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 <[email protected]
<mailto:[email protected]>> 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
========================================
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