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At least 163 records · Page 9

Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗

Decentralized Failure-Tolerant Optimization of Electric Vehicle Charging

We present a decentralized failure-tolerant algorithm for optimizing electric vehicle (EV) charging, using charging stations as computing agents. The algorithm is based on the alternating direction method of multipliers (ADMM) and it has the following features: (i) It handles capacity, peak demand, and ancillary services coupling constraints. (ii) It does not require a central agent collecting information and performing coordination (e.g. an aggregator), instead all agents exchange information and computations are carried out in a fully decentralized fashion. (iii) It can withstand the failure of any number of computing agents, as long as the remaining computing agents are in a connected communications network. We construct this algorithm by reformulating the optimal EV charging problem in a decomposable form, amenable to ADMM, and then developing efficient decentralized solution methods for the subproblems dealing with coupling constraints. We conduct numerical experiments on industry-scale synthetic EV charging datasets, with up to 1,152 charging stations, using a high performance computing cluster. The experiments demonstrate that the proposed algorithm can solve the optimal EV charging problem fast enough to permit the integration of EV charging with real-time electricity markets, even in the presence of failures.

42 ENGINEERING↗

Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict

The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Cooperative Data Sharing: Simple Support for Clusters of SMP Nodes

Libraries like PVM and MPI send typed messages to allow for heterogeneous cluster computing. Lower-level libraries, such as GAM, provide more efficient access to communication by removing the need to copy messages between the interface and user space in some cases. still lower-level interfaces, such as UNET, get right down to the hardware level to provide maximum performance. However, these are all still interfaces for passing messages from one process to another, and have limited utility in a shared-memory environment, due primarily to the fact that message passing is just another term for copying. This drawback is made more pertinent by today's hybrid architectures (e.g. clusters of SMPs), where it is difficult to know beforehand whether two communicating processes will share memory. As a result, even portable language tools (like HPF compilers) must either map all interprocess communication, into message passing with the accompanying performance degradation in shared memory environments, or they must check each communication at run-time and implement the shared-memory case separately for efficiency. Cooperative Data Sharing (CDS) is a single user-level API which abstracts all communication between processes into the sharing and access coordination of memory regions, in a model which might be described as "distributed shared messages" or "large-grain distributed shared memory". As a result, the user programs to a simple latency-tolerant abstract communication specification which can be mapped efficiently to either a shared-memory or message-passing based run-time system, depending upon the available architecture. Unlike some distributed shared memory interfaces, the user still has complete control over the assignment of data to processors, the forwarding of data to its next likely destination, and the queuing of data until it is needed, so even the relatively high latency present in clusters can be accomodated. CDS does not require special use of an MMU, which can add overhead to some DSM systems, and does not require an SPMD programming model. unlike some message-passing interfaces, CDS allows the user to implement efficient demand-driven applications where processes must "fight" over data, and does not perform copying if processes share memory and do not attempt concurrent writes. CDS also supports heterogeneous computing, dynamic process creation, handlers, and a very simple thread-arbitration mechanism. Additional support for array subsections is currently being considered. The CDS1 API, which forms the kernel of CDS, is built primarily upon only 2 communication primitives, one process initiation primitive, and some data translation (and marshalling) routines, memory allocation routines, and priority control routines. The entire current collection of 28 routines provides enough functionality to implement most (or all) of MPI 1 and 2, which has a much larger interface consisting of hundreds of routines. still, the API is small enough to consider integrating into standard os interfaces for handling inter-process communication in a network-independent way. This approach would also help to solve many of the problems plaguing other higher-level standards such as MPI and PVM which must, in some cases, "play OS" to adequately address progress and process control issues. The CDS2 API, a higher level of interface roughly equivalent in functionality to MPI and to be built entirely upon CDS1, is still being designed. It is intended to add support for the equivalent of communicators, reduction and other collective operations, process topologies, additional support for process creation, and some automatic memory management. CDS2 will not exactly match MPI, because the copy-free semantics of communication from CDS1 will be supported. CDS2 application programs will be free to carefully also use CDS1. CDS1 has been implemented on networks of workstations running unmodified Unix-based operating systems, using UDP/IP and vendor-supplied high- performance locks. Although its inter-node performance is currently unimpressive due to rudimentary implementation technique, it even now outperforms highly-optimized MPI implementation on intra-node communication due to its support for non-copy communication. The similarity of the CDS1 architecture to that of other projects such as UNET and TRAP suggests that the inter-node performance can be increased significantly to surpass MPI or PVM, and it may be possible to migrate some of its functionality to communication controllers.

