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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Streaming data analytics via message passing with application to graph algorithms

The need to process streaming data, which arrives continuously at high-volume in real-time, arises in a variety of contexts including data produced by experiments, collections of environmental or network sensors, and running simulations. Streaming data can also be formulated as queries or transactions which operate on a large dynamic data store, e.g. a distributed database. We describe a lightweight, portable framework named PHISH which enables a set of independent processes to compute on a stream of data in a distributed-memory parallel manner. Datums are routed between processes in patterns defined by the application. PHISH can run on top of either message-passing via MPI or sockets via ZMQ. The former means streaming computations can be run on any parallel machine which supports MPI; the latter allows them to run on a heterogeneous, geographically dispersed network of machines. We illustrate how PHISH can support streaming MapReduce operations, and describe streaming versions of three algorithms for large, sparse graph analytics: triangle enumeration, subgraph isomorphism matching, and connected component finding. Lastly, we also provide benchmark timings for MPI versus socket performance of several kernel operations useful in streaming algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Integration Of PanDA Workload Management System With Supercomputers for ATLAS and Data Intensive Science

The.LHC, operating at CERN, is leading Big Data driven scientific explorations. Experiments at the LHC explore the fundamental nature of matter and the basic forces that shape our universe. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 150 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data centers are physically scattered all over the world. While PanDA currently uses more than 250,000 cores with a peak performance of 0.3 petaFLOPS, LHC data taking runs require more resources than grid can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, in particular with Titan supercomputer at Oak Ridge Leadership Computing Facility. Current approach utilizes modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single threaded workloads in parallel on LCFs multi-core worker nodes. This implementation was tested with a variety of Monte-Carlo workloads on several supercomputing platforms for ALICE and ATLAS experiments and it is in full pro duction for the ATLAS since September 2015. We will present our current accomplishments with running PanDA at supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facilities infrastructure for High Energy and Nuclear Physics as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

PROTEUS-SN User Manual

PROTEUS-SN is a three-dimensional, highly scalable, high-fidelity neutron transport code developed at Argonne National Laboratory. The code is applicable to all spectrum reactor transport calculations, particularly those in which a high degree of fidelity is needed either to represent spatial detail or to resolve solution gradients. PROTEUS-SN solves the second order formulation of the transport equation using the continuous Galerkin finite element method in space, the discrete ordinates approximation in angle, and the multigroup approximation in energy. PROTEUS-SN’s parallel methodology permits the efficient decomposition of the problem by both space and angle, permitting large problems to run efficiently on hundreds of thousands of cores. PROTEUS-SN can also be used in serial or on smaller compute clusters (10’s to 100’s of cores) for smaller homogenized problems, although it is generally more computationally expensive than traditional homogenized methodology codes. PROTEUS-SN has been used to model partially homogenized systems, where regions of interest are represented explicitly and other regions are homogenized to reduce the problem size and required computational resources. PROTEUS-SN solves forward and adjoint eigenvalue problems and permits both neutron upscattering and downscattering. An adiabatic kinetics option has recently been included for performing simple time-dependent calculations in addition to standard steady state calculations. PROTEUS-SN handles void and reflective boundary conditions. Multigroup cross sections can be generated externally using the MC2-3 fast reactor multigroup cross section generation code or internally using the cross section application programming interface (API) which can treat the subgroup or resonance table libraries. PROTEUS-SN is written in Fortran 90 and also includes C preprocessor definitions. The code links against the PETSc, METIS, HDF5, and MPICH libraries. It optionally links against the MOAB library and is a part of the SHARP multi-physics suite for coupled multi-physics analysis of nuclear reactors. This user manual describes how to set up a neutron transport simulation with the PROTEUS-SN code. A companion methodology manual describes the theory and algorithms within PROTEUS-SN.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Institute for Sustained Performance, Energy, and Resilience (SuPER)

