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At least 181 records · Page 10

Effective Software Design and Development for the New Graph Architecture HPC Machines

Software applications need to change and adapt as modern architectures evolve. Nowadays advancement in chip design translates to increased parallelism. Exploiting such parallelism is a major challenge in modern software engineering. Multicore processors are about to introduce a significant change in the way we design and use fundamental data structures. In this work we describe the design and programming principles of a software library of highly concurrent scalable and nonblocking data containers. In this project we have created algorithms and data structures for handling fundamental computations in massively multithreaded contexts, and we have incorporated these into a usable library with familiar look and feel. In this work we demonstrate the first design and implementation of a wait-free hash table. Our multiprocessor data structure design allows a large number of threads to concurrently insert, remove, and retrieve information. Non-blocking designs alleviate the problems traditionally associated with the use of mutual exclusion, such as bottlenecks and thread-safety. Lock-freedom provides the ability to share data without some of the drawbacks associated with locks, however, these designs remain susceptible to starvation. Furthermore, wait-freedom provides all of the benefits of lock-free synchronization with the added assurance that every thread makes progress in a finite number of steps. This implies deadlock-freedom, livelock-freedom, starvation-freedom, freedom from priority inversion, and thread-safety. The challenges of providing the desirable progress and correctness guarantees of wait-free objects makes their design and implementation difficult. There are few wait-free data structures described in the literature. Using only standard atomic operations provided by the hardware, our design is portable; therefore, it is applicable to a variety of data-intensive applications including the domains of embedded systems and supercomputers.Our experimental evaluation shows that our hash table design outperforms the most advanced locking solution, provided by Intel's TBB library, by 22%. When compared to more traditional locking designs we show a performance improvement by a factor of 7.92. When compared to alternative non-blocking designs, our hash table demonstrates solid performance gains in a large majority of cases, typically by a factor of 3.44.

99 GENERAL AND MISCELLANEOUS↗

Final Report: Correctness Tools for Petascale Computing

In the course of developing parallel programs for leadership computing systems, subtle programming errors often arise that are extremely difficult to diagnose without tools. To meet this challenge, University of Maryland, the University of Wisconsin—Madison, and Rice University worked to develop lightweight tools to help code developers pinpoint a variety of program correctness errors that plague parallel scientific codes. The aim of this project was to develop software tools that help diagnose program errors including memory leaks, memory access errors, round-off errors, and data races. Research at Rice University focused on developing algorithms and data structures to support efficient monitoring of multithreaded programs for memory access errors and data races. This is a final report about research and development work at Rice University as part of this project.

97 MATHEMATICS AND COMPUTING↗

Block-Parallel Data Analysis with DIY2

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial, parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.

97 MATHEMATICS AND COMPUTING↗

PIPER: Performance Insight for Programmers and Exascale Runtimes: Guiding the Development of the Exascale Software Stack

The PIPER project set out to develop methodologies and software for measurement, analysis, attribution, and presentation of performance data for extreme-scale systems. Goals of the project were to support analysis of massive multi-scale parallelism, heterogeneous architectures, multi-faceted performance concerns, and to support both post-mortem performance analysis to identify program features that contribute to problematic performance and on-line performance analysis to drive adaptation. This final report summarizes the research and development activity at Rice University as part of the PIPER project. Producing a complete suite of performance tools for exascale platforms during the course of this project was impossible since both hardware and software for exascale systems is still a moving target. For that reason, the project focused broadly on the development of new techniques for measurement and analysis of performance on modern parallel architectures, enhancements to HPCToolkit’s software infrastructure to support our research goals or use on sophisticated applications, engaging developers of multithreaded runtimes to explore how support for tools should be integrated into their designs, engaging operating system developers with feature requests for enhanced monitoring support, engaging vendors with requests that they add hardware measure- ment capabilities and software interfaces needed by tools as they design new components of HPC platforms including processors, accelerators and networks, and finally collaborations with partners interested in using HPCToolkit to analyze and tune scalable parallel applications.

97 MATHEMATICS AND COMPUTING↗

Humin to Human: Organic carbon, sediment, and water fluxes along river corridors in a changing world

This is a presentation with slides on What does it mean to be human? ...humin?; River flow and Hydrographs; Snake River altered hydrograph (Marston et al., 2005); Carbon dynamics are important in rivers; Rivers and streams as carbon sink; Reservoirs for organic carbon; Study sites in Colorado; River morphology; Soil sample collection; Surveys at RMNP; Soil organic carbon content at RMNP; Abandoned channels and Cutoffs; East River channel migration and erosion; Linking hydrology to floodplain sediment flux; Impact of Extreme Floods on Floodplain Sediment; Channel Geometry: RMNP; Beavers dams and multithread channels; Geomorphology and carbon in N. St. Vrain Creek; Geomorphology and carbon along the East River; Geomorphology and carbon in N. St. Vrain Creek; San Marcos River, etc.

