[ITK-users] stand-alone lib -- ITKApps/ITKFilterLib -- Solved (maybe)
Matt McCormick
matt.mccormick at kitware.com
Wed Mar 23 13:21:07 EDT 2016
Hi Robert,
If CMake is new enough, just set CMAKE_POSITION_INDEPENDENT_CODE to
ON. This automatically add -fPIC to the build flags.
Otherwise, add -fPIC to the build flags. Those libraries were still
causing issues likely because they contain both C and C++ code; add
the flag to both CMAKE_C_FLAGS and CMAKE_CXX_FLAGS if
CMAKE_POSITION_INDEPENDENT_CODE is not used.
HTH,
Matt
On Wed, Mar 23, 2016 at 1:04 PM, <Robert.Atwood at diamond.ac.uk> wrote:
> Hi, Matt
> I did that but it didn't work. Exactly the same error. See a little further back in the thread:
>
> That's where I lost patience with 'combinatorial trial and error approach' , I added -fPIC everywhere I could think of
> The position-independent-code seems to be generated for all libs except a small selction of i/o libs ; gdcm* ,Nrrd , and a couple of others (trial-and-error)
>
> If I don't include these in the final link, then the link is successful. All other libraries appear to have PIC generated.
>
> But, the final library isn't usable. I wonder what these ones have in common?? Is there a 'glitch' in the makefile generation that omits -fPIC in these cases somehow?
>
>
> libitkgdcmjpeg8-4.10.a
> libitkgdcmjpeg12-4.10.a
> libitkgdcmjpeg16-4.10.a
> libitkgdcmopenjpeg-4.10.a
> libitkgdcmuuid-4.10.a
> libITKEXPAT-4.10.a
> libITKniftiio-4.10.a
> libITKNrrdIO-4.10.a
> libitkhdf5-4.10.a
> libitksys-4.10.a
>
> (using system jpeg, tiff, zlib and png)
>
> Ironically , it's only .mhd I actually want to use and it is not on the problem list. But the io-objects need all these to be available just in case they get used, I suppose.
>
>
>
>
>> > I have tried some combinations of these options but, you know, it
>> > takes a while to rebuild ITK even though the computer is pretty good.
>> > BUILD_POSITION_DEPENDENT_CODE OFF (I don’t think this should be ON
>> > because that really wouldn’t work? )
>> > BUILD_SHARED_LIBS OFF (or ON)
>> > CMAKE_CXX_FLAGS -fPIC (or default)
>> > CMAKE_EXE_LINKER_FLAGS -fPIC (or default)
>> > CMAKE_STATIC_LINKER_FLAGS (should this be set too? )
>
> Regards, Robert
>
>
>
>
>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: 23 March 2016 16:29
>> To: Atwood, Robert (DLSLtd,RAL,SCI)
>> Cc: Dženan Zukić; insight-users at itk.org
>> Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib -- Solved
>> (maybe)
>>
>> Hi Robert,
>>
>> > /usr/bin/ld:
>> > /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c
>> > .o): relocation R_X86_64_32S against `.text' can not be used when
>> > making a shared object; recompile with -fPIC
>>
>> This means that "-fPIC" should be added to the CMAKE_CXX_FLAGS for ITK.
>>
>> HTH,
>> Matt
>>
>> On Wed, Mar 23, 2016 at 11:58 AM, <Robert.Atwood at diamond.ac.uk>
>> wrote:
>> > Hi, Dženan, and List :
>> >
>> >
>> >
>> > Thanks for the tips, but, building the executable by pointing to the
>> > itk-build folder for linking is exactly what I did not want to do. I
>> > want the compiled instances of the specific templated objects to be
>> > put into a stand-alone library that could then be linked , in an
>> > environment where the ITK build directory may not be available, and
>> > within a project that’s not using cmake (yet? J ) just for a small
>> > single-data-type-specific filter chain that would be a bit nontrivial to just re-
>> implement myself!
