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Pararhombi: Parallel Implementation of 3-D Seismic Wave Propagation in Orthorhombic Media
Many earth materials and minerals are seismically anisotropic; however, due to the weakness of anisotropy and for simplicity, the earth is often approximated as an isotropic medium. Specific circumstances, such as in shales, tectonic fabrics, or oriented fractures, for example, require the use of anisotropic simulations in order to accurately model the earth. This report details the development of a new massively parallel 3-D full seismic waveform simulation algorithm within the principle coordinate system of an orthorhombic material, which is a specific form of anisotropy common in layered, fractured media. The theory and implementation of Pararhombi is described along with verification of the code against other solutions.
Pararhombi: Parallel Implementation of 3-D Seismic Wave Propagation in Orthorhombic Media
Many earth materials and minerals are seismically anisotropic; however, due to the weakness of anisotropy and for simplicity, the earth is often approximated as an isotropic medium. Specific circumstances, such as in shales, tectonic fabrics, or oriented fractures, for example, require the use of anisotropic simulations in order to accurately model the earth. This report details the development of a new massively parallel 3-D full seismic waveform simulation algorithm within the principle coordinate system of an orthorhombic material, which is a specific form of anisotropy common in layered, fractured media. The theory and implementation of Pararhombi is described along with verification of the code against other solutions.
Research software engineering: Professionalization, roles, and identity
This report summarizes the results of a study of research software professionals based on 17 interviews conducted at U.S. national laboratories and academic institutions. The study focuses on understanding the emerging professional role of research software engineer (RSE) and examining how the history of software engineering might be relevant to the emergence of research software engineering as a professional movement. The report first uses interview data to identify several models of professional identity for research software professionals. These include dominance models in which a person strongly identifies with a single professional identity (such as RSE), and multiplicity models in which an individual sees an identity like RSE as just one facet of their overall professional role. Next, it identifies three types of work situations for software professionals at national laboratories, covering those who work in dedicated RSE organizations, those who play an integral role in large multiphysics code projects, and those who work in a more isolated capacity to provide software development support for less computationally intensive research projects. It then reviews some key ideas from the sociology of professions in the context of the software engineering profession, suggesting parallels between the current RSE professional movement and aspects of the history of software engineering. It concludes by suggesting some potential practical implications of these findings for the RSE movement and professional organizations.
Correlation and analysis of elevon seal test results
The heating rate and pressure distributions in and around the elevon coves were correlated. An analytical approach incorporating such a correlation into a thermal structure computer code to examine the elevon seal and cover structure in flight was developed. Emphasis was placed on the design of a thermal model that predicts gas and wall temperatures in the cove area. The elevon cove area was modelled analytically by a parallel plate flow channel, incorporating effects of axial wall conduction, axial and environmental radiant energy exchanges, and effects of laminar and turbulent convection entrance regions. Comparisons were made between computed and measured values of (1) cove wall temperatures; (2) local gas temperature within the cove; and (3) local heating rates.
A high-performance FFT algorithm for vector supercomputers
Many traditional algorithms for computing the fast Fourier transform (FFT) on conventional computers are unacceptable for advanced vector and parallel computers because they involve nonunit, power-of-two memory strides. A practical technique for computing the FFT that avoids all such strides and appears to be near-optimal for a variety of current vector and parallel computers is presented. Performance results of a program based on this technique are given. Notable among these results is that a FORTRAN implementation of this algorithm on the CRAY-2 runs up to 77-percent faster than Cray's assembly-coded library routine.
Precipitation of ions induced by magnetotail collapse
The precipitation of ions triggered by dipolarization of magnetospheric field lines during substorm expansion phase is examined by means of single-particle codes. As large but short-lived electric fields develop and particles experience transient nonadiabatic motions, it is demonstrated that 'de-trapping' of inner plasma sheet populations can be achieved either via damping of magnetic moment or impulsive accelerations in the parallel direction. It is shown that the former precipitation mechanism results from phasing between gyromotion and the surging electric field. It preferentially affects heavy and low-charge state ions which can display large de-energization rates within a cyclotron period. The latter mechanism rather favors the loss of lighter and/or higher-charge state ions which are less sensitive to temporal nonadiabaticity. In this case, injection into the loss cone may result from enhanced curvature related acceleration. As this latter acceleration occurs on the dipolarization time scale, it affects a limited amount of plasma sheet populations, namely those intercepting the region of maximum curvature at the time of peak induced electric field.
