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

Tue Sep 9 15:37:56 CEST 2014

Thank you very much to all of you. That should explain the difference in
performance.

I'll also discuss it with a more gromacs-knowledgeable colleague of mine.

Best Regards.

2014-09-06 8:58 GMT+02:00 Abhi Acharya <abhi117acharya at gmail.com>:

> Thank you Mark and Szilard for your replies. It gave more clarity on how
> the new gromacs works,
> especially in greater support for streamed computing.
>
> I hope David's problem is sorted too. :)
>
> Thanks again,
>
> Regards,
> Abhishek Acharya
>
>
> On Fri, Sep 5, 2014 at 10:45 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > On Fri, Sep 5, 2014 at 6:40 PM, Abhishek Acharya
> > <abhi117acharya at gmail.com> wrote:
> > > Dear Mark,
> > >
> > > Thank you for the insightful reply.
> > > In the manual for gromacs 5.0 it was mentioned that verlet scheme is
> > better for GPU systems.
> >
> > More correctly, only the Verlet scheme supports GPU acceleration. The
> > algorithms used by the group scheme are not appropriate for GPUs or
> > other wide-SIMD accelerators.
> >
> > > Does that mean that we should give up on the group scheme scheme, even
> > though we get good performance compared to verlet?
> >
> > That's up to you to decide. The algorithms are different, the group
> > scheme does not use a buffer by default, while the verlet scheme does
> > and aims to control the drift (and keep it quite low by default).
> >
> > > Future plan of removing group cut-off scheme indicates that it must
> have
> > been associated with a high cost-benefit ratio.
> >
> > What makes you conclude that? The reasons are described here:
> > http://www.gromacs.org/Documentation/Cut-off_schemes
> >
> > In very brief summary: i) the groups scheme is not suitable for
> > accelerators and wide SIMD architectures ii)  energy conservation =
> > high performance penalty iii) inconvenient for high parallalelization
> > as it increases load imbalance
> >
> > Cheers,
> > --
> > Szilárd
> >
> > > Could you please shed little light on this  ?
> > > Thanks.
> > >
> > > Regards,
> > > Abhishek
> > >
> > > -----Original Message-----
> > > From: "Mark Abraham" <mark.j.abraham at gmail.com>
> > > Sent: ‎9/‎5/‎2014 7:57 PM
> > > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > > Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5.
> What
> > wentwrong ?
> > >
> > > 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
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