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At least 847 records · Page 47

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DOE OSTI2018

Scalable molecular dynamics with NAMD on the Summit system

According to the article, NAnoscale Molecular Dynamics (NAMD) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like HIV and various types of influenza. State-of-the-art biomolecular simulations often require integration of billions of timesteps, computing all interatomic forces for each femtosecond timestep. Molecular dynamics simulation of large biomolecular systems and long-timescale biological phenomena requires tremendous computing power. NAMD harnesses the power of thousands of heterogeneous processors to meet this demand. In this paper, we present algorithmic improvements and performance optimizations that enable NAMD to achieve high performance on the IBM Newell platform (with IBM POWER9 processors and NVIDIA Volta V100 GPUs), which underpins the Oak Ridge National Laboratory's Summit and Lawrence Livermore National Laboratory's Sierra supercomputers. The Top-500 supercomputers November 2018 list shows Summit at the number one spot, with 200 petaflop/s peak performance, and Sierra second with 125 petaflop/s. Optimizations for NAMD on Summit include: data layout changes for GPU acceleration and CPU vectorization, improving GPU offload efficiency, increasing performance with Parallel Active Messaging Interface support in Charm++, improving efficiency of fast Fourier transform calculations, improving load balancing, enabling better CPU vectorization and cache performance, and providing an alternative thermostat through stochastic velocity rescaling. We also present performance scaling results on early Newell systems.

Computer Science↗

DOE OSTI2021

The research into the propagation law of the shock wave of a gas explosion inside a building

Based on the dissipation rate conservation equations of turbulent kinetic energy in the k‐ ε turbulence model, a complicated three‐dimensional finite element model of a kitchen filled with gas mixture is developed by using the open source field operation and manipulation (OpenFOAM). Two representative kitchens were used to investigate the propagation law of the shock wave of a gas explosion inside a building by considering the key characteristics of the blast shock wave. The influence of some crucial parameters, such as initial conditions and kitchen parameters, on the properties of the blast shock wave is investigated. The basic steps to predict the peak pressure of the blast shock wave are given in consideration of the initial condition and the kitchen whilst the injury effect of the blast shock wave on the humans and animals is evaluated. The research results indicate that the pressure time history and the peak pressure space distribution are greatly influenced by the kitchen design layout. The coupled interaction between the initial temperature and gas volume concentration, especially at the upper and lower explosion limits of the gas, significantly affects the peak pressure. The peak pressure varies significantly with the opening and the buffer; however, it has little relation with the width, length, and height of the kitchen. The proposed method can accurately and effectively predict the peak pressure of the blast shock wave inside buildings. In terms of the peak pressure space distribution of the explosion shock wave, the peak pressure is much higher than the threshold of the killing pressure, which is unsafe for the humans and animals in the building.

Lin, Shu-Chao↗

DOE OSTI2022

Research on Deformation Law of Deep Foundation Pit of Station in Core Region of Saturated Soft Loess Based on Monitoring

Saturated soft loess has a large pore structure, high compressibility, low strength, fluid plastic state, and poor engineering properties. It is still one of the key problems that engineering needs to solve. In order to study the influence of deep foundation pit excavation in the saturated soft loess area on the deformation of foundation pits, the deformation laws of ground settlement, enclosure structure, and supporting axial force were clarified based on the field tests on the deformation characteristics of deep foundation pits in areas with the high-water level in saturated soft loess, combined with geological conditions and on-site construction procedures. The results indicate the following: water supply and construction process were found to be the main factor in changing the surface settlement curve of deep foundation pits in saturated soft loess; increasing the construction speed of the pit bottom floor, inverted braces, floor frame beams, and sidewall frame beams to close the structure, which is conducive to restraining the deformation of the continuous underground wall and foundation pits in similar areas. In the initial stage of support layout, the axial force of steel support tends to increase too fast or even exceed the standard control value. Therefore, a reasonable preadding axial force is an effective means to control the deformation of the continuous underground wall and the axial force of the steel support. The current research results may provide a reference for constructing deep foundation pits in similar areas.

