SEARCH · Search NASA

Results for “parallel clustering”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28

All sources NASA NTRS DOE OSTI

DOE OSTI2017

High Fidelity Simulations of Large-scale Wireless Networks (Part II - FY2017)

The ability to simulate wireless networks at large-scale for meaningful amount of time is considerably lacking in today's network simulators. For this reason, many published work in this area often limit their simulation studies to less than a 1,000 nodes and either over-simplify channel characteristics or perform studies over time scales much less than a day. In this report, we show that one can overcome these limitations and study problems of high practical consequence. This work presents two key contributions to high fidelity simulation of large-scale wireless networks: (a) wireless simulations can be sped up by more than 100X in runtime using ideas from spatial indexing algorithms and clipping of negligible signals and (b) clustering and task-oriented programming paradigm can be used to reduce inter- process communication in a parallel discrete event simulation resulting in a better scaling efficiency.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Randomized Cholesky Preconditioning for Graph Partitioning Applications

A graph is a mathematical representation of a network; we say it consists of a set of vertices, which are connected by edges. Graphs have numerous applications in various fields, as they can model all sorts of connections, processes, or relations. For example, graphs can model intricate transit systems or the human nervous system. However, graphs that are large or complicated become difficult to analyze. This is why there is an increased interest in the area of graph partitioning, reducing the size of the graph into multiple partitions. For example, partitions of a graph representing a social network might help identify clusters of friends or colleagues. Graph partitioning is also a widely used approach to load balancing in parallel computing. The partitioning of a graph is extremely useful to decompose the graph into smaller parts and allow for easier analysis. There are different ways to solve graph partitioning problems. For this work, we focus on a spectral partitioning method which forms a partition based upon the eigenvectors of the graph Laplacian (details presented in Acer, et. al.). This method uses the LOBPCG algorithm to compute these eigenvectors. LOBPCG can be accelerated by an operator called a preconditioner. For this internship, we evaluate a randomized Cholesky (rchol) preconditioner for its effectiveness on graph partitioning problems with LOBPCG. We compare it with two standard preconditioners: Jacobi and Incomplete Cholesky (ichol). This research was conducted from August to December 2021 in conjunction with Sandia National Laboratories.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1982

Content-addressable read/write memories for image analysis

The commonly encountered image analysis problems of region labeling and clustering are found to be cases of search-and-rename problem which can be solved in parallel by a system architecture that is inherently suitable for VLSI implementation. This architecture is a novel form of content-addressable memory (CAM) which provides parallel search and update functions, allowing speed reductions down to constant time per operation. It has been proposed in related investigations by Hall (1981) that, with VLSI, CAM-based structures with enhanced instruction sets for general purpose processing will be feasible.

Snyder, W. E.↗

DOE OSTI2022

Shocks in the stacked Sunyaev-Zel’dovich profiles of clusters II: Measurements from SPT-SZ + Planck Compton- y map

ABSTRACT We search for the signature of cosmological shocks in stacked gas pressure profiles of galaxy clusters using data from the South Pole Telescope (SPT). Specifically, we stack the latest Compton-y maps from the 2500 deg2 SPT-SZ survey on the locations of clusters identified in that same data set. The sample contains 516 clusters with mean mass $\langle M_{\rm 200m}\rangle = 10^{14.9} \, {\rm M}_\odot$ and redshift 〈z〉 = 0.55. We analyse in parallel a set of zoom-in hydrodynamical simulations from the three hundred project. The SPT-SZ data show two features: (i) a pressure deficit at R/R200m = 1.08 ± 0.09, measured at 3.1σ significance and not observed in the simulations, and; (ii) a sharp decrease in pressure at R/R200m = 4.58 ± 1.24 at 2.0σ significance. The pressure deficit is qualitatively consistent with a shock-induced thermal non-equilibrium between electrons and ions, and the second feature is consistent with accretion shocks seen in previous studies. We split the cluster sample by redshift and mass, and find both features exist in all cases. There are also no significant differences in features along and across the cluster major axis, whose orientation roughly points towards filamentary structure. As a consistency test, we also analyse clusters from the Planck and Atacama Cosmology Telescope Polarimeter surveys and find quantitatively similar features in the pressure profiles. Finally, we compare the accretion shock radius ($R_{\rm sh,\, acc}$) with existing measurements of the splashback radius (Rsp) for SPT-SZ and constrain the lower limit of the ratio, $R_{\rm sh,\, acc}/R_{\rm sp}\gt 2.16 \pm 0.59$.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

