[gmx-users] Paralellization limit?
and.carotti at farmchim.uniba.it
Wed Apr 19 14:41:51 CEST 2006
thanks for your quick reply.
Could you plese confrim me that gromacs 3.3.1 works and compile fine with
Cause this is the first time that I hear that from a user and I'll go ahead
on this way instead of usin LAM.
----- Original Message -----
From: "Carsten Kutzner" <ckutzne at gwdg.de>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, April 19, 2006 2:15 PM
Subject: Re: [gmx-users] Paralellization limit?
> Hi Andrea,
> Andrea Carotti wrote:
>> Hi all,
>> I'm trying to simulate a system with two identical proteins (42aa each
>> one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100
>> Now the "problem" is that if I run the MD on 4 nodes everything works
>> fine, but when I try to use 6 or 8 cpus the process stops on the master
>> and continue only on the last two slaves (4 cpus, the systems are dual
>> xeon). The problem is that I can't find any error message on the log
>> I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6
>> and 8 cpus.
>> So my question is: is there a limit of parallelization in gromacs
>> depending on the simulated system?
>> I'm using gromacs 3.3.1, mpich 188.8.131.52 and fftw 2.1.5.
> I have encountered similar problems when using mpich 1.2.x on
> Ethernet. Upgrading to mpich-2.x or using LAM solved the problems.
> There is only a parallelisation limit in the sense that using more
> CPUs does not always result in faster execution. 56 k atoms should
> run happily on 8 CPUs.
> Good luck,
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