DiNucci, David C.↗

Data Storage for HEP Experiments in the Era of High-Performance Computing

As particle physics experiments push their limits on both the energy and the intensity frontiers, the amount and complexity of the produced data are also expected to increase accordingly. With such large data volumes, next-generation efforts like the HL-LHC and DUNE will rely even more on both high-throughput (HTC) and high-performance (HPC) computing clusters. Full utilization of HPC resources requires scalable and efficient data-handling and I/O. For the last few decades, ROOT has been used by most HEP experiments to store data. However, other storage technologies like HDF5 may perform better in HPC environments. Initial explorations with HDF5 have begun using ATLAS, CMS and DUNE data; the DUNE experiment has also adopted HDF5 for its data-acquisition system. This paper presents the future outlook of the HEP computing and the role of HPC, and a summary of ongoing and future works to use HDF5 as a possible data storage technology for the HEP experiments to use in HPC environments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Enabling Pulse-level Programming, Compilation, and Execution in XACC

Noisy gate-model quantum processing units (QPUs) are currently available from vendors over the cloud, and digital quantum programming approaches exist to run low-depth circuits on physical hardware. These digital representations are ultimately lowered to pulse-level instructions by vendor quantum control systems to affect unitary evolution representative of the submitted digital circuit. Vendors are beginning to open this pulse-level control system to the public via specified interfaces. Robust programming methodologies, software frameworks, and backend simulation technologies for this analog model of quantum computation will prove critical to advancing pulse-level control research and development. Prototypical use cases for this include error mitigation, optimal pulse control, and physics-inspired pulse construction. Here we present an extension to the XACC quantum-classical software framework that enables pulse-level programming for superconducting, gate-model quantum computers, and a novel, general, and extensible pulse-level simulation backend for XACC that scales on classical compute clusters via MPI. Our work enables custom backend Hamiltonian definitions and gate-level compilation to available pulses with a focus on performance and scalability. We end with a demonstration of this capability, and show how to use XACC for pertinent pulse-level programming tasks.

97 MATHEMATICS AND COMPUTING↗

An Extension of the Athena++ Code Framework for Radiation-magnetohydrodynamics in General Relativity Using a Finite-solid-angle Discretization

We extend the general-relativistic magnetohydrodynamics (GRMHD) capabilities of Athena++ to incorporate radiation. The intensity field in each finite-volume cell is discretized in angle, with explicit transport in both space and angle properly accounting for the effects of gravity on null geodesics, and with matter and radiation coupled in a locally implicit fashion. Here we describe the numerical procedure in detail, verifying its correctness with a suite of tests. Motivated in particular by black hole accretion in the high-accretion-rate, thin-disk regime, we demonstrate the application of the method to this problem. With excellent scaling on flagship computing clusters, the port of the algorithm to the GPU-enabled AthenaK code now allows the simulation of many previously intractable radiation-GRMHD systems.

