[ITK] [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib -- Solved (maybe)

Wed Mar 23 13:04:19 EDT 2016

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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> > Any opinions expressed within this e-mail are those of the individual
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> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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> > any damage which you may sustain as a result of software viruses which
> > may be transmitted in or with the message.
> > 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
> >
> >
> >
> >
> >
> >
> > --
> >
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you are not the intended addressee or an authorised
> > recipient of the addressee please notify us of receipt by returning
> > the e-mail and do not use, copy, retain, distribute or disclose the
> > information in or attached to the e-mail.
> > Any opinions expressed within this e-mail are those of the individual
> > and not necessarily of Diamond Light Source Ltd.
> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability for
> > any damage which you may sustain as a result of software viruses which
> > may be transmitted in or with the message.
> > 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
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
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