[gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

[Mark Abraham]

On Mon, Jul 28, 2014 at 6:05 PM, qiaobf <qiaobf at gmail.com> wrote:

> Dear Mark,
>
> 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'
>>
>
Yes, you can add linker flags using the normal CMake mechanisms. Google's
your friend here, but probably cmake -DCMAKE_EXE_LINKER_FLAGS=-lm might
help.


>  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?
>

Things change. ;-) If you're deliberately bypassing the new wrapper binary,
then you won't get the functionality it supports, like the new help module
output.

Mark


> I am looking forward to your kind help, and appreciate your time!
>
> best regards,
> Baofu
>
>
> 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[2]: *** [CMakeFiles/gmx_density2.dir/gmx_density2.c.o] Error 1
>>> make[1]: *** [CMakeFiles/gmx_density2.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>
>> best wishes,
>> Baofu
>>
>
> --
> Baofu Qiao
> Department of Materials Science and Engineering,
> Northwestern University
> Tel: 224-420-1019
> Email: qiaobf at gmail.com
>
>
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