[vtkusers] Migration to VTK6
Arno Klein
binarybottle at gmail.com
Fri Dec 11 02:48:20 EST 2015
Thank you for clarifying this for me!!
When I set the SDK to 10.9:
SET(CMAKE_OSX_SYSROOT "macosx10.9")
I get the error:
clang: warning: no such sysroot directory: 'macosx10.9'
I don't get this error when I set the SDK to 'macosx10.11', but would this
setting place an unreasonable demand on the target architecture?
Cheers,
@rno
On Thu, Dec 10, 2015 at 11:09 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> Ah, so you're building a binary package to share with others. I strongly
> advise against using these:
>
> SET(CMAKE_OSX_DEPLOYMENT_TARGET "")
> SET(CMAKE_OSX_SYSROOT /)
>
> The resulting binary will only work with your own version of OS X or
> later. Your best bet is to name a reasonably old deployment target (e.g.
> 10.7) and SDK (e.g. 10.9).
>
> CMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.7
> CMAKE_OSX_SYSROOT:STRING=macosx10.9
>
> These will provide a binary package that will work on 10.7 or later.
>
> What is the minimum supported OS X that the anaconda VTK supports?
> Ideally, you should use that version as your deployment target.
>
> As for AGL, it might be missing from some SDKs because it is obsolete
> (modern programs should not be using it). However, it is in my 10.9 SDK,
> so it will probably also be in yours.
>
> - David
>
>
> On Thu, Dec 10, 2015 at 11:57 PM, Arno Klein <binarybottle at gmail.com>
> wrote:
>
>> I forgot to mention that the other reason for not explicitly setting the
>> version of OSX in the CMakeLists.txt file is because when I do set it
>> appropriately (as you suggested), compilation inexplicably raises the
>> following error, suggesting that outdated SDKs are required:
>>
>> make[2]: *** No rule to make target
>> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/AGL.framework',
>> needed by `travel_depth/TravelDepthMain'. Stop.
>>
>> Cheers,
>> @rno
>>
>> On Thu, Dec 10, 2015 at 10:46 PM, Arno Klein <binarybottle at gmail.com>
>> wrote:
>>
>>> I built VTK 6 through the Anaconda Python distribution ("conda install
>>> vtk" installed 6.3).
>>>
>>> I placed the three lines you recommended in the top-level CMakeLists.txt
>>> file in my library:
>>> SET(CMAKE_OSX_DEPLOYMENT_TARGET "10.11")
>>> SET(CMAKE_OSX_ARCHITECTURES "x86_64")
>>> SET(CMAKE_OSX_SYSROOT "macosx10.11")
>>>
>>> This enabled the make command to compile farther than I have been able
>>> to get so far. However, it requires someone to explicitly specify which
>>> version of MacOSX, which I was hoping to avoid. Previously, I was using:
>>>
>>> #https://forums.developer.apple.com/thread/17334
>>> SET(CMAKE_OSX_DEPLOYMENT_TARGET "")
>>> SET(CMAKE_OSX_SYSROOT /)
>>>
>>> or:
>>>
>>> # https://cmake.org/Bug/view.php?id=14695
>>> SET(MACOSX_DEPLOYMENT_TARGET
>>> ${DARWIN_MAJOR_SDK_VERSION}.${DARWIN_MINOR_SDK_VERSION})
>>> SET(CMAKE_CXX_FLAGS "--sysroot ${CMAKE_OSX_SYSROOT} ${CMAKE_CXX_FLAGS}")
>>>
>>>
>>>
>>> Cheers,
>>> @rno
>>>
>>> On Thu, Dec 10, 2015 at 10:14 PM, David Gobbi <david.gobbi at gmail.com>
>>> wrote:
>>>
>>>> Actually I might have misunderstood your issue. Did you build VTK 6
>>>> yourself, or did you download a binary package? In either case, the three
>>>> cmake variables that I mentioned above should be set the same in your own
>>>> project as they are in the VTK that you are building against.
>>>>
>>>> On Thu, Dec 10, 2015 at 11:00 PM, David Gobbi <david.gobbi at gmail.com>
>>>> wrote:
>>>>
>>>>> You can try setting the SDK info in the CMakeCache.txt:
>>>>>
>>>>> CMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.11
>>>>> CMAKE_OSX_ARCHITECTURES:STRING=x86_64
>>>>> CMAKE_OSX_SYSROOT:STRING=macosx10.11
>>>>>
>>>>> I recommend deleting your entire build directory, creating a new
>>>>> CMakeCache.txt that has only these three lines, and then re-running cmake.
>>>>>
>>>>> - David
>>>>>
>>>>>
>>>>> On Thu, Dec 10, 2015 at 10:49 PM, Arno Klein <binarybottle at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> 'gcc tmp.cpp' created an 'a.out' file, and I have been able to
>>>>>> compile other things, so I guess my Xcode installation is fine. What do
>>>>>> you recommend I try next?
>>>>>>
>>>>>> Cheers,
>>>>>> @rno
>>>>>>
>>>>>> On Thu, Dec 10, 2015 at 7:52 PM, David Gobbi <david.gobbi at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> The header unistd.h is posix standard and comes with every Xcode
>>>>>>> SDK. Try compiling the following trivial program. If it doesn't compile,
>>>>>>> then there must be something awry with your Xcode installation:
>>>>>>>
>>>>>>> #include <unistd.h>
>>>>>>> int main()
>>>>>>> {
>>>>>>> return 0;
>>>>>>> }
>>>>>>>
>>>>>>> - David
>>>>>>>
>>>>>>> On Thu, Dec 10, 2015 at 7:39 PM, Arno Klein <binarybottle at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Thank you for your help!
