[gmx-users] mpi version of gromacs

[Justin A. Lemkul]

Amit Choubey wrote:
> ok here the pbs file for the job
> 
> #!/bin/bash         
> #PBS -l nodes=1:ppn=1
> #PBS -l walltime=00:01:59
> #PBS -o output.out 
> #PBS -j oe
> #PBS -N mdrun 
> WORK_HOME=/auto/hpc-08/knomura/choubey/GROMACS/test
> cd $WORK_HOME
> source /usr/usc/mpich/default/setup.sh
> mdrun_mpi -v -s em -o em -c after_em -g emlog
> 
> Is my command line wrong? 
> 

Yes.  The mdrun_mpi executable must be launched as an mpirun process, i.e.:

mpirun -np X mdrun_mpi (etc)

-Justin

> On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amit Choubey wrote:
> 
>         Hi everyone,
> 
>         I have the gromacs mpi version on my system and everything in
>         the simulation works fine until i get to mdrun_mpi and when i
>         use this executable the following pops error comes up
> 
>         MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX
>         device entry in /dev.
> 
>         Then i tried the to do mdrun_mpi -h on the terminal and the same
>         thing comes out.
> 
>         MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX
>         device entry in /dev.
> 
>         Is this an installation problem? I am also not able to find the
>         online manual for mpi version of gromacs, could someone send me
>         the link?
> 
> 
>     Because MPI only applies to mdrun, so there's no need for a separate
>     manual. All the information for mdrun applies to mdrun_mpi, except
>     that it can be executed in parallel.
> 
>     It looks like there is either a problem with the MPI implementation
>     of the machine, or you're calling the command wrong.  If you can
>     post your command line or the contents of whatever submission script
>     you might be using, we might be able to implicate (or rule out) the
>     latter.
> 
>     -Justin
> 
>         Thank you,
>         Amit
> 
>         ------------------------------------------------------------------------
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================