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On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote:
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<title>mpi run in Gromacs 4.5.3</title>
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<p><font size="2">Hi,<br>
I have been trying to run Gromacs 4.5.3 parallel simulations
using openmpi 1.4.2. From my understanding, mdrun_mpi is not
used in this version of Gromacs.</font></p>
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<br>
I don't understand what (you think) you mean. You can use
thread-based parallelism for processors that share common silicon,
or MPI-based parallelism if a network connection is involved, but
not both. The latter is named mdrun_mpi by default.<br>
<br>
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<p><font size="2"> Our system administrator told me that all mpi
related options have been turned on while installing Gromacs.
With either commands:<br>
mdrun -np X -deffnm topol -N X (run in an 8-cpu node)<br>
</font></p>
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<br>
This won't run in parallel at all. mdrun ignores -np and -N<br>
<br>
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or<br>
mpirun -np X mdrun -deffnm topol -N X (submitted in a number
of nodes depending on availability)<br>
</font></p>
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<br>
This will get you the symptoms below, but -N is still ignored.<br>
<br>
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I get X identical simulations instead of a parallel run. If
X=4, I get 4 identical simulations (the same simulation ran 4
times) instead of 1 parallel simulation in 4 processors. The
performance difference between a single-processor run and the
X=4 run are also similar (no marked difference in the time it
takes to finish the simulation).<br>
Has anyone encountered this problem?<br>
</font></p>
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<br>
You're using a serial mdrun. Use a parallel mdrun.<br>
<br>
Mark<br>
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