Progress Towards Petascale Applications in Biology: Status in 2006
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.
computational biology, grand challenge problem, high performance computing, life sciences, peak theoretical capacity, petabytes, petaflops, petascale computing
C. A. Stewart, M. S. Müller, M. Lingwall. Progress Towards Petascale Applications in Biology: Status in 2006. In Proceedings of Euro-Par 2006 Workshops, Aug. 29 - Sept. 1, Dresden, LNCS 4375, pages 289-303, Springer Verlag, 2007.
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