BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications
Author(s)
Bader, David A.
Li, Yue
Li, Tao
Sachdeva, Vipin
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Abstract
The exponential growth in the amount of genomic data
has spurred growing interest in large scale analysis of
genetic information. Bioinformatics applications, which
explore computational methods to allow researchers to sift
through the massive biological data and extract useful
information, are becoming increasingly important
computer workloads. This paper presents BioPerf, a
benchmark suite of representative bioinformatics
applications to facilitate the design and evaluation of high-performance
computer architectures for these emerging
workloads. Currently, the BioPerf suite contains codes
from 10 highly popular bioinformatics packages and
covers the major fields of study in computational biology
such as sequence comparison, phylogenetic reconstruction,
protein structure prediction, and sequence homology &
gene finding. We demonstrate the use of BioPerf by
providing simulation points of pre-compiled Alpha
binaries and with a performance study on IBM Power
using IBM Mambo simulations cross-compared with Apple
G5 executions.
The BioPerf suite (available from www.bioperf.org)
includes benchmark source code, input datasets of various
sizes, and information for compiling and using the
benchmarks. Our benchmark suite includes parallel codes
where available.
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Date
2006
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Text
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Technical Report