Computational Strategies for Scalable Genomics Analysis.

The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications

Two-level pipelined systolic array graphics engine

The authors report a VLSI design of an advanced systolic array graphics (SAG) engine built from pipelined functional units which can generate realistic images interactively for high-resolution displays. They introduce a structured frame store system as an environment for the advanced SAG engine and present the principles and architecture of the advanced SAG engine. They introduce pipelined functional units into this SAG engine to meet the performance requirements. This is done by a formal approach where the original systolic array is represented at bit level by a finite, vertex-weighted, edge-weighted, directed graph. Two architectures built from pipelined functional units are described. A prototype containing nine processing elements was fabricated in a 1.6-¿m CMOS technolog

A two-level structure for advanced space power system automation

The tasks to be carried out during the three-year project period are: (1) performing extensive simulation using existing mathematical models to build a specific knowledge base of the operating characteristics of space power systems; (2) carrying out the necessary basic research on hierarchical control structures, real-time quantitative algorithms, and decision-theoretic procedures; (3) developing a two-level automation scheme for fault detection and diagnosis, maintenance and restoration scheduling, and load management; and (4) testing and demonstration. The outlines of the proposed system structure that served as a master plan for this project, work accomplished, concluding remarks, and ideas for future work are also addressed

Avionics systems integration technology

A very dramatic and continuing explosion in digital electronics technology has been taking place in the last decade. The prudent and timely application of this technology will provide Army aviation the capability to prevail against a numerically superior enemy threat. The Army and NASA have exploited this technology explosion in the development and application of avionics systems integration technology for new and future aviation systems. A few selected Army avionics integration technology base efforts are discussed. Also discussed is the Avionics Integration Research Laboratory (AIRLAB) that NASA has established at Langley for research into the integration and validation of avionics systems, and evaluation of advanced technology in a total systems context

QCDGPU: open-source package for Monte Carlo lattice simulations on OpenCL-compatible multi-GPU systems

The multi-GPU open-source package QCDGPU for lattice Monte Carlo simulations of pure SU(N) gluodynamics in external magnetic field at finite temperature and O(N) model is developed. The code is implemented in OpenCL, tested on AMD and NVIDIA GPUs, AMD and Intel CPUs and may run on other OpenCL-compatible devices. The package contains minimal external library dependencies and is OS platform-independent. It is optimized for heterogeneous computing due to the possibility of dividing the lattice into non-equivalent parts to hide the difference in performances of the devices used. QCDGPU has client-server part for distributed simulations. The package is designed to produce lattice gauge configurations as well as to analyze previously generated ones. QCDGPU may be executed in fault-tolerant mode. Monte Carlo procedure core is based on PRNGCL library for pseudo-random numbers generation on OpenCL-compatible devices, which contains several most popular pseudo-random number generators.Comment: Presented at the Third International Conference "High Performance Computing" (HPC-UA 2013), Kyiv, Ukraine; 9 pages, 2 figure

Evaluating Cache Coherent Shared Virtual Memory for Heterogeneous Multicore Chips

The trend in industry is towards heterogeneous multicore processors (HMCs), including chips with CPUs and massively-threaded throughput-oriented processors (MTTOPs) such as GPUs. Although current homogeneous chips tightly couple the cores with cache-coherent shared virtual memory (CCSVM), this is not the communication paradigm used by any current HMC. In this paper, we present a CCSVM design for a CPU/MTTOP chip, as well as an extension of the pthreads programming model, called xthreads, for programming this HMC. Our goal is to evaluate the potential performance benefits of tightly coupling heterogeneous cores with CCSVM

Simulator verification techniques study. Integrated simulator self test system concepts

Software and hardware requirements for implementing hardware self tests are presented in support of the development of training and procedures development simulators for the space shuttle program. Self test techniques for simulation hardware and the validation of simulation performance are stipulated. The requirements of an integrated simulator self system are analyzed. Readiness tests, fault isolation tests, and incipient fault detection tests are covered

Three Dimensional Pseudo-Spectral Compressible Magnetohydrodynamic GPU Code for Astrophysical Plasma Simulation

This paper presents the benchmarking and scaling studies of a GPU accelerated three dimensional compressible magnetohydrodynamic code. The code is developed keeping an eye to explain the large and intermediate scale magnetic field generation is cosmos as well as in nuclear fusion reactors in the light of the theory given by Eugene Newman Parker. The spatial derivatives of the code are pseudo-spectral method based and the time solvers are explicit. GPU acceleration is achieved with minimal code changes through OpenACC parallelization and use of NVIDIA CUDA Fast Fourier Transform library (cuFFT). NVIDIAs unified memory is leveraged to enable over-subscription of the GPU device memory for seamless out-of-core processing of large grids. Our experimental results indicate that the GPU accelerated code is able to achieve upto two orders of magnitude speedup over a corresponding OpenMP parallel, FFTW library based code, on a NVIDIA Tesla P100 GPU. For large grids that require out-of-core processing on the GPU, we see a 7x speedup over the OpenMP, FFTW based code, on the Tesla P100 GPU. We also present performance analysis of the GPU accelerated code on different GPU architectures - Kepler, Pascal and Volta