To get debug symbols, you need to recompile with the -g flag and no
optimization (so only -O0, not -O1, -O2, etc.). You can add these straight
to the config.h file. Google will be your friend here, and if it's a little
over your experience level, hopefully a guru can reproduce the error and
find out what's happening.
All the best,
Jason
On Wed, May 12, 2010 at 5:57 PM, Omair A. Khan <oak3.psu.edu> wrote:
> Jason, thanks for clarifying how to use gdb. I ran tleap again, with the
> "loadOff solvents.lib" command which resulted in the same segfault:
>
> /opt/amber10/bin/tleap: line 17: 5135 Segmentation fault (core
> dumped)
> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
>
>
> gdb gave the following output:
>
> [oak3.proton09 building_in_leap]$ gdb $AMBERHOME/bin/teLeap core.5135
> GNU gdb (GDB) Fedora (7.0.1-44.fc12)
> Copyright (C) 2009 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html
> >
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /opt/amber10/bin/teLeap...(no debugging symbols
> found)...done.
> Missing separate debuginfo for
> Try: yum --disablerepo='*' --enablerepo='*-debuginfo' install
> /usr/lib/debug/.build-id/8b/6feabeeae377da1938171057f8180e62ad90f0
> Reading symbols from /lib64/libm.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libm.so.6
> Reading symbols from /lib64/libc.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libc.so.6
> Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/ld-linux-x86-64.so.2
> Core was generated by `/opt/amber10/bin/teLeap -I/opt/amber10/dat/leap/prep
> -I/opt/amber10/dat/leap/li'.
> Program terminated with signal 11, Segmentation fault.
> *#0 0x000000000043e4c9 in zUnitIOBuildFromTables ()*
> Missing separate debuginfos, use: debuginfo-install glibc-2.11.1-4.x86_64
>
>
> I'm guessing the penultimate line is important but I have no idea what it
> means.
>
> Prof. Case, I'm using Fedora Core 12 x86_64, csh shell, gcc/gfortran
> version
> 4.4.3 20100127 (Red Hat 4.4.3-4). The system is running on an Intel Core
> i5-750 with 8 GB of RAM. I compiled AmberTools simply with "./configure
> gnu"
> and the config.h file is pasted here: http://pastebin.com/CkHr0V2X. The
> segfault occurred when I tested it with AmberTools 1.0, 1.3, and 1.4.
>
> Any suggestions?
>
> On 11 May 2010 17:57, case <case.biomaps.rutgers.edu> wrote:
>
> > On Tue, May 11, 2010, Omair A. Khan wrote:
> > >
> > > I ran gdb on teLeap, tried loading the all_nucleic94 library and
> received
> > > the following output. I have no idea how to decode it...
> > >
> > > > loadOff /opt/amber10/dat/leap/lib/all_nucleic94.lib
> > > Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
> > >
> > > Program received signal SIGSEGV, Segmentation fault.
> > > 0x000000000041ba9b in bAtomCoordinationSaturated ()
> > > Missing separate debuginfos, use: debuginfo-install
> glibc-2.11.1-4.x86_64
> > > (gdb) where
> > > #0 0x000000000041ba9b in bAtomCoordinationSaturated ()
> > > #1 0x000000000041bbe8 in bBondAtomProblem ()
> > > #2 0x000000000041c564 in AtomBondToFlags ()
> > > #3 0x000000000043e4f1 in zUnitIOBuildFromTables ()
> > > #4 0x0000000000431d70 in uUnitLoad ()
> > > #5 0x000000000045a918 in oLibraryLoad ()
> > > #6 0x0000000000474677 in oCmd_loadOff ()
> > > #7 0x000000000046d013 in yyparse ()
> > > #8 0x000000000046ec8a in ParseBlock ()
> > > #9 0x00000000004843ef in main ()
> >
> > This is moderately useful, but if you don't know how to proceed, we need
> to
> > figure out how to reproduce the problem, so that someone with the proper
> > experience can follow up.
> >
> > Can you (re-)post exactly what OS and compilers you are using? Please
> > include the arguments you gave to the configure script, and any other
> > details
> > you can about your system.
> >
> > Also, have you tried either AmberTools 1.3 or 1.4? It would be good to
> > know
> > if this is something unique to an older release.
> >
> > ...thx...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.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
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Received on Wed May 12 2010 - 15:30:04 PDT
