AMBER Archive (2006)

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

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Thu Apr 20 2006 - 11:30:51 CDT

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

I then typed "x 0x8f3ff4" and got;

0x8f3ff4: 0x008f3d3c

If i type "break main" i get the following response;

Note: breakpoint 1 also set at pc 0x804b9cc.
Breakpoint 2 at 0x804b9cc: file respgen.c, line 271.

"x 0x804b9cc" then gave;

0x804b9cc <main+12>: 0x02087d83

This does not mean anything to me does anyone else have an ideas?

Kind Regards

Simon

----------------------------------------------------------------------------------------------------
You've not compiled the respgen binary with debugging symbols. To do
this, go to

$AMBERHOME/src/antechamber

do a
        make clean

then do a
        make -e AMBERBUILDFLAGS="-DDEBUG -g"

At the end of this process, the compiled respgen will be moved to
../../exe by the makefile, but gdb makes use of the sources in the same
dir, hence copy respgen back to the build dir:

        cp ../../exe/respgen .

Now run "gdb ./respgen" and when in gdb, passing commandline options using:

        run -i tp.ac -o something -f resp1

I also recommend a read of:
        http://users.actcom.co.il/~choo/lupg/tutorials/debugging/debugging-with-gdb.html

regards,

Mark
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