[gmx-users] Reg: Running gromacs on a condor cluster

Esztermann, Ansgar Ansgar.Esztermann at mpi-bpc.mpg.de
Fri Apr 30 16:04:27 CEST 2010

On Apr 30, 2010, at 14:46 , Rohit Farmer wrote:
> Hi everyone..
> I just made a small two node condor cluster and was trying to run gromacs on it ... so i used the vanilla environment and placed the gromacs mdrun command in a shell script and used the shell script to run the command ... and it is running also ... but only one one system .. my pool is showing four processor on doing condor_status ... but only one processor is clamed ... not all ... so if anyone works on gromacs and condor both then please help ...

Does it work locally, i.e. without Condor? After all, Condor is just a batch system. It will help you start mdrun on one or more nodes of your cluster, but it does not magically parallelize things.
You would either use an MPI distribution or pthreads. (I am not sure if the latter is already available in a release version.)
How do you call mdrun? Do you use mpiexec? What are the parameters?



Ansgar Esztermann
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

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