[gmx-developers] Problem submitting GROMACS script

[Justin A. Lemkul]

rainy908 at yahoo.com wrote:
> Hi,
> 
> I'm trying to carry out an MD simulation on 4 processors but am having 
> trouble with the MPI ("Can't read MPIRUN_HOST").  My error is:
> 
> -catch_rsh 
> /opt/gridengine/default/spool/compute-0-32/active_jobs/176501.1/pe_hostfile
> compute-0-32
> compute-0-32
> compute-0-32
> compute-0-32
> Got 4 slots.
> compute-0-32
> compute-0-32
> compute-0-32
> compute-0-32
> OSU MVAPICH VERSION 0.9.5-SingleRail
> Can't read MPIRUN_HOST
> # Cleaning local host (compute-0-32) for lpeng (lpeng)... done.
> 
> 
> My submission script is:
> 
> # Define locations of MPIRUN, MDRUN, and grompp
> MPIRUN=/usr/local/topspin/mpi/mpich/bin/mpirun
> MDRUN=/share/apps/gromacs-3.3.1/bin/mdrun-mpi
> grompp=/share/apps/gromacs-3.3.1/bin/grompp
> 
> cd /nas2/lpeng/nexil/gromacs/cg_setup
> 
> # Running Gromacs: read TPR and write output to /nas2 disk
> $MPIRUN -v -machinefile $TMPDIR/machines -np $NSLOTS $grompp -f md.mdp 
> -c confout.gro -o md3.tpr -n index.ndx
> 
> # Run MD
> $MDRUN -v -nice -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g 
> md3.log -x md3.xtc
> 

The problem could be that you're trying to run grompp using mpirun (which you 
shouldn't), and then trying to run a parallel job with mdrun without invoking 
mpirun.

Probably something like:

$grompp -f md.mdp -c confout.gro -o md3.tpr -n index.ndx

$MPIRUN -v -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice -np $NSLOTS 
-s md3.tpr -o md3.trr -c confout.gro -g md3.log -x md3.xtc

is more appropriate.  Without knowing the specifics of your system, a guess is 
about all I can give.

-Justin

> 
> Does anyone have any insight on what the problem could be?  Is the 
> problem with the MPI or the submission script?
> 
> Thanks,
> Lili
> 
> 
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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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