AMBER Archive (2009)

Subject: Re: [AMBER] amber 10 test failures...

From: peker milas (pekermilas_at_gmail.com)
Date: Tue Nov 03 2009 - 08:11:01 CST

Thank you dear Ross,Jason, and Mark,

You helped me much. By the way, i may use abmd in future but i definitely
don't need it right now. As parallel to your advice, i will try it with
different set of compilers and if necessary with different optimization
levels when i need abmd. Right now i just needed it to run as smoothly as
possible because as i said i just started to learn it. Thank you so much
again for your helps...

best
peker

On Mon, Nov 2, 2009 at 7:19 PM, Jason Swails <jason.swails_at_gmail.com> wrote:

> The same named bug was happening on a Mac with gfortran 4.5.0 (or something
> like that). Did you try recompiling with a lower optimization? (i.e.
> dropping from -O3 to -O2 was enough to get my problem module compiled).
>
> All the best,
> Jason
>
> On Mon, Nov 2, 2009 at 7:11 PM, Mark Williamson <mjw_at_sdsc.edu> wrote:
>
> > Ross Walker wrote:
> >
> >> Hi Peker,
> >>
> >> ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>'
> instead
> >>
> >> I suspect this is because they use some new namelist option in the input
> >> files that your compiler is not supporting. That said I am sure others
> >> have
> >> used gfortran 4.1.2 and have not seen this problem. The nice thing at
> >> least
> >>
> >
> > This is specific to the gfortran 4.1.2 compiler; I see it on my RHEL4
> > desktop machine. I think it is some form of compiler bug; I do not see
> this
> > issue with ifort or later versions of gfortran.
> >
> > The error message is being emitted by the type_mismatch() routine, which
> I
> > think has been called by node_lookup_list() which has been called by
> > colvar_mdread() whilst I think parsing the section:
> >
> > # list of participating atoms
> > i = (1, 5, 8, 10, 12, 29, 31, 33, 41,
> > 43, 53, 55, 57, 59, 70, 72, 74,
> > 84, 86, 88, 91, 93, 95, 105, 107,
> > 109, 129, 131, 133, 136)
> >
> > of the test/ncsu/abmd_ANALYSIS/mdin file. I had a look at this a while
> ago
> > with the aim to generating some form of workaround, but I could not
> > ascertain what specifically was causing it. I've started to look into it
> > again, but I'm not sure how much joy I will have: compiler bugs are a
> real
> > time sink.
> >
> > --
> > Mark Williamson, Post Doc
> > Walker Molecular Dynamics Group
> > Room 395E
> > San Diego Supercomputer Center
> > 9500 Gilman Drive
> > La Jolla, CA 92093-0505
> > Email: mjw at sdsc.edu
> > Office: 858-246-0827
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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