[MINC-users] Building minc-toolkit for debugging

[Vladimir S. FONOV]

Hello,

I prefer to build all the underlying libraries instead of relying on the 
system ones.

On 15-04-15 02:09 PM, Andrew Wood wrote:
> I think I figured out the answer to my own question - the configuration
> settings from the above email belong in CMakeCache.txt in the build
> directory.
>
>
> I did come across another though when I used your configuration options
> though:
>
> [  1%] Built target NETCDF
> make[2]: *** No rule to make target `external/opt/minc/lib/libz.a', needed
> by `libminc/libminc2.so.2.3.00'.  Stop.
> make[1]: *** [libminc/CMakeFiles/minc2.dir/all] Error 2
> make: *** [all] Error 2
>
> I got around this by setting USE_SYSTEM_ZLIB:BOOL=OFF, but is this a
> generic problem that others might come across?
>
>
> On somewhat a different topic, I'm curious about your suggestion to force
> the old amoeba initialization with MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON.
> It's my understanding that the new initialization is an improvement
> (removing a directional bias). Have you found that it actually creates its
> own sort of problems?

Just for compatibility.


>
> Thanks,
> Andrew
>
> On Wed, Apr 15, 2015 at 11:22 AM, Andrew Wood <andrew at biospective.com>
> wrote:
>
>> Hi Vlad,
>>
>> My issue wasn't with the missing netcdf library (I already had a copy
>> lying around that I dropped into where the download was supposed to go) but
>> rather getting executables suitable for use in gdb.
>>
>> I'm less than a CMake novice, so I'm still confused.. I normally specify
>> cmake variables on the command like "-MCMAKE_BUILD_TYPE=Debug" but you're
>> suggesting a lot of options, so I'm trying to drop them in a config file.
>>
>> If I understand CMake correctly, I should drop these settings at the end
>> of the CMakeLists.txt file in the root directory. To satisfy CMake syntax,
>> I copy/pasted from your email then translated everything to SET calls:
>>
>> SET( BUILD_TESTING ON )
>> SET( CMAKE_BUILD_TYPE Debug )
>> etc...
>>
>> Then I did the standard `mkdir build; cd build; cmake ..` and everything
>> happily built (the netcdf download worked this time - thanks!). The
>> executables still aren't suited for gdb though:
>>
>> $ gdb build_debug/mni_autoreg/minctracc/minctracc
>> ...
>> Reading symbols from build_debug/mni_autoreg/minctracc/minctracc...(no
>> debugging symbols found)...done.
>> (gdb)
>>
>> I must have put those settings in the wrong place?
>>
>> Thanks,
>> Andrew
>>
>>
>>
>>
>>
>>
>> On Wed, Apr 15, 2015 at 12:31 AM, Vladimir S. Fonov <
>> vladimir.fonov at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I noticed that URL of netcdf library changed - I updated it in the
>>> repository.
>>> Otherwise it compiles fine with the following settings:
>>>
>>>
>>> BUILD_TESTING:BOOL=ON
>>> CMAKE_BUILD_TYPE:STRING=Debug
>>> CMAKE_INSTALL_PREFIX:PATH=/opt/minc
>>> GLUT_X11_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so
>>> GLUT_Xi_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXi.so
>>> GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXmu.so
>>> MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON
>>> MT_BUILD_C3D:BOOL=ON
>>> MT_BUILD_ITK_TOOLS:BOOL=ON
>>> MT_BUILD_LITE:BOOL=OFF
>>> MT_BUILD_MINC_ANTS:BOOL=ON
>>> MT_BUILD_SHARED_LIBS:BOOL=ON
>>> MT_BUILD_VISUAL_TOOLS:BOOL=ON
>>> MT_USE_OPENMP:BOOL=ON
>>> USE_SYSTEM_FFTW3F:BOOL=OFF
>>> USE_SYSTEM_GLUT:BOOL=OFF
>>> USE_SYSTEM_GSL:BOOL=OFF
>>> USE_SYSTEM_HDF5:BOOL=OFF
>>> USE_SYSTEM_ITK:BOOL=OFF
>>> USE_SYSTEM_NETCDF:BOOL=OFF
>>> USE_SYSTEM_PCRE:BOOL=OFF
>>> USE_SYSTEM_ZLIB:BOOL=OFF
>>>
>>>
>>>
>>>
>>> On 15-04-14 05:36 PM, Andrew Wood wrote:
>>>
>>>> Hi all,
>>>>
>>>> I'm having trouble getting the minc-toolkit built with debugging symbols
>>>> (specifically trying to dive into minctracc).
>>>>
>>>> I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG.
>>>>
>>>> Am I missing something obvious?
>>>>
>>>> Thanks,
>>>> Andrew
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com