[gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What went wrong ?

[Abhi Acharya]

Hello,

>From the log files it is clear that out of 48 cores, the 5.0 run had 8
cores allocated to PME while the 4.6.5 run had 12 cores. This seems to have
caused a greater load imbalance in case of the 5.0 run.

 If you notice the last table in both .mdp files, you will notice that the
PME spread/gather wall time values for 5.0 is more than double the wall
time value in case of the 4.6.5.

Try running the simulation by explicitly setting the -npme flag as 12.

Regards,
Abhishek Acharya


On Fri, Sep 5, 2014 at 4:43 PM, David McGiven <davidmcgivenn at gmail.com>
wrote:

> Thanks Szilard, here it goes! :
>
> 4.6.5 : http://pastebin.com/nqBn3FKs
> 5.0 : http://pastebin.com/kR4ntHtK
>
> 2014-09-05 12:47 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
>
> > mdrun writes a log file, named md.log by default, which contains among
> > other things results of hardware detection and performance
> > measurements. The list does not accept attachments, please upload it
> > somewhere (dropbox, pastebin, etc.) and post a link.
> >
> > Cheers,
> > --
> > Szilárd
> >
> >
> > On Fri, Sep 5, 2014 at 12:37 PM, David McGiven <davidmcgivenn at gmail.com>
> > wrote:
> > > Command line in both cases is :
> > > 1st :     grompp -f grompp.mdp -c conf.gro -n index.ndx
> > > 2nd :    mdrun -nt 48 -v -c test.out
> > >
> > > Log file you mean the standard output/error ? Attached to the email ?
> > >
> > > Thanks
> > >
> > > 2014-09-05 12:30 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
> > >
> > >> Please post the command lines you used to invoke mdrun as well as the
> > >> log files of the runs you are comparing.
> > >>
> > >> Cheers,
> > >> --
> > >> Szilárd
> > >>
> > >>
> > >> On Fri, Sep 5, 2014 at 12:10 PM, David McGiven <
> davidmcgivenn at gmail.com
> > >
> > >> wrote:
> > >> > Dear Gromacs users,
> > >> >
> > >> > I just compiled gromacs 5.0 with the same compiler (gcc 4.7.2), same
> > OS
> > >> > (RHEL 6) same configuration options and basically everything than my
> > >> > previous gromacs 4.6.5 compilation and when doing one of our typical
> > >> > simulations, I get worst performance.
> > >> >
> > >> > 4.6.5 does 45 ns/day
> > >> > 5.0 does 35 ns/day
> > >> >
> > >> > Do you have any idea of what could be happening ?
> > >> >
> > >> > Thanks.
> > >> >
> > >> > Best Regards,
> > >> > D.
> > >> > --
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