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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 25 14:34:19 CEST 2006

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 
> 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 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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