79 ASTRONOMY AND ASTROPHYSICS↗

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗

Summary of VERA Core Simulator Performance Improvements

This report describes the performance improvements made to the VERA Core Simulator (VERA CS) during FY2016. At the beginning of the year, a timing study was performed to identify areas of the code where the run-times could be improved. This study identified six broad areas for improvement: • Cross section lookup and CMFD stabilization, • CTF parallel partitioning, • MOC methodology, • Subgroup methodology, • MOC parallel partitioning, and • CMFD Krylov solution techniques. The goal of this work was to reduce the VERA-CS run-times so a complete cycle depletion could be run with 1,000 cores overnight (i.e., the “1,000 core depletion” criterion). This goal was set by our industry partners so they could achieve reasonable turnaround on medium-sized computer clusters. The results presented in this report show a code speed-up by a factor of 5, which successfully satisfies the goal set by industry.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Numerical Modeling of Nanoelectronic Devices

Nanoelectronic Modeling 3-D (NEMO 3-D) is a computer program for numerical modeling of the electronic structure properties of a semiconductor device that is embodied in a crystal containing as many as 16 million atoms in an arbitrary configuration and that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantummechanical behavior of the device resolved to the atomistic level of granularity. The system of electrons in the device is represented by a sparse Hamiltonian matrix that contains hundreds of millions of terms. NEMO 3-D solves the matrix equation on a Beowulf-class cluster computer, by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. In a recent update of NEMO 3-D, a new strain treatment, parameterized for bulk material properties of GaAs and InAs, was developed for two tight-binding submodels. The utility of the NEMO 3-D was demonstrated in an atomistic analysis of the effects of disorder in alloys and, in particular, in bulk In(x)Ga(l-x)As and in In0.6Ga0.4As quantum dots.

Klimeck, Gerhard↗

Molecular-Level Insights into Oxygen Reduction Catalysis by Graphite-Conjugated Active Sites

With a combination of experimental and computational investigations, we design a consistent mechanistic model for the oxygen reduction reaction (ORR) at molecularly well-defined graphite-conjugated catalyst ( GCC ) active sites featuring aryl-pyridinium moieties ( N+-GCC ). ORR catalysis at glassy carbon surfaces modified with N+-GCC fragments displays near-first-order dependence in O 2 partial pressure and near-zero-order dependence on electrolyte pH. Tafel analysis suggests an equilibrium one-electron transfer process followed by a rate-limiting chemical step at modest overpotentials that transitions to a rate-limiting electron transfer sequence at higher overpotentials. Finite-cluster computational modeling of the N+-GCC active site reveals preferential O 2 adsorption at electrophilic carbons alpha to the pyridinium moiety. Together, the experimental and computational data indicate that ORR proceeds via a proton-decoupled O 2 activation sequence involving either concerted or stepwise electron transfer and adsorption of O 2 , which is then followed by a series of electron/proton transfer steps to generate water and turn over the catalytic cycle. The introduced mechanistic model serves as a roadmap for the bottom-up synthesis of highly active N-doped carbon ORR catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From Data to Models and Analytics: An Integrated Scientific Computing Platform to Accelerate Environmental Research SBIR Phase I (Final Technical Report)

Phase I research was conducted to investigate the technical feasibility of an integrated open source platform GeoLib to provide turnkey solutions for model-data integration for environmental systems science (ESS), using modern web technologies, advances in HPC and cloud computing and high-performance visualization. A key feature of our platform is that it minimizes and automates data movement between data storage and computing systems. Another critical feature of the design is that it enables users to perform high-fidelity post-processing by performing high-performance visualization server-side and in-situ on the compute cluster close to the data. The investigation, which was performed over a 12-month period ending April 2019, centered on developing prototype software to demonstrate the key enabling technologies required for this system. This included: (i) rapid access to data from multiple remote sources, via a unified data interface; (ii) software for scalable geospatial visualization of raster, vector, and point cloud data on the web; (iii) development of an easy-to-use API for creating simulation and modeling workflows; (iv) remote data visualization and processing on middle-tier servers; and (v) remote data processing on high-performance computing systems. A critical part of this work is that all of these capabilities be accessible to end users through standard desktop tools such as Project Jupyter, which is widely adopted for ESS simulation and modeling.

