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At least 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Scalar quantum field theories as a benchmark for near-term quantum computers

Quantum field theory (QFT) simulations are a potentially important application for noisy intermediate scale quantum (NISQ) computers. The ability of a quantum computer to emulate a QFT therefore constitutes a natural application-centric benchmark. Foundational quantum algorithms to simulate QFT processes rely on fault-tolerant computational resources, but to be useful on NISQ machines, error-resilient algorithms are required. Here we outline and implement a hybrid algorithm to calculate the lowest energy levels of the paradigmatic 1+1–dimensional $\phi$ 4 interacting scalar QFT. We calculate energy splittings and compare results with experimental values obtained on currently available quantum hardware. We show that the accuracy of mass-renormalization calculations represents a useful metric with which near-term hardware may be benchmarked. Finally, we also discuss the prospects of scaling the algorithm to full simulation of interacting QFTs on future hardware.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Exploiting communication concurrency on high performance computing systems

Although logically available, applications may not exploit enough instantaneous communication concurrency to maximize hardware utilization on HPC systems. This is exacerbated in hybrid programming models such as SPMD+OpenMP. We present the design of a "multi-threaded" runtime able to transparently increase the instantaneous network concurrency and to provide near saturation bandwidth, independent of the application configuration and dynamic behavior. The runtime forwards communication requests from application level tasks to multiple communication servers. Our techniques alleviate the need for spatial and temporal application level message concurrency optimizations. Experimental results show improved message throughput and bandwidth by as much as 150% for 4KB bytes messages on InfiniBand and by as much as 120% for 4KB byte messages on Cray Aries. For more complex operations such as all-to-all collectives, we observe as much as 30% speedup. This translates into 23% speedup on 12,288 cores for a NAS FT implemented using FFTW. We also observe as much as 76% speedup on 1,500 cores for an already optimized UPC+OpenMP geometric multigrid application using hybrid parallelism.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

New technologies as decision aids for the advancement of ecological risk assessment

Moore's law states that the number of transistors that can be placed on an integrated circuit doubles every two years (Moore, 1975). This has led to a steady increase in the processing power of computers over time, and technology is now enhancing and advancing software and scientific applications, which has enabled computationally intensive methods such as machine learning, data science, modeling, and simulation. The advancement of computers and data-driven algorithms is profoundly impacting people's lives. It is changing the way we work, the way we learn, and the way we interact with the world around us. Here, this editorial will discuss how scientists can benefit from the latest technology advancements and related tools by incorporating them into the ecological risk assessment (ERA) to study ecosystems as a way to create refined assessments and accelerate the turnaround times.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The SODA Approach: Leveraging High-Level Synthesis for Hardware/Software Co-design and Hardware Specialization: Invited

Novel "converged" applications combine phases of scientific simulation with data analysis and machine learning. Each computational phase can benefit from specialized accelerators. However, algorithms evolve so quickly that mapping them on existing accelerators is suboptimal or even impossible. This paper presents the SODA (Software Defined Accelerators) framework, a modular, multi-level, open-source, no-human-in-the-loop, hardware synthesizer that enables end-to-end generation of specialized accelerators. SODA is composed of SODA-Opt, a high-level frontend developed in MLIR that interfaces with domain-specific programming frameworks and allows performing system level design, and Bambu, a state-of-the-art high-level synthesis engine that can target different device technologies. The framework implements design space exploration as compiler optimization passes. We show how the modular, yet tight, integration of the high-level optimizer and lower-level HLS tools enables the generation of accelerators optimized for the computational patterns of converged applications. We then discuss some of the research opportunities that such a framework allows, including system-level design, profile driven optimization, and supporting new optimization metrics.

Bohm Agostini, Nicolas↗
DOE OSTI2022

Neuromorphic Computing is Turing-Complete

Neuromorphic computing is a non-von Neumann computing paradigm that performs computation by emulating the human brain. Neuromorphic systems are extremely energy-efficient and known to consume thousands of times less power than CPUs and GPUs. They have the potential to drive critical use cases such as autonomous vehicles, edge computing and internet of things in the future. For this reason, they are sought to be an indispensable part of the future computing landscape. Neuromorphic systems are mainly used for spike-based machine learning applications, although there are some non-machine learning applications in graph theory, differential equations, and spike-based simulations. These applications suggest that neuromorphic computing might be capable of general-purpose computing. However, general-purpose computability of neuromorphic computing has not been established yet. In this work, we prove that neuromorphic computing is Turing-complete and therefore capable of general-purpose computing. Specifically, we present a model of neuromorphic computing, with just two neuron parameters (threshold and leak), and two synaptic parameters (weight and delay). We devise neuromorphic circuits for computing all the μ-recursive functions (i.e., constant, successor and projection functions) and all the μ-recursive operators (i.e., composition, primitive recursion and minimization operators). Given that the μ-recursive functions and operators are precisely the ones that can be computed using a Turing machine, this work establishes the Turing-completeness of neuromorphic computing.

