Progress towards petascale applications in biology: status in 2006

Authors:
Craig A. Stewart;Matthias Müller;Malinda Lingwall
Affiliations:
Office of the Vice President for Information Technology, Indiana University, Bloomington, IN;Center for Information Services and High Performance Computing, Technische Universitaet Dresden;University Information Technology Services, Indiana University, Bloomington, IN
Venue:
Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
Year:
2006

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Abstract

Petascale computing is currently a common topic of discussion in the high performance computing community. Biological applications, particularly protein folding, are often given as examples of the need for petascale computing. There are at present biological applications that scale to execution rates of approximately 55 teraflops on a special-purpose supercomputer and 2.2 teraflops on a general-purpose supercomputer. In comparison, Qbox, a molecular dynamics code used to model metals, has an achieved performance of 207.3 teraflops. It may be useful to increase the extent to which operation rates and total calculations are reported in discussion of biological applications, and use total operations (integer and floating point combined) rather than (or in addition to) floating point operations as the unit of measure. Increased reporting of such metrics will enable better tracking of progress as the research community strives for the insights that will be enabled by petascale computing.