[gmx-users] mpi version of gromacs

[Amit Choubey]

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?

On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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