[gmx-users] running GROMACS-MPI on Rocks cluster- strange results

kala kalabharath at gmail.com
Fri Mar 6 09:34:48 CET 2009

i have ran a particular MD of protein in water for 100ps (50,000 steps) in a
variety of combinations

1. on a single processor( non-mpi) intel core2duo 2.2Ghz 2 GB ram time taken
: 1hr 30 min
2. 2 processors on a single machine (MPI) similar specs time taken : 35 min
3 .2 processors on different machines (mpi) similar specs time taken : 1hr 5
4 .5 processors on 5 different machines (mpi) similar specs time taken: 38
5.10 processors on 5 different machines(mpi) similar specs time taken: 45

for 1- open discovery ( fedora 9)
for 2-5 Rocks cluster 5.1

network connectivity Gigabit on cat6
Are the above specified time intervals normal or i am making big big
comments are invited.
kala bharath
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