PPAAC @ IEEE Cluster 2010

Workshop on Parallel Programming and Applications on Accelerator Clusters (PPAAC)

held in conjunction with IEEE Cluster 2010

20 September, Heraklion, Crete, Greece

Call for Papers

Accelerator-based parallel architectures, heterogeneous multi-core processors, FPGAs and GPUs, are rapidly becoming mainstream components for cluster computing. While the potential of accelerators for addressing problems such as memory latency and bandwidth has long been recognized, accelerators present several challenges to programmers and cluster systems designers. Conventional parallel programming models and libraries, parallel algorithms, and system software need to be restructured and redesigned to exploit the architectural strengths of accelerators and mitigate their lack of efficient general-purpose computing capabilities.

Computing on accelerator-based nodes is mainly driven by applications. Bioinformatics, in particular, has emerged as a primary application area for the use of accelerators in scientific computing. Recent advances in DNA sequencing technologies have generated an unprecedented data "tsunami" that poses new challenges for exploiting parallelism and deploying accelerators for Bioinformatics algorithms, including at the production-level. Because of the DNA sequencing revolution (the amount of molecular data grows faster than Moore's law), we expect Bioinformatics applications to play a leading role in future accelerator-based cluster systems and applications.

This workshop will bring together researchers from academia and industry to discuss the latest developments in parallel programming models, languages, tools, system software and applications for accelerators and accelerator-based clusters. Of particular interest are papers focused on experiences with accelerator-based Bioinformatics applications; a focused track of the workshop will be devoted to this topic.

Topics for the general track include, but are not limited to:

Programming models for accelerator-based custers, including systems using GPUs, heterogeneous multi-core processors and FPGAs.
Compiler and runtime support for accelerator-based clusters, including support for scheduling, communication, and memory management.
Operating systems and virtualization support for accelerator-based clusters.
Performance evaluation of accelerator-based clusters, in particular with relation to conventional homogeneous clusters.
Performance analysis, profiling and debugging tools.
Application studies on accelerator-based clusters.
Power and energy-efficiency studies of accelerator-based clusters.

Topics for the Bioinformatics track include, but are not limited to, accelerator usage for:

Metagenomics algorithms
Computational genomics and proteomics
DNA assembly, clustering, and mapping
Gene expression and microarrays
Gene identification and annotation
Phylogeny reconstruction algorithms
Protein structure prediction and modeling
Hardware architectures for Bioinformatics functions
Production-level mappings to accelerators of widely used algorithms
Systems Biology

Schedule and Submissions

Papers due:	Closed
Author notification:	July 23, 2010
Final papers due:	August 10, 2010
PPAAC workshop:	September 20, 2010

Submitted manuscripts should be formatted according to IEEE Cluster 2010 proceedings guidelines.

The maximum length is 8 pages.
Single-spaced
8.5x11-inch, two-column numbered pages in IEEE Xplore format

Submissions must be in pdf format and should be uploaded to http://www.easychair.org/conferences/?conf=ppaac10. (Note: an EasyChair account is required.)

Organizers

Apostolos Dollas	Technical University of Crete, Greece
Dimitris Nikolopoulos	FORTH-ICS and University of Crete, Greece
Cal Ribbens	Virginia Tech, USA
Bertil Schmidt	Nanyang Technological University, Singapore
Alexandros Stamatakis	Technical University of Munich, Germany
Jaroslaw Zola	Iowa State University, USA

Program Committee

Dmitry Afonikov	Institute of Cytology and Genetics, Russia
Srinivas Aluru	Iowa State University, USA
Peter Athanas	Virginia Tech, USA
Eduard Ayguade	Barcelona Supercomputing Center, Spain
Kevin Barker	Los Alamos National Laboratory, USA
Filip Blagojevic	Lawrence Berkeley National Laboratory, USA
Scott Emrich	University of Notre Dame, USA
Mathieu Giraud	INRIA Lille, France
Martin Herbordt	Boston University, USA
Mike Heroux	Sandia National Laboratory, USA
Ananth Kalyanaraman	Washington State University, USA
Sven Karlsson	Technical University of Denmark, Denmark
Jakub Kurzak	University of Tennessee, USA
Kamesh Madduri	Lawrence Berkeley National Laboratory, USA
Bernard Moret	Swiss Federal Institute of Technology, Switzerland
Yannis Papaefstathiou	Technical University of Crete, Greece
Michela Taufer	University of Delaware, USA
Jeffrey Vetter	Oak Ridge National Laboratory, USA
John P. Walters	University of Southern California, USA