[gmx-users] Re: help with gmx C source code

[aherz]

You will have to set the right environment variable for CFLAGS to get
debug symbols:


cd gromacs_directory
CFLAGS="-O0 -g3"
./configure

might do the trick.

you can use gdb to check whether there are debug symbols in an executable.

Alex


Inon Sharony schrieb:
>
> reply to:
> http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html
>
>
> "...
> My usual advice is to compile GROMACS with -g, get a graphical
> debugger(Totalview, ddd, insight, whatever) and spend a day stepping
> through ashort mdrun to get some understanding about what is really
> happening.
> You will find it simpler if you've set the environment
> variableGMX_NB_GENERIC=1 so that the nonbonded kernels are more
> transparent.
> ..."
>
>
>
>
> Dear Mark and other GMX users,
>
> I've been trying to compile GMX for debugging, as you suggested, and
> itappears that I'm not doing it correctly. I've added the "-g" flag
> onthe "make" command's "CFLAGS" variable, and the installation seemed
> tohave completed successfully, however when I try to preform some
> simpledebugging (suggested
> byhttp://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide)I
> get error messages.
> I've included the commands I ran for the installation of gromacs
> withdebugging enabled, and the debugging commands I issued and their
> result.
>
>
>
> A. *********************
> fftw-3.2.2 installation:
> ------------------------
>
> ./configure
> make
> make install
>
>
> B. ********************************************
>
> gromacs-4.0.5 installation in double-precission
> -----------------------------------------------
>
> ./configure --disable-float
> make CFLAGS=-g
> make install
>
>
> C. *****************
>
> "cat /tmp/gdb_cmds":
> --------------------
>
> break _gmx_error
> break do_force
> run -v
>
>
> D. ******************************
>
> "gdb -x gdb_cmds /usr/bin/mdrun":
> ---------------------------------
>
> GNU gdb 6.8-debian
> Copyright (C) 2008 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 "i486-linux-gnu"...
> (no debugging symbols found)
> Function "_gmx_error" not defined.
> Make breakpoint pending on future shared library load? (y or [n])
> [answered N; input not
> from terminal]
> Function "do_force" not defined.
> Make breakpoint pending on future shared library load? (y or [n])
> [answered N; input not
> from terminal]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> [Thread debugging using libthread_db enabled]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
>
> --
> Inon   Sharony
> ינון     שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this
> e-mail.
>
> ------------------------------------------------------------------------
>
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