[MINC-users] Building minc-toolkit for debugging

[Andrew Wood]

Hi again,

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?

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
>>
>
>