Large Scale Biomolecular Dynamics Simulations - prace
Large Scale Biomolecular Dynamics Simulations - prace
Large Scale Biomolecular Dynamics Simulations - prace
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Efficient PME Parallelization<br />
• Almost all accurate simulations today<br />
use Particle-Mesh Ewald lattice<br />
summation<br />
• Small 3D Fourier Transforms scale<br />
bad - all-to-all communication<br />
• Direct space & PME are mostly<br />
independent, though!<br />
• Dedicate a subset of nodes to run a<br />
separate PME-only version of the<br />
program to improve scaling<br />
X<br />
Y<br />
• FFT over 5 instead of 25 nodes!<br />
Original implementation with<br />
help of RZG of MPI<br />
PME nodes<br />
onsdag, 2009 maj 13
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