[gmx-users] about parallel work

Carsten Kutzner ckutzne at gwdg.de
Tue Apr 21 17:30:22 CEST 2009

On Apr 21, 2009, at 5:04 PM, sheerychen wrote:

> Hello, every body. I have a question about parallel running of  
> mdrun_mpi. I doubt that sometimes the parallel running of mdrun_mpi  
> can not utilize the domain decomposition.
> This is the case when I use the batch work in the computer cluster  
> which install the MPICH2. In the case, I use commond like ''mpirun - 
> np 8 mdrun_mpi -deffnm *** -v'' . (The command ''mpirun -np 3 /usr/ 
> bin/mdrun_mpi -deffnm *** -v'' doesn't work) .The working didn't  
> show any information about domain decomposition. And the computing  
> rate is rather slow, which is only a little bit higher than
So what exactly is the output of mdrun? What is the content of the  
md.log file?


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