The University of Tennessee (UTK) and University of Texas at El Paso (UTEP) partnership supported the three main thrusts of the SUPER project---performance, energy, and resilience. The UTK-UTEP effort thus helped advance the main goal of SUPER, which was to ensure that DOE's computational scientists can successfully exploit the emerging generation of high performance computing (HPC) systems. This goal is being met by providing application scientists with strategies and tools to productively maximize performance, conserve energy, and attain resilience. The primary vehicle through which UTK provided performance measurement support to SUPER and the larger HPC community is the Performance Application Programming Interface (PAPI). PAPI is an ongoing project that provides a consistent interface and methodology for collecting hardware performance information from various hardware and software components, including most major CPUs, GPUs and accelerators, interconnects, I/O systems, and power interfaces, as well as virtual cloud environments. The PAPI software is widely used for performance modeling of scientific and engineering applications---for example, the HOMME (High Order Methods Modeling Environment) climate code, and the GAMESS and NWChem computational chemistry codes---on DOE supercomputers. PAPI is widely deployed as middleware for use by higher-level profiling, tracing, and sampling tools (e.g., CrayPat, HPCToolkit, Scalasca, Score-P, TAU, Vampir, PerfExpert), making it the de facto standard for hardware counter analysis. PAPI has established itself as fundamental software infrastructure in every application domain (spanning academia, government, and industry), where improving performance can be mission critical. Ultimately, as more application scientists migrate their applications to HPC platforms, they will benefit from the extended capabilities this grant brought to PAPI to analyze and optimize performance in these environments, whether they use PAPI directly, or via third-party performance tools. Capabilities added to PAPI through this grant include support for new architectures such as the lastest GPU and Xeon Phi accelerators, and advanced power measurement and management features. Another important topic for the UTK team was providing support for a rich ecosystem of different fault management strategies in the context of parallel computing. Our long term efforts have been oriented toward proposing flexible strategies and providing building boxes that application developers can use to build the most efficient fault management technique for their application. These efforts span across the entire software spectrum, from theoretical models of existing strategies to easily assess their performance, to algorithmic modifications to take advantage of specific mathematical properties for data redundancy and to extensions to widely used programming paradigms to empower the application developers to deal with all types of faults. We have also continued our tight collaborations with users to help them adopt these technologies to ensure their application always deliver meaningful scientific data. Large supercomputer systems are becoming more and more power and energy constrained, and future systems and applications running on them will need to be optimized to run under power caps and/or minimize energy consumption. The UTEP team contributed to the SUPER energy thrust by developing power modeling methodologies and investigating power management strategies. Scalability modeling results showed that some applications can scale better with respect to an increasing power budget than with respect to only the number of processors. Power management, in particular shifting power to processors on the critical path of an application execution, can reduce perturbation due to system noise and other sources of runtime variability, which are growing problems on large-scale power-constrained computer systems.

42 ENGINEERING↗
DOE OSTI2022

High-performance and high-fidelity Monte Carlo solutions to the BEAVRS benchmark

The BEAVRS (Benchmark for Evaluation and Validation of Reactor Simulation) benchmark is solved by PRAGMA, the GPU-based continuous energy Monte Carlo code. The resulting solutions are comprised of the detailed simulation results of two cycles, each of which consists of the zero power physics test (ZPPT) and the core depletion calculations. The ZPPT consists of characteristic parameters, such as critical boron concentration (CBC), control rod bank worth, isothermal temperature coefficients, and assembly-wise detector signal, which are compared with measured data provided by the benchmark administration. The core depletion calculations were performed for both the hot full power and the load follow modes, and the comparison was made with the measured or deduced CBCs and assembly-wise detector signals. In the load follow calculations, the operating power history was approximately applied to simulate the real operation as closely as possible. PRAGMA performed the various calculations with a tremendous number of histories ranging up to hundreds of millions per cycle, exploiting GPUs' massively parallel performance. The load follow run time was shorter than 16 hours on a single rack of computing nodes mounded with 24 gaming GPUs with a remarkable agreement with the measurements for most comparisons. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2019

High resolution ENDOR spectroscopy combined with quantum chemical calculations reveals the structure of the nitrogenase Janus intermediate E4(4H)

We have shown that the key state in N2 reduction to two NH3 by the enzyme nitrogenase is the E4(4H), ‘Janus’ intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed the catalytic multi-metallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of structure - the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of ‘anchor’ Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties of the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed by DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a pulsed-ENDOR protocol (‘PESTRE’) to obtain absolute hyperfine-interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its ‘anchoring’ Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result: the freeze-trapped, lowest-energy Janus intermediate structure is E4(4H)(a).

