[gmx-users] mpi run

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Thu Jul 8 10:53:03 CEST 2010

During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work.
I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run.
Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too.


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Carsten Kutzner [ckutzne at gwdg.de]
Sent: Thursday, July 08, 2010 4:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mpi run

Hi Mahmoud,

for anyone to be able to help you, you need to provide
a lot more information, at least:
- which mpi library are you using?
- how did you compile and/or install Gromacs?
- what commands do you use to run mdrun and what was
the output of it?


On Jul 8, 2010, at 9:41 AM, nanogroup wrote:

Dear GMX Users,

I have a PC with 4 CPU, but the Gromacs only use one CPU.

the command of mpiru works on linux; however, the command of mdrun_mpi does not work.

Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4

Many thanks,

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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
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