David A. Bader
IEEE Fellow
AAAS Fellow
Professor
College of Computing
Georgia Tech
Atlanta, GA 30332


 
 

 

BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation performance computer systems

BioSPLASH is a suite of representative applications that we have assembled from the computational biology community, where the codes are carefully selected to span a breadth of algorithms and performance characteristics. The main results of this paper are the assembly of a scalable bioinformatics workload with impact to the DARPA High Productivity Computing Systems Program to develop revolutionarily-new economically-viable high-performance computing systems, and analyses of the performance of these codes for computationally demanding instances using the cycle-accurate IBM MAMBO simulator and real performance monitoring on an Apple G5 system. Hence, our work is novel in that it is one of the first efforts to incorporate life science application performance for optimizing high-end computer system architectures.

Publication History

Versions of this paper appeared as:
  1. D.A. Bader, V. Sachdeva, V. Agarwal, G. Goel, A.N. Singh, ``BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation performance computer systems,'' Technical Report, University of New Mexico, May 2005.
  2. D.A. Bader and V. Sachdeva, "BioSPLASH: A sample workload from bioinformatics and computational biology for
    optimizing next-generation high-performance computer systems," (Poster Session), 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, MI, June 25-29, 2005.

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Last updated: May 28, 2005

 




Computational Biology



Parallel Computing



Combinatorics