54 ENVIRONMENTAL SCIENCES↗

Subcritical Multiplication Ex-Core Calculations with Shift

This report details the development and testing of Virtual Environment for Reactor Applications (VERA) as applied to full core subcritical multiplication ex-core calculations with Shift. The limiting factor in being able to run these detector calculations with Monte Carlo is the amount of computational memory used by a fully-loaded full core problem. The main development features added to VERA in this effort were enabling source biasing and separable weight windows and integrating multithreading in Shift. With these capabilities, a subcritical multiplication detector response calculation on a full core Watts Bar Nuclear Plant Unit 1 (WBN1) ex-core model was successfully run on a moderately sized computing cluster.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NEAMS Milestone Report: M2MS–20OR030102 FW–CADIS PWR Ex-Core Analysis with Shift Through VERA

This report presents the work completed for the NEAMS milestone M2MS–20OR030102 titled "FW–CADIS PWR Ex-Core Analysis with Shift through VERA." The work completed for this milestone includes the implementation, integration, and optimization of memory and performance improvement methods in Shift for fully coupled ex-core calculations through Virtual Environment for Reactor Applications (VERA). Fully coupled in this context means the transfer of moderator boron concentration, pin-wise fission source, depleted compositions, temperatures, and moderator densities from MPACT (with COBRA-TF (CTF)) to Shift. The ability to run ex-core calculations with VERA has been enabled and used for several years by Consortium for Advanced Simulation of Light Water Reactors (CASL) partners. However, this implementation was limited and potentially computationally burdensome. This work has enabled the ability to run higher-fidelity ex-core calculations on moderate computing clusters by focusing on multithreading, domain decomposition, and Forward-Weighted CADIS (FW-CADIS) variance reduction. Tests performed on small cores, a small modular reactor (SMR), and CASL progression problems show very promising memory reduction and computational performance. Recommendations for settings when running fully coupled high-fidelity ex-core calculations with VERA are documented. Without these optimization methods, many processors on a compute node would be left unused for the entire ex-core calculation. Therefore, these methods enable the user to better use the resources available and reduce computation time.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Celeritas R&D Report: Accelerating Geant4

Celeritas is a new Monte Carlo (MC) detector simulation code designed for computationally intensive applications on high-performance heterogeneous architectures. In the past two years Celeritas has advanced from prototyping a Graphics Processing Unit (GPU)-based single physics model in infinite medium to implementing a full set of electromagnetic (EM) physics processes in complex geometries. The current release of Celeritas, version 0.4, has incorporated full device-based navigation, an event loop in the presence of magnetic fields, and detector hit scoring. New functionality incorporates a scheduler to offload electromagnetic physics to the GPU within a Geant4-driven simulation, enabling straightforward integration of Celeritas into the high energy physics (HEP) experimental frameworks CMSSW and ATLAS FullSimLight. On the Perlmutter supercomputer, Celeritas performs EM physics between 3× and 18× faster using the machine’s Nvidia GPUs compared to using only CPUs, corresponding to an electrical power efficiency up to a factor of 5. When running a multithreaded Geant4 ATLAS test beam application with full hadronic physics, using Celeritas to accelerate the EM physics results in an overall simulation speedup of 1.7–2.2× on GPU and 1.2× on CPU. In a CMS test application using tt¯ events and the prototype Run 4 configuration, compared to Geant4 CPU, Celeritas with a Nvidia A100 improves overall throughput up to a factor of 2.7× but cannot be efficiently shared with more than 8 cores.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Developing a GUI for the Robotic Test Stand

The introduction of this poster explains the technology behind DUNE’s far and near detectors and how passing neutrinos generate electrons that drift into a wire grid. I then explain how 3 ASICs manage signals received from electron interception. Next, the poster states how COLDATA chips are undergoing quality control by a Robotic Test Stand using a state machine. I further explained how earlier tests were done via a command line script and the necessity to implement a user-friendly Graphical User Interface with new features a command line can’t implement. For the implementation section, tools and methods for implementation are listed such as Python, tkinter, and GitHub as well as how multithreading and queue implementation was necessary for GUI functionality. Then, I elaborated on the GUIs new features. Finally, I explain how the GUI will be distributed across multiple institutions and future changes planned for the GUI. Photos of the RTS, far detector cave, diagram of anode assembly plane, COLDATA chips, set up tab, result tab, and legacy command line interface are shown.

