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 - 08:23:55 CDT

Simon Whitehead wrote:
> After a quick look on google i found some info on gdb (is that suitable) and ran it which gave the following information;
>
> Reading symbols from shared object read from target memory...(no debugging symbols found)...done.
> Loaded system supplied DSO at 0x40000000
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0804b90e in respin ()
>
> Is this of any use?
>
> 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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