[gmx-users] How can I best setup the nodes number
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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. example 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. Regards Vinoth On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA# zhao0...@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] How can I best setup the nodes number
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, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of vinothkumar mohanakrishnan [kmvin...@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. example 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. Regards Vinoth On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sgmailto:zhao0...@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 -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How can I best setup the nodes number
- Original Message -
From: #ZHAO LINA# zhao0...@e.ntu.edu.sg
Date: Wednesday, October 6, 2010 19:44
Subject: [gmx-users] How can I best setup the nodes number
To: gmx-users@gromacs.org gmx-users@gromacs.org
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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.
There's some discussion in manual 3.17.5.
Mark
|
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