[gmx-users] PME nodes

[David van der Spoel]

XAvier Periole wrote:
> 
> 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.
> 
Depends a lot on the interconnect and the ratio atoms/node. You may also 
want to play with cut-offs, the tool will help you with this.

> 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
> 
> _______________________________________________
> 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


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++