Re: [otb-users] Re: undefined reference to fftwf*

Thu, 13 Mar 2014 05:40:56 -0700

Good news is that I was right about FFTWF, since you do not have the issue with fftwf symbols anymore. 

This next issue seems related to openMP support.
Could you please run "cmake ." in your build dir and post the output of the configure step ? You can also do "ctest -D Experimental" as Mickaël suggested.
Last, openmp is only used in the siftfast third party. You can try to set OTB_USE_SIFTFAST configuration option to False if you do not need this function. 

Regards,

Julien

Le 13/03/2014 13:29, [email protected] a écrit :


Hi,
I tried with ITK_USE_FFTWF=OFF

and I got this:
[ 75%] Building CXX object Testing/Code/FeatureExtraction/CMakeFiles/otbFeatureExtractionTests10.dir/otbImageToFastSIFTKeyPointSetFilterOutputInterestPointAscii.cxx.o 
Linking CXX executable ../../../bin/otbFeatureExtractionTests10
../../../bin/libsiftfast.a(libsiftfast.o): In function `GradOriImages':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:970: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:970: undefined reference to `GOMP_parallel_end' 
../../../bin/libsiftfast.a(libsiftfast.o): In function `SubtractImage':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:449: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:449: undefined reference to `GOMP_parallel_end' ../../../bin/libsiftfast.a(libsiftfast.o): In function `GradOriImagesFast': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1006: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1006: undefined reference to `GOMP_parallel_end' 
../../../bin/libsiftfast.a(libsiftfast.o): In function `MakeKeypoint':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1424: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1431: undefined reference to `GOMP_critical_end' 
../../../bin/libsiftfast.a(libsiftfast.o): In function `InterpKeyPoint':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1201: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1205: undefined reference to `GOMP_critical_end' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1205: undefined reference to `GOMP_critical_end' 
../../../bin/libsiftfast.a(libsiftfast.o): In function `FindMaxMin':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:902: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:902: undefined reference to `GOMP_parallel_end' 
../../../bin/libsiftfast.a(libsiftfast.o): In function `ConvVerticalFast':
/home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:778: undefined reference to `omp_get_max_threads' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:753: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:753: undefined reference to `GOMP_parallel_end' ../../../bin/libsiftfast.a(libsiftfast.o): In function `ConvHorizontalFast': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:634: undefined reference to `omp_get_max_threads' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:601: undefined reference to `GOMP_parallel_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:601: undefined reference to `GOMP_parallel_end' ../../../bin/libsiftfast.a(libsiftfast.o): In function `ConvHorizontalFast.omp_fn.4': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:601: undefined reference to `GOMP_loop_dynamic_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:650: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:659: undefined reference to `GOMP_critical_end' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:745: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:747: undefined reference to `GOMP_critical_end' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:601: undefined reference to `GOMP_loop_dynamic_next' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:601: undefined reference to `GOMP_loop_end_nowait' ../../../bin/libsiftfast.a(libsiftfast.o): In function `ConvVerticalFast.omp_fn.3': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:753: undefined reference to `omp_get_num_threads' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:753: undefined reference to `omp_get_thread_num' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:800: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:807: undefined reference to `GOMP_critical_end' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:892: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:894: undefined reference to `GOMP_critical_end' ../../../bin/libsiftfast.a(libsiftfast.o): In function `FindMaxMin.omp_fn.2': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:902: undefined reference to `GOMP_loop_dynamic_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:958: undefined reference to `GOMP_critical_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:961: undefined reference to `GOMP_critical_end' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:902: undefined reference to `GOMP_loop_dynamic_next' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:902: undefined reference to `GOMP_loop_end_nowait' ../../../bin/libsiftfast.a(libsiftfast.o): In function `GradOriImagesFast.omp_fn.0': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1006: undefined reference to `GOMP_loop_dynamic_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1006: undefined reference to `GOMP_loop_dynamic_next' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:1006: undefined reference to `GOMP_loop_end_nowait' ../../../bin/libsiftfast.a(libsiftfast.o): In function `SubtractImage.omp_fn.5': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:449: undefined reference to `GOMP_loop_dynamic_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:449: undefined reference to `GOMP_loop_dynamic_next' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:449: undefined reference to `GOMP_loop_end_nowait' ../../../bin/libsiftfast.a(libsiftfast.o): In function `GradOriImages.omp_fn.1': /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:970: undefined reference to `GOMP_loop_dynamic_start' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:970: undefined reference to `GOMP_loop_dynamic_next' /home/lwasquel/OTB/OTB_code_source/OTB/Utilities/otbsiftfast/libsiftfast.cpp:970: undefined reference to `GOMP_loop_end_nowait' 
collect2: ld returned 1 exit status
make[2]: *** [bin/otbFeatureExtractionTests10] Error 1
make[1]: *** [Testing/Code/FeatureExtraction/CMakeFiles/otbFeatureExtractionTests10.dir/all] Error 2 
make: *** [all] Error 2



Regards,
Loïc
Le mercredi 12 mars 2014 14:30:39 UTC+1, [email protected] a écrit : 

    Hello everyone,

    I got an undefined reference while building OTB when
    BUILD_TESTING=ON in CMake.
    The error *does not* appear when BUILD_TESTING is OFF.

