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At least 19 records

All sources NASA NTRS DOE OSTI

DOE OSTI2011

Energy Proportionality and Performance in Data Parallel Computing Clusters

Energy consumption in datacenters has recently become a major concern due to the rising operational costs andscalability issues. Recent solutions to this problem propose the principle of energy proportionality, i.e., the amount of energy consumedby the server nodes must be proportional to the amount of work performed. For data parallelism and fault tolerancepurposes, most common file systems used in MapReduce-type clusters maintain a set of replicas for each data block. A coveringset is a group of nodes that together contain at least one replica of the data blocks needed for performing computing tasks. In thiswork, we develop and analyze algorithms to maintain energy proportionality by discovering a covering set that minimizesenergy consumption while placing the remaining nodes in lowpower standby mode. Our algorithms can also discover coveringsets in heterogeneous computing environments. In order to allow more data parallelism, we generalize our algorithms so that itcan discover k-covering sets, i.e., a set of nodes that contain at least k replicas of the data blocks. Our experimental results showthat we can achieve substantial energy saving without significant performance loss in diverse cluster configurations and workingenvironments.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Scalable deep text comprehension for Cancer surveillance on high-performance computing

Background: Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by larger and larger data sets. This vastly increased computational demand challenges the feasibility of conducting cutting-edge research. One solution is to distribute the vast computational workload across multiple computing cluster nodes with data parallelism algorithms. In this study, we used a High-Performance Computing environment and implemented the Downpour Stochastic Gradient Descent algorithm for data parallelism to train a Convolutional Neural Network (CNN) for the natural language processing task of information extraction from a massive dataset of cancer pathology reports. We evaluated the scalability improvements using data parallelism training and the Titan supercomputer at Oak Ridge Leadership Computing Facility. To evaluate scalability, we used different numbers of worker nodes and performed a set of experiments comparing the effects of different training batch sizes and optimizer functions.Results: We found that Adadelta would consistently converge at a lower validation loss, though requiring over twice as many training epochs as the fastest converging optimizer, RMSProp. The Adam optimizer consistently achieved a close 2nd place minimum validation loss significantly faster; using a batch size of 16 and 32 allowed the network to converge in only 4.5 training epochs.Conclusions: We demonstrated that the networked training process is scalable across multiple compute nodes communicating with message passing interface while achieving higher classification accuracy compared to a traditional machine learning algorithm.

Qiu, John X.↗

DOE OSTI2014

Parallel Optical Flow Processing of 4D Cardiac CT Data on Multicore Clusters, In: 2014 IEEE 17th International Conference on Computational Science and Engineering

Optical flow is the distribution of apparent velocities of movement of brightness patterns in a sequence of images. For large 3D image sequences, optical flow applications are time consuming and memory-bound. To cope with these problems, in this paper, we present parallel optical flow processing of 4D cardiac CT data on multicore cluster systems to significantly shorten the time for computing velocity fields of the heart in order to aid cardiologists in diagnosing heart disease such as myocardial infarction and cardiac dysrhythmia in time. First, we modify and extend two traditional 2D optical flow methods Horn-Schunck and Lucas-Kanade to three-dimensional cases to process the 4D cardiac CT data. Second, we extend Mat lab MPI to support parallel computing with Mat lab and Octave on these cluster systems. Then we develop the parallel Mat lab/Octave optical flow applications for the 4D cardiac CT data in detail. Our experimental results show that these parallel optical flow applications have good scalability with close to linear speedup, and are able to shorten the image processing time significantly from more than 5 hours on 4 cores to 1.5 minutes on 1024 cores.

Engineering↗

DOE OSTI2018

Parallel multiple-chain DRAM MCMC for large-scale geosteering inversion and uncertainty quantification

Geosteering is the proactive control of a wellbore placement based on the downhole measurements, aiming at maximizing economic production from the well. We report the recent development of azimuthal resistivity logging-whiledrilling (LWD) tools have a much larger depth of detection, thus sets higher demands for geosteering inversion as more unknown parameters need to be taken into account in the earth model to be inverted. For complicated nonlinear problems, traditional deterministic inversion methods are more likely to be trapped near local optima. In general, Markov chain Monte Carlo (MCMC) inversion methods are more capable of finding the global optimal solution and providing additional uncertainty analyses by sampling from the target distribution. However, MCMC methods usually have the problem of slow convergence. Even though optimization methods like delayed rejection (DR) and adaptive Metropolis (AM) were proposed to speed up the convergence, using MCMC methods to solve geosteering inversion problems may still incur unacceptable time cost. To reduce the sampling cost of MCMC methods, we use parallel multiple-chain DRAM MCMC methods to solve geosteering inverse problems and estimate the corresponding uncertainty. A clustering method, density-based spatial clustering of applications with noise (DBSCAN), is applied to select the best solution among many results. Lastly, the simulation results show that running many relatively short MCMC chains for one problem can obtain a similar result as running a long single chain. Besides, avoiding communications between multiple Markov chains during the sampling process yields almost linear scalability.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2012

