AMBER Archive (2006)

Subject: Re: AMBER: RE: Respgen segemtation fault - debug attempt

From: Mark Williamson (Mark.Williamson_at_imperial.ac.uk)
Date: Thu Apr 20 2006 - 11:56:55 CDT

Simon Whitehead wrote:
> Dear Mark,
>
> Many thanks for you mail, I did not realised that this had to be done. I did what you said and got the following response;
>
> Reading symbols from shared object read from target memory...done.
> Loaded system supplied DSO at 0x40000000
>
> Breakpoint 1, main (argc=7, argv=0x8f3ff4) at respgen.c:271
> 271 if (argc == 2
>

Dear Simon,

Initially, don't start messing with breakpoints, just execute respgen
with the input file / options that causes it to segfault. If the program
crashes, gdb should then generate a backtrace from the point where it
crashed.

 From you email, I assume you've provided respgen with any command line
parameters; remember this has to be done WITHIN gdb using the run command:

[mjw99_at_mjw antechamber]$ gdb ./respgen
GNU gdb Red Hat Linux (6.1post-1.20040607.43.0.1rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you
arewelcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux-gnu"...Using host
libthread_db library "/lib/tls/libthread_db.so.1".

(gdb) run -i tp.ac -o something -f resp1
Starting program: /tmp/src/antechamber/respgen -i tp.ac -o something -f
resp1
Reading symbols from shared object read from target memory...done.
Loaded system supplied DSO at 0xb7f2e000

Program exited normally.

c.f. The following will NOT work:
        
        gdb ./respgen -i tp.ac -o something -f resp1
        

In a previous mail some of the output you pasted indicated that the
segfault was in the respin() function. gdb should now (with debugging
symbols compiled in) be able to provide more info on what went wrong at
that point.

regards,

Mark
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