Hoeke, Veronica↗
DOE OSTI2019

IAEA Coordinated Research Project on HTGR Physics, Thermal Hydraulics, and Depletion Uncertainty Analysis: PHISICS/RELAP5-3D Results for the Phase III Coupled Core Exercises

This report details the Parallel and Highly Innovative Simulation for INL Code System (PHISICS)/Reactor Excursions and Leak Analysis Program (RELAP5)-3D results obtained for the neutronics stand-alone core exercises defined for Phase II of the International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on high-temperature gas cooled reactor (HTGR) uncertainty analysis in modeling (UAM). The Phase II models and results are linked to the earlier Standardized Computer Analyses for Licensing Evaluation (SCALE)/Sampler/New ESC-based Weighting Transport (NEWT) data generated for the lattice physics (lattice) stage Phase I of the CRP. The focus of this report is the propagation of cross-section uncertainties from the lattice to the core calculation (core) phase of the prismatic 350 megawatt (MW) General Atomics (GA) Modular HTGR (MHTGR). The Phase II neutronics exercises consist of two sub-cases (II-2a and II-2b) specified for the fresh and mixed core loading of the MHTGR-350 prismatic high-temperature reactor design. Exercises II-2a and II-2b are performed without temperature feedback using isothermal temperature profiles. For the nominal lattice physics (i.e., best-estimate) model, a series of fresh and depleted single block and super cell SCALE/KENO and SCALE/NEWT models were developed at Idaho National Laboratory (INL) to assess the impact of spectral effects on the few-group cross sections. A combination of these lattice cells were used in a super cell calculation to construct 8-group cross-section libraries for use in the INL-developed PHISICS/RELAP5-3D code suite. The block-level homogenized libraries were assigned to the 220 fuel zones utilized in the MHTGR-350 PHISICS core model, according to the fresh and mixed fresh/depleted core loading pattern. In order to evaluate the effect of uncertainty propagation, several sets consisting of 1,000 perturbed NEWT lattice and PHISICS/RELAP5-3D core calculations were performed using the SCALE 6.2 ENDF/B-VII.1 cross-section co-variance data and the stochastic sampling module Sampler in SCALE 6.2.0. The Figures of Merit (FOM) investigated include the mean and standard deviation uncertainty values obtained for the eigenvalues, control rod worth values, block-averaged power profiles, power axial offsets, and isothermal temperature feedback coefficients. A sensitivity study on the main nuclide reaction contributors to the FOM uncertainties has not yet been performed since the SCALE/PHISICS/RAVEN coupling with ENDF/B-VII co-variance data is still being developed. It was found that uncertainties in the cross sections lead to uncertainties in the local power values of up to 1.5%. The variances between the fresh and mixed/depleted core models are not as large as the axial variations between the top and bottom within each core model. The core eigenvalue uncertainty is approximately 0.5%, which is significant in comparison to typical eigenvalue difference targets (less than ~0.1% for LWRs). The power peaking and axial offset uncertainties are smaller (0.10% – 0.15%) and probably below the level of significance in typical core design metrics. The use of an 8-group energy structure slightly under-estimates some of the uncertainties, but in absolute terms, the uncertainty results are reasonably close to the 26-group results. The 26- and 8-group mean and nominal results differ by a larger degree, and if it can be afforded in terms of calculation resources, the 26-group structure should be used for HTGR calculations. The 8-group structure can, however, still be useful for reasonably accurate uncertainty assessments of transient cases where computational time is important. It was furthermore found that the use of a super cell during the cross-section generation process for better representation of the spectral environment at the core periphery did not lead to significant changes in the core eigenvalues, axial offset, and power peaking uncertainties. The impact of the super cell cross sections on the nominal and mean eigenvalues is, however, important enough (0.6% – 1.1% lower) to justify the use of these super cells for HTGR core simulation to represent the softer spectral environment in the core peripheral regions for nominal best-estimate calculations. The use of super cells for HTGR uncertainty studies is, therefore, not strictly necessary, but the improvements in nominal results could justify their use.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

