[gmx-developers] Problem submitting GROMACS script

[rainy908 at yahoo.com]

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.

Lili

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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