[gmx-users] SMP/Parallel mdrun

Ian Stokes-Rees 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:

$ lamboot
$ 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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