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

[Inon Sharony]

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
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