integration. Tiramisu is now open source and is available for public use (http://tiramisu-compiler.org/). A paper about Tiramisu was published, it shows that Tiramisu extends Halide with many new capabilities and that Tiramisu can generate efficient code for multicores, GPUs, FPGAs and distributed heterogeneous systems. The performance of code generated by the Tiramisu backends matches or exceeds hand optimized reference implementations. For example, the multicore backend matches the highly optimized Intel MKL library on many kernels and shows speedups reaching 4x over the original Halide. In addition to making Tiramisu more robust, we have used Tiramisu to implement a set of representative tensor operation for constructing baryon building blocks required for multi baryon contractions in LQCD. In order to implement this code, we needed to generalize Tiramisu in two ways: first we needed to support indirect array accesses, and second, we needed to add support for complex numbers to Tiramisu. The code generated by Tiramisu is 6x faster than the reference code. Our efforts towards an MPI based multi-node version of tiramisu have matured and the resulting code scales well on multiple nodes (tests up to 512 KNL nodes have been undertaken).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A comparison using APPL and PVM for a parallel implementation of an unstructured grid generation program

Efforts to parallelize the VGRIDSG unstructured surface grid generation program are described. The inherent parallel nature of the grid generation algorithm used in VGRIDSG was exploited on a cluster of Silicon Graphics IRIS 4D workstations using the message passing libraries Application Portable Parallel Library (APPL) and Parallel Virtual Machine (PVM). Comparisons of speed up are presented for generating the surface grid of a unit cube and a Mach 3.0 High Speed Civil Transport. It was concluded that for this application, both APPL and PVM give approximately the same performance, however, APPL is easier to use.

Arthur, Trey↗