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

Mark Abraham mark.j.abraham at gmail.com
Fri Sep 5 16:26:34 CEST 2014 

This cutoff-scheme difference is probably caused by using an .mdp file that
does not specify the cutoff scheme, and the default changed in 5.0. grompp
issued a note about this, if you go and check it. The change in the -npme
choice is a direct consequence of this; the heuristics underlying the
splitting choice approximately understand the relative performance
characteristics of the two implementations, and you can see that in
practice the reported PP/PME balance is decent in each case.

There is indeed a large chunk of water (which you can see in group-scheme
log files e.g. the line in the FLOP accounting that says NB VdW & Elec.
[W3-W3,F] dominates the cost), and David's neighbour list is unbuffered.
This is indeed the regime where the group scheme might still out-perform
the Verlet scheme (depending whether you value buffering in the neighbour
list, which you generally should!).

Mark


On Fri, Sep 5, 2014 at 4:06 PM, Abhi Acharya <abhi117acharya at gmail.com>
wrote:

> Hello,
> Is you system solvated with water molecules?
>
> The reason I ask is that, in case of the run with 4.6.5 you gromacs has
> used a group cut-off scheme, whereas 5.0 has used verlet scheme. For system
> with water molecules, group scheme gives better performance than verlet.
>
> For more check out:
> http://www.gromacs.org/Documentation/Cut-off_schemes
>
> Regards,
> Abhishek Acharya
>
> On Fri, Sep 5, 2014 at 7:28 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>
> > Hi,
> >
> > you might want to use g_tune_pme to find out the optimal number
> > of PME nodes for 4.6 and 5.0.
> >
> > Carsten
> >
> >
> >
> > On 05 Sep 2014, at 15:39, David McGiven <davidmcgivenn at gmail.com> wrote:
> >
> > > What is even more strange is that I tried with 10 pme nodes (mdrun
> -ntmpi
> > > 48 -v -c TEST_md.gro -npme 16), got a 15,8% performance loss and ns/day
> > are
> > > very similar : 33 ns/day
> > >
> > > D.
> > >
> > > 2014-09-05 14:54 GMT+02:00 David McGiven <davidmcgivenn at gmail.com>:
> > >
> > >> 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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> > --
> > Dr. Carsten Kutzner
> > Max Planck Institute for Biophysical Chemistry
> > Theoretical and Computational Biophysics
> > Am Fassberg 11, 37077 Goettingen, Germany
> > Tel. +49-551-2012313, Fax: +49-551-2012302
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