97 MATHEMATICS AND COMPUTING↗

Rapid Calculation of Max-Min Fair Rates for Multi-Commodity Flows in Fat-Tree Networks

Max-min fairness is often used in the performance modeling of interconnection networks. Existing methods to compute max-min fair rates for multi-commodity flows have high complexity and are computationally infeasible for large networks. In this paper, we show that by considering topological features, this problem can be solved efficiently for the fat-tree topology that is widely used in data centers and high performance compute clusters. Several efficient new algorithms are developed for this problem, including a parallel algorithm that can take advantage of multi-core and shared-memory architectures. Using these algorithms, we demonstrate that it is possible to find the max-min fair rate allocation for multi-commodity flows in fat-tree networks that support tens of thousands of nodes. We evaluate the run-time performance of the proposed algorithms and show improvement in orders of magnitude over the previously best known method. Finally, we further demonstrate a new application of max-min fair rate allocation that is only computationally feasible using our new algorithms.

97 MATHEMATICS AND COMPUTING↗

Thermal Management for FPGA Nodes in HPC Systems

The integration of FPGAs into large-scale computing systems is gaining attention. In these systems, real-time data handling for networking, tasks for scientific computing, and machine learning can be executed with customized datapaths on reconfigurable fabric within heterogeneous compute nodes. At the same time, thermal management, particularly battling the cooling cost and guaranteeing the reliability, is a continuing concern. The introduction of new heterogeneous components into HPC nodes only adds further complexities to thermal modeling and management. The thermal behavior of multi-FPGA systems deployed within large compute clusters is less explored. Here, we first show that the thermal behaviors of different FPGAs of the same generation can vary due to their physical locations in a rack and process variation, even though they are running the same tasks. We present a machine learning–based model to capture the thermal behavior of each individual FPGA in the cluster. We then propose two thermal management strategies guided by our thermal model. First, we mitigate thermal variation and hotspots across the cluster by proactive thermal-aware task placement. Under the tested system and benchmarks, we achieve up to 26.4° C and on average 13.3° C system temperature reduction with no performance penalty. Second, we utilize this thermal model to guide HLS parameter tuning at the task design stage to achieve improved thermal response after deployment.

97 MATHEMATICS AND COMPUTING↗

Ocelot: An Interactive, Efficient Distributed Compression-As-a-Service Platform With Optimized Data Compression Techniques

Large volumes of data generated by scientific simulations, genome sequencing, and other applications need to be moved among clusters for data collection/analysis. Data compression techniques have effectively reduced data storage and transfer costs. However, users' requirements on interactively controlling both data quality and compression ratios are non-trivial to fulfill. Here, we propose a novel Compression-as-a-Service (CaaS) platform called Ocelot with four important contributions: (1) It offers real-time visualization, interactive compression, and transfer of scientific datasets. (2) It incorporates new strategies for compressing diverse types of datasets more effectively than traditional methods. (3) It provides an effective method for estimating the compression ratio and execution time of compression tasks. (4) Experiments on multiple real-world datasets on geographically distributed computers show that Ocelot can significantly improve data transfer efficiency with a performance gain of more than 10x in computing clusters with relatively slow networks.

compression as a service (CaaS)↗

Open-Source Software for Modeling of Nanoelectronic Devices

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

Oyafuso, Fabiano↗

PATCHWORK: A Multipatch Infrastructure for Multiphysics/Multiscale/Multiframe Fluid Simulations

Here, we present a "multipatch" infrastructure for the numerical simulation of fluid problems in which subregions require different grid scales, different grid geometries, different physical equations, or different reference frames. Its key element is a sophisticated client–router–server framework for efficiently linking processors supporting different regions ("patches") that must exchange boundary data. This infrastructure may be used with a wide variety of fluid dynamics codes; the only requirement is that their primary dependent variables be the same in all patches, e.g., fluid mass density, internal energy density, and velocity. Its structure can accommodate either Newtonian or relativistic dynamics. The overhead imposed by this system is both problem and computer cluster architecture dependent. Compared to a conventional simulation using the same number of cells and processors employed on a problem not requiring multipatch methods, the cell update per processor rate decreases by an amount that can range from negligible to a factor of a few; however, even in these problems, the infrastructure can permit substantial decreases in the total number of cell updates required.

97 MATHEMATICS AND COMPUTING↗