[gmx-users] PME nodes

[XAvier Periole]

On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote:

>
>
> XAvier Periole wrote:
>> Dears,
>> I am having troubles finding the better balance between the PME  
>> CPUs and the rest.
>> I played with the rdd, rcon and -npme options but nothing really  
>> appears very
>> straightforwardly best.
>> I'd appreciate if some of you could post their experience in that  
>> matter. I mean the
>> number of pme nodes as compared the total number of CPUs used.
>> I think this info as been discussed recently on the list but the  
>> archive is not accessible.
>> It may matter that I have a system containing about 70000 atoms, a  
>> protein in a bilayer.
>
> Some advice that I got from Berk long ago has worked beautifully for  
> me.  You want a 3:1 PP:PME balance for a regular triclinic cell  
> (grompp will report the relative PME load as 25% if your parameters  
> create such a balance), 2:1 for an octahedron.  My scaling has been  
> great using this information, without having to alter -rdd, -rcon,  
> etc.

Thanks for the info. I got more or less to that ratio. Although a 2:1  
PP:PME sometimes is better.

However my problem now is to get 256 CPUs more efficient (ns/day) than  
128 CPUs. The communications
become a limiting factor ... can't get it to go faster! The system  
might be small, but not sure.

I'll take a look at the CVS tool.

XAvier.
>
> -Justin
>
>> Best,
>> XAvier.
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before  
>> posting!
>> Please don't post (un)subscribe requests to the list. Use thewww  
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php