[gmx-developers] Problem submitting GROMACS script

[rainy908 at yahoo.com]

So I've been able to get access to Gromacs v4.0.4 on another supercomputer
cluster.  However, I've been told that there are compatibility issues
regarding the MPI with Gromacs v4.  Also, I'm using the MARTINI force field
with Gromacs, but I'm not sure how well it is tested with v4?

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

> Justin A. Lemkul wrote:
>
>>
>>
>> rainy908 at yahoo.com wrote:
>>
>>> 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?
>>>
>>>
>> Correct.  As I originally indicated, mdrun must be called as an mpirun
>> process, i.e.:
>>
>> mpirun -np 4 mdrun -options
>>
>> I believe I once read (in a previous thread) that the -np option of mdrun
>> is actually ignored.  My memory could be failing, though :)
>>
>
> Something like that, yes. It certainly can find out from the mpirun
> environment.
>
> Mark
>
>
>  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.
>>>
>>>
>> It would probably be best to use the most recent version to take advantage
>> of all the nice new features, among which is a major speed upgrade.  Getting
>> used to Gromacs is not version-dependent.  Most tutorial material is broadly
>> applicable.
>>
>> -Justin
>>
>>  Lili
>>>
>>> 2009/8/2 Mark Abraham <Mark.Abraham at anu.edu.au <mailto:
>>> Mark.Abraham at anu.edu.au>>
>>>
>>>    rainy908 at yahoo.com <mailto: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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>>>
>>>
>>>
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>>
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