----- Original Message -----
From: #ZHAO LINA# <[email protected]>
Date: Thursday, July 8, 2010 18:53
Subject: RE: [gmx-users] mpi run
To: Discussion list for GROMACS users <[email protected]>
P {margin-top:0;margin-bottom:0;}
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|
> 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: [email protected] [[email protected]] on
> behalf of Carsten Kutzner [[email protected]]
> 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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>
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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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