[gmx-users] question about parallel runing of gromacs

Diego Enry Gomes diego.enry at gmail.com
Tue Mar 10 05:03:10 CET 2009

On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote:

> Xiang Mao wrote:
>> My PC has a intel core2 cpu. I compiled gromacs under cygwin, and  
>> using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi .... to  
>> run EM, MD.
> OK that might be working right. Now you need to look in the log file  
> for an indication of whether the run has two component processes or  
> one - right at the top, usually.
> Mark

Hi Xiang, maybe the solution is simple and you just didn't use the "-- 
enable-mpi" flag in the ./configure step.
That explains the duplicate steps.

Try a quick "ldd" test to check if MPI compilation worked.

% which mdrun_mpi     (find where mdrun was installed, mine is at /usr/ 
% ldd /usr/local/gmx4/bin/mdrun_mpi

You should see "libmpi.so.0" in the list of libraries, if not, go back  
to the ./configure step.


Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
diegoenry.gomes at pnl.gov
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