Wang, Xueyan↗

DOE OSTI2015

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗

DOE OSTI2014

Sandia National Laboratories Environmental Fluid Dynamics Code V. 1 0.0 (Beta)

Jones, Craig↗

DOE OSTI2016

Simple Ontology Format (SOFT)

Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

Sorokine, Alexandre↗

DOE OSTI2016

Delft3D turbine turbulence module

Chartrand, Chris↗

DOE OSTI2018

SolarPILOT™

SolarPILOT™advances the analytical flux image Hermite series approximation used in DELSOL3 by applying it to individual heliostat images rather than "zones", allowing characterization of a wide variety of heliostat field layouts. SolarPILOT also integrates the SolTrace Monte-Carlo ray tracing engine, providing improved receiver optical modeling capability, a user-friendly front end for geometry definition, and side-by-side validation of the analytical algorithms. The tool and source code are publicly available and are designed for third-party modification and extendability. The software is intended as a replacement for the more antiquated DELSOL3 algorithm originally developed at Sandia National Laboratory. The software will be used at NREL for power tower component design analysis and may be used at other laboratories, in academia, or as a third-party validation tool by some industry groups.

Wagner, Michael↗

DOE OSTI2019

Fluorescent Amplification of Next Generation Sequencing Libraries Tools (FA-NGS tools) v1

This is a software utility for calculating pooling volumes and graphing quality control data of next generation sequencing libraries amplified with fluorescent intercalating agents and monitored by real-time quantitative PCR (qPCR). The tool is used to calculate pooling volumes of individual next generation sequencing libraries based on experimentally determined fluorescence values. To do this, fluorescent values are used as a proxy for relative concentration to determine the ratio of transfer volumes. The output is a "transfer file" that specifies the transfer volume and destination well of a given library. The tool can also be used to assess the quality of individual next generation sequencing libraries by melting curve analysis. The output are small-multiples graphs of the melting curves of individual sequencing libraries according to the specified plate layout.

Garber, Megan↗

DOE OSTI2020

FieLDS

Field Landscape Decision Support (FieLDS) is a decision support tool that assists agricultural producers and farm managers in selecting parts of the field that can be converted to bioenergy plants, like perennial grasses, from the conventional use, like corn or soybean growth. That conversion of parts of the field is done based on the specific landscape properties and the agricultural producer’s priorities. The decision support tool generates a map of the field layout and spatially marks where to place each plant based on the spatial input from the user. Also, the user selects which priorities (sustainability indicators) are most relevant to them in their decision-making. By allowing the user to set the weights among the priorities, the tool empowers the user to generate field designs specific to their needs instead of imposing the developer’s set of priorities, and increases the transparency of the decision process.

Vazhnik, Veronika↗

DOE OSTI2016

TuckerCompressMPI v. 1.0

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. This software provides a method for compressing large-scale multiway data.

Austin, Woody↗

DOE OSTI2019

NAMSA

In NAMSA, we introduce two main solutions to address the limitations of MSA-type algorithms for simulation of electron scattering/microscopy data: just-in-time compilation and work partitioning via MPI and GPU-to-GPU communication. First, the just-in-time (JIT) compilation strategy produces optimally tuned CUDA C++ kernels due to the data layout being perfectly known at runtime and compiled via calls from the Python interpreter. NAMSA automatically optimizes the 2-D FFT planning, and CUDA multi-streams scheduling/launching of probe simulations. With NAMSA, we can simulate electron scattering/microscopy on hundreds to thousands of GPUs, while removing the major limitations of memory and bandwidth from MSA.

Laanait, Nouamane↗

DOE OSTI2021

diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0

In this work we present a 2D distributed memory algorithm for overlap detection and introduce a novel design and implementation for layout simplification where we perform a transitive reduction from overlap graph to string graph in the context of de novo genome assembly.