Date, Prasanna↗
DOE OSTI2021

Bringing OpenCL to Commodity RISC-V CPUs

The importance of open-source hardware has been increasing in recent years with the introduction of the RISC-V Open ISA. This has also accelerated the push for support of the open-source software stack from compiler tools to full-blown operating systems. Parallel computing with today’s Application Programming Interfaces such as OpenCL has proven to be effective at leveraging the parallelism in commodity multi-core processors and programmable parallel accelerators. However, to the best of our knowledge, there is currently no publicly available implementation of OpenCL targeting commodity RISC-V processors that is accessible to the open-source community. Besides opening RISC-V to the existing rich variety of scientific parallel applications, OpenCL also provides access to a unique genre of benchmarks useful in computer architecture research. In this work, we extended an Open-source implementation of OpenCL to target RISC-V CPUs. Our work not only cover commodity multi-core RISC-V processors, but also plethora of low- profile embedded RISC-V CPUs that often do not support atomic instructions or multi-threading.

Tine, Blaise↗
DOE OSTI2022

Constant-depth circuits for dynamic simulations of materials on quantum computers

Abstract Dynamic simulation of materials is a promising application for near-term quantum computers. Current algorithms for Hamiltonian simulation, however, produce circuits that grow in depth with increasing simulation time, limiting feasible simulations to short-time dynamics. Here, we present a method for generating circuits that are constant in depth with increasing simulation time for a specific subset of one-dimensional (1D) materials Hamiltonians, thereby enabling simulations out to arbitrarily long times. Furthermore, by removing the effective limit on the number of feasibly simulatable time-steps, the constant-depth circuits enable Trotter error to be made negligibly small by allowing simulations to be broken into arbitrarily many time-steps. For an N -spin system, the constant-depth circuit contains only $\mathcal {O}(N^{2})$ O ( N 2 ) CNOT gates. Such compact circuits enable us to successfully execute long-time dynamic simulation of ubiquitous models, such as the transverse field Ising and XY models, on current quantum hardware for systems of up to 5 qubits without the need for complex error mitigation techniques. Aside from enabling long-time dynamic simulations with minimal Trotter error for a specific subset of 1D Hamiltonians, our constant-depth circuits can advance materials simulations on quantum computers more broadly in a number of indirect ways.

Materials simulation↗
DOE OSTI2015

Superconducting thin films of (100) and (111) oriented indium doped topological crystalline insulator SnTe

Recent discovery of the topological crystalline insulator SnTe has triggered a search for topological superconductors, which have potential application to topological quantum computing. The present work reports on the superconducting properties of indium doped SnTe thin films. The (100) and (111) oriented thin films were epitaxially grown by pulsed-laser deposition on (100) and (111) BaF2 crystalline substrates respectively. The onset superconducting transition temperatures are about 3.8 K for (100) and 3.6 K for (111) orientations, slightly lower than that of the bulk. Magneto-resistive measurements indicate that these thin films may have upper critical fields higher than that of the bulk. With large surface-to-bulk ratio, superconducting indium doped SnTe thin films provide a rich platform for the study of topological superconductivity and potential device applications based on topological superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

LANL ARM Benchmarking Efforts

Overview of LANL ARM benchmarking efforts; ASC application performance on current ARM systems; ARM future technologies investigations; and external collaborations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Computing system operational methods and apparatus

Computing system operational methods and apparatus are described. According to one aspect, a computing system operational method includes accessing user information regarding a user logging onto a computing device of the computing system, processing the user information to determine if the user information is authentic, as a result of the processing determining that the user information is authentic, first enabling the computing device to execute an application segment, and as a result of the processing determining that the user information is authentic, second enabling the application segment to communicate data externally of the computing device via one of a plurality of network segments of the computing system.