Gutierrez Villanueva, Jaziel [DuPage Coll.]↗

A Parallel Graph Environment for Real-World Data Analytics Workflows

Economic competitiveness and national security depend increasingly on the insightful analysis of large data sets. The diversity of real-world data sources and analytic workflows impose challenging hardware and software requirements for parallel graph platforms. The irregular nature of graph methods is not supported well by the deep memory hierarchies of conventional distributed systems, requiring new processor and runtime system designs to tolerate memory and synchronization latencies. Moreover, the efficiency of relational table operations and matrix computations are not attainable when data is stored in common graph data structures. In this paper, we present HAGGLE, a high-performance, scalable data analytics platform. The platform’s hybrid data model supports a variety of distributed, thread-safe data structures, parallel programming constructs, and persistent and streaming data. An abstract runtime layer enables us to map the stack to conventional, distributed computer systems with accelerators. The runtime uses multithreading, active messages, and data aggregation to hide memory and synchronization latencies on large-scale systems.

Graph Analytics↗

AN MHD AVALANCHE IN A MULTI-THREADED CORONAL LOOP

For the first time, we demonstrate how an MHD avalanche might occur in a multithreaded coronal loop. Considering 23 non-potential magnetic threads within a loop, we use 3D MHD simulations to show that only one thread needs to be unstable in order to start an avalanche even when the others are below marginal stability. This has significant implications for coronal heating in that it provides for energy dissipation with a trigger mechanism. The instability of the unstable thread follows the evolution determined in many earlier investigations. However, once one stable thread is disrupted, it coalesces with a neighboring thread and this process disrupts other nearby threads. Coalescence with these disrupted threads then occurs leading to the disruption of yet more threads as the avalanche develops. Magnetic energy is released in discrete bursts as the surrounding stable threads are disrupted. The volume integrated heating, as a function of time, shows short spikes suggesting that the temporal form of the heating is more like that of nanoflares than of constant heating.

79 ASTRONOMY AND ASTROPHYSICS↗

HOOKED FLARE RIBBONS AND FLUX-ROPE-RELATED QSL FOOTPRINTS

We studied the magnetic topology of active region 12158 on 2014 September 10 and compared it with the observations before and early in the flare that begins at 17:21 UT (SOL2014-09-10T17:45:00). Our results show that the sigmoidal structure and flare ribbons of this active region observed by the Solar Dynamics Observatory /Atmospheric Imaging Assembly can be well reproduced from a Grad–Rubin nonlinear force-free field extrapolation method. Various inverse-S- and inverse-J-shaped magnetic field lines, which surround a coronal flux rope, coincide with the sigmoid as observed in different extreme-ultraviolet wavelengths, including its multithreaded curved ends. Also, the observed distribution of surface currents in the magnetic polarity where it was not prescribed is well reproduced. This validates our numerical implementation and setup of the Grad–Rubin method. The modeled double inverse-J-shaped quasi-separatrix layer (QSL) footprints match the observed flare ribbons during the rising phase of the flare, including their hooked parts. The spiral-like shape of the latter may be related to a complex pre-eruptive flux rope with more than one turn of twist, as obtained in the model. These ribbon-associated flux-rope QSL footprints are consistent with the new standard flare model in 3D, with the presence of a hyperbolic flux tube located below an inverse-teardrop-shaped coronal QSL. This is a new step forward forecasting the locations of reconnection and ribbons in solar flares and the geometrical properties of eruptive flux ropes.

79 ASTRONOMY AND ASTROPHYSICS↗

DATA-DRIVEN RADIATIVE HYDRODYNAMIC MODELING OF THE 2014 MARCH 29 X1.0 SOLAR FLARE

Spectroscopic observations of solar flares provide critical diagnostics of the physical conditions in the flaring atmosphere. Some key features in observed spectra have not yet been accounted for in existing flare models. Here we report a data-driven simulation of the well-observed X1.0 flare on 2014 March 29 that can reconcile some well-known spectral discrepancies. We analyzed spectra of the flaring region from the Interface Region Imaging Spectrograph ( IRIS ) in Mg ii h and k, the Interferometric BIdimensional Spectropolarimeter at the Dunn Solar Telescope (DST/IBIS) in H α 6563 Å and Ca ii 8542 Å, and the Reuven Ramaty High Energy Solar Spectroscope Imager ( RHESSI ) in hard X-rays. We constructed a multithreaded flare loop model and used the electron flux inferred from RHESSI data as the input to the radiative hydrodynamic code RADYN to simulate the atmospheric response. We then synthesized various chromospheric emission lines and compared them with the IRIS and IBIS observations. In general, the synthetic intensities agree with the observed ones, especially near the northern footpoint of the flare. The simulated Mg ii line profile has narrower wings than the observed one. This discrepancy can be reduced by using a higher microturbulent velocity (27 km s{sup −1}) in a narrow chromospheric layer. In addition, we found that an increase of electron density in the upper chromosphere within a narrow height range of ≈800 km below the transition region can turn the simulated Mg ii line core into emission and thus reproduce the single peaked profile, which is a common feature in all IRIS flares.

