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

[David van der Spoel]

-------- 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,

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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