Graphics Processing Unit Assisted Thermographic Compositing

Objective: To develop a software application utilizing general purpose graphics processing units (GPUs) for the analysis of large sets of thermographic data. Background: Over the past few years, an increasing effort among scientists and engineers to utilize the GPU in a more general purpose fashion is allowing for supercomputer level results at individual workstations. As data sets grow, the methods to work them grow at an equal, and often great, pace. Certain common computations can take advantage of the massively parallel and optimized hardware constructs of the GPU to allow for throughput that was previously reserved for compute clusters. These common computations have high degrees of data parallelism, that is, they are the same computation applied to a large set of data where the result does not depend on other data elements. Signal (image) processing is one area were GPUs are being used to greatly increase the performance of certain algorithms and analysis techniques. Technical Methodology/Approach: Apply massively parallel algorithms and data structures to the specific analysis requirements presented when working with thermographic data sets.

Ragasa, Scott↗

NASA NTRS2013

Graphics Processing Unit Assisted Thermographic Compositing

Objective: To develop a software application utilizing general purpose graphics processing units (GPUs) for the analysis of large sets of thermographic data. Background: Over the past few years, an increasing effort among scientists and engineers to utilize the GPU in a more general purpose fashion is allowing for supercomputer level results at individual workstations. As data sets grow, the methods to work them grow at an equal, and often greater, pace. Certain common computations can take advantage of the massively parallel and optimized hardware constructs of the GPU to allow for throughput that was previously reserved for compute clusters. These common computations have high degrees of data parallelism, that is, they are the same computation applied to a large set of data where the result does not depend on other data elements. Signal (image) processing is one area were GPUs are being used to greatly increase the performance of certain algorithms and analysis techniques.

Ragasa, Scott↗

NASA NTRS2003

Access and visualization using clusters and other parallel computers

JPL's Parallel Applications Technologies Group has been exploring the issues of data access and visualization of very large data sets over the past 10 or so years. this work has used a number of types of parallel computers, and today includes the use of commodity clusters. This talk will highlight some of the applications and tools we have developed, including how they use parallel computing resources, and specifically how we are using modern clusters. Our applications focus on NASA's needs; thus our data sets are usually related to Earth and Space Science, including data delivered from instruments in space, and data produced by telescopes on the ground.

data sets↗

DOE OSTI2011

Data mining in earth system science (DMESS 2011).

From field-scale measurements to global climate simulations and remote sensing, the growing body of very large and long time series Earth science data are increasingly difficult to analyze, visualize, and interpret. Data mining, information theoretic, and machine learning techniques - such as cluster analysis, singular value decomposition, block entropy, Fourier and wavelet analysis, phase-space reconstruction, and artificial neural networks - are being applied to problems of segmentation, feature extraction, change detection, model-data comparison, and model validation. The size and complexity of Earth science data exceed the limits of most analysis tools and the capacities of desktop computers. New scalable analysis and visualization tools, running on parallel cluster computers and supercomputers, are required to analyze data of this magnitude. This workshop will demonstrate how data mining techniques are applied in the Earth sciences and describe innovative computer science methods that support analysis and discovery in the Earth sciences.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2011

Data Mining in Earth System Science (DMESS 2011)

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2017

Parallel Multivariate Spatio-Temporal Clustering of Large Ecological Datasets on Hybrid Supercomputers

A proliferation of data from vast networks of remote sensing platforms (satellites, unmanned aircraft systems (UAS), airborne etc.), observational facilities (meteorological, eddy covariance etc.), state-of-the-art sensors, and simulation models offer unprecedented opportunities for scientific discovery. Unsupervised classification is a widely applied data mining approach to derive insights from such data. However, classification of very large data sets is a complex computational problem that requires efficient numerical algorithms and implementations on high performance computing (HPC) platforms. Additionally, increasing power, space, cooling and efficiency requirements has led to the deployment of hybrid supercomputing platforms with complex architectures and memory hierarchies like the Titan system at Oak Ridge National Laboratory. The advent of such accelerated computing architectures offers new challenges and opportunities for big data analytics in general and specifically, large scale cluster analysis in our case. Although there is an existing body of work on parallel cluster analysis, those approaches do not fully meet the needs imposed by the nature and size of our large data sets. Moreover, they had scaling limitations and were mostly limited to traditional distributed memory computing platforms. We present a parallel Multivariate Spatio-Temporal Clustering (MSTC) technique based on k-means cluster analysis that can target hybrid supercomputers like Titan. We developed a hybrid MPI, CUDA and OpenACC implementation that can utilize both CPU and GPU resources on computational nodes. We describe performance results on Titan that demonstrate the scalability and efficacy of our approach in processing large ecological data sets.

