[gmx-users] Number of processors in parallel running

[Justin A. Lemkul]

Peggy Yao wrote:
> Thank you, Justin.
> 
> I am using GMX 4.0.2. Do I need to have the -np option in all grompp and 
> mdrun commands? Thanks in advance!
> 

Read the -h of each program, as well as the numerous threads on the topic in the 
list archive.

-Justin

> Peggy
> 
> On Tue, Feb 17, 2009 at 3:02 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Peggy Yao wrote:
> 
>         Dear all,
> 
>         In order to run Gromacs on multiple processors, I should put the
>         number of processors in the commands. For example,
> 
>         grompp -np <nr> -o topol.tpr <other options>
> 
> 
>     Only if you're using GMX < 4.0.
> 
> 
> 
>         My question is: nr should be the number of processors, or the
>         number of cores? If I have a quad-core processor, should I put 4?
> 
> 
>     Number of cores.  Try it and you will see.
> 
>     -Justin
> 
>         Thanks,
>         Peggy
> 
> 
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================