A cloud computing approach to massively-parallel distributed stochastic optimization with application to geomechanical reservoir characterization

Many search strategies used to optimize parameters during hydrologic model calibration are inherently limited in that simulations must be performed sequentially in order for the algorithm to converge. As a result, the overall time required to reach a solution increases linearly with the number of steps necessary. In contrast, sampling strategies that attempt to approximate the posterior distribution of the parameters do not require the model simulations to be run in sequence and therefore invite the use of a massively parallel approach across heterogeneous computing environments. We apply a cloud computing methodology to this problem where a head node running on Amazon Web Services continuously produces candidate models that are distributed to arbitrary compute environments to run the simulation, in our case Clemson’s Palmetto cluster computer. Thus the time required to obtain a sufficient number of samples to produce an adequate approximation of the posterior distribution of the parameters is limited by the number of available compute sites. Monte Carlo sampling of the posterior space would be duplicative and inefficient, thus we combine Latin hypercube methods with genetic algorithms to ensure that no large regions of the parameter space are left unexplored, and that high probability regions are investigated thoroughly. We independently assess the fit to different types of data sets without the need to construct a single objective function. Sets of Pareto optimal models are particularly valuable when the quality and information content of data is poorly known or conceptual model errors exist in our simulation. We illustrate our approach for a problem where in situ strain data are used to calibrate the parameters of an oil reservoir in the Avant oil field in Oklahoma. We use well injection and shut-in to stress a deep (500m) confined formation, and observe the geomechanical response using borehole strainmeters installed in the shallow subsurface (30m). These data were then used to calibrate the poroelastic properties of the reservoir and caprock along with the geometry of an elliptic channel associated with the formation. Using our approach we are able to identify issues with model error as well as substantial tradeoffs that occur within the parameters.

inversion, stochastic, geomechanics, poroelastic, ↗
DOE OSTI2015

Improving Block-level Efficiency with scsi-mq

Current generation solid-state storage devices are exposing a new bottlenecks in the SCSI and block layers of the Linux kernel, where IO throughput is limited by lock contention, inefficient interrupt handling, and poor memory locality. To address these limitations, the Linux kernel block layer underwent a major rewrite with the blk-mq project to move from a single request queue to a multi-queue model. The Linux SCSI subsystem rework to make use of this new model, known as scsi-mq, has been merged into the Linux kernel and work is underway for dm-multipath support in the upcoming Linux 4.0 kernel. These pieces were necessary to make use of the multi-queue block layer in a Lustre parallel filesystem with high availability requirements. We undertook adding support of the 3.18 kernel to Lustre with scsi-mq and dm-multipath patches to evaluate the potential of these efficiency improvements. In this paper we evaluate the block-level performance of scsi-mq with backing storage hardware representative of a HPC-targerted Lustre filesystem. Our findings show that SCSI write request latency is reduced by as much as 13.6%. Additionally, when profiling the CPU usage of our prototype Lustre filesystem, we found that CPU idle time increased by a factor of 7 with Linux 3.18 and blk-mq as compared to a standard 2.6.32 Linux kernel. Our findings demonstrate increased efficiency of the multi-queue block layer even with disk-based caching storage arrays used in existing parallel filesystems.

Cluster Computing↗
DOE OSTI2016

Algorithmic Improvements for Portable Event-Based Monte Carlo Transport Using the Nvidia Thrust Library

