Results for “parallelization” — Page 75

DOE OSTI2020

Fast and Accurate Core Analysis by the Full-Immersion Pressure-Pulse Decay: Part 1—Theory

Summary Core-scale measurements are considered the ground truth that oil and gas or electric utility companies use to predict the migration of fluids such as oil, natural gas, carbon dioxide, or brine deep underground during their extraction or injection operations. To provide a greater understanding of petrophysical properties of low-permeability geologic formations such as shales and tight gas sandstones, this study introduces a novel core-analysis procedure. The technique follows conventional pressure-pulse-decay permeametry, where the pressure in an inlet chamber adjacent to a cylindrical core plug undergoes a rapid pressurization, the system is shut in, and the pressure reaches a new equilibrium. However, unlike a standard unidirectional pressure-pulse decay, the full-immersion pressure-pulse decay (Hannon 2019) applies a pressure disturbance to the entire outer surface area of the sample. This article covers the numerical simulator designed to model flow through an anisotropic porous sample in this scenario. The model assumes distinct but uniform permeabilities along the radial and axial directions of the cylindrical plug sample. When extracting a plug vertically (or perpendicular to bedding), the permeability along the radial direction associates with the horizontal permeability (i.e., parallel to bedding), whereas in the axial direction, flow occurs perpendicular to bedding (a vertical permeability). Investigations of these model outputs demonstrate an approximately 20-fold decrease in time to complete a full-immersion experiment compared with conventional pressure-pulse decay. Furthermore, the pressure-decay curves resulting from the full-immersion method have slightly different shapes than those resulting from other unidimensional transient methods. These differences begin to demonstrate that, under achievable experimental conditions, the analysis of pressure data from one full-immersion test could enable the simultaneous estimation of the apparent permeabilities parallel and perpendicular to bedding of a cylindrical sample in addition to its porosity. A follow-up article finalizes the proof of this capability with a parameter-estimation procedure and presents experimental verification through a proof-of-concept study. Described in greater detail in that article, the parameter estimator requires multiple forward simulations to analyze the data, which behooves minimizing the compute time for each simulation. By using an alternating direction implicit time-marching scheme and a structured but variably spaced grid, the numerical simulator built for this purpose provides a forward model output with suitable accuracy in approximately 0.5 seconds.

Energy & Fuels↗

DOE OSTI2020

PIPER: Performance Insight for Programmers and Exascale Runtimes (Final Technical Report)

This project concentrated on the development of novel performance tools and analysis techniques for large scale parallel systems and applications, eventually targeting exascale platforms. Activities conducted included work to novel root cause detection approaches and an auto-tuning framework for parallel systems. The work has led to several software solutions, which are available as open source.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

SIERRA/Aero User Manual - Version 4.56

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2020

SIERRA/Aero Theory Manual - Version 4.56

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2020

EBS Task Force: Task 9/FEBEX Modeling Final Report: Thermo-Hydrological Modeling with PFLOTRAN

This report outlines Sandia National Laboratories modeling studies applied to Stage 1 and Stage 2 of the Full-scale Engineered Barriers Experiment in Crystalline Host Rock (FEBEX) in situ test for the SKB EBS Task Force Task 9. The FEBEX test was a full-scale test conducted over ~18 years at the Grimsel, Switzerland Underground Research Laboratory (URL) managed by NAGRA. It involved emplacing simulated waste packages, in the form of welded cylindrical heaters, inside a tunnel in crystalline granitic rock and surrounded by a bentonite barrier and cement plug. Sensors emplaced within the bentonite monitored the wetting-up, heating, and drying out of the bentonite barrier, and the large resulting data set provides an excellent opportunity for validation of multiphysics Thermal-Hydrological (TH), Thermal-Hydrologic-Chemical (THC), and Thermal-Hydrological-Mechanical (THM) modeling approaches for underground nuclear waste storage and the performance of engineered bentonite barriers. The present status of the EBS Task Force is finalizing Task 9, which follows years of modeling studies of the FEBEX test, by many notable modeling teams (Gens et al., 2009; Sanchez et al. 2010; 2012; Samper et al., 2018). These modeling studies generally use two-dimensional axisymmetric meshes, ignoring threedimensional effects, gravity and asymmetric wetting and dry out of the bentonite engineered barrier. This study investigates these effects with use of the PFLOTRAN THC code with massively parallel computational methods in modeling FEBEX Stage 1 and Stage 2 results. The PFLOTRAN numerical code is an open source, state-of-the-art, massively parallel subsurface flow and reactive transport code operating in a high-performance computing environment (Hammond et al., 2014). Section 2 describes the applied partial differential equations describing mass, momentum and energy balance used in this study, considerations derived by assuming phase equilibrium between gas and liquid phases, constitutive equations for granite, cement plug, and bentonite domains, and specific approaches for use inthe PFLOTRAN code. Section 3 describes the geometry, meshing, and model set-up. Section 4 describes modeling results, Section 5 compares modeling results to field testing data, and Section 6 gives conclusions. The Appendix provides detailed information required by the EBSTask Force for final reporting.

