TY - GEN
T1 - BioPerf
T2 - 2005 IEEE International Symposium on Workload Characterization, IISWC-2005
AU - Bader, David A.
AU - Li, Yue
AU - Li, Tao
AU - Sachdeva, Vipin
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33749079198&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33749079198&partnerID=8YFLogxK
U2 - 10.1109/IISWC.2005.1526013
DO - 10.1109/IISWC.2005.1526013
M3 - Conference contribution
AN - SCOPUS:33749079198
SN - 0780394615
SN - 9780780394612
T3 - Proceedings of the 2005 IEEE International Symposium on Workload Characterization, IISWC-2005
SP - 163
EP - 173
BT - Proceedings of the 2005 IEEE International Symposium on Workload Characterization, IISWC-2005
Y2 - 6 October 2005 through 8 October 2005
ER -