[gmx-users] Re: GROMACS + MOSIX (fwd)

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 17 15:40:06 CEST 2002

---------- Forwarded message ----------
Date: Wed, 17 Apr 2002 15:33:28 +0200 (CEST)
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Chandrasekar Ramamoorthy <sekar_ceg at yahoo.com>
Subject: Re: GROMACS + MOSIX

On Tue, 16 Apr 2002, Chandrasekar Ramamoorthy wrote:

>Dear Sir,
>   I have a 16 node beowulf cluster configured using
>MOSIX. I want to run MD simulation using GROMACS.
>Instead of using LAM to transfer processes to another
>node is it possible to make mdrun spawn several
>processes on the same node and let MOSIX balance the
Mosix can not handle processes that access sockets, i.e. the mechanism to 
transport data between unix machines, that is it can not move suche 
processes to other nodes. Having said that, it may be able to handle 
processes that use shared memory. Since LAM can use shared memory within a 
node, maybe you can fool LAM into running all the processes through shared 
memory on one node, and then let MOSIX handle the process scheduling. In 
effect this would come down to having one large virtual shared memory 
machine, composed out of many normal PCs. 

This is hypothetical, check www.openmosix.org for more information. If it 
doesn't work, you can either run a lot of single machine jobs or remove 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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