OpenMP and MPI implementations of an elasto-viscoplastic fast Fourier transform-based micromechanical solver for fast crystal plasticity modeling

Here, we explore several parallel implementations of an elasto-viscoplastic fast Fourier transform (EVPFFT) model using Message Passing Interface (MPI), OpenMP, and a hybrid of MPI and OpenMP to efficiently predict micromechanical response of polycrystals. Performance studies using EVPFFT are performed based on domain decomposition over voxels of a periodic cell, which is a representative volume element (RVE) of polycrystalline copper. We begin by parallelizing the computationally intensive Newton–Raphson (NR) single crystal solver within EVPFFT. Next, we compare the performance of the serial and parallel FFTW (Fastest Fourier Transform in the West) using OpenMP (OpenMP-FFTW) and MPI (MPI-FFTW) with the original Numerical Recipes-based FOURN routine within EVPFFT. In the parallel environment, we find that the FFT calculations are best performed using the MPI version of FFTW. Finally, the remainder of the code, except read/write subroutines, is parallelized. Significant speedups of the original EVPFFT model are achieved using MPI on shared memory multicore workstations. Furthermore, results achieved on a distributed memory Cray supercomputer show promising strong and weak scalability and in some cases even super scalability for the single crystal NR solver in EVPFFT. MPI-FFTW also scales perfectly for microstructure RVEs larger than 64 3 FFT voxels. For example, the MPI-EVPFFT parallel version of the code accelerates the simulations for approximately two orders of magnitude using 64 cores over the old serial code for an RVE size of 128 3 . Finally, the parallel EVPFFT code developed in this work can run massive voxel-based microstructural RVEs taking the advantages of thousands of logical cores provided by more advanced clusters.

42 ENGINEERING↗

DOE OSTI2013

Performance modeling of microsecond scale biological molecular dynamics simulations on heterogeneous architectures

Performance improvements in biomolecular simulations based on molecular dynamics (MD) codes are widely desired. Unfortunately, the factors, which allowed past performance improvements, particularly the microprocessor clock frequencies, are no longer increasing. Hence, novel software and hardware solutions are being explored for accelerating performance of widely used MD codes. In this paper, we describe our efforts on porting, optimizing and tuning of Large-scale Atomic/Molecular Massively Parallel Simulator, a popular MD framework, on heterogeneous architectures: multi-core processors with graphical processing unit (GPU) accelerators. Our implementation is based on accelerating the most computationally expensive non-bonded interaction terms on the GPUs and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs and allows extension of the implementation on GPU-enabled clusters. We hypothesize that the optimal benefit of heterogeneous architectures for applications will come by utilizing all possible resources (for example, CPU-cores and GPU devices on GPU-enabled clusters). Benchmarks for a range of biomolecular system sizes are provided, and an analysis is performed on four generations of NVIDIA's GPU devices. On GPU-enabled Linux clusters, by overlapping and pipelining computation and communication, we observe up to 10-folds application acceleration in multi-core and multi-GPU environments illustrating significant performance improvements. Detailed analysis of the implementation is presented that allows identification of bottlenecks in algorithm, indicating that code optimization and improvements on GPUs could allow microsecond scale simulation throughput on workstations and inexpensive GPU clusters, putting widely desired biologically relevant simulation time-scales within reach of a large user community. In order to systematically optimize simulation throughput and to enable performance prediction, we have developed a parameterized performance model that will allow developers and users to explore the performance potential of future heterogeneous systems for biological simulations.