Buluc, Aydin↗

DOE OSTI2015

Global Feedback Simulator

GFS is a simulation engine that is used for the characterization of Accelerator performance parameters based on the machine layout, configuration and noise sources. It combines extensively tested Feedback models with a longitudinal phase space tracking simulator along with the interaction between the two via beam-based feedback using a computationally efficient simulation engine. The models include beam instrumentation, considerations on loop delays for in both the R and beam-based feedback loops, as well as the ability to inject noise (both correlated and uncorrelated) at different points of the machine including a full characterization of the electron gun performance parameters.

Doolittle, Lawrence↗

DOE OSTI2021

UMT

UMT is a Sn deterministic thermal radiative transport Fortran proxy application. Its primary purpose is to research how data layout, programming paradigms and architectures effect the implementation and performance of Sn transport in Fortran on unstructured meshes. It is based on the LLNL Teton Sn deterministic thermal radiative transport code.

Yee, BenC.↗

DOE OSTI2022

Trace Crawler SOFTWARE

The trace crawler is a tool for selective web crawling to archive web resources with well-defined boundaries. The specific web navigation steps (or trace) are formulated for the families of webpages, where layout or HTML structure can be similar but the content is different, for example, GitHub, Slideshare, blogs, etc. The trace is recorded in a json file format.

Balakireva, Lyudmila↗

DOE OSTI2018

Sandia's Current Energy Conversion module for Flexible-Mesh Delft3D flow solver v. 1.0

The DOE has funded Sandia National Labs (SNL) to develop an open-source modeling tool to guide the design and layout of marine hydrokinetic (MHK) arrays to maximize power production while minimizing environmental effects. This modeling framework simulates flows through and around a MHK arrays while quantifying environmental responses. As an augmented version of the Dutch company, Deltares’s, environmental hydrodynamics code, Delft3D, SNL-Delft3D-CEC-FM includes a new module that simulates energy conversion (momentum withdrawal) by MHK current energy conversion devices with commensurate changes in the turbulent kinetic energy and its dissipation rate. SNL-Delft3D-CEC-FM modified the Delft3D flexible mesh flow solver, DFlowFM. The Following is a description of Deltares’s open-source code Delft3D from which Delft3D-CEC is built upon. “Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. As per 1 January 2011, the Delft3D flow (FLOW), morphology (MOR) and waves (WAVE) modules are available in open source. The software is used and has proven his capabilities on many places around the world, like the Netherlands, USA, Hong Kong, Singapore, Australia, Venice, etc. The software is continuously improved and developed with innovating advanced modelling techniques as consequence of the research work of our institute and to stay world leading. The FLOW module is the heart of Delft3D and is a multi-dimensional (2D or 3D) hydrodynamic (and transport) simulation program which calculates non-steady flow and transport phenomena resulting from tidal and meteorological forcing on a curvilinear, boundary fitted grid or spherical coordinates. In 3D simulations, the vertical grid is defined following the so-called sigma coordinate approach or Z-layer approach. The MOR module computes sediment transport (both suspended and bed total load) and morphological changes for an arbitrary number of cohesive and non-cohesive fractions. Both currents and waves act as driving forces and a wide variety of transport formulae have been incorporated. For the suspended load this module connects to the 2D or 3D advection-diffusion solver of the FLOW module; density effects may be taken into account. An essential feature of the MOR module is the dynamic feedback with the FLOW and WAVE modules, which allow the flows and waves to adjust themselves to the local bathymetry and allows for simulations on any time scale from days (storm impact) to centuries (system dynamics). It can keep track of the bed composition to build up a stratigraphic record. The MOR module may be extended to include extensive features to simulate dredging and dumping scenarios. For over 30 years Deltares has been in the forefront of these types of combined morphological simulation techniques.”

Chartand, Chris↗

DOE OSTI2022

Binary Driller

Binary Driller (BD) is a visualization tool which uses the data produced from the Troglodyte tool developed on the Deep Learning Malware project. Binary Driller performs function matching using the provided function embeddings (function representations), then displays the matches for each function in a layout that mimics the location of each function within the binary.

Cutsha, Michael↗