[gmx-developers] Any known gcc 4.1 issues?

[Roland Schulz]

On Mon, Jul 5, 2010 at 5:59 PM, <hess at sbc.su.se> wrote:

> Hi,
>
> Which Gromacs version is this?
>
 Head from two weeks ago (commit: 0541796)

> And this is not with GBSA?
>
no GBSA. PME.

> I assume this is in parallel?
>
yes

> In all 4.0 versions there is a bug in the graph code,
> but I have never seen that being triggered.
>
you mean GCC 4 or GROMACS 4?

>
> You probably wouldn't know if 4.1.3 does better?
>
no. Only tested those two GCC versions.

BTW: Are MDP files supposed to be upward compatible? Because the default for
nstcalcenergy is -1 in grompp. Thus if one has an old mdp file without the
nstcalcenergy option one gets a different tpr file with grompp from HEAD
than grompp 4.0.7. Should we set nstcalcenergy to 1 if it is missing or
print a NOTICE if is it is missing and we set it to -1?

(We noticed this while looking at the origin of the large
energy fractionation. The  (short-term)  fluctuation are increased with
nstcalcenergy -1 (it is using 10) but much smaller than the increase caused
by GCC 4.1 - which are longer term fluctuations)

Roland

>
> Berk
>
> > Hi,
> >
> > we have a simulation in our group (Xiaohu's system) which shows much
> > larger
> > energy fluctuations (on a ~10ns time-scale) if compiled with 4.1.2.
> > These fluctuation are large enough for the system to explode
> infrequently.
> > The system behaves as expected (without the large
> fluctuations/explosions)
> > when compiled with 4.4.4.
> >
> > Roland
> >
> > On Thu, Jun 24, 2010 at 11:05 AM, Berk Hess <hess at cbr.su.se> wrote:
> >
> >> Hi,
> >>
> >> We just found out a that a bug that frequently showed up and we thought
> >> might be due to a bug in gcc 4.1
> >> was actually a bug in the GB sse2 (not sse3) code that only got
> >> triggered with gcc 4.1 with -O2 or -O3.
> >>
> >> So my question is now:
> >> Do you know of any issues with gcc 4.1.x on non-GB simulations?
> >>
> >> Thanks,
> >>
> >> Berk
> >>
> >> --
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> >
> >
> >
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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