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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 26 09:23:12 CEST 2006

-------- Original Message --------
Subject: Re: problem with gromacs on cluster
Date: Wed, 26 Jul 2006 08:53:18 +0530
From: Mr. M.N. Manoj <manoj at vmsrf.org>
To: David van der Spoel <spoel at xray.bmc.uu.se>
References: <44C60C4A.1080801 at vmsrf.org> <44C60FCB.1010706 at xray.bmc.uu.se>

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,


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 
>> 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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