[gmx-developers] Problem submitting GROMACS script

rainy908 at yahoo.com rainy908 at yahoo.com
Mon Aug 3 02:04:22 CEST 2009

Hi Mark,

I originally specified my $NSLOTS as 4 in my original scripts (didn't
include the header portion in my previous email).  Are you saying that even
though I specified 4 nodes as "-np 4", I'm still running my job on a single
processor, based on the way I've written my script?

I'm pretty new to using GROMACS so I figured it would be faster for me to do
a test run on the GROMACS 3.3.1 that's currently available on the cluster
I'm using rather to compile the new version 4(?) that is out.  Thanks for
your recommendation though.


2009/8/2 Mark Abraham <Mark.Abraham at anu.edu.au>

> rainy908 at yahoo.com wrote:
>> Justin,
>> You are correct about my attempt to run grompp using MPIRUN - it doesn't
>> work.  Actually I realized that I was using a version of Gromacs that
>> wasn't
>> compiled for MPI!  Gromacs-3.3.1-dev is compiled for MPI, however.  The
>> submission script that worked is as follows:
>> # Define locations of MPIRUN, MDRUN
>> MPIRUN=/usr/local/topspin/mpi/mpich/bin/mpirun
>> MDRUN=/share/apps/gromacs-3.3.1-dev/bin/mdrun
>> cd /nas2/lpeng/nexil/gromacs/cg_setup
>> # Run MD
>> $MDRUN -v -nice 0 -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g
>> md3.log -x md3.xtc
>> ..This was carried out  after I ran grompp on a single node.
> That still won't run a parallel mdrun. Justin indicated the correct
> approach.
> Also, unless you know a good reason for using a version of GROMACS 3(?)
> years old, use an up-to-date one. It'll be heaps faster.
> Mark
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