Durango: Scalable Synthetic Workloard Generation for Extreme-Scale Application Performance Modeling & Simulation
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Carothers, Christopher D.↗
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Reduced-thickness backlighter for autostereoscopic display and display using the backlighter
A reduced-thickness backlighter for an autostereoscopic display is disclosed having a lightguide and at least one light source parallel to an edge of the lightguide so as to be substantially coplanar with the lightguide. The lightguide is provided with a first surface which has a plurality of reflective linear regions, such as elongated grooves or glossy lines, parallel to the illuminated edge of the lightguide. Preferably the lightguide further has a second surface which has a plurality of lenticular lenses for reimaging the reflected light from the linear regions into a series of thin vertical lines outside the guide. Because of the reduced thickness of the backlighter system, autostereoscopic viewing is enabled in applications requiring thin backlighter systems. In addition to taking up less space, the reduced-thickness backlighter uses less lamps and less power. For accommodating 2-D applications, a 2-D diffuser plate or a 2-D lightguide parallel to the 3-D backlighter is disclosed for switching back and forth between 3-D viewing and 2-D viewing.
Eichenlaub, Jesse B↗
Analysis of the Mutual Inductance between Two Parallel Plates for the Detection of Surface Flaws
There has recently been much effort behind the development of NDE methods applicable to the detection of surface/subsurface flaws in thin metallic structures with a rapid scan capability. One such method, an electromagnetic technique using a current-sheet parallel to the surface of a specimen in order to induce eddy current flow shows a high potential for satisfying the rapid scan requirement stated above. The technique is based on the detection of flaw-induced magnetic field components normal to the specimen surface by an appropriate detection mechanism positioned above the current-sheet as shown schematically in Fig. 1. As indicated in this figure, the current-sheet separates the source of the normal magnetic field components from the detector in such a way that the electric and magnetic properties of the current-sheet can be a major factor affecting the strength of the detected signals. The purpose of the present study is, therefore, to perform a detailed investigation on the effect of the material properties of the current-sheet on the detected signal strength and to establish a simple theoretical model for the detection mechanism.
Namking, M.↗
Performance Analysis of a Hybrid Overset Multi-Block Application on Multiple Architectures
This paper presents a detailed performance analysis of a multi-block overset grid compu- tational fluid dynamics app!ication on multiple state-of-the-art computer architectures. The application is implemented using a hybrid MPI+OpenMP programming paradigm that exploits both coarse and fine-grain parallelism; the former via MPI message passing and the latter via OpenMP directives. The hybrid model also extends the applicability of multi-block programs to large clusters of SNIP nodes by overcoming the restriction that the number of processors be less than the number of grid blocks. A key kernel of the application, namely the LU-SGS linear solver, had to be modified to enhance the performance of the hybrid approach on the target machines. Investigations were conducted on cacheless Cray SX6 vector processors, cache-based IBM Power3 and Power4 architectures, and single system image SGI Origin3000 platforms. Overall results for complex vortex dynamics simulations demonstrate that the SX6 achieves the highest performance and outperforms the RISC-based architectures; however, the best scaling performance was achieved on the Power3.
Djomehri, M. Jahed↗
TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics
TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.
74 ATOMIC AND MOLECULAR PHYSICS↗
Parallel streaming between heterogeneous HPC resources for real-time analysis
Performing analysis or generating visualizations concurrently with high performance simulations can yield great benefits compared to post-processing data. Writing and reading large volumes of data can be reduced or eliminated, thereby producing an I/O cost savings. One such method for concurrent simulation and analysis is in transit - streaming data from the resource running the simulation to a separate resource running the analysis. In transit analysis can be beneficial since computational resources may not have certain resources needed for visualization and analysis (e.g. GPUs) and to reduce the impact of performing analysis tasks to the run time of the simulation. When sending and receiving data in transit, data redistribution mechanisms are needed in order to support heterogeneous data layouts that may be required by the simulation and analysis applications. The work described in this paper compares two mechanisms for on-the-fly data redistribution when streaming data in parallel between two distributed memory applications. Finally, our results show that it is often more advantageous to stream data in the same layout as the sender and redistribute data amongst processes on the receiving end than to stream data in the final layout needed by the receiver.
97 MATHEMATICS AND COMPUTING↗
Merlin - Massively parallel heterogeneous computing
Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.