42 ENGINEERING↗

DOE OSTI2020

Program Verification for Extreme-Scale Applications (Final Scientific/Technical Report)

The project seeks to develop tools and techniques to help software developers verify the correctness and accuracy of their code. The target domain is scientific software of the kind widely used and developed in the Department of Energy research community, with a particular focus on "extreme scale" programs - those that are expected to involve possibly millions of parallel threads of execution. The report covers the University of Delaware contribution to the collaborative project. The project had a number of successful outcomes, especially regarding the development and extension of the CIVL software verification framework. CIVL is a verification tool for C or Fortran programs that use MPI, OpenMP, CUDA, and/or Pthreads for parallelization. CIVL went through vast improvements and extensions, and was successfully applied to a number of challenging codes. It found a subtle bug in the Devito PDE framework. It was able to verify the functional correctness of a conjugate gradient solver using a novel probabilistic technique with vanishingly small chance of error. CIVL was used very successfully in verification competitions, and the CIVL solutions to the competition challenges were presented and published. CIVL was also used successfully by other researchers on a computational chemistry kernel.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

HPC-enabled computation of demand models at scale

The purpose of this project is to examine the energy impact of urban-scale traffic for the Los Angeles Basin by developing and implementing a scalable traffic assignment model. An energy optimization function will be posed and when integrated into the optimization code for travel assignment it can be mathematically proven to converge. The energy optimization function can then be compared to the typical travel time optimization that is traditionally used in traffic assignment models. The analysis will begin with static traffic assignment models with the routing for all origin and destinations computed in parallel on high performance computing facilities. Convergence of the numerical methods rely on the solution of convex programs (or extensions of these). This step will mostly consist of demonstrating the ability to parallelize the Frank Wolfe algorithm on various platforms.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

HPC4Mobilty w/ UCB

The purpose of this project is to examine the energy impact of urban-scale traffic for the Los Angeles Basin by developing and implementing a scalable traffic assignment model. An energy optimization function will be posed and when integrated into the optimization code for travel assignment it can be mathematically proven to converge. The energy optimization function can then be compared to the typical travel time optimization that is traditionally used in traffic assignment models. The analysis will begin with static traffic assignment models with the routing for all origin and destinations computed in parallel on high performance computing facilities. Convergence of the numerical methods rely on the solution of convex programs (or extensions of these). This step will mostly consist of demonstrating the ability to parallelize the Frank Wolfe algorithm on various platforms. This work will contribute to LBNL’s efforts to develop new processes, analytical tools, program designs, and business models to advance the state of the art in next-generation sustainable transportation solutions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Multigrid-Reduction-in-Time for the Rotating Shallow Water Equations

We consider multilevel time-parallel methods for the numerical solution of the rotating shallow water equations. In particular, the multigrid-reduction-in-time (MGRIT) algorithm is used for the parallel time integration. An asymptotic model is used at the coarse levels while the full model is employed at the finer levels. The asymptotic model is well-suited for highly oscillatory partial differential equations like the rotating shallow water equations because it can accurately and stably take the required large time-steps on coarse levels. Our work exploits the flexibility of the MGRIT algorithm in terms of the number of levels and relaxation schemes to show some computational benefits, especially with respect to FCF-relaxation and data reuse.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

ECP ST Capability Assessment Report (CAR) for VTK-m (FY20)

The ECP/VTK-m project is providing the core capabilities to perform scientific visualization on Exascale architectures. The ECP/VTK-m project fills the critical feature gap of performing visualization and analysis on processors like graphics-based processors. The results of this project will be delivered in tools like ParaView, Vislt, and Ascent as well as in stand-alone form. Moreover, these projects are depending on this ECP effort to be able to make effective use of ECP architectures. One of the biggest recent changes in high-performance computing is the increasing use of accelerators. Accelerators contain processing cores that independently are inferior to a core in a typical CPU, but these cores are replicated and grouped such that their aggregate execution provides a very high computation rate at a much lower power. Current and future CPU processors also require much more explicit parallelism. Each successive version of the hardware packs more cores into each processor, and technologies like hyper threading and vector operations require even more parallel processing to leverage each core's full potential. VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures. The ECP/VTK-m project is building up the VTK-m codebase with the necessary visualization algorithm implementations that run across the varied hardware platforms to be leveraged at the Exascale. We will be working with other ECP projects, such as ALPINE, to integrate the new VTK-m code into production software to enable visualization on our HPC systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

