[gmx-users] Running gromacs in parallel on multicore machine

[Mark Abraham]

----- Original Message -----
From: Sikandar Mashayak <symashayak at gmail.com>
Date: Wednesday, June 2, 2010 8:39
Subject: Re: [gmx-users] Running gromacs in parallel on multicore machine
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> well I installed the mpi enabled mdrun and execute it with option -np 8, but still I see only core is being used at 100% instead of 8.
> 
> Is there additional settings to be done to correct this.?

Copying and pasting your actual input and output is much more useful than filtering things through your head.

What's your actual command line? Does the top of the GROMACS logfile indicate you're running on 8 processors? If so, what time does -np1 take to run vs -np 8?

Indications of core utilization can be meaningless, since they rely on definitions of work that may not be valid.

Mark

> 
> thanks
> sikandar
 > 
> On Tue, Jun 1, 2010 at 4:18 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
 > 
> 
> ----- Original Message -----
> From: Sikandar Mashayak <symashayak at gmail.com>
> Date: Wednesday, June 2, 2010 7:17
>  Subject: [gmx-users] Running gromacs in parallel on multicore machine
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
> > Hi
 > > 
> > I am wondering whether its possible to run gromacs in parallel on single processor machine with multiple cores?
 > > 
> > I have 8 core processor, when I run mdrun in serial I see only one of those is used at 100%. I am thinking, if possible, to use all cores approximately equally by running mdrun in parallel and hoping to get results faster.
  > > 
> > Any suggestions?
 > 
> Compiling with MPI and running in parallel is your only current option. See GROMACS webpage.
 > 
> Mark 
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