[gmx-users] how to compile and make a C analyzing code under GROMACS 5.0
qiaobf at gmail.com
Mon Jul 28 18:05:43 CEST 2014
Thanks a lot for your kind help. I have corrected the linkages to the
heading files. However, I got a few more problems:
1) The math library is not recognized when compiling. See below for the
error message. Is there a way to add the flag of "-lm" under cmake? For
instance, "gcc test.c -lm -o test" works where sqrt is also used.
> undefined reference to symbol 'sqrt@@GLIBC_2.2.5'
2) If the line with "sqrt" function is commented out, the g_density2 can
be successfully generated. however, the "./g_density2 -h" is not working
to display the help contents. Could you please give me some suggestions?
I am looking forward to your kind help, and appreciate your time!
On 07/24/2014 04:47 PM, qiaobf wrote:
> Dear all,
> Please help me out. Thanks in advance.
> I had written some analyzing codes, which can be easily compiled under
> Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to
> re-compile them under GMX5.0. But the GMX5.0 seems quite different
> from GMX4.5.5. Anyone can help me? Thanks a lot!
> I have tried the following methods:
> 1) (a) save the gmx_density2.c under
> $HOME/programmes/backup/gromacs-5.0/src/gromacs/gmxana, which is the
> folder to save all the gmx_XXX.c analyzing codes under the
> distribution folder;
> (b) re-install the whole package of GMX5.0 (cmake-->make--->make
> install). I got no error message. All regular analyzing programs are
> correctly installed, but not the gmx_density2!
> 2) (a) run "source $HOME/programmes/GROMACS-5.0/bin/GMXRC";
> (b) save the gmx_density2.c under
> $HOME/programmes/GROMACS-5.0/share/gromacs/template, which is under
> the executable folder;
> (c) modify the content of CMakeList.txt to change "template" to
> "gmx_density2", and "template.cpp" to "gmx_density2.c";
> (d) run "cmake .". No error message, and the Makefile and the
> folder CMakeFiles are created;
> (e) run "make". Then I get the error message
>> gmx_density2.c:42:22: fatal error: sysstuff.h: No such file or directory
>> #include "sysstuff.h"
>> compilation terminated.
>> make: *** [CMakeFiles/gmx_density2.dir/gmx_density2.c.o] Error 1
>> make: *** [CMakeFiles/gmx_density2.dir/all] Error 2
>> make: *** [all] Error 2
> best wishes,
Department of Materials Science and Engineering,
Email: qiaobf at gmail.com
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