[gmx-users] PME scaling

Erik Lindahl lindahl at sbc.su.se
Tue Jan 10 18:02:26 CET 2006

Hi Rob,

The head branch of CVS has major scaling improvements, but it's  
changing quite a lot right now, so unless you really like to iron out  
bugs I'd recommend waiting a couple of weeks until it's stabilized a  

For instance, the current version partitions the system into separate  
PME and direct space nodes, but depending on the performance we might  
actually decide to reverse that and do PME on all nodes again.



On Jan 10, 2006, at 5:45 PM, Robert Bjornson wrote:

> Hi,
> I'm experiencing very poor scaling when using PME on gromacs-3.3, and
> looking through the list indicates that this is a known issue with
> that release.  However, there was some indication that work has been
> done on parallelizing PME, and that the top of CVS might contain a
> version that is worth trying.
> Has anyone tried this?  Did your PME performance improve?  If so, did
> you simply take the top of cvs, or is there a tag that is more likely
> to work successfully?
> thanks,
> Rob Bjornson
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Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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