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Scaling NAMD into the Petascale and Beyond
Joint Laboratory for Petascale Computing Workshop (JLPC) 2010
Publication Type: Talk
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Summary
Many challenges arise when employing ever larger supercomputers for the simulation of biological molecules in the context of a mature molecular dynamics code. Issues stemming from the scaling up of problem size, such as input and output require both parallelization and revisions to legacy file formats. Order of magnitude increases in the number of processor cores evoke problems with O(P) structures, load balancing, and performance analysis. New architectures present code optimization opportunities (VSX SIMD) which must be carefully applied to provide the desired performance improvements without dire costs in implementation time and code quality. Looking beyond these imminent concerns for sustained petaflop performance on Blue Waters, we will also consider scalability concerns for future exascale machines. pdf
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