-------- Original Message --------
Subject: Re: problem with gromacs on cluster
Date: Wed, 26 Jul 2006 08:53:18 +0530
From: Mr. M.N. Manoj <[EMAIL PROTECTED]>
To: David van der Spoel <[EMAIL PROTECTED]>
References: <[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
Dear Sir,
Thanx for the reply
Sorry for to trouble u once more ....
I have been using grompp & mpirn with -np [x] for my cluster. But there
is no scale up in compute power happening
Our cluster has been checked & bechmarked with XHPL, and gives ~30 GFLOPS
I have been browsing thru the mailing list, but none gives a complete answer
Thats why I have mailed direct to support team
Hope u could give a complete instr to get out of this problem
With best regards,
Manoj
VMSRF
David van der Spoel wrote:
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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