I have a fix - I will post details shortly...
> -----Original Message-----
> From: owner-amber-developers.scripps.edu [mailto:owner-amber-
> developers.scripps.edu] On Behalf Of Scott Brozell
> Sent: Friday, July 11, 2008 3:20 PM
> To: amber-developers.scripps.edu
> Subject: RE: amber-developers: Serious problems with Antechamber runs due
> to faulty Mopac in AmberTools?
>
> Hi,
>
> I also verify that x86_64 with both g77 and gfortran has the mopac
> problem:
> Linux opt-login01.osc.edu 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT
> 2008 x86_64 x86_64 x86_64 GNU/Linux
> Red Hat Enterprise Linux Server release 5.2 (Tikanga)
> g77: gcc version 3.4.6 20060404 (Red Hat 3.4.6-4)
> gfortran: gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)
>
> I tried reverting to revision 1.1 of block.f eliminating the only recent
> mopac source changes; this had no effect.
> -O0 -g also had no effect.
> One avenue is -fbounds-check which yields a quick:
> Subscript out of range on file line 43, procedure jcarin.f/jcarin.
> Attempt to access the 4-th element of variable coord[subscript-1-of-2].
> And now Im punting since Ross is the mopac expert ;-)
>
>
> I agree that we should be very very careful when updating .save outputs.
> I agree that we should be testing mopac.
> But Im distancing myself from the sky is falling world of Ross since
> I have seen similar partial charge differences have little affect
> on docking results.
> In addition, broken stuff has great pedagogical potential.
>
> For the record these platform do not have the mopac problem:
>
> Darwin rooster.compbio.ucsf.edu 7.9.0 Darwin Kernel Version 7.9.0: Wed Mar
> 30 20:11:17 PST 2005; root:xnu/xnu-517.12.7.obj~1/RELEASE_PPC Power
> Macintosh powerpc
> gcc version 3.3 20030304 (Apple Computer, Inc. build 1495)
> g77: gcc version 3.4.0 20040107 (experimental)
>
> Linux piv-login1 2.6.18.1 #12 SMP Sun Feb 10 17:08:11 EST 2008 i686 i686
> i386 GNU/Linux
> Red Hat Enterprise Linux AS release 3 (Taroon Update 6)
> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-53)
>
> good luck,
> Scott
>
> On Fri, 11 Jul 2008, Ross Walker wrote:
>
> > Okay here is a summary of the mopac problems on my machine
> >
> > RHEL4, Intel Pentium-D x86_64
> >
> > g77 (gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)) - Suffers from the
> > problems discussed.
> >
> > gfortran (gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)) - Also suffers
> from
> > the same problem.
> >
> > g95 (gcc version 4.0.3 (g95 0.92!)) - Gives a segfault very early on.
> >
> > ifort (Version 10.1 Build 20070913 Package ID: l_fc_p_10.1.008) -
> Works
> > correctly (with extra output issues)
> >
> > Using -O0 with g77 or gfortran does not fix things.
> >
> > Trying to print the values of TIMITR, TIMES and DEBUG that control the
> > printing of all the extra info that appears in the ifort output fixes
> the
> > problem implying that there is some memory issue somewhere that is
> > scrambling things.
> >
> > I will see if I can track down where the problems are - this is all due
> to
> > numerous memory stomping issues and missing variable initializations -
> mopac
> > 6.0 is full these :-(.
Received on Sun Jul 13 2008 - 06:07:54 PDT
