Hello,
I can verify your segfault, and I'm looking into it. I also know where it
happens (line 114 of model.c), but I haven't tracked down why this memory
wasn't allocated yet.
Another thing to try is to use sleap instead (but make sure that you load
the proper frcmod file!). sleap doesn't segfault for me.
I'll report back if/when I find the cause of the bug in tleap (unless
someone with better knowledge of the code finds it first).
HTH,
Jason
On Tue, Aug 2, 2011 at 4:42 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> Dear Jason and David,
>
> Many thanks for the useful hints.
>
> Following your advises, I decided to install AmberTools 1.5 in my local
> machine
> and everything seemed to work fine.
> All the tests passed, apart from those that required the installation
> of Amber11 (sander),
> as you can see:
>
> 481 file comparisons passed
> 2 file comparisons failed
> 0 tests experienced errors
> Test log file saved as logs/test_at_serial/2011-08-02_20-21-38.log
> Test diffs file saved as logs/test_at_serial/2011-08-02_20-21-38.diff
>
> But unfortunately I got again segmentation fault with loadPdb in
> executing the same
> procedure I posted yesterday, that is:
>
> :~>tleap
> >source leaprc.ff99SBildn
> >set default PBradii mbondi2
> >loadOff seh.lib
> >peptide = loadPdb peptide.pdb
>
> This time I enclosed also the pdb file of the peptide (and my library
> seh.library as well).
>
> Any kind suggestion?
>
> Cheers,
>
>
>
> 2011/8/1 Jason Swails <jason.swails.gmail.com>:
> > On Mon, Aug 1, 2011 at 4:03 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Mon, Aug 01, 2011, Massimiliano Porrini wrote:
> >> >
> >> > Since it was not me to install both Amber and AmberTools in the
> >> > cluster I am running on, is there any way to check which version I am
> >> using?
> >> >
> >> > And in case I am using the not fixed version 1.4, how can I
> >> > patch it?
> >>
> >> Either (a) go to http://ambermd.org, click on "bug fixes" and follow
> the
> >> instructions to patch version 1.4; or (b) download AmberTools1.5 from
> the
> >> same
> >> web site. I would recommend the latter.
> >>
> >> [I don't think there is any easy way to determine which version someone
> >> else
> >> installed, although Jason probably knows....]
> >
> >
> > It's not nearly as good as a --version flag, but the following can help
> tell
> > what version you have (as long as you haven't done anything like renaming
> > directories and adding/removing files and directories):
> >
> > If you have AmberTools 1.2, then it unpacks into an amber10/ directory
> and
> > builds alongside amber10.
> > If you have AmberTools 1.3, then it unpacks into an amber11/ directory,
> but
> > I don't think it can build with Amber11. In any case, it's unlikely
> anybody
> > is using this version. (since it was only ~6 months between 1.3 and 1.4
> > releases IIRC)
> > If you have AmberTools 1.4, then it unpacks into an amber11/ directory,
> and
> > it *can* build with Amber11. Furthermore, it has no
> > $AMBERHOME/AmberTools/src/cpptraj/ directory or
> $AMBERHOME/AT15_Amber11.py
> > script.
> > If you have AmberTools 1.5, then it unpacks into an amber11/ directory
> and
> > it *can* build with Amber11 as long as you run AT15_Amber11.py, and it
> > *does* have a cpptraj directory. This is also the first release to build
> > mdgx by default, IIRC.
> >
> > If you're just trying to distinguish between AT 1.4 and AT 1.5, look for
> the
> > cpptraj and mmpbsa_py directories in $AMBERHOME/AmberTools/src and the
> > AT15_Amber11.py script (these are only in AmberTools 1.5). (The easiest
> > file to trace, though, is probably the configure file, if you know what
> to
> > look for).
> >
> > The only packages you can download right *now* are AmberTools 1.5 and
> > AmberTools 1.2 (to build amber10).
> >
> > Looking at git logs, it appears as though Mengjuei fixed tleap's huge
> > segfaulting issue (caused by 64-bit builds) ~6/1/2010. So it appears
> that
> > anything older than AmberTools 1.4 will experience frequent segfaults
> with
> > tleap.
> >
> > Perhaps we should add the AmberTools version to *something*? Each
> package's
> > Makefiles? Require each package to recognize a --version flag? The
> master
> > Makefile?
> >
> > Of course if you have the original tarball it says there.
> >
> > I don't know how helpful this is. (To Massimiliano, I suggest that you
> > build your own AmberTools 1.5, since that's the package that will get the
> > most support. If something doesn't work in older versions, the
> maintainer
> > will probably just ask you to upgrade to see if the problem goes away,
> > anyway).
> >
> > HTH,
> > Jason
> >
> >
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 02 2011 - 20:30:02 PDT
