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At least 1,225 records · Page 68

Hybrid Parallel Contour Trees, Version 1.0

A common operation in scientific visualization is to compute and render a contour of a data set. Given a function of the form f : R^d -> R, a level set is defined as an inverse image f^-1(h) for an isovalue h, and a contour is a single connected component of a level set. The Reeb graph can then be defined to be the result of contracting each contour to a single point, and is well defined for Euclidean spaces or for general manifolds. For simple domains, the graph is guaranteed to be a tree, and is called the contour tree. Analysis can then be performed on the contour tree in order to identify isovalues of particular interest, based on various metrics, and render the corresponding contours, without having to know such isovalues a priori. This code is intended to be the first data-parallel algorithm for computing contour trees. Our implementation will use the portable data-parallel primitives provided by Nvidia’s Thrust library, allowing us to compile our same code for both GPUs and multi-core CPUs. Native OpenMP and purely serial versions of the code will likely also be included. It will also be extended to provide a hybrid data-parallel / distributed algorithm, allowing scaling beyond a single GPU or CPU.

Sewell, Christopher↗

ARES v1.x - Performance Portable Tool to Simulate Supernovae based on Parthenon Framework

Historically, codes for simulating supernovae (such as Arepo, FLASH or LEAFS) have been at the forefront of scientific high-performance computing to the immense computational resources required for full 3D simulations. However, given the shift towards heterogenous HPC architectures, many current-generation codes are at the risk of losing their competitiveness as they are only designed to run on homogeneous CPU-only systems. There exist several efforts to enable these codes for GPU’s, however, these efforts only consider specific architectures or vendors (e.g., implement only CUDA or HIP), limiting themselves to a small range of exascale computing systems. Frameworks such as Kokkos aim to provide a framework which is agnostic of the targeted architecture, enabling the development of performant and portable code. In the Ares code, we develop a performance portable tool to simulate supernovae based on the Parthenon Framework, which in turn uses Kokkos in the background. Here, the Parthenon Framework provides an interface to the underlying mesh-refinement routines, which form the backbone of our code. In addition, we incorporate the already existing Singularity-EOS toolkit to provide us with various equations of state, primarily the Helmholtz equation of state. We also include the JINA Reaclib as a basis for our nuclear network solver. Finally, we implement a gravity solver to complete the required physics. This setup will provide us with a minimal code base to simulate supernova in a similar style to the tried-and-tested Arepo code, but in a futureproof performance portable framework.

Lim, Hyun↗

Workshop on Incomplete Network Data Held at Sandia National Labs – Livermore

While network analysis is applied in a broad variety of scientific fields (including physics, computer science, biology, and the social sciences), how networks are constructed and the resulting bias and incompleteness have drawn more limited attention. For example, in biology, gene networks are typically developed via experiment -- many actual interactions are likely yet to be discovered. In addition to this incompleteness, the data-collection processes can introduce significant bias into the observed network datasets. For instance, if you observe part of the World Wide Web network through a classic random walk, then high degree nodes are more likely to be found than if you had selected nodes at random. Unfortunately, such incomplete and biasing data collection methods must be often used.

97 MATHEMATICS AND COMPUTING↗

Accelerated Climate Modeling for Energy (ACME) Final Scientific/Technical Report

Seven Department of Energy (DOE) national laboratories, Universities, and Kitware, undertook a coordinated effort to build an Earth system modeling capability tailored to meet the climate change research strategic objectives of the DOE Office of Science, as well as the broader climate change application needs of other DOE programs.

97 MATHEMATICS AND COMPUTING↗

Final Report: Optimal Model Complexity in Geological Carbon Sequestration: A Response Surface Uncertainty Analysis

