[gmx-developers] Problem submitting GROMACS script

[Justin A. Lemkul]

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 :)

> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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