EUPDF: An Eulerian-Based Monte Carlo Probability Density Function (PDF) Solver. User's Manual
EUPDF is an Eulerian-based Monte Carlo PDF solver developed for application with sprays, combustion, parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with the coding required to couple the PDF code to any given flow code and a basic understanding of the EUPDF code structure as well as the models involved in the PDF formulation. The source code of EUPDF will be available with the release of the National Combustion Code (NCC) as a complete package.
Forecasting of Storm-Surge Floods Using ADCIRC and Optimized DEMs
Increasing the accuracy of storm-surge flood forecasts is essential for improving preparedness for hurricanes and other severe storms and, in particular, for optimizing evacuation scenarios. An interactive database, developed by WorldWinds, Inc., contains atlases of storm-surge flood levels for the Louisiana/Mississippi gulf coast region. These atlases were developed to improve forecasting of flooding along the coastline and estuaries and in adjacent inland areas. Storm-surge heights depend on a complex interaction of several factors, including: storm size, central minimum pressure, forward speed of motion, bottom topography near the point of landfall, astronomical tides, and, most importantly, maximum wind speed. The information in the atlases was generated in over 100 computational simulations, partly by use of a parallel-processing version of the ADvanced CIRCulation (ADCIRC) model. ADCIRC is a nonlinear computational model of hydrodynamics, developed by the U.S. Army Corps of Engineers and the US Navy, as a family of two- and three-dimensional finite-element-based codes. It affords a capability for simulating tidal circulation and storm-surge propagation over very large computational domains, while simultaneously providing high-resolution output in areas of complex shoreline and bathymetry. The ADCIRC finite-element grid for this project covered the Gulf of Mexico and contiguous basins, extending into the deep Atlantic Ocean with progressively higher resolution approaching the study area. The advantage of using ADCIRC over other storm-surge models, such as SLOSH, is that input conditions can include all or part of wind stress, tides, wave stress, and river discharge, which serve to make the model output more accurate. To keep the computational load manageable, this work was conducted using only the wind stress, calculated by using historical data from Hurricane Camille, as the input condition for the model. Hurricane storm-surge simulations were performed on an eight-node Linux computer cluster. Each node contained dual 2-GHz processors, 2GB of memory, and a 40GB hard drive. The digital elevation model (DEM) for this region was specified using a combination of Navy data (over water), NOAA data (for the coastline), and optimized Interferometric Synthetic Aperture Radar data (over land). This high-resolution topographical data of the Mississippi coastal region provided the ADCIRC model with improved input with which to calculate improved storm-surge forecasts.
Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels
Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.
Exploiting Modern C++ for Portable Parallel Programming in Lattice QCD Applications
The evolution of ISO C++ standards increasingly serves the needs of scientific computing, offering potential benefits for developing portable applications. The recent revisions of C++ programming language, for instance, introduces a suite of algorithms capable of being executed on accelerators. Although this approach may not yield best performance, it can present a viable balance between code productivity and computational efficiency. In this report, we discuss the implementation of the HISQ operator utilizing a range of features from the C++17/20/23 standards and include an assessment of their performance.
Performance effects of irregular communications patterns on massively parallel multiprocessors
A detailed study of the performance effects of irregular communications patterns on the CM-2 was conducted. The communications capabilities of the CM-2 were characterized under a variety of controlled conditions. In the process of carrying out the performance evaluation, extensive use was made of a parameterized synthetic mesh. In addition, timings with unstructured meshes generated for aerodynamic codes and a set of sparse matrices with banded patterns on non-zeroes were performed. This benchmarking suite stresses the communications capabilities of the CM-2 in a range of different ways. Benchmark results demonstrate that it is possible to make effective use of much of the massive concurrency available in the communications network.
Performance effects of irregular communications patterns on massively parallel multiprocessors
A detailed study of the performance effects of irregular communications patterns on the CM-2 was conducted. The communications capabilities of the CM-2 were characterized under a variety of controlled conditions. In the process of carrying out the performance evaluation, extensive use was made of a parameterized synthetic mesh. In addition, timings with unstructured meshes generated for aerodynamic codes and a set of sparse matrices with banded patterns on non-zeroes were performed. This benchmarking suite stresses the communications capabilities of the CM-2 in a range of different ways. Benchmark results demonstrate that it is possible to make effective use of much of the massive concurrency available in the communications network.
