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<p>
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 <http://gnu.org/licenses/gpl.html><br />
This is free software: you are free to change and redistribute it.<br />
There is NO WARRANTY, to the extent permitted by law.  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   Sharony<br />
ינון     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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