Sreepathi, Sarat↗

NASA NTRS2004

Development of Message Passing Routines for High Performance Parallel Computations

Computational Fluid Dynamics (CFD) calculations require a great deal of computing power for completing the detailed computations involved. In an effort shorten the time it takes to complete such calculations they are implemented on a parallel computer. In the case of a parallel computer some sort of message passing structure must be used to communicate between the computers because, unlike a single machine, each computer in a parallel computing cluster does not have access to all the data or run all the parts of the total program. Thus, message passing is used to divide up the data and send instructions to each machine. The nature of my work this summer involves programming the "message passing" aspect of the parallel computer. I am working on modifying an existing program, which was written with OpenMP, and does not use a multi-machine parallel computing structure, to work with Message Passing Interface (MPI) routines. The actual code is being written in the FORTRAN 90 programming language. My goal is to write a parameterized message passing structure that could be used for a variety of individual applications and implement it on Silicon Graphics Incorporated s (SGI) IRIX operating system. With this new parameterized structure engineers would be able to speed up computations for a wide variety of purposes without having to use larger and more expensive computing equipment from another division or another NASA center.

Summers, Edward K.↗

DOE OSTI2020

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2003

Access and visualization using clusters and other parallel computers

JPL's Parallel Applications Technologies Group has been exploring the issues of data access and visualization of very large data sets over the past 10 years. this work has used a number of types of parallel computers, and today includes the use of commodity clusters. This talk will highlight some of the applications and tools we have developed, including how they use parallel computing resources, and specifically how we are using modern clusters.

parallel computers clusters↗

DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2004

Accessing and Visualizing scientific spatiotemporal data

This paper discusses work done by JPL 's Parallel Applications Technologies Group in helping scientists access and visualize very large data sets through the use of multiple computing resources, such as parallel supercomputers, clusters, and grids These tools do one or more of the following tasks visualize local data sets for local users, visualize local data sets for remote users, and access and visualize remote data sets The tools are used for various types of data, including remotely sensed image data, digital elevation models, astronomical surveys, etc The paper attempts to pull some common elements out of these tools that may be useful for others who have to work with similarly large data sets.

data sets↗

NASA NTRS2001

Arthropod phylogeny based on eight molecular loci and morphology

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Non-NASA Center↗

DOE OSTI2018

Parallel k-means Clustering of Geospatial Data Sets Using Manycore CPU Architectures

The increasing availability of high-resolution geospatiotemporal data sets from sources such as observatory networks, remote sensing platforms, and computational Earth system models has opened new possibilities for knowledge discovery and mining of weather, climate, ecological, and other geoscientific data sets fused from disparate sources. Many of the standard tools used on individual workstations are impractical for the analysis and synthesis of data sets of this size; however, new algorithmic approaches that can effectively utilize the complex memory hierarchies and the extremely high levels of parallelism available in state-of-the-art high-performance computing platforms can enable such analysis. Here, we describe pKluster, an open-source tool we have developed for accelerated k-means clustering of geospatial and geospatiotemporal data, and discuss algorithmic modifications and code optimizations we have made to enable it to effectively use parallel machines based on novel CPU architectures—such as the Intel “Knights Landing” Xeon Phi and Skylake Xeon processors—with many cores and hardware threads, and employing significant single instruction, multiple data (SIMD) parallelism. We outline some applications of the code in ecology and climate science contexts and present a detailed discussion of the performance of the code for one such application, LiDAR-derived vertical vegetation structure classification.

Mills, Richard T↗

DOE OSTI2011

Creating a Parallel Version of VisIt for Microsoft Windows

VisIt is a popular, free interactive parallel visualization and analysis tool for scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images or movies for presentations. VisIt was designed from the ground up to work on many scales of computers from modest desktops up to massively parallel clusters. VisIt is comprised of a set of cooperating programs. All programs can be run locally or in client/server mode in which some run locally and some run remotely on compute clusters. The VisIt program most able to harness today's computing power is the VisIt compute engine. The compute engine is responsible for reading simulation data from disk, processing it, and sending results or images back to the VisIt viewer program. In a parallel environment, the compute engine runs several processes, coordinating using the Message Passing Interface (MPI) library. Each MPI process reads some subset of the scientific data and filters the data in various ways to create useful visualizations. By using MPI, VisIt has been able to scale well into the thousands of processors on large computers such as dawn and graph at LLNL. The advent of multicore CPU's has made parallelism the 'new' way to achieve increasing performance. With today's computers having at least 2 cores and in many cases up to 8 and beyond, it is more important than ever to deploy parallel software that can use that computing power not only on clusters but also on the desktop. We have created a parallel version of VisIt for Windows that uses Microsoft's MPI implementation (MSMPI) to process data in parallel on the Windows desktop as well as on a Windows HPC cluster running Microsoft Windows Server 2008. Initial desktop parallel support for Windows was deployed in VisIt 2.4.0. Windows HPC cluster support has been completed and will appear in the VisIt 2.5.0 release. We plan to continue supporting parallel VisIt on Windows so our users will be able to take full advantage of their multicore resources.

97 MATHEMATICS AND COMPUTING↗