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

[David McGiven]

Hi Abhi,

Yes I noticed that imbalance but I thought gromacs knew better than the
user how to split PP/PME!!

How is it possible that 4.6.5 guesses better than 5.0 ?

Anyway, I tried :
mdrun -nt 48 -v -c test.out

Exits with an error "You need to explicitly specify the number of MPI
threads (-ntmpi) when using separate PME ranks"

Then:
mdrun -ntmpi 48 -v -c TEST_md.gro -npme 12

Then again 35 ns/day with the warning :
NOTE: 8.5 % performance was lost because the PME ranks
      had less work to do than the PP ranks.
      You might want to decrease the number of PME ranks
      or decrease the cut-off and the grid spacing.


I don't know much about Gromacs so I am puzzled.




2014-09-05 14:32 GMT+02:00 Abhi Acharya <abhi117acharya at gmail.com>:

> 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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