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

[David McGiven]

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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