High performance computing environments are progressively moving towards many-core computing architectures. The Los Alamos National Laboratory Trinity machine, available in late 2016, will use both Intel Xeon Haswell processors and Intel Xeon Phi Knights Landing many integrated core (MIC) coprocessors. The Lawrence Livermore National Laboratory Sierra machine, available in 2018, will use an IBM PowerPC architecture along with Nvidia graphics processing units (GPUs). Applications that must work in this supercomputing environment must continue to adapt in order to take advantage of the diverse hardware architectures that are coming. A significant consideration is not only the performance of the application on a given platform but also the portability of the application to other platforms. The algorithmic improvements presented in this paper build upon recently-reported work on event-based Monte Carlo transport in the ALPSMC code that models particle transport in one-dimensional binary stochastic media. That paper discussed the lack of available vectorization in the traditional history-based algorithm used for Monte Carlo transport and presented a data parallel event-based algorithm implemented using the Nvidia Thrust library for portability. The performance of the data parallel event-based algorithm implemented using Thrust was compared to a native CUDA implementation. The conclusions from that work were that the Thrust library abstraction technique caused too significant a loss in performance but that the event-based method was a viable option that should be further investigated. In this paper, we describe algorithmic improvements to the data parallel event-based algorithm previously presented. We made further algorithmic optimizations to the event-based CUDA implementation, most notably: data structure changes, a new conditional particle removal scheme in the event-based process, and the use of multiple GPUs. In addition to improvements to the algorithm, we re-implemented the Thrust version from the now further optimized CUDA version, giving a greater chance for success at a performant abstraction. Finally, we revisited our previous assumptions about the inability of the history-based method to achieve performance on vector style architectures such as the MICs and GPUs, with surprising and promising results. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

A rheological model for loose sands with insights from DEM

A rheological model for loose granular media is developed to capture both solid-like and fluid-like responses during shearing. The proposed model is built by following the mathematical structure of an extended Kelvin–Voigt model, where an elastic spring and plastic slider act in parallel to a viscous damper. This arrangement requires the partition of the total stress into rate-independent and rate-dependent stress components. To model the solid-like behavior, a simple frictional plasticity model is adopted without modifications, thus contributing to the rate-independent stress. Instead, the fluid-like or rate-dependent stress is further decomposed into deviatoric and volumetric parts, by proposing a new formulation based on a combination of the μ(I) relation, originally developed under pressure-controlled shear, with a pressure-shear rate relation derived under volume-controlled shear. The proposed formulation allows the model to capture both the increase in the friction coefficient and the enhanced dilation at high shear rates. High-fidelity simulation data, obtained from discrete element method and multiscale modelling, are used to evaluate the performance of the proposed constitutive model. The model provides accurate results under both drained and undrained simple shear paths across a wide range of shear rates. Furthermore, it successfully reproduces at much lower computational cost the flowslide mobility computed through multiscale simulations, which is primarily regulated by the shear rate dependence of the material properties during the dynamic runout stage.

Elasticity↗
DOE OSTI2015

Parallel Tensor Compression for Large-Scale Scientific Data.

As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8 TB of data. By viewing the data as a dense five way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 10000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed memory parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. We provide accompanying analysis of the computation and communication costs of the algorithms. To demonstrate the compression and accuracy of the method, we apply our approach to real-world data sets from combustion science simulations. We also provide detailed performance results, including parallel performance in both weak and strong scaling experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Status Report on the Water-Based NSTF RCCS Capability: Preparations and Design for the Transformation of the Natural Convection Shutdown Heat Removal Test Facility (NSTF) From Air to Water-based Cooling

The following report provides an overview of the current status of the water-based transformation, including details of the design, geometry, and fabrication of the test section and network piping, for the ½ scale water-based NSTF program at Argonne National Laboratory. In early FY2015, efforts towards a water-based design began in parallel with on-going air-based work, and began by identifying top level objectives of the transformation. Scaling studies and preparation tasks with computational modeling were carried out to guide the design decisions, minimize distortions, and ensure relevant data among scales. This entailed close collaboration with AREVA, whose water-based RCCS (included as part of their 625 MWt SC-HTGR) served as the primary design basis for incorporation into the NSTF. A literature review of previous works was made, with an emphasis placed on similar facilities, relevance to passive decay heat removal, and details pertaining to two-phase flow and measurement techniques. The study focused on input from key designers and a thermal analysis of existing cooling panels (e.g. at TAMU and UW-Madison) and two proposed AREVA cooling panels. A base case was used as a reference point for parametric studies of effects from varying tube spacing (pitch), tube diameter, fin thickness, and materials. Then, a structural analysis was performed to ensure safe material stresses during high temperature operation. Details of the pipe network geometry and guidelines for design of the water storage tank are finally presented, followed by engineering drawings in the appendix. The results of this study have identified a suitable configuration to support both the ANL/DOE project goals and the DOE vision to provide AREVA with data suitable for characterizing the RCCS of their full scale HTGR design. The dimensions were not selected for optimal RCCS performance, but instead to serve as a representative yet bounding configuration for future implementation into a full scale design. Scaling distortions are unavoidable; however, they can be accurately predicted based on earlier works of derived similarity solutions. Flexibility remained a primary design philosophy, and will allow the test facility to easily accommodate future alterations. The final design for the test section and network piping is as follows: riser tubes: 1.5” Schedule 160, 5.91” (150-mm) pitch, 304L stainless, heat transfer panels: 5/16” plates, 4.01” (102-mm) width, full penetration weld to risers, 304L stainless, split into 4 panels per riser separated by horizontal 1/8” gaps, test section: Eight (x8) riser tubes and nine (x9) heat transfer panels, fabricated into banks of two (x2) riser tubes and three (x3) fins, joined to form single section, and network geometry: 4.0” Schedule 40, 304L stainless. Details of the water storage tank will reflect competing effects such as thermal hydraulic phenomena during single and two-phase operation. These considerations include mixing during single-phase jet penetration, condensation of rising bubbles during two-phase discharge, bubble entrainment into the liquid outlet, and liquid carry-over into the steam outlet.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

