[gmx-users] GROMACS Parallel Runs

[David van der Spoel]

Sunny wrote:
>> From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: RE: [gmx-users] GROMACS Parallel Runs
>> Date: Fri, 06 Oct 2006 09:35:31 +1000
>>
>> > I have successfully run gmx on up to 128 cpus. When I scale
>> > to 256 cpus, the
>> > following error occurs. Does it mean that gmx can't be run on
>> > 256 nodes?
>> >
>> > Fatal error:
>> > could not find a grid spacing with nx and ny divisible by the
>> > number of
>> > nodes (256)
>>
>> Isn't that just due to the reasoning pointed out previously ....
>>
> 
> I think that's not the same problem. This time I have set fourier_nx=512 
> (or nkx=512, I've tried both setting). When running grompp ... -np 256, 
> it reports the error:
> 
> Fatal error:
> could not find a grid spacing with nx and ny divisible by the number of 
> nodes (256)
> 
> If I run the same grompp with the same .mdp file and less -np (i.e., 
> 128), the error doesn't occur.
> 
> Thanks,
> 
> Sunny
> 
>> >>the current version of gmx requires at least pme_order/2 grid points
>> >>per
>> >>processor
>> >>for the x-dimension of the pme grid. With pme_order=4 and
>> fourier_nx=64
>> >>you end up with
>> >>only one grid point per processor. On 64 CPUs you would have to set
>> >>fourier_nx to 128
>> >>then (or alternatively choose a smaller fourierspacing). These
>> settings
>> >>are not
>> >>useful for 32 or less CPUs though, because they would unnecessarily
>> slow
>> >>down your
>> >>calculation.
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
> 
> _________________________________________________________________
> Try the new Live Search today!  
> http://imagine-windowslive.com/minisites/searchlaunch/?locale=en-us&FORM=WLMTAG 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
set all of them to 256

do not expect to get any performance gain though.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++