The critical component of a risk assessment study in evaluating GCS is an analysis of uncertainty in CO2 modeling. In such analyses, direct numerical simulation of CO2 flow and leakage requires many time-consuming model runs. Alternatively, analytical methods have been developed which allow fast and efficient estimation of CO2 storage and leakage, although restrictive assumptions on formation rock and fluid properties are employed. In this study, an intermediate approach is proposed based on the Design of Experiment and Response Surface methodology, which consists of using a limited number of numerical simulations to estimate a prediction outcome as a combination of the most influential uncertain site properties. The methodology can be implemented within a Monte Carlo framework to efficiently assess parameter and prediction uncertainty while honoring the accuracy of numerical simulations. The choice of the uncertain properties is flexible and can include geologic parameters that influence reservoir heterogeneity, engineering parameters that influence gas trapping and migration, and reactive parameters that influence the extent of fluid/rock reactions. The method was tested and verified on modeling long-term CO2 flow, non-isothermal heat transport, and CO2 dissolution storage by coupling two-phase flow with explicit miscibility calculation using an accurate equation of state that gives rise to convective mixing of formation brine variably saturated with CO2. All simulations were performed using three-dimensional high-resolution models including a target deep saline aquifer, overlying caprock, and a shallow aquifer. To evaluate the uncertainty in representing reservoir permeability, sediment hierarchy of a heterogeneous digital stratigraphy was mapped to create multiple irregularly shape stratigraphic models of decreasing geologic resolutions: heterogeneous (reference), lithofacies, depositional environment, and a (homogeneous) geologic formation. To ensure model equivalency, all the stratigraphic models were successfully upscaled from the reference heterogeneous model for bulk flow and transport predictions (Zhang & Zhang, 2015). GCS simulation was then simulated with all models, yielding insights into the level of parameterization complexity that is needed for the accurate simulation of reservoir pore pressure, CO2 storage, leakage, footprint, and dissolution over both short (i.e., injection) and longer (monitoring) time scales. Important uncertainty parameters that impact these key performance metrics were identified for the stratigraphic models as well as for the heterogeneous model, leading to the development of reduced/simplified models at lower characterization cost that can be used for the reservoir uncertainty analysis. All the CO2 modeling was conducted using PFLOTRAN – a massively parallel, multiphase, multi-component, and reactive transport simulator developed by a multi-laboratory DOE/SciDAC (Scientific Discovery through Advanced Computing) project (Zhang et al., 2017, in review). Within the uncertainty analysis framework, increasing reservoir depth were investigated to explore its effect on the uncertainty outcomes and the potential for developing gravity-stable injection with increased storage security (Dai et al., 20126; Dai et al., 2017, in review). Finally, to accurately model CO2 fluid-rock reactions and resulting long-term storage as secondary carbonate minerals, a modified kinetic rate law for general mineral dissolution and precipitation was proposed and verified that is invariant to a scale transformation of the mineral formula weight. This new formulation will lead to more accurate assessment of mineral storage over geologic time scales (Lichtner, 2016).

58 GEOSCIENCES↗

Compiler and Runtime Approaches to Enable Large-Scale Irregular Programs. Final report, July 2013 - July 2019

While regular algorithms, characterized by operations on dense matrices and arrays, have long been the mainstay of scientific, high-performance computing, irregular algorithms, which feature unpredictable accesses to pointer-based data structures, are becoming increasingly common in high performance computing, arising in graph analysis, data mining and visualization, among other domains. Unfortunately, the defining characteristics of irregular applications, their dynamic, unpredictable, data-dependent access patterns and data layouts, make achieving high performance on large scale systems difficult. Scaling applications to peta- and exa-scale requires carefully controlling communication and data movement and placement, an inherently difficult task when access patterns and data layouts are unpredictable! Most irregular applications that attain high performance must be painstakingly hand-written and hand-tuned, with few common principles or paradigms uniting various implementations and easing future development. Despite the increasing importance of irregular applications, there is little programmer knowledge, and even less compiler ability, devoted to optimizing them. This project aims to solve these problems. By allowing programmers to write irregular applications in high level forms, with at most a few annotations highlighting key structural properties, programmers can focus on developing their algorithms and methods. The compiler and run-time system can take on the tedious task of optimizing the application for execution at large scales, and can automatically provide efficient implementations. This will provide portability and ease maintenance for existing irregular applications, but, more importantly, open up whole new domains of computational science to large-scale, high-performance simulation codes.

97 MATHEMATICS AND COMPUTING↗

The SciDAC QuantOm Framework: A composable Workflow

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Jefferson Lab and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event-level by leveraging nuclear theory models and accounting for experimental conditions. In order to efficiently run multiple analyses under varying conditions, a composable workflow was designed where each section (theory, experiment, objective minimization, etc.) has its own dedicated module. The optimization, i.e. the fit of theory to experimental data is carried out by deep learning techniques, such as Generative Adversarial Networks (GANs) or Reinforcement Learning (RL). This presentation gives an overview of the current status of the workflow, highlights present and future challenges, and highlights possible extensions to other projects with similar requirements.

Lersch, Daniel↗

Scaling the SciDAC QuantOm Workflow

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Jefferson Lab and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event-level by combining the input from theoretical and experimental nuclear physics into a single, composable workflow. The optimization itself (I.e. fitting the experimental data with theoretical predictions) is carried out by a machine / deep learning algorithm. The size of the acquired DIS data as well as the complexity of the workflow itself require that the analysis is performed across multiple GPUs on high performance computing systems, such as Polaris at Argonne National Laboratory. This presentation discusses the novelties and challenges that came along with parallelizing this workflow. Recent results are compared to common distributed training techniques.

