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
>
>
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>
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Received on Wed May 12 2010 - 15:00:05 PDT
