[gmx-users] How can I best setup the nodes number

vinothkumar mohanakrishnan kmvinoth at gmail.com
Wed Oct 6 10:48:56 CEST 2010

I think the PME mesh part is ok and it should be less than 0.5 always.

Regarding the nodes ask your administrator how many ppn one node have.
suppose if one node has 6 ppn then 12 nodes will have 72ppn which is
sufficient to run md.

hope the above explanation helps you.


On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg> wrote:

>  Hi,
> Estimate for the relative computational load of the PME mesh part: 0.33
> How do I set how many nodes I should use?
> #PBS -l nodes=12:ppn=4
> What if the PME mesh part has different values?
> is it okay? Before I did those kind of very blindly, just based on the most
> nodes I can use to hopefully run quickly.
> Thanks and best regards,
> lina
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