[gmx-users] Reg Gromacs in cluster problem
vidhya sankar
scvsankar_agr at yahoo.com
Wed Mar 26 15:54:52 CET 2014
Dear Justin,
Thank you for your Previous reply I am Running Gromacs on Cluster with 16 Processor
I am using the following script to submit Job
#!/bin/bash
#PBS -l nodes=compute-0-5:ppn=16
#PBS -l walltime=900:10:5
hostname
date
cd $PBS_O_WORKDIR
echo "files copied from" $PBS_O_WORKDIR
echo "to computing directory" $TMPDIR
cd $TMPDIR
cp $PBS_O_WORKDIR/newplumed04RestartHILLS.dat $TMPDIR/
mpirun=/opt/openmpi/bin/mpirun
LD_LIBRARY_PATH=/share/apps/gromacsplu/lib
source="/share/apps/gromacsplu//bin"
MDRUN="/share/apps/gromacsplu/bin/mdrun_mpi_d"
$mpirun -np 16 $MDRUN -s CNTPEPRSOLIONSfullplumed.tpr -npme 0 -cpi CNTPEPRSOLIONSfullplumed_prev.cpt -append -nt 1 -plumed newplumed04RestartHILLS.dat -v -deffnm CNTPEPRSOLIONSfullplumed &>/dev/null
cp --force $TMPDIR/* $PBS_O_WORKDIR/out14/
rm -rf $TMPDIR
date
But after 19 hours Running My Node Become down and shows as follows
state = down,job-exclusive
np = 16
ntype = cluster
When i Try to Access My node using the following Command
ssh compute-0-5 then it shows the follwong error
ssh: connect to host compute-0-5 port 22: No route to host
I would be very garteful if you Give any suggestion
Thanks in Advance
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