[gmx-users] GROMACS on a parallel Linux cluster

Peter Spijker pspijker at wag.caltech.edu
Mon Mar 1 18:44:00 CET 2004

Hi all,

With the help of David van der Spoel I was able to get GROMACS running on a
parallel machine. But it behaves very awkward. Using the same PBS-script to
submit jobs (except for the differnence in number of nodes and processors)
result in a random acceptance of the job. I was wondering if this has
happened to someone else before. I thought maybe GROMACS failed with a
certain request. Below there is some technical information. Thanks for
helping me.

Kind regards,

Peter Spijker
California Institute of Technology


I am using the DPPC-benchmark system downloadable from the GROMACS website.

Lines from the PBS-script (with $MDP the MDP-file is mentioned, and so on ;
for MPIRUN the number of nodes is needed as input, not the number of


#PBS -l nodes=4:ppn=1
#PBS -q workq
#PBS -o std.out
#PBS -e std.err

### Set variables
set NOD=4


### Script Commands

### Set Environments
setenv CONV_RSH ssh
setenv LAMRSH "ssh -x"
setenv LD_LIBRARY_PATH "/usr/lib"

### Write info about nodes used
set n=`wc -l < $PBS_NODEFILE`
echo 'PBS_NODEFILE ' $PBS_NODEFILE ' has ' $n ' lines'


### Run simulation
/gromacs_mpi/i686-pc-linux-gnu/bin/grompp -f $MDP -c $GRO -p $TOP -o
$TPR -np $NOD -deshuf $NDX -shuffle -sort
mpirun -c $NOD /gromacs_mpi/i686-pc-linux-gnu/bin/mdrun -s $TPR -np $NOD

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