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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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