Planning for Pre-Exascale Platform Environment (Fiscal Year 2015 Level 2 Milestone 5216)

This Plan for ASC Pre-Exascale Platform Environments document constitutes the deliverable for the fiscal year 2015 (FY15) Advanced Simulation and Computing (ASC) Program Level 2 milestone Planning for Pre-Exascale Platform Environment. It acknowledges and quantifies challenges and recognized gaps for moving the ASC Program towards effective use of exascale platforms and recommends strategies to address these gaps. This document also presents an update to the concerns, strategies, and plans presented in the FY08 predecessor document that dealt with the upcoming (at the time) petascale high performance computing (HPC) platforms. With the looming push towards exascale systems, a review of the earlier document was appropriate in light of the myriad architectural choices currently under consideration. The ASC Program believes the platforms to be fielded in the 2020s will be fundamentally different systems that stress ASC’s ability to modify codes to take full advantage of new or unique features. In addition, the scale of components will increase the difficulty of maintaining an errorfree system, thus driving new approaches to resilience and error detection/correction. The code revamps of the past, from serial- to vector-centric code to distributed memory to threaded implementations, will be revisited as codes adapt to a new message passing interface (MPI) plus “x” or more advanced and dynamic programming models based on architectural specifics. Development efforts are already underway in some cases, and more difficult or uncertain aspects of the new architectures will require research and analysis that may inform future directions for program choices. In addition, the potential diversity of system architectures may require parallel if not duplicative efforts to analyze and modify environments, codes, subsystems, libraries, debugging tools, and performance analysis techniques as well as exploring new monitoring methodologies. It is difficult if not impossible to selectively eliminate some of these activities until more information is available through simulations of potential architectures, analysis of systems designs, and informed study of commodity technologies that will be the constituent parts of future platforms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

ICED: An Integrated CGRA Framework Enabling DFVS-Aware Acceleration

oarse-grained reconfigurable arrays (CGRAs) are a promising solution to enable energy-efficient acceleration of applications from different domains. By leveraging reconfiguration at the functional level, they can adapt to significantly different computational patterns. Existing CGRA mapping approaches extract instruction-level parallelism, exploit loop-pipelining opportunities, guarantee the data dependency, and target high throughput of a given loop. However, the recurrence data-dependency in the DFG and the mismatch between required and available computing/communication resources complicate the mapping, and might lead to significant unbalances in the utilization of the CGRA's tiles. This results in wasted power for tiles with low utilization. Applying dynamic voltage and frequency scaling (DVFS) can potentially solve this challenge and improve energy efficiency by adjusting voltage and frequency of different tiles independently. CGRAs have also been successful in accelerating data-dependent streaming applications. However, in these applications, the execution time of each kernel in the pipeline might dynamically vary depending on the characteristics of the input. This also leads to under-utilization of resources for the dynamically changing kernels that do not limit the application throughput. DVFS can also improve energy efficiency for these applications by dynamically changing the voltage and frequency levels of tiles that host non performance-constraining kernels. This paper proposes ICEDTEA -- an integrated DVFS-aware framework to map applications on CGRAs that support power islands. ICEDTEA proposes a CGRA architecture supporting DVFS islands at varying granularity (from a single tile to a group of tiles) and the related DVFS-aware compilation and mapping toolchain. ICEDTEA is the first work that introduces DVFS support for spatio-temporal CGRAs at power-island levels. The experimental evaluation shows that ICEDTEA improves average utilization by 2.3$\times$ and energy-efficiency by 1.32$\times$ over a conventional CGRA. With streaming applications, ICEDTEA improves energy efficiency by 1.12$\times$ over a state-of-the-art CGRA that introduces partial dynamic reconfiguration to adapt to variations in kernels' throughput.