>> >
>> >
>> >
>> > I had some success with the following, for the example ITKFilterLib:
>> >
>> >
>> >
>> > Using the itk-master-git-static as built before, (BUILD_SHARED_LIBS
>> > OFF)
>> >
>> >
>> >
>> >
>> >
>> > In CMakeLists.txt for the project, add SHARED keyword to the library
>> > defninition:
>> >
>> >
>> >
>> > 15 ADD_LIBRARY(Example_ITKFilterLib SHARED ITKFilterLib.cxx )
>> >
>> > Then use cmake + make to build the libExample_ITKFilterLib.so library.
>> >
>> >
>> >
>> >
>> >
>> > Then I can invoke g++ as follows
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > build]$ g++ ../ITKFilterLib/ITKFilterLibTest.cxx -o testcomp -L . -l
>> > Example_ITKFilterLib -I ../ITKFilterLib/
>> >
>> >
>> >
>> > Even if the itk-master-static is not available in that environment,
>> > this succeeds, and I believe this is what I want. I don’t want to have
>> > a statically linked final executable, but rather a .so library.
>> >
>> >
>> >
>> >
>> >
>> > However …
>> >
>> >
>> >
>> > I encountered another hitch trying to apply this to my actual project.
>> > If there were any FileWriter and FileReader present in the library, it
>> > would not build, complaining about position-dependent symbols in
>> > several IO libraries , most of which I was not actually wanting to use
>> > at all. This happened at the step of trying to build the .so library
>> > using the makefile created by cmake:
>> >
>> >
>> >
>> > /usr/bin/ld:
>> > /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c.o):
>> > relocation R_X86_64_32S against `.text' can not be used when making a
>> > shared object; recompile with -fPIC
>> >
>> > /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a: could
>> > not read symbols: Bad value
>> >
>> >
>> >
>> >
>> >
>> > Removing any reference to FileReader and FileWriter gets rid of this
>> > problem.
>> >
>> >
>> >
>> > Thanks!
>> >
>> >
>> >
>> >
>> >
>> > As a further note:
>> >
>> >
>> >
>> > There are also some directions in the comments of the ITKFilterLib
>> > example that did not turn out to be necessary in my project. I did not
>> > have to create global objects for poitners or image containiers
>> > outside the scope of the class and still did not have to #include itkImage.h in
>> the main program.
>> > I placed the typedef’s inside the class and the instantiations of the
>> > smart poitners in the class constructor. I don’t see that this extra
>> > complication in the example is necessary unless it is platform dependent?
>> >
>> >
>> >
>> > ITKFilterLib.cxx from ItkApps example:
>> >
>> >
>> >
>> >
>> >
>> > 23 #include "ITKFilterLib.h"
>> >
>> > 24
>> >
>> > 25 // Nasty local globals inside .cxx file to hide itk from the real world.
>> >
>> > 26 // Can't put this variable in the class definition otherwise we'd have
>> > to
>> >
>> > 27 // include itkImage.h in every program using this class.
>> >
>> > 28 // The typedef h_itkFilterLibeDataType is in itkFilterLib.h to hide
>> >
>> > 29 // templates
>> >
>> > 30 typedef itk::Image<g_ItkFilterLibDataType,3> g_ImageType;
>> >
>> > 31 g_ImageType::Pointer g_InputImage;
>> >
>> > 32 g_ImageType::Pointer g_OutputImage;
>> >
>> >
>> >
>> > I did not find this to be necessary in my project.
>> >
>> >
>> >
>> >
>> >
>> > 33
>> >
>> > 34
>> >
>> > 35 //
>> >
>> > 36 //
>> >
>> > 37 // The first filter in the .lib
>> >
>> > 38 //
>> >
>> > 39 //
>> >
>> > 40
>> >
>> > 41 /** The next lines are used to include the definition of the filter
>> >
>> > 42 * we want to install in the .lib, define a typedef for it, and create
>> >
>> > 43 * a "smart" pointer to hold it.
>> >
>> > 44 * CHANGE HERE: The filter to be instantiated.
