On Tue, May 11, 2010 at 3:55 PM, Omair A. Khan <oak3.psu.edu> wrote:
> That doesn't seem to work. The output is:
>
> "/opt/amber10/bin/tleap": not in executable format: File format not
> recognized
> /opt/amber10/bin/core: No such file or directory.
>
Bill's instructions were generic, since he has no way of knowing details of
what happened on your machine. His instructions regarding tleap are correct
-- it is a script and you have to look at the executable it's actually
calling (for me, its:
#!/bin/sh
if [ "$AMBERHOME" ]; then
$AMBERHOME/bin/teLeap \
-I$AMBERHOME/dat/leap/prep \
-I$AMBERHOME/dat/leap/lib \
-I$AMBERHOME/dat/leap/parm \
-I$AMBERHOME/dat/leap/cmd \
$*
else
echo "Error: you must set the AMBERHOME environment variable!"
exit 1
fi
) so teLeap is the actual executable file. Also the core file is not simply
named core. Whenever the core is dumped following a segfault, it names it
"core.something", where the something varies from instance to instance. You
need to use this core-dump file, not "core".
You need to type "gdb $AMBERHOME/bin/teLeap core.########" where the
.####### corresponds to your particular core file name (we have no way of
knowing what that is). Do not type core.######## literally.
Good luck!
Jason
> I verified that tleap is executable by all users. Am I typing it in wrong?
>
> Omair
>
> On 11 May 2010 13:39, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > *tleap: line 17: 26980 Segmentation fault (core dumped)
> >
> > Whenever you see 'core dumped' you can try debug by finding the
> > tleap binary and 'gdb <binary> core' followed by 'where' to the
> > gdb prompt, which will show the place where the error occurred.
> >
> > Bill
> >
> > _______________________________________________
> > 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 Tue May 11 2010 - 14:30:04 PDT
