13789

Posts

Mar, 28

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach […]
Mar, 28

Shortest-Path Queries in Planar Graphs on GPU-Accelerated Architectures

We develop an efficient parallel algorithm for answering shortest-path queries in planar graphs and implement it on a multi-node CPU/GPU clusters. The algorithm uses a divide-and-conquer approach for decomposing the input graph into small and roughly equal subgraphs and constructs a distributed data structure containing shortest distances within each of those subgraphs and between their […]
Mar, 28

PErasure: a Parallel Cauchy Reed-Solomon Coding Library for GPUs

In recent years, erasure coding has been adopted by large-scale cloud storage systems to replace data replication. With the increase of disk I/O throughput and network bandwidth, the speed of erasure coding becomes one of the key system bottlenecks. In this paper, we propose to offload the task of erasure coding to Graphics Processing Units […]
Mar, 25

Pseudorandom Numbers Generation for Monte Carlo Simulations on GPUs: OpenCL Approach

General principles of pseudorandom numbers production for Monte Carlo simulations on GPUs are discussed by creating an OpenCL open-source library of pseudorandom number generators PRNGCL. The library contains implementation of a number of the most popular uniform generators. The most popular pseudorandom number generators for Monte Carlo simulations and libraries for GPUs are reviewed. Some […]
Mar, 25

Energy-efficient Computing on Distributed GPUs using Dynamic Parallelism and GPU-controlled Communication

GPUs are widely used in high performance computing, due to their high computational power and high performance per Watt. Still, one of the main bottlenecks of GPU-accelerated cluster computing is the data transfer between distributed GPUs. This not only affects performance, but also power consumption. The most common way to utilize a GPU cluster is […]
Mar, 25

Analysis of illumination conditions at the lunar south pole using parallel computing techniques

In this Master Thesis an analysis of illumination conditions at the lunar south pole using parallel computing techniques is presented. Due to the small inclination (1.54o) of the lunar rotational axis with respect to the ecliptic plane and the topography of the lunar south pole, which allows long illumination periods, the study of illumination conditions […]
Mar, 25

The Feasibility of Using OpenCL Instead of OpenMP for Parallel CPU Programming

OpenCL, along with CUDA, is one of the main tools used to program GPGPUs. However, it allows running the same code on multi-core CPUs too, making it a rival for the long-established OpenMP. In this paper we compare OpenCL and OpenMP when developing and running compute-heavy code on a CPU. Both ease of programming and […]
Mar, 25

Data driven scheduling approach for the multi-node multi-GPU Cholesky decomposition

Recently large scale scientific computation on heterogeneous supercomputers equipped with accelerators is receiving attraction. However, traditional static job execution methods and memory management methods are insufficient in order to harness heterogeneous computing resources including memory efficiently, since they introduce larger data movement costs and lower resource usage. This paper takes the Cholesky decomposition computation, which […]
Mar, 23

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

The analysis of next-generation sequencing (NGS) data is a major topic in bioinformatics: short reads obtained from DNA, the molecule encoding the genome of living organisms, are processed to provide insight into biological or medical questions. This thesis provides novel solutions to major topics within the analysis of NGS data, focusing on parallelization, scalability and […]
Mar, 23

Curracurrong: a stream processing system for distributed environments

Advances in technology have given rise to applications that are deployed on wireless sensor networks (WSNs), the cloud, and the Internet of things. There are many emerging applications, some of which include sensor-based monitoring, web traffic processing, and network monitoring. These applications collect large amount of data as an unbounded sequence of events and process […]
Mar, 23

GPU Kernels for High-Speed 4-Bit Astrophysical Data Processing

Interferometric radio telescopes often rely on computationally expensive O(N^2) correlation calculations; fortunately these computations map well to massively parallel accelerators such as low-cost GPUs. This paper describes the OpenCL kernels developed for the GPU based X-engine of a new hybrid FX correlator. Channelized data from the F-engine is supplied to the GPUs as 4-bit, offset-encoded […]
Mar, 23

Massively Parallel Construction of the Cell Graph

Motion planning is an important and well-studied field of robotics. A typical approach to finding a route is to construct a cell graph representing a scene and then to find a path in such a graph. In this paper we present and analyze parallel algorithms for constructing the cell graph on a SIMD-like GPU processor. […]
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Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

The platforms are

Node 1
  • GPU device 0: nVidia GeForce GTX 560 Ti 2GB, 822MHz
  • GPU device 1: AMD/ATI Radeon HD 6970 2GB, 880MHz
  • CPU: AMD Phenom II X6 @ 2.8GHz 1055T
  • RAM: 12GB
  • OS: OpenSUSE 13.1
  • SDK: nVidia CUDA Toolkit 6.5.14, AMD APP SDK 3.0
Node 2
  • GPU device 0: AMD/ATI Radeon HD 7970 3GB, 1000MHz
  • GPU device 1: AMD/ATI Radeon HD 5870 2GB, 850MHz
  • CPU: Intel Core i7-2600 @ 3.4GHz
  • RAM: 16GB
  • OS: OpenSUSE 12.3
  • SDK: AMD APP SDK 3.0

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