[gmx-users] Running GROMACS in PBS

[Triguero, Luciano O]

Hi Mark,
 
If I would have had more information about my PBS problem with gromacs, I would have then, probably, solved it myself, but I turn to the list because I konw of the great experincies of the people in the list, though your unpleasent humor. 
 
I submit my gromacs job to the PBS with the script below. The job goes to the queue, remains there for few seconds with a status E and then dies without giving any trace of why is going on? 
 
I appreciate any help from you.
 
Thank in advance,
 
Luciano
 
============================ Script follows ================================================
##############################################################
#!/bin/bash
#
# runmd: Submit a GROMACS MD job to our PBS batch queue.
#
# $1      -- queue's name
# $2      -- name of the .tpr file
# $3      -- .gro input filename
# $4      -- directory name to be created in the /chk dist
#############################################################
#Assign first argument to variable queue
queue=$1
case $queue in 
 long)      ;;
 medium)     ;;
 large)     ;;
 small)     ;;
 *) echo "This script can only be used with queues long large medium small" 
  echo "Submit this job by '$0 [queue_name] [filename([.tpr] initial)] [.gro input filename] [directory name]'"
  exit  ;;
esac
#Assign second argument to variable md_input
md_input=$2
if ! test -e $2.tpr 
then
 echo "$2.tpr DOES NOT exist"
 echo "This job is not submitted"
 exit 1
fi
#Assign the third argument to variable gro_input
gro_input=$3
if ! test -e $3.gro 
then
 echo "$2.gro DOES NOT exist"
 echo "This job is not submitted"
 exit 1
fi
###################################################################
md_homedir=`pwd`
md_workdir=/chk/$USER/$4
###################################################################
#
#Create the job file that is to be submitted to the queue with qsub
#
####################################################################
cat <<END >$2.job
#PBS -S /bin/bash 
#PBS -q $queue
#PBS -l nodes=1:ppn=4
#PBS -N $2
cd $md_homedir
echo "Current directory: $md_homedir" >> $md_homedir/run.log
if ! test -d $md_workdir
then
   mkdir $md_workdir
fi
cp $md_homedir/$md_input.tpr $md_workdir/$md_input.tpr 
cp $md_homedir/$gro_input.gro $md_workdir/$gro_input.gro
cd $md_workdir
######################################################################################################
gmx=/usr/local2/gromacs/bin/mpimdrun
mpix=/usr/local2/mpich/bin/mpirun
${mpix} -np 4 ${gmx} -s $md_input.tpr -o md_minim_traj.trr -c md_$gro_input.gro -e md_minim_energy.edr 
######################################################################################################
END
#
# Now submit $2.job to the queue.
#
case $queue in 
 long) 
   qsub   $2.job   ;;
 medium)  
   qsub   $2.job   ;;
 large)  
   qsub   $2.job   ;;
 small)  
   qsub   $2.job   ;;
esac

sleep 1
exit
 
=======================================================================================
 
Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Sat 3/31/2007 10:31 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Running GROMACS in PBS



Triguero, Luciano O wrote:
> Hello Everyone,
> 
> I have a small problem here and need your help. Let start telling that I had spend some time trying to solve the problem with the recommendations I found in the internet, however my problem persist.
> 
> I am running gromacs in a cluster and want to use one single machine with 4 nodes. When I submit mpimdrun directly to one of the node as (mpimdrun -np 4 -s filename.tpr -N 4) the program runs without problems. However, when I do the same command inside a script and sibmit it to the PBS system. I mean (qsub -q long run.job), mpimdrun doesn't work. Is there anybody in the list who has experienced a similar problem and know how to solve it.

"Hello, Bill's Car Repairs"

"Hi, my car doesn't work. Do you know how to solve it?"

"Probably, but you'll have to tell me a bit more information than that."

Mark
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