Agarwal, Pratul K.↗

DOE OSTI2013

Parallel multiscale simulations of a brain aneurysm

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Optimized coordinates in vibrational coupled cluster calculations

The use of variationally optimized coordinates, which minimize the vibrational self-consistent field (VSCF) ground state energy with respect to orthogonal transformations of the coordinates, has recently been shown to improve the convergence of vibrational configuration interaction (VCI) towards the exact full VCI [K. Yagi, M. Keçeli, and S. Hirata, J. Chem. Phys. 137, 204118 (2012)]. The present paper proposes an incorporation of optimized coordinates into the vibrational coupled cluster (VCC), which has in the past been shown to outperform VCI in approximate calculations where similar restricted state spaces are employed in VCI and VCC. An embarrassingly parallel algorithm for variational optimization of coordinates for VSCF is implemented and the resulting coordinates and potentials are introduced into a VCC program. The performance of VCC in optimized coordinates (denoted oc-VCC) is examined through pilot applications to water, formaldehyde, and a series of water clusters (dimer, trimer, and hexamer) by comparing the calculated vibrational energy levels with those of the conventional VCC in normal coordinates and VCI in optimized coordinates. For water clusters, in particular, oc-VCC is found to gain orders of magnitude improvement in the accuracy, exemplifying that the combination of optimized coordinates localized to each monomer with the size-extensive VCC wave function provides a supreme description of systems consisting of weakly interacting sub-systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Solvers for $\mathcal{O} (N)$ Electronic Structure in the Strong Scaling Limit

Here we present a hybrid OpenMP/Charm\tt++ framework for solving the $\mathcal{O} (N)$ self-consistent-field eigenvalue problem with parallelism in the strong scaling regime, $P\gg{N}$, where $P$ is the number of cores, and $N$ is a measure of system size, i.e., the number of matrix rows/columns, basis functions, atoms, molecules, etc. This result is achieved with a nested approach to spectral projection and the sparse approximate matrix multiply [Bock and Challacombe, SIAM J. Sci. Comput., 35 (2013), pp. C72--C98], and involves a recursive, task-parallel algorithm, often employed by generalized $N$-Body solvers, to occlusion and culling of negligible products in the case of matrices with decay. Lastly, employing classic technologies associated with generalized $N$-Body solvers, including overdecomposition, recursive task parallelism, orderings that preserve locality, and persistence-based load balancing, we obtain scaling beyond hundreds of cores per molecule for small water clusters ([H${}_2$O]${}_N$, $N \in \{ 30, 90, 150 \}$, $P/N \approx \{ 819, 273, 164 \}$) and find support for an increasingly strong scalability with increasing system size $N$.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Active Flash: Performance-Energy Tradeoffs for Out-of-Core Processing on Non-Volatile Memory Devices