Wittie, Larry↗
Parallel algorithm for dominant points correspondences in robot binocular stereo vision
This paper presents an algorithm to find the correspondences of points representing dominant feature in robot stereo vision. The algorithm consists of two main steps: dominant point extraction and dominant point matching. In the feature extraction phase, the algorithm utilizes the widely used Moravec Interest Operator and two other operators: the Prewitt Operator and a new operator called Gradient Angle Variance Operator. The Interest Operator in the Moravec algorithm was used to exclude featureless areas and simple edges which are oriented in the vertical, horizontal, and two diagonals. It was incorrectly detecting points on edges which are not on the four main directions (vertical, horizontal, and two diagonals). The new algorithm uses the Prewitt operator to exclude featureless areas, so that the Interest Operator is applied only on the edges to exclude simple edges and to leave interesting points. This modification speeds-up the extraction process by approximately 5 times. The Gradient Angle Variance (GAV), an operator which calculates the variance of the gradient angle in a window around the point under concern, is then applied on the interesting points to exclude the redundant ones and leave the actual dominant ones. The matching phase is performed after the extraction of the dominant points in both stereo images. The matching starts with dominant points in the left image and does a local search, looking for corresponding dominant points in the right image. The search is geometrically constrained the epipolar line of the parallel-axes stereo geometry and the maximum disparity of the application environment. If one dominant point in the right image lies in the search areas, then it is the corresponding point of the reference dominant point in the left image. A parameter provided by the GAV is thresholded and used as a rough similarity measure to select the corresponding dominant point if there is more than one point the search area. The correlation is used as a final decision tool when there is still more than one point in the search area. If there is no dominant point in the search area of if the points in the search area are below a correlation threshold, then the dominant point in the reference image is occluded and can not be corresponded. The algorithm has been modeled, implemented and shown to be fast, robust and parallel. The parallelism is created from three main features: locality of the operators; a memory optimization scheme; and the ability to fully parallelize the extraction phase which is the most computational intensive task in the algorithm. The last feature is achieved by performing the extraction phase on the two images simultaneously.
Al-Tammami, A.↗
Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation
Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optimization of Microelectronic Devices for Sensor Applications
The NASA/JPL goal to reduce payload in future space missions while increasing mission capability demands miniaturization of active and passive sensors, analytical instruments and communication systems among others. Currently, typical system requirements include the detection of particular spectral lines, associated data processing, and communication of the acquired data to other systems. Advances in lithography and deposition methods result in more advanced devices for space application, while the sub-micron resolution currently available opens a vast design space. Though an experimental exploration of this widening design space-searching for optimized performance by repeated fabrication efforts-is unfeasible, it does motivate the development of reliable software design tools. These tools necessitate models based on fundamental physics and mathematics of the device to accurately model effects such as diffraction and scattering in opto-electronic devices, or bandstructure and scattering in heterostructure devices. The software tools must have convenient turn-around times and interfaces that allow effective usage. The first issue is addressed by the application of high-performance computers and the second by the development of graphical user interfaces driven by properly developed data structures. These tools can then be integrated into an optimization environment, and with the available memory capacity and computational speed of high performance parallel platforms, simulation of optimized components can proceed. In this paper, specific applications of the electromagnetic modeling of infrared filtering, as well as heterostructure device design will be presented using genetic algorithm global optimization methods.
Cwik, Tom↗
Parallel Anisotropic Tetrahedral Adaptation
An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.
Park, Michael A.↗
O(N) Quantum Molecular Dynamics (QMD) Algorithms, Code Requirements, Release Notes, and Library Deployment
The Exascale Computing Project (ECP) Co-design Center for Particle Applications (CoPA) is addressing the challenges for particle applications to run on upcoming exascale computing architectures. This includes short- and long-range molecular dynamics (MD), particle-in-cell (PIC), and quantum molecular dynamics (QMD). This document addresses $\mathcal{O}(N)$ QMD. The goal of this CoPA team is to develop $\mathcal{O}(N)$ linear scaling methods for QMD optimized for new and next generation architectures. This will provide the capability to simulate larger systems and run for longer timeframes than is possible today. Focus is initially on the density matrix construction. This requires efficient matrix formats and linear algebra operations for distributed architectures. A significant reduction in the wallclock time for an MD timestep is necessary to achieve practical large scale QMD. Equally challenging is to develop scalable distributed implementations. This requires the exploration of efficient data formats (dense, sparse, etc.), data decomposition and distribution across compute nodes using block- and graph-based methods. Traditional programming models such as MPI/OpenMP, hybrid MPI/OpenMP/Accelerator, as well as asynchronous task-based models will be explored to achieve maximum parallelism. Parallelism at the level of a matrix operation, solver, and/or application needs to be explored to gain the most benefit on new and emerging architectures. This report serves as a “living document” of the additions and enhancements throughout the ECP CoPA project for $\mathcal{O}(N)$ QMD. The following sections address the applications we are working with, the quantum chemistry libraries (BML and PROGRESS), and our co-design exploration through the use of a proxy application.