>> >
>> > 45 **/
>> >
>> > 46 #include "itkCurvatureAnisotropicDiffusionImageFilter.h"
>> >
>> > 47 typedef itk::CurvatureAnisotropicDiffusionImageFilter<g_ImageType,
>> >
>> > 48 g_ImageType> g_AnisoFilterType;
>> >
>> > 49 g_AnisoFilterType::Pointer g_anisoFilter;
>> >
>> > 50
>> >
>> >
>> >
>> > I also did not find it to be necessary to have this sort of typedef
>> > and instantiation of the object at global scope in my project.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > From: Dženan Zukić [mailto:dzenanz at gmail.com]
>> > Sent: 23 March 2016 14:39
>> > To: Atwood, Robert (DLSLtd,RAL,SCI)
>> > Cc: Insight-users
>> > Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
>> >
>> >
>> >
>> > Hi Robert,
>> >
>> >
>> >
>> > BUILD_SHARED_LIBS OFF is the crucial setting. You can keep the rest of
>> > options on defaults.
>> >
>> >
>> >
>> > Your CMake code looks OK. You should execute the following from your
>> folder:
>> >
>> > cmake .
>> >
>> > make
>> >
>> >
>> >
>> > During CMake step you should configure options (point to the itk-build
>> > folder which was configured with BUILD_SHARED_LIBS OFF). Afterwards,
>> > do not invoke g++ directly - invoke make, which supplies correct
>> > include directories and link libraries so you don't run into a thousand errors.
>> >
>> >
>> >
>> > Regards,
>> >
>> > Dženan
>> >
>> >
>> >
>> > On Tue, Mar 22, 2016 at 6:25 AM, <Robert.Atwood at diamond.ac.uk>
>> wrote:
>> >
>> > Hi,
>> > Thanks, Dženan, for the hint. But, does anyone have specific
>> > information on exactly which options to set in each of: the ITK cmake
>> > options; and the project cmake options, or the plain g++ for building
>> > an external program to link to the library, for this to work ? There
>> > appear to be a few that might be related to this. Because, so far,
>> > simply changing the build options of the ITK installation didn’t work. See
>> below for even more details .
>> >
>> > Thanks
>> >
>> > Robert
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > Options selected in the project:
>> >
>> > ITK_DIR
>> > /dls_sw/apps/itk/itk-master-static/lib/cmake/ITK-4.10
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > In the ITK with installation to itk-master-static:
>> >
>> > I have tried some combinations of these options but, you know, it
>> > takes a while to rebuild ITK even though the computer is pretty good.
>> >
>> >
>> >
>> > BUILD_POSITION_DEPENDENT_CODE OFF (I don’t think this should be ON
>> > because that really wouldn’t work? )
>> >
>> > BUILD_SHARED_LIBS OFF (or ON)
>> >
>> > CMAKE_CXX_FLAGS -fPIC (or default)
>> >
>> > CMAKE_EXE_LINKER_FLAGS -fPIC (or default)
>> >
>> > CMAKE_STATIC_LINKER_FLAGS (should this be set too? )
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > The CMakeLists in the project file – only small modification from the
>> > original to ‘BUILD_OUTSIDE_INSIGHT_APPICATIONS’. The project builds
>> > using the Cmake makefile, producing the library and the executable
>> >
>> > But trying to build either the ‘main’ procedure provided with linking
>> > to that library, or even simplifying the ‘main’ to do virtually
>> > nothing except instantiate the object, results in 1000 error messages
>> > of ‘undefined symbols’
>> >
>> >
>> >
>> > 1 PROJECT(Example_ITKFilterLib)
>> >
>> > 2
>> >
>> > 3 #REMOVED 'IF (BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
>> >
>> > 4
>> >
>> > 5 FIND_PACKAGE(ITK)
>> >
>> > 6 IF(ITK_FOUND)
>> >
>> > 7 INCLUDE(${ITK_USE_FILE})
>> >
>> > 8 ELSE(ITK_FOUND)
>> >
>> > 9 MESSAGE(FATAL_ERROR
>> >
>> > 10 "Cannot build ITKApps without ITK. Please set ITK_DIR.")
