[gmx-users] Re: problem with gromacs on cluster

[David van der Spoel]

Mr. M.N. Manoj wrote:
> Dear Sir/Madam
> 
> We have been using gromacs 3.3 on our workstation succesfully
> Now we have purchased a Rocks 4.2 based cluster (dual xeon processor 
> with 5 nodes)
> We have been able to compile Gromacs 3.3 with fftw 2.1.5 and MPI-LAM 
> 7.1.2 on front node, its working there.
> Then we  have copied the installation folder /usr/local/gromacs to each 
> node
> 
> But when we run it, the performance is not better than one single node 
> (master) in terms of ps/day
> Also from the ganglia it can be seen that hardly anything is happening 
> on compute nodes, though it says its running mdrun_mpi
> 
> Now we have few questions:
> 
> 1. What is the exact procedure for installing gromacs on the the FULL 
> CLUSTER ?
> 2. Do we have to install it (gmx and fftw2) on each node?
> 3. Any other way ?
> 

your installation is probably fine.
you have to tell mpirun to use more than one node, try "man mpirun"


please ask further questions on the mailing list.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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