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

Fri Sep 5 15:39:28 CEST 2014

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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