Edgar, Thomas W.↗
DOE OSTI2019

Explore: An Advanced Computing Agenda for Competitiveness

Over the course of this three-year grant, the Council on Competitiveness (Council) hosted six meetings of its Advanced Computing Roundtable made up of experts from a broad cross section of advanced computing users and manufacturers, and four Advanced Computing for Competitiveness Regional Forums to explore issues related to advanced computing in regions, states and localities. More than two hundred experts, stakeholders and policymakers from the federal and state levels participated in this work and provided their time and expertise to help define the opportunity in advanced computing and the barriers to it reaching its full potential as a game-changing competitive advantage for the United States economy and national security. Building on the insights of the Council’s Advanced Computing Roundtable and findings and recommendations from the four U.S. Department of Energy-supported Forums, the Council has identified several broad policy objectives for the United States related to advanced computing leadership and implementation. The United States must: Compete at the high end of advanced computing. Continue investing to be a technology leader as the world moves toward exascale computing, including in hardware, software and applications. America also must lead in strategic areas like extending Moore’s Law and quantum computing. Improve the ability of HPC-using firms to leverage advanced computing. The Council recommends steps to improve computational skills, increase industry partnerships with laboratories and academia, and expand and strengthen software partnerships. Regulatory agencies also should accelerate efforts to use modeling and simulation within the regulatory process. Expand the number of HPC-using companies in America. Too few firms are able to leverage advanced computing to innovate and compete. Federal, state and local economic development efforts should be utilized to lower barriers and teach small and medium-sized firms, particularly manufacturers, to use advanced modeling, simulation and analytics. Coordinate federal action. Federal agencies should continue to act in a coordinated fashion on advanced computing challenges through the Joint Program Office for Strategic Computing. Leverage HPC to compete in strategic technologies and applications. Leadership in advanced computing is tightly linked to leadership in artificial intelligence, the Internet of Things, cybersecurity, additive manufacturing and other emerging technologies. Public and private sector leaders should collaborate on research and partnership efforts that ensure world-class computing environments for strategic technology leadership.

advanced computing↗
DOE OSTI2018

APPLICATION OF THE FAVOR-OCI FRACTURE MECHANICS COMPUTER PROGRAM TO ASME CODE SECTION XI, IWB-3610 FLAW ACCEPTANCE CRITERIA EVALUATIONS

This paper presents an overview of added features in a new version of the FAVOR (Fracture Analysis of Vessels Oak Ridge) computer code called FAVOR-OCI. The original FAVOR code was developed at the US Department of Energy’s Oak Ridge National Laboratory (ORNL) under the sponsorship of the US Nuclear Regulatory Commission (NRC). FAVOR is applied by US and international nuclear power industries to perform deterministic and probabilistic fracture mechanics analyses of commercial nuclear reactor pressure vessels (RPVs). Appli-cations of FAVOR are focused on insuring that the structural integrity of aging, and increasingly embrittled, RPVs is main-tained throughout their licensed service life. Based on the final ORNL release of FAVOR, v16.1, FAVOR-OCI extends existing deterministic features of FAVOR while preserving all prev-iously-existing probabilistic capabilities of FAVOR.The objective of this paper is to describe new deterministic features in FAVOR-OCI that can be applied to analytical evaluations of planar flaws. These evaluations are consistent with the acceptance criteria of ASME Code, Section XI, Article IWB-3610, including Subarticles IWB-3611 (acceptance based on flaw size) and IWB-3612 (acceptance based on applied stress intensity factor). The linear elastic fracture mechanics (LEFM) capabilities of FAVOR-OCI also incorporate the analytical procedures presented in the Nonmandatory Appendix A, Analysis of Flaws, Article A-3000, Method of KI Determination, for both surface and subsurface (embedded) flaws.The paper describes a computational methodology for determining critical values of fracture-related parameters that satisfy ASME Code Section XI acceptance criteria for flaws exposed to multiple thermal-hydraulic transients. These com-pute-intensive analyses can be carried out with a single execution of FAVOR-OCI. The new methodology determines critical values by solving for either the point of tangency or point of intersection between applied KI versus time histories and a user-selected fracture toughness material property (e.g., ASME KIc, FAVOR Weibull KIc, or Master Curve Weibull KJc) for surface or subsurface flaws. Situations where warm prestress conditions apply can also be addressed. The paper highlights a need for this new capability via applications to a recent independent review of safety cases for RPVs in two Belgian nuclear power plants (NPPs). That review required ASME Section XI assessments of several thousand embedded, quasi-laminar flaws in the wall of each RPV. Analysis results provided by the new capability contributed to the technical bases compiled from several sources by the Belgian nuclear regulatory agency (FANC) and eventually used by FANC to justify the restart of these NPPs.

