Hah!!! I am vindicated!
Thanks Dan, I'll check in the patch to the tree.
All the best
Ross
> -----Original Message-----
> From: amber-developers-bounces.ambermd.org [mailto:amber-developers-
> bounces.ambermd.org] On Behalf Of Daniel Roe
> Sent: Thursday, March 25, 2010 10:09 AM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] Current parallel test failures in the
> tree
>
> Hi All,
>
> I found a few bugs in the NEB code, including the one that was causing
> the
> test cases to fail. The end beads in NEB exit before they do any of the
> tangent calculation since for them it is not needed. However, the
> neb_force
> array was not being zeroed on these beads before their early exit,
> hence the
> problem was only with compilers that don't automatically zero
> everything.
> There was also a smaller but significant bug where the variable ncopy
> was
> being used instead of neb_nbead, which led to incorrect energies being
> used
> in the tangent calculation (this is what was causing the issues that
> Mark
> was seeing with the NEB_NRG_ALL array since ncopy is not used in NEB
> and is
> 0).
>
> The attached patch fixes said bugs, as well as updates the NEB test
> runscripts to use up to 12 processors only, test output from all beads,
> and
> use absolute error criterion instead of truncating floating point
> digits
> with the dacdif script (which sometimes caused weird and inconsistent
> conversion of 0.000 to 0. and a fake Fail).
>
> Let me know if the patch doesn't work for you. It should be applied
> from
> $AMBERHOME.
>
> -Dan
>
> On Wed, Mar 24, 2010 at 5:56 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > > > possible FAILURE: check neb_gb_partial_01.out.dif
> > > > /home/rcw/cvs_checkouts/amber11/test/neb-testcases/neb_gb_partial
> > > >> vlimit exceeded for step 1; vmax = **********
> > > > etc
> > > > etc
> >
> >
> > > Did you get my email (cc'd to Dan and Carlos) about these ones
> > > specifically? I concluded that it was a compiler bug; (ifort
> 10.1.018).
> > > What version of ifort did you use?
> >
> > I don't buy this. 10.1.018 has been a version we have been
> recommending for
> > years because of it's stability. I would be surprised to find an
> error now.
> > More likely this test case has VERY bad initial structures since just
> > naively setting up end points and allowing an interpolation will lead
> to
> > vlimit errors in NEB. Chances are there is a division by a very small
> > number
> > occurring here, due to the images being on top of each other, and
> some
> > compilers are more sensitive to rounding this to zero than others. It
> would
> > probably be better if an actual restart from an equilibrated set of
> > coordinates was used as the test case, this would likely give a more
> > reliable regression test. I'm cc'ing this email to Christina who I
> hope can
> > put together a more realistic test case.
> >
> > > > The ti_decomp_1 also has issues:
> > > > possible FAILURE: check ti_decomp_1.out.dif
> > > > /home/rcw/cvs_checkouts/amber11/test/ti_decomp
> >
> > > > This is way beyond rounding errors, even with having values
> printed
> > > to way
> > > > too much precision for a test case in the output. Who is
> responsible
> > > for
> > > > ti_decomp these days? They should probably look at this ASAP.
> > >
> > > I think this fail has been present for a long while and was
> discussed
> > > before on here the other week; Dave has cc'd Holger about it.
> >
> > We need volunteers to fix this ASAP hence why I posted it.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> > be read every day, and should not be used for urgent or sensitive
> issues.
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
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Received on Thu Mar 25 2010 - 10:30:07 PDT
