[gmx-developers] Problem submitting GROMACS script

[Mark Abraham]

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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