Tan, Cheng↗
DOE OSTI2016

Reducing I/O variability using dynamic I/O path characterization in petascale storage systems

In petascale systems with a million CPU cores, scalable and consistent I/O performance is becoming increasingly difficult to sustain mainly because of I/O variability. Furthermore, the I/O variability is caused by concurrently running processes/jobs competing for I/O or a RAID rebuild when a disk drive fails. We present a mechanism that stripes across a selected subset of I/O nodes with the lightest workload at runtime to achieve the highest I/O bandwidth available in the system. In this paper, we propose a probing mechanism to enable application-level dynamic file striping to mitigate I/O variability. We also implement the proposed mechanism in the high-level I/O library that enables memory-to-file data layout transformation and allows transparent file partitioning using subfiling. Subfiling is a technique that partitions data into a set of files of smaller size and manages file access to them, making data to be treated as a single, normal file to users. Here, we demonstrate that our bandwidth probing mechanism can successfully identify temporally slower I/O nodes without noticeable runtime overhead. Experimental results on NERSC’s systems also show that our approach isolates I/O variability effectively on shared systems and improves overall collective I/O performance with less variation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Improving I/O-aware Workflow Scheduling via Data Flow Characterization and trade-off Analysis

The scientific computing paradigm has transitioned from compute-intensive to I/O-intensive and memory-intensive in the past decade, especially when data-driven science has become common practice. Numerous empirical I/O-aware scheduling optimizations have been developed by incorporating I/O capacity and bandwidth as constraints into scheduling. Unfortunately, there is a lack of data flow (I/O) characterization tool and an understanding of trade-offs between concurrency, locality, and I/O bandwidth. To bridge the gap, this work 1) presents a set of descriptors to characterize, organize, and visualize I/O profiles, including flow size, I/O bandwidth, and operation count, which group data flows by I/O types, tasks, and files; 2) proposes an I/O Roofline model-based trade-off analysis to find the optimal trade-off between flow operational intensity, concurrency, and flow performance. The I/O descriptors generate useful insights into complicated I/O behaviors, suggesting distinct concurrency, storage, and scheduling to be used by types, tasks, and files. The proposed trade-off analysis guides scheduling decisions that generate resource assignment with the best flow parallelism. We evaluate our I/O-aware scheduling methodology on a highly I/O-intensive workflow–1000 Genomes. The experimental results demonstrate speedups of up to 2.4× compared to the state-of-the- art methods.

Guo, Luanzheng [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2022

Advanced architectures for high-performance quantum networking

As practical quantum networks prepare to serve an ever-expanding number of nodes, there has grown a need for advanced auxiliary classical systems that support the quantum protocols and maintain compatibility with the existing fiber-optic infrastructure. We propose and demonstrate a quantum local area network design that addresses current deployment limitations in timing and security in a scalable fashion using commercial off-the-shelf components. First, we employ White Rabbit switches to synchronize three remote nodes with ultra-low timing jitter, significantly increasing the fidelities of the distributed entangled states over previous work with Global Positioning System clocks. Second, using a parallel quantum key distribution channel, we secure the classical communications needed for instrument control and data management. Therefore, the conventional network that manages our entanglement network is secured using keys generated via an underlying quantum key distribution layer, preserving the integrity of the supporting systems and the relevant data in a future-proof fashion.

97 MATHEMATICS AND COMPUTING↗