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

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Wed Oct 6 10:52:44 CEST 2010

I think I know how many ppn one nodes have. :-)

My question was that the number of ppn has something to do with the PME mesh part number or not?

Why sometimes I had a big load imbalance.

Thanks and best regards,


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of vinothkumar mohanakrishnan [kmvinoth at gmail.com]
Sent: Wednesday, October 06, 2010 4:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How can I best setup the nodes number

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<mailto:ZHAO0139 at e.ntu.edu.sg>> wrote:

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,


gmx-users mailing list    gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101006/61772afe/attachment.html>

More information about the gromacs.org_gmx-users mailing list