Dickson, Terry L.↗
DOE OSTI2017

Domain Specific Language Support for Exascale

A multi-institutional project known as D-TEC (short for “Domain- specific Technology for Exascale Computing”) set out to explore technologies to support the construction of Domain Specific Languages (DSLs) to map application programs to exascale architectures. DSLs employ automated code transformation to shift the burden of delivering portable performance from application programmers to compilers. Two chief properties contribute: DSLs permit expression at a high level of abstraction so that a programmer’s intent is clear to a compiler and DSL implementations encapsulate human domain-specific optimization knowledge so that a compiler can be smart enough to achieve good results on specific hardware. Domain specificity is what makes these properties possible in a programming language. If leveraging domain specificity is the key to keep exascale software tractable, a corollary is that many different DSLs will be needed to encompass the full range of exascale computing applications; moreover, a single application may well need to use several different DSLs in conjunction. As a result, developing a general toolkit for building domain-specific languages was a key goal for the D-TEC project. Different aspects of the D-TEC research portfolio were the focus of work at each of the partner institutions in the multi-institutional project. D-TEC research and development work at Rice University focused on on three principal topics: understanding how to automate the tuning of code for complex architectures, research and development of the Rosebud DSL engine, and compiler technology to support complex execution platforms. This report provides a summary of the research and development work on the D-TEC project at Rice University.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Work stealing for GPU-accelerated parallel programs in a global address space framework

Task parallelism is an attractive approach to automatically load balance the computation in a parallel system and adapt to dynamism exhibited by parallel systems. Exploiting task parallelism through work stealing has been extensively studied in shared and distributed-memory contexts. In this paper, we study the design of a system that uses work stealing for dynamic load balancing of task-parallel programs executed on hybrid distributed-memory CPU-graphics processing unit (GPU) systems in a global-address space framework. We take into account the unique nature of the accelerator model employed by GPUs, the significant performance difference between GPU and CPU execution as a function of problem size, and the distinct CPU and GPU memory domains. We consider various alternatives in designing a distributed work stealing algorithm for CPU-GPU systems, while taking into account the impact of task distribution and data movement overheads. These strategies are evaluated using microbenchmarks that capture various execution configurations as well as the state-of-the-art CCSD(T) application module from the computational chemistry domain

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

An efficient computational method for solving nonlinear stochastic Itô integral equations: Application for stochastic problems in physics

Because of the nonlinearity, closed-form solutions of many important stochastic functional equations are virtually impossible to obtain. Thus, numerical solutions are a viable alternative. In this paper, a new computational method based on the generalized hat basis functions together with their stochastic operational matrix of Itô-integration is proposed for solving nonlinear stochastic Itô integral equations in large intervals. In the proposed method, a new technique for computing nonlinear terms in such problems is presented. The main advantage of the proposed method is that it transforms problems under consideration into nonlinear systems of algebraic equations which can be simply solved. Error analysis of the proposed method is investigated and also the efficiency of this method is shown on some concrete examples. The obtained results reveal that the proposed method is very accurate and efficient. As two useful applications, the proposed method is applied to obtain approximate solutions of the stochastic population growth models and stochastic pendulum problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Oppenheimer Science and Energy Leadership Program (OSELP) Software and Computing Strategy for the Future of Weapons Physics Applications [Slides]

Mission drivers at the national level are evolving to accommodate a broadening landscape. The U.S. faces a rapidly evolving, threat-based environment with an associated expansion of national-level priorities. Priorities continue to include all aspects of sustaining the existing, aging stockpile. Now, however, we must also include consideration of options for a future deterrent, including efficacy of the deterrent against new threats (threat assessment and response), capability needs associated with new materials and modern manufacturing and production processes, and efficiency requirements for a modern workflow for weapons design. Executing this complex strategy will come with challenges. We must execute our current mission, while we prepare for future missions and an increasingly uncertain future.

42 ENGINEERING↗
DOE OSTI2017

Sequential Infiltration Synthesis for the Design of Low Refractive Index Surface Coatings with Controllable Thickness

Control over refractive index and thickness of surface coatings is central to the design of low refraction films used in applications ranging from optical computing to antireflective coatings. Here, we introduce gas-phase sequential infiltration synthesis (SIS) as a robust, powerful, and efficient approach to deposit conformal coatings with very low refractive indices. We demonstrate that the refractive indices of inorganic coatings can be efficiently tuned by the number of cycles used in the SIS process, composition, and selective swelling of the of the polymer template. We show that the refractive index of Al2O3 can be lowered from 1.76 down to 1.1 using this method. The thickness of the Al2O3 coating can be efficiently controlled by the swelling of the block copolymer template in ethanol at elevated temperature, thereby enabling deposition of both single-layer and graded-index broadband antireflective coatings. Using this technique, Fresnel reflections of glass can be reduced to as low as 0.1% under normal illumination over a broad spectral range.

Berman, Diana↗