John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
Early experiences porting the NAMD and VMD molecular simulation
and analysis software to GPU-accelerated OpenPOWER platforms.
International Workshop on OpenPOWER for HPC (IWOPH'16), pp.
188-206, 2016.
STON2016D
All-atom molecular dynamics simulations of biomolecules provide
a powerful tool for exploring the structure and dynamics of large
protein complexes within realistic cellular environments.
Unfortunately, such simulations are extremely demanding in terms of
their computational requirements, and they present many challenges
in terms of preparation, simulation methodology,
and analysis and visualization of results.
We describe our early experiences porting the popular molecular
dynamics simulation program NAMD and the
simulation preparation, analysis, and visualization tool VMD
to GPU-accelerated OpenPOWER hardware platforms.
We report our experiences with compiler-provided autovectorization
and compare with hand-coded vector intrinsics for the POWER8 CPU.
We explore the performance benefits obtained from unique POWER8
architectural features such as 8-way SMT and its value for
particular molecular modeling tasks.
Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.
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