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At least 415 records · Page 23

Parallel processors and nonlinear structural dynamics algorithms and software

A nonlinear structural dynamics program with an element library that exploits parallel processing is under development. The aim is to exploit scheduling-allocation so that parallel processing and vectorization can effectively be treated in a general purpose program. As a byproduct an automatic scheme for assigning time steps was devised. A rudimentary form of the program is complete and has been tested; it shows substantial advantage can be taken of parallelism. In addition, a stability proof for the subcycling algorithm has been developed.

Belytschko, T.↗

Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs

Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.

Dash, Sajal↗

Image segmentation by iterative parallel region growing with application to data compression and image analysis

Image segmentation can be a key step in data compression and image analysis. However, the segmentation results produced by most previous approaches to region growing are suspect because they depend on the order in which portions of the image are processed. An iterative parallel segmentation algorithm avoids this problem by performing globally best merges first. Such a segmentation approach, and two implementations of the approach on NASA's Massively Parallel Processor (MPP) are described. Application of the segmentation approach to data compression and image analysis is then described, and results of such application are given for a LANDSAT Thematic Mapper image.

Tilton, James C.↗

Using Clustering to Establish Climate Regimes from PCM Output

A multivariate statistical clustering technique--based on the k-means algorithm of Hartigan has been used to extract patterns of climatological significance from 200 years of general circulation model (GCM) output. Originally developed and implemented on a Beowulf-style parallel computer constructed by Hoffman and Hargrove from surplus commodity desktop PCs, the high performance parallel clustering algorithm was previously applied to the derivation of ecoregions from map stacks of 9 and 25 geophysical conditions or variables for the conterminous U.S. at a resolution of 1 sq km. Now applied both across space and through time, the clustering technique yields temporally-varying climate regimes predicted by transient runs of the Parallel Climate Model (PCM). Using a business-as-usual (BAU) scenario and clustering four fields of significance to the global water cycle (surface temperature, precipitation, soil moisture, and snow depth) from 1871 through 2098, the authors' analysis shows an increase in spatial area occupied by the cluster or climate regime which typifies desert regions (i.e., an increase in desertification) and a decrease in the spatial area occupied by the climate regime typifying winter-time high latitude perma-frost regions. The patterns of cluster changes have been analyzed to understand the predicted variability in the water cycle on global and continental scales. In addition, representative climate regimes were determined by taking three 10-year averages of the fields 100 years apart for northern hemisphere winter (December, January, and February) and summer (June, July, and August). The result is global maps of typical seasonal climate regimes for 100 years in the past, for the present, and for 100 years into the future. Using three-dimensional data or phase space representations of these climate regimes (i.e., the cluster centroids), the authors demonstrate the portion of this phase space occupied by the land surface at all points in space and time. Any single spot on the globe will exist in one of these climate regimes at any single point in time. By incrementing time, that same spot will trace out a trajectory or orbit between and among these climate regimes (or atmospheric states) in phase (or state) space. When a geographic region enters a state it never previously visited, a climatic change is said to have occurred. Tracing out the entire trajectory of a single spot on the globe yields a 'manifold' in state space representing the shape of its predicted climate occupancy. This sort of analysis enables a researcher to more easily grasp the multivariate behavior of the climate system.

Oglesby, Robert↗

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

Hsieh, Shang-Hsien↗

Investigations on the usefulness of the Massively Parallel Processor for study of electronic properties of atomic and condensed matter systems

The usefulness of the Massively Parallel Processor (MPP) for investigation of electronic structures and hyperfine properties of atomic and condensed matter systems was explored. The major effort was directed towards the preparation of algorithms for parallelization of the computational procedure being used on serial computers for electronic structure calculations in condensed matter systems. Detailed descriptions of investigations and results are reported, including MPP adaptation of self-consistent charge extended Hueckel (SCCEH) procedure, MPP adaptation of the first-principles Hartree-Fock cluster procedure for electronic structures of large molecules and solid state systems, and MPP adaptation of the many-body procedure for atomic systems.

