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            reply to: http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html<br />
            <br />
            <br />
            "...<br />
            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.<br />
            You will find it simpler if you've set the environment variableGMX_NB_GENERIC=1 so that the nonbonded kernels are more transparent.<br />
            ..."<br />
            <br />
            <br />
            <br />
            <br />
            Dear Mark and other GMX users,<br />
            <br />
            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.<br />
            I've included the commands I ran for the installation of gromacs withdebugging enabled, and the debugging commands I issued and their result.<br />
            <br />
            <br />
            <br />
            A. *********************<br />
            fftw-3.2.2 installation:<br />
            ------------------------<br />
            <br />
            ./configure<br />
            make<br />
            make install<br />
            <br />
            <br />
            B. ********************************************<br />
            <br />
            gromacs-4.0.5 installation in double-precission<br />
            -----------------------------------------------<br />
            <br />
            ./configure --disable-float<br />
            make CFLAGS=-g<br />
            make install<br />
            <br />
            <br />
            C. *****************<br />
            <br />
            "cat /tmp/gdb_cmds":<br />
            --------------------<br />
            <br />
            break _gmx_error<br />
            break do_force<br />
            run -v<br />
            <br />
            <br />
            D. ******************************<br />
            <br />
            "gdb -x gdb_cmds /usr/bin/mdrun":<br />
            ---------------------------------<br />
            <br />
            GNU gdb 6.8-debian<br />
            Copyright (C) 2008 Free Software Foundation, Inc.<br />
            License GPLv3+: GNU GPL version 3 or later &lt;http://gnu.org/licenses/gpl.html&gt;<br />
            This is free software: you are free to change and redistribute it.<br />
            There is NO WARRANTY, to the extent permitted by law.&#160; Type "show copying"<br />
            and "show warranty" for details.<br />
            This GDB was configured as "i486-linux-gnu"...<br />
            (no debugging symbols found)<br />
            Function "_gmx_error" not defined.<br />
            Make breakpoint pending on future shared library load? (y or [n]) [answered N; input not<br />
            from terminal]<br />
            Function "do_force" not defined.<br />
            Make breakpoint pending on future shared library load? (y or [n]) [answered N; input not<br />
            from terminal]<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            [Thread debugging using libthread_db enabled]<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)<br />
            (no debugging symbols found)
        </p>
        <p class="imp-signature">
            --<br />
            Inon&#160; &#160;Sharony<br />
            ינון&#160; &#160; &#160;שרוני<br />
            +972(3)6407634<br />
            atto.TAU.ac.IL/~inonshar<br />
            Please consider your environmental responsibility before printing this e-mail.
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