[gmx-users] mpi run

[Mark Abraham]

----- Original Message -----
From: #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg>
Date: Thursday, July 8, 2010 18:53
Subject: RE: [gmx-users] mpi run
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


   P {margin-top:0;margin-bottom:0;} -----------------------------------------------------------
| 

 
 > During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work.

--program-suffix merely appends that suffix. --enable-mpi is necessary to actually create MPI-enable mdrun. It is normal to use both of them together.

Mark

>  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.
 > 
>  Best,
 > 
>  lina
   -----------------------------------------------------------
 > 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? > 
  > Best, >   Carsten > 
  > 
  > 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,
>  Mahmoud
 > 
  | 
  -----------------------------------------------------------
 > 
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   > >  -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > 
   >  >   > 
      |
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