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Unless otherwise noted benchmarks run for 20 ps (10000 steps * with dt = 2 fs), Langevin thermostat, Berendsen barostat.

Lonepeak

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intel

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pmemd.mpi

Atoms1 node2 nodes4 nodes8 nodes
129756.8411.7918.8530.97
155997.1710.1917.2637.36
194344.528.1613.9022.38
294532.985.168.5814.86
323742.754.807.9617.20
330222.474.547.6812.12

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, OpenMPI, pmemd.MPI, 800 ps, 2015-03-31

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intel, IntelMPI, pmemd.MPI, 200 ps, 2015-10-15

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Ember

intel, mvapich2, pmemd.MPI, 200 ps, 2015-10-15

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Kingspeak

intel, mvapich2, pmemd.MPI, 20 ps, 2015-03-30

MPI: /uufs/ember.arches/sys/pkg/mvapich2/std_intel/etc/mvapich2.sh (X)

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Note the performance drop for small systems (< 30k atoms). Using ember-specific mvapich2 appears to help somewhat at higher processor counts. Of course, this could also be because the benchmark is too short to be very accurate. May need to re-run these numbers.

pmemd.mpi