[gmx-users] GROMACS parallel set up Questions.

[David van der Spoel]

Mark Abraham wrote:
> Subhrangshu Supakar wrote:
>> Dear All,
>> I have a few questions about installing gromacs in a parallel set up:
>> I am planning to use a parallel system consisting of 4 x3650 boxes 
>> connected to each other with a gigabit switch and the same OS 
>> installed in all the three. The MPI would be LAM/MPICH and the boxes 
>> will use their own HDDs. GROMACS will be installed in all of them with 
>> the mpi option.
>> Now, does GROMACS (mdrun) write the output files on NODE0 only? 
> 
> No.
> 
>> Do I have to copy the run input files to all the boxes?
> 
> Each MPI process needs to run the same executable with the same input 
> file - both need to be on a file system visible to the processor.

The input file is needed on node0 only, but all nodes write a small log 
file. You probably need to setup NFS between the boxes.

> 
>> It would be of great help to me if somebody can suggest a particular 
>> type of cluster setup procedure (if any) suitable for running GROMACS .
www.rocksclusters.org

> 
> Mark
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se