Efficacy of Code Optimization on Cache-based Processors
The current common wisdom in the U.S. is that the powerful, cost-effective supercomputers of tomorrow will be based on commodity (RISC) micro-processors with cache memories. Already, most distributed systems in the world use such hardware as building blocks. This shift away from vector supercomputers and towards cache-based systems has brought about a change in programming paradigm, even when ignoring issues of parallelism. Vector machines require inner-loop independence and regular, non-pathological memory strides (usually this means: non-power-of-two strides) to allow efficient vectorization of array operations. Cache-based systems require spatial and temporal locality of data, so that data once read from main memory and stored in high-speed cache memory is used optimally before being written back to main memory. This means that the most cache-friendly array operations are those that feature zero or unit stride, so that each unit of data read from main memory (a cache line) contains information for the next iteration in the loop. Moreover, loops ought to be 'fat', meaning that as many operations as possible are performed on cache data-provided instruction caches do not overflow and enough registers are available. If unit stride is not possible, for example because of some data dependency, then care must be taken to avoid pathological strides, just ads on vector computers. For cache-based systems the issues are more complex, due to the effects of associativity and of non-unit block (cache line) size. But there is more to the story. Most modern micro-processors are superscalar, which means that they can issue several (arithmetic) instructions per clock cycle, provided that there are enough independent instructions in the loop body. This is another argument for providing fat loop bodies. With these restrictions, it appears fairly straightforward to produce code that will run efficiently on any cache-based system. It can be argued that although some of the important computational algorithms employed at NASA Ames require different programming styles on vector machines and cache-based machines, respectively, neither architecture class appeared to be favored by particular algorithms in principle. Practice tells us that the situation is more complicated. This report presents observations and some analysis of performance tuning for cache-based systems. We point out several counterintuitive results that serve as a cautionary reminder that memory accesses are not the only factors that determine performance, and that within the class of cache-based systems, significant differences exist.
Asynchronous-many-task systems: Challenges and opportunities - Scaling an AMR astrophysics code on exascale machines using Kokkos and HPX
Dynamic and adaptive mesh refinement is pivotal in high-resolution, multi-physics, multi-model simulations, necessitating precise physics resolution in localized areas across expansive domains. Today’s supercomputers’ extreme heterogeneity presents a significant challenge for dynamically adaptive codes, highlighting the importance of achieving performance portability at scale. Our research focuses on astrophysical simulations, particularly stellar mergers, to elucidate early universe dynamics. Here, we present Octo-Tiger, leveraging Kokkos, HPX, and SIMD for portable performance at scale in complex, massively parallel adaptive multi-physics simulations. Octo-Tiger supports diverse processors, accelerators, and network backends. Experiments demonstrate exceptional scalability across several heterogeneous supercomputers including Perlmutter, Frontier, and Fugaku, encompassing major GPU architectures and x86, ARM, and RISC-V CPUs. Parallel efficiency of 47.59% (110,080 cores and 6880 hybrid A100 GPUs) on a full-system run on Perlmutter (26% HPCG peak performance) and 51.37% (using 32,768 cores and 2048 MI250X) on Frontier are achieved.
The Viskores User's Guide (V.1.0)
High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created Viskores: the visualization toolkit for multi-/many-core architectures. Viskores supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. Viskores also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although Viskores provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.
The Viskores User's Guide, Release 1.1
High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created Viskores: the visualization toolkit for multi/many-core architectures. Viskores supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. Viskores also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although Viskores provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.
Eucalyptus – An Analysis Suite for Fault Trees with Uncertainty Quantification
Eucalyptus is a novel code developed at Lawrence Livermore National Laboratory to incorporate uncertainty quantification into Fault Tree Analysis (FTA). This tool addresses the challenge of imperfect knowledge in “grey-box” systems by allowing analysts to incorporate and propagate uncertainty from component-level assessments to system-level effects. Eucalyptus facilitates a consistent evaluation of the impact of subject matter expert judgment and knowledge gaps on overall system response by Monte Carlo generation of possible system fault trees, sampling probabilities of the existence of subsystems and components. Here, the code supports the specification of fault trees through text and allows export to various formats, including auto-generated images, easing analysis and reducing errors. It has undergone extensive verification testing, demonstrating its reliability and readiness for deployment, and leverages on-node parallelism for rapid analysis. Example analyses are shown that include the identification of system failure paths and quantification of the value of further information about system components.