In this abstract, we study the performance and energy tradeoffs involved in migrating data analysis into the flash device, a process we refer to as Active Flash. The Active Flash paradigm is similar to 'active disks', which has received considerable attention. Active Flash allows us to move processing closer to data, thereby minimizing data movement costs and reducing power consumption. It enables true out-of-core computation. The conventional definition of out-of-core solvers refers to an approach to process data that is too large to fit in the main memory and, consequently, requires access to disk. However, in Active Flash, processing outside the host CPU literally frees the core and achieves real 'out-of-core' analysis. Moving analysis to data has long been desirable, not just at this level, but at all levels of the system hierarchy. However, this requires a detailed study on the tradeoffs involved in achieving analysis turnaround under an acceptable energy envelope. To this end, we first need to evaluate if there is enough computing power on the flash device to warrant such an exploration. Flash processors require decent computing power to run the internal logic pertaining to the Flash Translation Layer (FTL), which is responsible for operations such as address translation, garbage collection (GC) and wear-leveling. Modern SSDs are composed of multiple packages and several flash chips within a package. The packages are connected using multiple I/O channels to offer high I/O bandwidth. SSD computing power is also expected to be high enough to exploit such inherent internal parallelism within the drive to increase the bandwidth and to handle fast I/O requests. More recently, SSD devices are being equipped with powerful processing units and are even embedded with multicore CPUs (e.g. ARM Cortex-A9 embedded processor is advertised to reach 2GHz frequency and deliver 5000 DMIPS; OCZ RevoDrive X2 SSD has 4 SandForce controllers, each with 780MHz max frequency Tensilica core). Efforts that take advantage of the available computing cycles on the processors on SSDs to run auxiliary tasks other than actual I/O requests are beginning to emerge. Kim et al. investigate database scan operations in the context of processing on the SSDs, and propose dedicated hardware logic to speed up scans. Also, cluster architectures have been explored, which consist of low-power embedded CPUs coupled with small local flash to achieve fast, parallel access to data. Processor utilization on SSD is highly dependent on workloads and, therefore, they can be idle during periods with no I/O accesses. We propose to use the available processing capability on the SSD to run tasks that can be offloaded from the host. This paper makes the following contributions: (1) We have investigated Active Flash and its potential to optimize the total energy cost, including power consumption on the host and the flash device; (2) We have developed analytical models to analyze the performance-energy tradeoffs for Active Flash, by treating the SSD as a blackbox, this is particularly valuable due to the proprietary nature of the SSD internal hardware; and (3) We have enhanced a well-known SSD simulator (from MSR) to implement 'on-the-fly' data compression using Active Flash. Our results provide a window into striking a balance between energy consumption and application performance.

42 ENGINEERING↗

DOE OSTI2019

Detecting galaxy–filament alignments in the Sloan Digital Sky Survey III

Abstract Previous studies have shown the filamentary structures in the cosmic web influence the alignments of nearby galaxies. We study this effect in the LOWZ sample of the Sloan Digital Sky Survey using the ‘Cosmic Web Reconstruction' filament catalogue. We find that LOWZ galaxies exhibit a small but statistically significant alignment in the direction parallel to the orientation of nearby filaments. This effect is detectable even in the absence of nearby galaxy clusters, which suggests it is an effect from the matter distribution in the filament. A non-parametric regression model suggests that the alignment effect with filaments extends over separations of 30–40 Mpc. We find that galaxies that are bright and early-forming align more strongly with the directions of nearby filaments than those that are faint and late-forming; however, trends with stellar mass are less statistically significant, within the narrow range of stellar mass of this sample.

Chen, Yen-Chi↗

DOE OSTI2021

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

CSRI Summer Proceedings 2021

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1989

Balanced-Load Real-Time Multiprocessor System

Modularity and parallelism provide tolerance to faults and high throughput capacity. System, called MAX, is network of interconnected computers. MAX cluster consists of group of modules - each semiautonomous computer. Modules connected to each other and to other clusters by global bus and circuit-switched communication mesh.

Rasmussen, Robert D.↗

NASA NTRS1994

A heterogeneous computing environment for simulating astrophysical fluid flows

In the Concurrent Computing Laboratory in the Department of Physics and Astronomy at Louisiana State University we have constructed a heterogeneous computing environment that permits us to routinely simulate complicated three-dimensional fluid flows and to readily visualize the results of each simulation via three-dimensional animation sequences. An 8192-node MasPar MP-1 computer with 0.5 GBytes of RAM provides 250 MFlops of execution speed for our fluid flow simulations. Utilizing the parallel virtual machine (PVM) language, at periodic intervals data is automatically transferred from the MP-1 to a cluster of workstations where individual three-dimensional images are rendered for inclusion in a single animation sequence. Work is underway to replace executions on the MP-1 with simulations performed on the 512-node CM-5 at NCSA and to simultaneously gain access to more potent volume rendering workstations.