>> >
>> > 11 ENDIF(ITK_FOUND)
>> >
>> > 12
>> >
>> > 13 #REMOVED 'ENDIF(BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
>> >
>> > 14
>> >
>> > 15 ADD_LIBRARY(Example_ITKFilterLib ITKFilterLib.cxx )
>> >
>> > 16 INSTALL_TARGETS(/lib Example_ITKFilterLib)
>> >
>> > 17 TARGET_LINK_LIBRARIES(Example_ITKFilterLib ${ITK_LIBRARIES})
>> >
>> > 18
>> >
>> > 19 ADD_EXECUTABLE(Example_ITKFilterLibTest ITKFilterLibTest.cxx )
>> >
>> > 20 INSTALL_TARGETS(/bin Example_ITKFilterLibTest)
>> >
>> > 21 TARGET_LINK_LIBRARIES(Example_ITKFilterLibTest
>> > Example_ITKFilterLib)
>> >
>> >
>> >
>> >
>> >
>> > build]$ ls -l
>> >
>> > total 2508
>> >
>> > -rw-rw-r-- 1 kny48981 kny48981 14393 Mar 22 10:02 CMakeCache.txt
>> >
>> > drwxrwxr-x 6 kny48981 kny48981 4096 Mar 22 10:05 CMakeFiles
>> >
>> > -rwxrwxr-x 1 kny48981 kny48981 1417263 Mar 22 10:05
>> > Example_ITKFilterLibTest
>> >
>> > drwxrwxr-x 2 kny48981 kny48981 4096 Mar 22 10:02
>> ITKIOFactoryRegistration
>> >
>> > -rw-rw-r-- 1 kny48981 kny48981 7933 Mar 22 10:02 Makefile
>> >
>> > -rw-rw-r-- 1 kny48981 kny48981 1092874 Mar 22 10:05
>> > libExample_ITKFilterLib.a
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > build]$ g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I
>> > ../ITKFilterLib -L . -l Example_ITKFilterLib >& out &
>> >
>> >
>> >
>> > … generates 1100 messages …
>> >
>> >
>> >
>> >
>> >
>> > 1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
>> > `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
>> > har,
>> > std::char_traits<char>, std::allocat
>> >
>> > 2
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
>> itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
>> > undefined reference to `itk::ExceptionObject:
>> >
>> > …
>> >
>> > 1106
>> > ITKFilterLib.cxx:(.text._ZNK3itk12NeighborhoodIPfLj3ENS_21Neighborhood
>> > AllocatorIS1_EEE9PrintSelfERSoNS_6IndentE[itk::Neighborhood<float*,
>> > 3u, itk::NeighborhoodAllocato
>> >
>> > 1107 collect2: ld returned 1 exit status
>> >
>> >
>> >
>> >
>> >
>> > Minimal example main:
>> >
>> >
>> >
>> > 1 #include "ITKFilterLib.h"
>> >
>> > 2 int main(int, char **) {
>> >
>> > 3 int inputDimSize[3];
>> >
>> > 4 float inputOrigin[3];
>> >
>> > 5 float inputSpacing[3];
>> >
>> > 6 inputDimSize[0] = 5;
>> >
>> > 7 inputDimSize[1] = 5;
>> >
>> > 8 inputDimSize[2] = 5;
>> >
>> > 9 inputOrigin[0] = 0;
>> >
>> > 10 inputOrigin[1] = 0;
>> >
>> > 11 inputOrigin[2] = 0;
>> >
>> > 12 inputSpacing[0] = 1;
>> >
>> > 13 inputSpacing[1] = 1;
>> >
>> > 14 inputSpacing[2] = 1;
>> >
>> > 15
>> >
>> > 16 itkFilterLib filter(inputDimSize, inputOrigin, inputSpacing);
>> >
>> > 17 return (true);
>> >
>> > 18 }
>> >
>> >
>> >
>> > g++ -o testmin minimal_example.cxx -I ../ITKFilterLib -L . -l
>> > Example_ITKFilterLib >& out
>> >
>> >
>> >
>> >
>> >
>> > Same output AFAICT:
>> >
>> >
>> >
>> >
>> >
>> > 1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
>> > `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
>> > har,
>> > std::char_traits<char>, std::alloca
>> >
>> > 2
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
>> itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
>> > undefined reference to `itk::ExceptionObject:
>> >
>> > ….
