[gmx-users] SMP/Parallel mdrun
ijstokes at crystal.harvard.edu
Thu Nov 27 02:35:09 CET 2008
I am a computational scientist working with a physical chemist to try to
parallelize her use of gromacs -- today is my first day using the
application and I am not succeeding in getting multiple threads.
I have an MPI-compiled version of gromacs v4.0 and am attempting to get
parallel execution on a 2x2 core AMD Opteron system via:
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4
however there is then only a single thread executing. Do I need to
preprocess the topology file?
In the first instance, getting mdrun going in parallel on an SMP machine
is the higher priority. Next I will look at running it on a cluster.
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
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