Cazes, J.↗

NASA NTRS2012

Ultrawideband asynchronous tracking system and method

A passive tracking system is provided with a plurality of ultrawideband (UWB) receivers that is asynchronous with respect to a UWB transmitter. A geometry of the tracking system may utilize a plurality of clusters with each cluster comprising a plurality of antennas. Time Difference of Arrival (TDOA) may be determined for the antennas in each cluster and utilized to determine Angle of Arrival (AOA) based on a far field assumption regarding the geometry. Parallel software communication sockets may be established with each of the plurality of UWB receivers. Transfer of waveform data may be processed by alternately receiving packets of waveform data from each UWB receiver. Cross Correlation Peak Detection (CCPD) is utilized to estimate TDOA information to reduce errors in a noisy, multipath environment.

Arndt, G. Dickey↗

DOE OSTI2017

The Peculiar Filamentary H i Structure of NGC 6145

In this paper, we report the peculiar H i morphology of the cluster spiral galaxy NGC 6145, which has a 150 kpc H i filament on one side that is nearly parallel to its major axis. This filament is made up of several H i clouds and the diffuse H i gas between them, with no optical counterparts. We compare its H i distribution with other one-sided H i distributions in the literature and find that the overall H i distribution is very different from the typical tidal and ram-pressure stripped H i shape, and that its morphology is inconsistent with that of a pure accretion event. Only ∼30% of the total H i gas is anchored on the stellar disk, while most of the H i gas forms the filament in the west. At a projected distance of 122 kpc, we find a massive elliptical companion (NGC 6146) with extended radio emission whose axis points to an H i gap in NGC 6145. The velocity of the H i filament shows an overall line-of-sight motion of 80–180 km s{sup −1} with respect to NGC 6145. Using the long-slit spectra of NGC 6145 along its major stellar axis, we find that some outer regions show enhanced star formation, while in contrast, almost no star formation activities are found in its center (<2 kpc). Pure accretion, tidal, or ram-pressure stripping are not likely to produce the observed H i filament. An alternative explanation is the jet stripping from NGC 6146, although direct evidence for a jet-cold gas interaction has not been found.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

ARENA: Asynchronous Reconfigurable Accelerator Ring to Enable Data-Centric Parallel Computing

The next generation HPC and data centers are likely to be reconfigurable and data-centric due to the trend of hardware specialization and the emergence of data-driven applications. In this work, we propose ARENA – an asynchronous reconfigurable accelerator ring architecture as a potential scenario on how the future HPC and data centers will be like. Despite using the coarse-grained reconfigurable arrays (CGRAs) as the substrate platform, our key contribution is not only the CGRA-cluster design itself, but also the ensemble of a new architecture and programming model that enables asynchronous tasking across a cluster of reconfigurable nodes, so as to bring specialized computation to the data rather than the reverse. We presume distributed data storage without asserting any prior knowledge on the data distribution. Hardware specialization occurs at runtime when a task finds the majority of data it requires are available at the present node. In other words, we dynamically generate specialized CGRA accelerators where the data reside. The asynchronous tasking for bringing computation to data is achieved by circulating the task token, which describes the dataflow graphs to be executed for a task, among the CGRA cluster connected by a fast ring network. Evaluations on a set of HPC and data-driven applications across different domains show that ARENA can provide better parallel scalability with reduced data movement (53.9 percent). Compared with contemporary compute-centric parallel models, ARENA can bring on average 4.37× speedup. The synthesized CGRAs and their task-dispatchers only occupy 2.93mm 2 chip area under 45nm process technology and can run at 800MHz with on average 759.8mW power consumption. ARENA also supports the concurrent execution of multi-applications, offering ideal architectural support for future high-performance parallel computing and data analytics systems.

97 MATHEMATICS AND COMPUTING↗