Lersch, Daniel↗

Tokamak Disruption Simulation (Final Technical Report)

The Tokamak Disruption Simulation collaboration was a SciDAC (Scientific Discovery through Advanced Computing) program led by Xianzhu Tang of the Los Alamos National Laboratory but with separate grants to each institution. I was the PI for Columbia University and the only person at Columbia directly funded by this SciDAC. Disruptions are a sudden loss of confinement in tokamaks, and a reliable method of preventing disruptions must be developed before tokamak fusion power plants become feasible. A related plasma confinement concept, the stellarator, is the only way known way of preventing disruptions with the required reliability. The largest devices, both existing and under construction, for confining plasmas for fusion using magnetic fields are tokamaks, so it is important to solve their disruption issues. The sudden loss of confinement in tokamaks can be from a bit of material falling into the plasma, which causes the plasma energy to be quickly lost by radiation, or by an instability causing a breakup of the confining surfaces formed by the magnetic field. This breakup can occur more than a million times faster than one would naively think possible. The sudden breakup of surfaces is called a fast magnetic reconnection and also results in a sudden cooling of the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SAGIPS: A scalable Framework for scidac quantom

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Thomas Jefferson National Accelerator Facility and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event level by taking into leveraging nuclear theory models and accounting for experimental conditions. In order to efficiently run multiple analyses under varying conditions, a composable workflow was designed where each section (theory, experiment, objective minimization, etc.) has its own dedicated module. This presentation gives an overview over of the current status of this workflow, highlights present and future challenges, and highlights possible extensions to other projects with similar requirements.

Lersch, Daniel [Thomas Jefferson National Accelera↗

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗

Monolithic parallel processor, phase 1A

A four-bit parallel processor LSI array was designed and fabricated using COS/MOS integrated-circuit technology. The design features include the provision for interconnecting groups of parallel-processor chips to form an expanded processor of any desired word length. This 800-transistor "computer on a chip' circuit has the logic capability of a medium-size, medium-speed, general-purpose computer suitable for sophisticated scientific data processing. The ability to fabricate this device repetitively was demonstrated.

Source record↗

A computer program for the calculation of laminar and turbulent boundary layer flows

The results are presented of a study to produce a computer program to calculate laminar and turbulent boundary layer flows. The program is capable of calculating the following types of flow: (1) incompressible or compressible, (2) two dimensional or axisymmetric, and (3) flows with significant transverse curvature. Also, the program can handle a large variety of boundary conditions, such as blowing or suction, arbitrary temperature distributions and arbitrary wall heat fluxes. The program has been specialized to the calculation of equilibrium air flows and all of the thermodynamic and transport properties used are for air. For the turbulent transport properties, the eddy viscosity approach has been used. Although the eddy viscosity models are semi-empirical, the model employed in the program has corrections for pressure gradients, suction and blowing and compressibility. The basic method of approach is to put the equations of motion into a finite difference form and then solve them by use of a digital computer. The program is written in FORTRAN 4 and requires small amounts of computer time on most scientific machines. For example, most laminar flows can be calculated in less than one minute of machine time, while turbulent flows usually require three or four minutes.

Dwyer, H. A.↗

Encounter with Venus - An update

This report deals with early results from the Pioneer Venus Orbiter and multiprobe missions, which encountered Venus on December 4 and December 9, 1978, respectively. Initial results for the multiprobe mission and for the first 30 days of the Orbiter mission have already been reported. Additional mission features and updated mission parameters based on refined tracking data and trajectory computations are presented here. Scientific results for both missions are discussed which cover the first 130 days (or orbits) of the nominal 243-day Orbiter mission.

Colin, L.↗

Planetary Data Workshop, Part 2

Technical aspects of the Planetary Data System (PDS) are addressed. Methods and tools for maintaining and accessing large, complex sets of data are discussed. The specific software and applications needed for processing imaging and non-imaging science data are reviewed. The need for specific software that provides users with information on the location and geometry of scientific observations is discussed. Computer networks and user interface to the PDS are covered along with Computer hardware available to this data system.

Source record↗

NASA's computer science research program

Following a major assessment of NASA's computing technology needs, a new program of computer science research has been initiated by the Agency. The program includes work in concurrent processing, management of large scale scientific databases, software engineering, reliable computing, and artificial intelligence. The program is driven by applications requirements in computational fluid dynamics, image processing, sensor data management, real-time mission control and autonomous systems. It consists of university research, in-house NASA research, and NASA's Research Institute for Advanced Computer Science (RIACS) and Institute for Computer Applications in Science and Engineering (ICASE). The overall goal is to provide the technical foundation within NASA to exploit advancing computing technology in aerospace applications.

Larsen, R. L.↗