>>>>>>>>
>>>>>>>> I am now able to compile with cmake on linux, but get the following
>>>>>>>> error on macosx 10.11, even though there is no "unistd.h" anywhere in my
>>>>>>>> github repo (https://github.com/nipy/mindboggle/issues/69):
>>>>>>>>
>>>>>>>> Scanning dependencies of target FsSurfaceReader
>>>>>>>> [ 3%] Building CXX object
>>>>>>>> CMakeFiles/FsSurfaceReader.dir/FsSurfaceReader.cpp.o
>>>>>>>> In file included from
>>>>>>>> /software/mindboggle/surface_cpp_tools/FsSurfaceReader.cpp:13:
>>>>>>>> In file included from
>>>>>>>> /software/mindboggle/surface_cpp_tools/FsSurfaceReader.h:16:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkPolyData.h:58:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkPointSet.h:30:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkDataSet.h:41:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkDataObject.h:36:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkObject.h:42:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkObjectBase.h:44:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkIndent.h:25:
>>>>>>>> In file included from
>>>>>>>> /usr/local/include/vtk-6.0/vtkSystemIncludes.h:36:
>>>>>>>> In file included from /usr/local/include/vtk-6.0/vtkIOStream.h:33:
>>>>>>>> In file included from
>>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iostream:37:
>>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:23:10:
>>>>>>>> fatal error:
>>>>>>>> 'unistd.h' file not found
>>>>>>>> #include
>>>>>>>> ^
>>>>>>>> 1 error generated.
>>>>>>>> make[2]: *** [CMakeFiles/FsSurfaceReader.dir/FsSurfaceReader.cpp.o]
>>>>>>>> Error 1
>>>>>>>> make[1]: *** [CMakeFiles/FsSurfaceReader.dir/all] Error 2
>>>>>>>> make: *** [all] Error 2
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> @rno
>>>>>>>>
>>>>>>>> On Thu, Dec 3, 2015 at 6:25 AM, David E DeMarle <
>>>>>>>> dave.demarle at kitware.com> wrote:
>>>>>>>>
>>>>>>>>> I agree with Cory on Update() being redundant before the Write().
>>>>>>>>>
>>>>>>>>> > vtkDataObject* dobj = someAlgorithm->GetOutput(1);
>>>>>>>>> > dobj->Update();
>>>>>>>>>
>>>>>>>>> should become:
>>>>>>>>>
>>>>>>>>> someAlgorithm->Update(1); //to make sure there is something valid
>>>>>>>>> vtkDataObject* dobj = someAlgorithm->GetOutput(1); //keep the
>>>>>>>>> output for later use
>>>>>>>>>
>>>>>>>>> Because since vtk6, dobj no longer has any connection to the
>>>>>>>>> algorithm, so updating it (which used to update the algorithm for you) no
>>>>>>>>> longer has any meaning.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> David E DeMarle
>>>>>>>>> Kitware, Inc.
>>>>>>>>> R&D Engineer
>>>>>>>>> 21 Corporate Drive
>>>>>>>>> Clifton Park, NY 12065-8662
>>>>>>>>> Phone: 518-881-4909
>>>>>>>>>
>>>>>>>>> On Thu, Dec 3, 2015 at 9:09 AM, Cory Quammen <
>>>>>>>>> cory.quammen at kitware.com> wrote:
>>>>>>>>>
>>>>>>>>>> Arno,
>>>>>>>>>>
>>>>>>>>>> That pattern should be valid in VTK6. Are you getting compile
>>>>>>>>>> errors?
>>>>>>>>>>
>>>>>>>>>> I believe the Update() and Write() calls to the writer are
>>>>>>>>>> redundant - you should need only one.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Cory
>>>>>>>>>>
>>>>>>>>>> On Wed, Dec 2, 2015 at 5:56 PM, Arno Klein <
>>>>>>>>>> binarybottle at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> I am trying to update my code to migrate to VTK6 according to:
>>>>>>>>>>>
>>>>>>>>>>> http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update
>>>>>>>>>>>
>>>>>>>>>>> According to the examples on that site, I understand that:
>>>>>>>>>>>
>>>>>>>>>>> vtkDataObject* dobj = someAlgorithm->GetOutput(1);
>>>>>>>>>>> dobj->Update();
>>>>>>>>>>>
>>>>>>>>>>> should become:
>>>>>>>>>>>
>>>>>>>>>>> someAlgorithm->Update(1);
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> However, I don’t know how to deal with the following pattern:
>>>>>>>>>>>
>>>>>>>>>>> void PointAreaComputer::WriteIntoFile(char *fileName)
>>>>>>>>>>> {
>>>>>>>>>>> vtkPolyDataWriter* writer=vtkPolyDataWriter::New();
>>>>>>>>>>> writer->SetFileName(fileName);
>>>>>>>>>>> m_mesh->GetPointData()->SetScalars(m_pointsArea);
>>>>>>>>>>> writer->SetInputData(m_mesh);
>>>>>>>>>>> writer->Update();
>>>>>>>>>>> writer->Write();
>>>>>>>>>>> writer->Delete();
>>>>>>>>>>> }
>>>>>>>>>>>
>>>>>>>>>>> What should I do to make this compatible with VTK6?
>>>>>>>>>>>
>>>>>>>>>>> Cheers,
>>>>>>>>>>> @rno
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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