Das, T. P.↗

Structural dynamic analysis on a parallel computer - The finite element machine

Recent and prospective advances in parallel multiple introduction multiple data (MIMD) computers offer significant improvements in the range of structural problems that can be solved, as well as the speed of solutions. These improvements have their basis in the effective selection and implementation of algorithms exploiting parallel computation. Attention is presently given to the solution of the transient response calculations of an experimental MIMD computer designated the 'Finite Element Machine', including its algorithm and its results for representative one- and two-dimensional dynamic response test problems. A factor of 6.5 is noted for the computational speed improvement.

Storaasli, O.↗

Concurrent extensions to the FORTRAN language for parallel programming of computational fluid dynamics algorithms

Experiments were conducted at NASA Ames Research Center to define multi-tasking software requirements for multiple-instruction, multiple-data stream (MIMD) computer architectures. The focus was on specifying solutions for algorithms in the field of computational fluid dynamics (CFD). The program objectives were to allow researchers to produce usable parallel application software as soon as possible after acquiring MIMD computer equipment, to provide researchers with an easy-to-learn and easy-to-use parallel software language which could be implemented on several different MIMD machines, and to enable researchers to list preferred design specifications for future MIMD computer architectures. Analysis of CFD algorithms indicated that extensions of an existing programming language, adaptable to new computer architectures, provided the best solution to meeting program objectives. The CoFORTRAN Language was written in response to these objectives and to provide researchers a means to experiment with parallel software solutions to CFD algorithms on machines with parallel architectures.

Weeks, Cindy Lou↗

Fast Fourier Transform algorithm design and tradeoffs

The Fast Fourier Transform (FFT) is a mainstay of certain numerical techniques for solving fluid dynamics problems. The Connection Machine CM-2 is the target for an investigation into the design of multidimensional Single Instruction Stream/Multiple Data (SIMD) parallel FFT algorithms for high performance. Critical algorithm design issues are discussed, necessary machine performance measurements are identified and made, and the performance of the developed FFT programs are measured. Fast Fourier Transform programs are compared to the currently best Cray-2 FFT program.

Kamin, Ray A., III↗

Parallel integer sorting with medium and fine-scale parallelism

Two new parallel integer sorting algorithms, queue-sort and barrel-sort, are presented and analyzed in detail. These algorithms do not have optimal parallel complexity, yet they show very good performance in practice. Queue-sort designed for fine-scale parallel architectures which allow the queueing of multiple messages to the same destination. Barrel-sort is designed for medium-scale parallel architectures with a high message passing overhead. The performance results from the implementation of queue-sort on a Connection Machine CM-2 and barrel-sort on a 128 processor iPSC/860 are given. The two implementations are found to be comparable in performance but not as good as a fully vectorized bucket sort on the Cray YMP.

Dagum, Leonardo↗

Computational requirements for on-orbit identification of space systems

For the future space systems, on-orbit identification (ID) capability will be required to complement on-orbit control, due to the fact that the dynamics of large space structures, spacecrafts, and antennas will not be known sufficiently from ground modeling and testing. The computational requirements for ID of flexible structures such as the space station (SS) or the large deployable reflectors (LDR) are however, extensive due to the large number of modes, sensors, and actuators. For these systems the ID algorithm operations need not be computed in real-time, only in near real-time, or an appropriate mission time. Consequently the space systems will need advanced processors and efficient parallel processing algorithm design and architectures to implement the identification algorithms in near real-time. The MAX computer currently being developed may handle such computational requirements. The purpose is to specify the on-board computational requirements for dynamic and static identification for large space structures. The computational requirements for six ID algorithms are presented in the context of three examples: the JPL/AFAL ground antenna facility, the space station (SS), and the large deployable reflector (LDR).