79 ASTRONOMY AND ASTROPHYSICS↗

Transition region and chromospheric signatures of impulsive heating events. II. Modeling

Results from the Solar Maximum Mission showed a close connection between the hard X-ray (HXR) and transition region (TR) emission in solar flares. Analogously, the modern combination of RHESSI and IRIS data can inform the details of heating processes in ways that were never before possible. We study a small event that was observed with RHESSI, IRIS, SDO, and Hinode, allowing us to strongly constrain the heating and hydrodynamical properties of the flare, with detailed observations presented in a previous paper. Long duration redshifts of TR lines observed in this event, as well as many other events, are fundamentally incompatible with chromospheric condensation on a single loop. We combine RHESSI and IRIS data to measure the energy partition among the many magnetic strands that comprise the flare. Using that observationally determined energy partition, we show that a proper multithreaded model can reproduce these redshifts in magnitude, duration, and line intensity, while simultaneously being well constrained by the observed density, temperature, and emission measure. We comment on the implications for both RHESSI and IRIS observations of flares in general, namely that: (1) a single loop model is inconsistent with long duration redshifts, among other observables; (2) the average time between energization of strands is less than 10 s, which implies that for a HXR burst lasting 10 minutes, there were at least 60 strands within a single IRIS pixel located on the flare ribbon; (3) the majority of these strands were explosively heated with an energy distribution well described by a power law of slope ≈−1.6; (4) the multi-stranded model reproduces the observed line profiles, peak temperatures, differential emission measure distributions, and densities.

79 ASTRONOMY AND ASTROPHYSICS↗

Open-Source GIS

The components making up an Open Source GIS are explained in this chapter. A map server (Sect. 30.1) can broadly be defined as a software platform for dynamically generating spatially referenced digital map products. The University of Minnesota MapServer (UMN Map Server) is one such system. Its basic features are visualization, overlay, and query. Section 30.2 names and explains many of the geospatial open source libraries, such as GDAL and OGR. The other libraries are FDO, JTS, GEOS, JCS, MetaCRS, and GPSBabel. The application examples include derived GIS-software and data format conversions. Quantum GIS, its origin and its applications explained in detail in Sect. 30.3. The features include a rich GUI, attribute tables, vector symbols, labeling, editing functions, projections, georeferencing, GPS support, analysis, and Web Map Server functionality. Future developments will address mobile applications, 3-D, and multithreading. The origins of PostgreSQL are outlined and PostGIS discussed in detail in Sect. 30.4. It extends PostgreSQL by implementing the Simple Feature standard. Section 30.5 details the most important open source licenses such as the GPL, the LGPL, the MIT License, and the BSD License, as well as the role of the Creative Commons.

Vatsavai, Raju↗

Multicore and Accelerator Development for a Leadership-Class Stellar Astrophysics Code

We describe recent development work on the core-collapse supernova code CHIMERA. CHIMERA has consumed more than 100 million cpu-hours on Oak Ridge Leadership Computing Facility (OLCF) platforms in the past 3 years, ranking it among the most important applications at the OLCF. Most of the work described has been focused on exploiting the multicore nature of the current platform (Jaguar) via, e.g., multithreading using OpenMP. In addition, we have begun a major effort to marshal the computational power of GPUs with CHIMERA. The impending upgrade of Jaguar to Titan a 20+ PF machine with an NVIDIA GPU on many nodes makes this work essential.

Messer, Bronson↗

Enabling Graph Appliance for Genome Assembly

In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

Big data↗

Framework for Network Co-Simulation

The Framework for Network Co-Simulation (FNCS) uses a federated approach to integrate simulations which may have differing time scales. Special consideration is given to integration with a communication network simulation such that inter-simulation messages may be optionally routed through and delayed by such a simulation. In addition, FNCS uses novel time synchronization algorithms to accelerate co-simulation including the application of speculative multithreading. FNCS accomplishes all of these improvements with minimal end user intervention. Simulations can be integrated using FNCS while maintaining their original model input files simply by linking with the FNCS library and making appropriate calls into the FNCS API.

Daily, Jeff↗