>> >
>> >
>> >
>> > From: Dženan Zukić [mailto:dzenanz at gmail.com]
>> > Sent: 21 March 2016 20:21
>> > To: Atwood, Robert (DLSLtd,RAL,SCI)
>> > Cc: Insight-users
>> > Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
>> >
>> >
>> >
>> > Hi Robert,
>> >
>> >
>> >
>> > maybe you need to link to ITK statically? To accomplish this you
>> > probably need to build ITK as static libraries (it is a configuration
>> > option in CMake).
>> >
>> >
>> >
>> > Regards,
>> >
>> > Dženan
>> >
>> >
>> >
>> > On Mon, Mar 21, 2016 at 12:50 PM, <Robert.Atwood at diamond.ac.uk>
>> wrote:
>> >
>> > Hi,
>> > This example, ITKApps/ITKFilterLib, appears to be an example of what I
>> > want to do , bundle or encapsulate a specific ITK-based filter into a
>> > library so that another program may just call it without having to
>> > have the ITK source installation available.
>> > However, a basic test for me is not working.
>> >
>> > I just tried to compile the test example from command line after
>> > building the library with Cmake as usual. I get hundreds of 'undefined
>> > reference', as if I have to link with all the ITK libs anyways.
>> > Am I missing something?
>> > Thanks
>> >
>> >
>> >
>> >
>> > g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I
>> > g++ ../ITKFilterLib/ -L
>> > . -l Example_ITKFilterLib
>> >
>> >
>> > First few lines of output:
>> >
>> > ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
>> > `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
>> > har, std::char_traits<char>, std::allocator<char> > const&, unsigned
>> > int, std::basic_string<char, std::char_traits<char>,
>> > std::allocator<char> > const&, std::basic_string<char,
>> > std::char_traits<char>, std::allocator<char>
>> >> const&)':
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
>> itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
>> > undefined reference to
>> > `itk::ExceptionObject::ExceptionObject(std::basic_string<char,
>> > std::char_traits<char>, std::allocator<char> > const&, unsigned int,
>> > std::basic_string<char, std::char_traits<char>, std::allocator<char> >
>> > const&, std::basic_string<char, std::char_trait
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
>> itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x44):
>> > undefined reference to `vtable for itk::MemoryAllocationError'
>> > ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
>> > `itk::ProcessAborted::ProcessAborted(char const*, unsigned int)':
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
>> ortedC5EPKcj]+0x33):
>> > undefined reference to `itk::ExceptionObject::ExceptionObject(char
>> > const*, unsigned int, char const*, char const*)'
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
>> ortedC5EPKcj]+0x3e):
>> > undefined reference to `vtable for itk::ProcessAborted'
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
>> ortedC5EPKcj]+0x4f):
>> > undefined reference to `itk::ExceptionObject::SetDescription(char const*)'
>> >
>> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
>> ortedC5EPKcj]+0x62):
>> > undefined reference to `itk::ExceptionObject::~ExceptionObject()'
>> >
>> >
>> >
>> > This is on a Linux Red Hat with ITK git master today (March 21 2016)
>> >
>> > cmake --version
>> > cmake version 2.8.12.2
>> >
>> > /proc/version:
>> >
>> > Linux version 2.6.32-573.18.1.el6.x86_64
>> > (mockbuild at x86-010.build.bos.redhat.com) (gcc version 4.4.7 20120313
>> > (Red Hat 4.4.7-16) (GCC) ) #1 SMP Wed Jan 6 11:20:49 EST 2016
>> >
>> >
>> >
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> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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