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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