Together with EuroPar-12, the 5th Workshop on UnConventional High Performance Computing 2012 (UCHPC 2012) will take place on August 27/28 at Rhodes Island, Greece. The workshop tries to capture solutions for HPC which are unconventional today but could become conventional and significant tomorrow. While GPGPU is already used a lot in HPC, there still are all kind of issues around best exploitation and productivity for the programmer. Submission deadline: June 6, 2012. For more details, see
http://www.lrr.in.tum.de/~weidendo/uchpc12

TunaCode has released CUVILib v1.2, a library to accelerate imaging and computer vision applications. CUVILib adds acceleration to Imaging applications from Medical, Industrial and Defense domains. It delivers very high performance and supports both CUDA and OpenCL. Modules include color operations (demosaic, conversions, correction etc), linear/non-linear filtering, feature extraction & tracking, motion estimation, image transforms and image statistics.

More information, including a free trial version: http://www.cuvilib.com/

Abstract:

Motivation: New high-throughput sequencing technologies have promoted the production of short reads with dramatically low unit cost. The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed.

Results: We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphics hardware as accelerators to achieve fast speed. Our algorithm employs a quality-aware bounded search approach based on the Burrows- Wheeler transform (BWT) and the Ferragina Manzini (FM)-index to reduce the search space and achieve high alignment quality. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units (GPUs) achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments compared to three popular BWT-based aligners: Bowtie, BWA and SOAP2. CUSHAW also delivers competitive performance in terms of SNP calling for an E.coli test dataset.

Availability: http://cushaw.sourceforge.net.

(Y. Liu, B. Schmidt, D. Maskell: “CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform”, Bioinformatics, 2012. [DOI])

Partnering with NVIDIA and Microsoft, this four day CUDA training course is designed for Researchers and Programmers in the life science industries who are looking to develop comprehensive skills in writing and optimizing applications that fully leverage the many-core processing capabilities of the GPU. It is held in Boston, MA, on June 4-7, 2012. This course will have a life science theme. Commonly used algorithms such as Monte Carlo methods, FFT and filtering will be used and profiled in examples. The case study on day 4 focuses on the efficient implementation of a molecular dynamics simulation. More information: http://www.acceleware.com/jun4boston

Submissions are cordially invited for MCC-III, to be held in Stuttgart, Germany, September 19-21. This conference is the 3rd in a series, starting in 2010 in Heidelberg at the Heidelberg Academy of Sciences (HAW) and 2011 at the Karlsruhe Institute of Technology (KIT) and the Engineering Mathematics and Computing Lab (EMCL). It aims to combine new aspects of multi-/manycore microprocessor technologies, parallel applications, numerical simulation, software development and tools. Contributions are welcome from all participating disciplines. Particular emphasis is placed on the support and advancement of young scientists, in addition to high-quality invited keynote talks and tutorials. More information including the full call for papers, topics of interest and submission instructions: http://www.multicore-challenge.org

The Intel® SDK for OpenCL Applications now supports the OpenCL 1.1 full-profile on 3rd generation Intel® Core™ processors with Intel® HD Graphics 4000/2500. For the first time, OpenCL developers using Intel® architecture can utilize compute resources across both Intel® Processor and Intel HD Graphics. More information: http://software.intel.com/en-us/articles/vcsource-tools-opencl-sdk

Libra Platform is a GPGPU-Heterogeneous Compute API and runtime environment available on Windows, Mac and Linux. Libra Compute API offers performance portability and direct compute access via standard programming environments C/C++, Java, C# and Matlab to execute math operations on top of current and future compute architectures, including the latest GPUs, x86/x64 CPUs and with broad support for compute devices compatible with low level specific APIs – OpenCL, CUDA, OpenGL and standard x86/x64 compute APIs.

Read more in the full announcement.

A 2 day CUDA workshop is taking place in Berlin, Germany on May 5 and 6 2012. Course details, outline and prices are available at http://cuda.eventbrite.com.

The rCUDA Team is proud to announce a new version of the rCUDA framework which will include many new functionalities as well as boosted performance. This new version, cooked for over a year, will incorporate pipelined transfers, full multi-thread and multi-node capabilities, CUDA 4.1 support, global scheduler integration, support for CUDA C extensions, and native InfiniBand support. A closed beta teting program has been started. See the complete text at http://www.rcuda.net/index.php/news/19-new-revolutionary-version-of-rcuda-to-be-launched.html.

Abstract:

Breadth-first search (BFS) is a core primitive for graph traversal and a basis for many higher-level graph analysis algorithms. It is also representative of a class of parallel computations whose memory accesses and work distribution are both irregular and data-dependent. Recent work has demonstrated the plausibility of GPU sparse graph traversal, but has tended to focus on asymptotically inefficient algorithms that perform poorly on graphs with non-trivial diameter.

We present a BFS parallelization focused on fine-grained task management constructed from efficient prefix sum that achieves an asymptotically optimal O(|V|+|E|) work complexity. Our implementation delivers excellent performance on diverse graphs, achieving traversal rates in excess of 3.3 billion and 8.3 billion traversed edges per second using single and quad-GPU configurations, respectively. This level of performance is several times faster than state-of-the-art implementations both CPU and GPU platforms.

(Duane Merrill, Michael Garland and  Andrew Grimshaw: “Scalable GPU graph traversal”, Proceedings of the 17th ACM SIGPLAN symposium on Principles and Practice of Parallel Programming (PPoPP’12), pp.117-128, Feburary 2012. [DOI])