    I am on Centos 5.4, i have installed my own FFTW library, I work
    with the latest bleeding-edge version of the OTB source code.

    First, I built FFTW without options and configured CMake with:

    FFTWD_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTWD_THREADS_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTWF_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTWF_THREADS_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTW_INCLUDE_PATH /home/lwasquel/fftw-3.3.3/api

    Next, I built FFTW with --enable-threads option and configured
    CMake with :
    FFTWD_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTWD_THREADS_LIB
    /home/lwasquel/fftw-3.3.3/threads/.libs/libfftw3_threads.a
    FFTWF_LIB /home/lwasquel/fftw-3.3.3/.libs/libfftw3.a
    FFTWF_THREADS_LIB
    /home/lwasquel/fftw-3.3.3/threads/.libs/libfftw3_threads.a
    FFTW_INCLUDE_PATH /home/lwasquel/fftw-3.3.3/api

    But it changes nothing, i got the next error during the make
    command of OTB:

    [ 69%] Built target otbBasicFiltersTests1
    Linking CXX executable ../../../bin/otbBasicFiltersTests10
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function
    `itk::FFTWGlobalConfiguration::ImportWisdomFileFloat(std::basic_string<char,
    std::char_traits<char>, std::allocator<char> > const&)':
    itkFFTWGlobalConfiguration.cxx:(.text+0x157): undefined reference
    to `fftwf_import_wisdom_from_file'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function `itk::FFTWGlobalConfiguration::FFTWGlobalConfiguration()':
    itkFFTWGlobalConfiguration.cxx:(.text+0x8fb): undefined reference
    to `fftwf_init_threads'
    itkFFTWGlobalConfiguration.cxx:(.text+0xacb): undefined reference
    to `fftwf_import_system_wisdom'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function `itk::FFTWGlobalConfiguration::FFTWGlobalConfiguration()':
    itkFFTWGlobalConfiguration.cxx:(.text+0x1cfb): undefined reference
    to `fftwf_init_threads'
    itkFFTWGlobalConfiguration.cxx:(.text+0x1ecb): undefined reference
    to `fftwf_import_system_wisdom'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function
    `itk::FFTWGlobalConfiguration::ExportWisdomFileFloat(std::basic_string<char,
    std::char_traits<char>, std::allocator<char> > const&)':
    itkFFTWGlobalConfiguration.cxx:(.text+0x3080): undefined reference
    to `fftwf_export_wisdom_to_file'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function `itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration()':
    itkFFTWGlobalConfiguration.cxx:(.text+0x36f8): undefined reference
    to `fftwf_cleanup_threads'
    itkFFTWGlobalConfiguration.cxx:(.text+0x36fd): undefined reference
    to `fftwf_cleanup'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function `itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration()':
    itkFFTWGlobalConfiguration.cxx:(.text+0x3b18): undefined reference
    to `fftwf_cleanup_threads'
    itkFFTWGlobalConfiguration.cxx:(.text+0x3b1d): undefined reference
    to `fftwf_cleanup'
    ../../../bin/libITKFFT-4.5.a(itkFFTWGlobalConfiguration.cxx.o): In
    function `itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration()':
    itkFFTWGlobalConfiguration.cxx:(.text+0x3f28): undefined reference
    to `fftwf_cleanup_threads'
    itkFFTWGlobalConfiguration.cxx:(.text+0x3f2d): undefined reference
    to `fftwf_cleanup'
    collect2: ld returned 1 exit status
    make[2]: *** [bin/otbBasicFiltersTests10] Error 1
    make[1]: ***
    [Testing/Code/BasicFilters/CMakeFiles/otbBasicFiltersTests10.dir/all]
    Error 2
    make: *** [all] Error 2

    Could you help me please?
    Thank you,

    Regards,
    Loïc Wasquel
    Capgemini

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Julien MICHEL
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18, avenue Edouard Belin
31401 Toulouse Cedex 09 - France
Tel: +33 561 282 894 - Fax: +33 561 283 109

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