SIX EPU Antiparallel Study: Estimating mechanical and magnetic performance of the distorted 3.5m EPU57 in antiparallel mode

The 3.5m long SIX EPU with 57 mm period shown schematically was manufactured to NSLS2 specification by Kyma of Italy. That specification called for operation to be limited to parallel mode. In parallel mode each of two diagonally opposing permanent magnet array quadrants drive in the same direction along its respective longitudinal axis by a half period relative to its adjacent fixed array quadrant. As such, at maximum shift the array pairs are only 180 degrees out of phase.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Sierra/SD - User's Manual - 4.56

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user's guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

UPC++ v1.0 Programmer’s Guide, Revision 2020.10.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

TChem v2.0 - A Software Toolkit for the Analysis of Complex Kinetic Models

TChem is an open source software library for solving complex computational chemistry problems and analyzing detailed chemical kinetic models. The software provides support for: complex kinetic models for gas-phase and surface chemistry; thermodynamic properties based on NASA polynomials; species production/consumption rates; stable time integrator for solving stiff time ordinary differential equations; and, reactor models such as homogenous gas-phase ignition (with analytical Jacobian matrices), continuously stirred tank reactor, plug-flow reactor. This toolkit builds upon earlier versions that were written in C and featured tools for gas-phase chemistry only. The current version of the software was completely refactored in C++, uses an object-oriented programming model, and adopts Kokkos as its portability layer to make it ready for the next generation computing architectures i.e., multi/many core computing platforms with GPU accelerators. We have expanded the range of kinetic models to include surface chemistry and have added examples pertaining to Continuously Stirred Tank Reactors (CSTR) and Plug Flow Reactor (PFR) models to complement the homogenous ignition examples present in the earlier versions. To exploit the massive parallelism available from modern computing platforms, the current software interface is designed to evaluate samples in parallel, which enables large scale parametric studies, e.g. for sensitivity analysis and model calibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

SIERRA/Aero Theory Manual - Version 4.58

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2020

SIERRA/Aero User Manual - Version 4.58

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

DOE OSTI2021

Efficient quadrature rules for finite element discretizations of nonlocal equations

In this paper we design efficient quadrature rules for finite element discretizations of nonlocal diffusion problems with compactly supported kernel functions. Two of the main challenges in nonlocal modeling and simulations are the prohibitive computational cost and the nontrivial implementation of discretization schemes, especially in three-dimensional settings. In this work we circumvent both challenges by introducing a parametrized mollifying function that improves the regularity of the integrand, utilizing an adaptive integration technique, and exploiting parallelization. We first showthat the “mollified” solution converges to the exact one as the mollifying parameter vanishes, then we illustrate the consistency and accuracy of the proposed method on several two- and three-dimensional test cases. Furthermore, we demonstrate the good scaling properties of the parallel implementation of the adaptive algorithm and we compare the proposed method with recently developed techniques for efficient finite element assembly.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Description of Sensor Assignment Optimization Method as Deployed on a Multi-Node Cluster

Data analytic methods are being developed to address the problem of how to assign a sensor set in a nuclear facility such that a requisite level of process monitoring capability is realized and that the sensor set is sufficiently rich to determine the status of the individual sensors with respect to need for calibration. There is an awareness in the nuclear industry that data analytics combined with rich sensor sets represent a means to improve operations and reduce costs. In the industry the calibration problem has been previously approached as an empirical data-driven problem with several methods having been developed. However, the experience of the utilities over the past ten years with these methods indicates that the absence of physics-based information renders the data-driven approach less reliable. Complicating factors such as the inherent variability of operation (both equipment alignment and operating condition) can confound a pure data-driven approach while there are no rigorous guidelines for determining what constitutes an adequate sensor set. The solution under development to overcome these shortcomings supplements the data analytic method with process information in a so-called process-constrained data-analytic approach. Simple balance equations are written for generic components (e.g., mechanical pump, valve, and heat exchanger). These do not require a priori knowledge of process parameters, such as heat transfer coefficients or friction factors. All that is needed on the part of the utility user is to identify the components and how they are connected. This report describes the development of a parallel computing capability for determining the optimal sensor set. The optimal sensor set problem suffers from the curse of dimensionality. Computation time increases exponentially as the size of the system grows. To overcome this difficulty a pre-conditioner algorithm is developed to find an approximate solution close the actual solution. This serves as a seed for the full-blown algorithm and acts to constrain the space that must searched. The optimization algorithms are described and the implementation on a parallel computing platform is described. The application of the method to a use case we are solving in collaboration with our utility partner served to illustrate how the default sensor set in a nuclear plant may not provide sufficient coverage to infer sensor calibration status.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