36 MATERIALS SCIENCE↗
Electromagnetic Design of a Magnetically-Coupled Spatial Power Combiner
The design of a two-dimensional beam-combining network employing a parallel-plate superconducting waveguide with a mono-crystalline silicon dielectric is presented. This novel beam-combining network structure employs an array of magnetically coupled antenna elements to achieve high coupling efficiency and full sampling of the intensity distribution while avoiding diffractive losses in the multi-mode region defined by the parallel-plate waveguide. These attributes enable the structures use in realizing compact far-infrared spectrometers for astrophysical and instrumentation applications. When configured with a suitable corporate-feed power-combiner, this fully sampled array can be used to realize a low-sidelobe apodized response without incurring a reduction in coupling efficiency. To control undesired reflections over a wide range of angles in the finite-sized parallel-plate waveguide region, a wideband meta-material electromagnetic absorber structure is implemented. This adiabatic structure absorbs greater than 99 of the power over the 1.7:1 operational band at angles ranging from normal (0 degree) to near parallel (180 degree) incidence. Design, simulations, and application of the device will be presented.
Bulcha, B.↗
h5bench: A unified benchmark suite for evaluating HDF5 I/O performance on pre‐exascale platforms
Summary Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community.
97 MATHEMATICS AND COMPUTING↗
Nebo: An efficient, parallel, and portable domain-specific language for numerically solving partial differential equations
This study presents Nebo, a declarative domain-specific language embedded in C++ for discretizing partial differential equations for transport phenomena on multiple architectures. Application programmers use Nebo to write code that appears sequential but can be run in parallel, without editing the code. Currently Nebo supports single-thread execution, multi-thread execution, and many-core (GPU-based) execution. With single-thread execution, Nebo performs on par with code written by domain experts. With multi-thread execution, Nebo can linearly scale (with roughly 90% efficiency) up to 12 cores, compared to its single-thread execution. Moreover, Nebo’s many-core execution can be over 140x faster than its single-thread execution.
97 MATHEMATICS AND COMPUTING↗
MPI jobs within MPI jobs: A practical way of enabling task-level fault-tolerance in HPC workflows
While the use of workflows for HPC is growing, MPI interoperability remains a challenge for workflow management systems. The MPI standard and/or its implementations provide a number of ways to build multiple-programs-multiple-data (MPMD) applications. These methods present limitations related to fault tolerance, and are not easy to use. In this paper, we advocate for a novel MPI_Comm_launch function acting as the parallel counterpart of a system(3) call. MPI_Comm_launch allows a child MPI application to be launched inside the resources originally held by processes of a parent MPI application. Two important aspects of MPI_Comm_launch is that it pauses the calling process, and runs the child processes on the parent’s CPU cores, but in an isolated manner with respect to memory. This function makes it easier to build MPMD applications with well-decoupled subtasks. We show how this feature can provide better flexibility and better fault tolerance in ensemble simulations and HPC workflows. Here, we report results showing 2x throughput improvement for application workflows with faults, and scaling results for challenging workloads up to 256 nodes.
97 MATHEMATICS AND COMPUTING↗
TRIO: Burst Buffer Based I/O Orchestration, In: 2015 IEEE International Conference on Cluster Computing
The growing computing power on leadership HPC systems is often accompanied by ever-escalating failure rates. Checkpointing is a common defensive mechanism used by scientific applications for failure recovery. However, directly writing the large and bursty checkpointing dataset to parallel file systems can incur significant I/O contention on storage servers. Such contention in turn degrades bandwidth utilization of storage servers and prolongs the average job I/O time of concurrent applications. Recently burst buffers have been proposed as an intermediate layer to absorb the bursty I/O traffic from compute nodes to storage backend. But an I/O orchestration mechanism is still desirable to efficiently move checkpointing data from burst buffers to storage backend. In this paper, we propose a burst buffer based I/O orchestration framework, named TRIO, to intercept and reshape the bursty writes for better sequential write traffic to storage servers. Meanwhile, TRIO coordinates the flushing orders among concurrent burst buffers to alleviate the contention on storage server. Our experimental results demonstrated that TRIO could efficiently utilize storage bandwidth and reduce the average job I/O time by 37% on average for data-intensive applications in typical checkpointing scenarios.
Computer Science↗
Impact of Module Configuration on Lithium-Ion Battery Performance and Degradation: Part I. Energy Throughput, Voltage Spread, and Current Distribution
Batteries are commonly connected in series and parallel to create modules that fulfill the power and energy requirements of specific applications. However, conclusions about battery performance and degradation under different conditions, as well as predictive models, are often derived from single cell cycling results. In this study, we evaluate the performance of six different series-parallel configurations of commercial lithium nickel manganese cobalt cells over hundreds of cycles. Each cell within the modules was individually instrumented for voltage, current, and temperature monitoring. We quantified the impact of module configuration on overall energy throughput, the voltage spread among series-connected cells, and the current heterogeneity in parallel-connected cells. This module cycling study, one of the broadest reported to date, supports systematic evaluation of the performance trade-offs, pack penalty, and safety implications of different module configurations.
25 ENERGY STORAGE↗