Hadaegh, Fred Y.↗

Geopotential Error Analysis from Satellite Gradiometer and Global Positioning System Observables on Parallel Architecture

The recovery of a high resolution geopotential from satellite gradiometer observations motivates the examination of high performance computational techniques. The primary subject matter addresses specifically the use of satellite gradiometer and GPS observations to form and invert the normal matrix associated with a large degree and order geopotential solution. Memory resident and out-of-core parallel linear algebra techniques along with data parallel batch algorithms form the foundation of the least squares application structure. A secondary topic includes the adoption of object oriented programming techniques to enhance modularity and reusability of code. Applications implementing the parallel and object oriented methods successfully calculate the degree variance for a degree and order 110 geopotential solution on 32 processors of the Cray T3E. The memory resident gradiometer application exhibits an overall application performance of 5.4 Gflops, and the out-of-core linear solver exhibits an overall performance of 2.4 Gflops. The combination solution derived from a sun synchronous gradiometer orbit produce average geoid height variances of 17 millimeters.

Schutz, Bob E.↗

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named NeuroGPU-EA. NeuroGPU-EA uses CPUs and GPUs concurrently to simulate and evaluate neuron membrane potentials with respect to multiple stimuli. We demonstrate a logarithmic cost for scaling the stimuli used in the fitting procedure. NeuroGPU-EA outperforms the typically used CPU based evolutionary algorithm by a factor of 10 on a series of scaling benchmarks. We report observed performance bottlenecks and propose mitigation strategies. Finally, we also discuss the potential of this method for efficient simulation and evaluation of electrophysiological waveforms.

59 BASIC BIOLOGICAL SCIENCES↗

An efficient three-dimensional Poisson solver for SIMD high-performance-computing architectures

We present an algorithm that solves the three-dimensional Poisson equation on a cylindrical grid. The technique uses a finite-difference scheme with operator splitting. This splitting maps the banded structure of the operator matrix into a two-dimensional set of tridiagonal matrices, which are then solved in parallel. Our algorithm couples FFT techniques with the well-known ADI (Alternating Direction Implicit) method for solving Elliptic PDE's, and the implementation is extremely well suited for a massively parallel environment like the SIMD architecture of the MasPar MP-1. Due to the highly recursive nature of our problem, we believe that our method is highly efficient, as it avoids excessive interprocessor communication.

Cohl, H.↗

Rectilinear partitioning of irregular data parallel computations

New mapping algorithms for domain oriented data-parallel computations, where the workload is distributed irregularly throughout the domain, but exhibits localized communication patterns are described. Researchers consider the problem of partitioning the domain for parallel processing in such a way that the workload on the most heavily loaded processor is minimized, subject to the constraint that the partition be perfectly rectilinear. Rectilinear partitions are useful on architectures that have a fast local mesh network. Discussed here is an improved algorithm for finding the optimal partitioning in one dimension, new algorithms for partitioning in two dimensions, and optimal partitioning in three dimensions. The application of these algorithms to real problems are discussed.

Nicol, David M.↗

Sage: parallel semi-asymmtric graph algorithms for NVRAMs

Non-volatile main memory (NVRAM) technologies provide an attractive set of features for large-scale graph analytics, including byte-addressability, low idle power, and improved memory-density. NVRAM systems today have an order of magnitude more NVRAM than traditional memory (DRAM). NVRAM systems could therefore potentially allow very large graph problems to be solved on a single machine, at a modest cost. However, a significant challenge in achieving high performance is in accounting for the fact that NVRAM writes can be much more expensive than NVRAM reads. In this paper, we propose an approach to parallel graph analytics using the Parallel Semi-Asymmetric Model (PSAM), in which the graph is stored as a read-only data structure (in NVRAM), and the amount of mutable memory is kept proportional to the number of vertices. Similar to the popular semi-external and semi-streaming models for graph analytics, the PSAM approach assumes that the vertices of the graph fit in a fast read-write memory (DRAM), but the edges do not. In NVRAM systems, our approach eliminates writes to the NVRAM, among other benefits. To experimentally study this new setting, we develop Sage, a parallel semi-asymmetric graph engine with which we implement provably-efficient (and often work-optimal) PSAM algorithms for over a dozen fundamental graph problems. We experimentally study Sage using a 48--core machine on the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) equipped with Optane DC Persistent Memory, and show that Sage outperforms the fastest prior systems designed for NVRAM. Importantly, we also show that Sage nearly matches the fastest prior systems running solely in DRAM, by effectively hiding the costs of repeatedly accessing NVRAM versus DRAM.

97 MATHEMATICS AND COMPUTING↗