[CCPPETMR/SIRF-SuperBuild] SIRF-SuperBuild Ubuntu 17.04 installation failed (#27)
Evan27
Hi all,
I tried to install the SIRF-SuperBuild on my Linux (Ubuntu 17.04) box following the instractions from the web page: https://github.com/CCPPETMR/SIRF/wiki/SIRF-SuperBuild-Ubuntu-16.04
I had to install some packages before but when I run the steps:
cmake .
make
in section 3 I get en error message when the configuration of gadgetron is performed without any obvious reason.
This is what I get:
[ 90%] Completed 'Armadillo'
[ 90%] Built target Armadillo
Scanning dependencies of target Gadgetron
[ 92%] Creating directories for 'Gadgetron'
[ 93%] Performing download step (git clone) for 'Gadgetron'
Cloning into 'Gadgetron'...
Already on 'master'
Your branch is up-to-date with 'origin/master'.
[ 94%] No patch step for 'Gadgetron'
[ 95%] Performing update step for 'Gadgetron'
Current branch master is up to date.
[ 96%] Performing configure step for 'Gadgetron'
-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for packages in : /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/
-- Found Git: /usr/bin/git (found version "2.11.0")
64bit system is found
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
OpenMP multithreading enabled
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- system
-- thread
-- program_options
-- filesystem
-- timer
-- chrono
-- date_time
-- atomic
-- Found ACE library: /usr/lib/libACE.so
-- Found ACE include: /usr/include
-- Found CUDA: /usr (found suitable version "8.0", minimum required is "5.5")
Compiling with -gencode arch=compute_30,code=sm_30;-gencode arch=compute_35,code=sm_35;-gencode arch=compute_50,code=sm_50;-gencode arch=compute_52,code=sm_52
-- Found GTest: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libgtest.a
-- Found Armadillo: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libarmadillo.so (found suitable version "7.800.2", minimum required is "4.600")
Armadillo found. Note that ARMADILLO_BLAS_LONG_LONG must be defined in /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/include/armadillo_bits/config.hpp to link against the MKL ILP64 interface.
-- Found HDF5: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5-shared.so (found suitable version "1.10.0.1", minimum required is "1.8") found components: C CXX HL
FFTW3 UNIX libraries: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3.a
-- Found FFTW3: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a
MKL is NOT found ...
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
LAPACK Found
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found suitable version "2.7.13", minimum required is "2")
-- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.13")
-- Found NumPy: version "1.12.1" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Could NOT find Matlab (missing: MATLAB_ROOT MATLAB_INCLUDE_DIR MATLAB_LIBRARIES)
Searching for OpenGL, GLEW, GLUT, and Qt. These libraries are only used in a single standalone application and are thus non-essential.
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
GLEW NOT FOUND
-- Could NOT find GLUT (missing: GLUT_glut_LIBRARY GLUT_INCLUDE_DIR)
qmake: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/qmake': No such file or directory
-- Found unsuitable Qt version "" from NOTFOUND
PLplot is found at /usr/include/plplot
-- Found HDF5: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5-shared.so (found version "1.10.0.1") found components: HL
Compiling cpu based optical flow registration toolbox.
Compiling gpu based optical flow registration toolbox.
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- date_time
-- filesystem
-- system
-- thread
-- regex
-- chrono
-- atomic
-- Found ACE library: /usr/lib/libACE.so
-- Found ACE include: /usr/include
-- Boost version: 1.63.0
-- A library with BLAS API found.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- python
-- system
-- thread
-- chrono
-- date_time
-- atomic
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.13")
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- python
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- thread
-- system
-- chrono
-- date_time
-- atomic
-- Found HDF5: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5-shared.so (found suitable version "1.10.0.1", minimum required is "1.8") found components: C
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- program_options
-- thread
-- system
-- chrono
-- date_time
-- atomic
Matlab not found. Matlab wrapper for registration toolbox will not be compiled.
MATLAB NOT FOUND: matlab wrapper for gtplus toolbox will not be compiled.
-- Found HDF5: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5-shared.so (found version "1.10.0.1") found components: HL
-- Found ACE library: /usr/lib/libACE.so
-- Found ACE include: /usr/include
FFTW3 UNIX libraries: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3.a/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3.a
ZFP NOT Found
-- Found HDF5: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5-shared.so (found suitable version "1.10.0.1", minimum required is "1.8") found components: C
Cuda found, compiling gpu accelerated gadgets
-- Boost version: 1.63.0
-- Found the following Boost libraries:
-- python
-- system
-- thread
-- chrono
-- date_time
-- atomic
PYTHON_INCLUDE_DIRS: /usr/include/python2.7
PYTHON_LIBRARIES: /usr/lib/x86_64-linux-gnu/libpython2.7.so
NUMPY_INCLUDE_DIRS: /usr/lib/python2.7/dist-packages/numpy/core/include
Compiling Python Gadgets
-- /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/include/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_python.so/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_system.so/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_thread.so/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_chrono.so/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_date_time.so/home/evan/Documents/devel/SIRF-SuperBuild/INSTALL/lib/libboost_atomic.so
-- Could NOT find DCMTK (missing: DCMTK_config_INCLUDE_DIR DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_oflog_INCLUDE_DIR DCMTK_oflog_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY)
DCMTK NOT found, not compiling DICOM gadget
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.13")
CMake Error at chroot/CMakeLists.txt:41 (get_filename_component):
get_filename_component unknown component
/usr/lib/x86_64-linux-gnu/libcublas_device.a
CPACK_PACKAGING_INSTALL_PREFIX: /home/evan/Documents/devel/SIRF-SuperBuild/INSTALL
-- Found CPack generators: DEB
-- Configuring incomplete, errors occurred!
See also "/home/evan/Documents/devel/SIRF-SuperBuild/Gadgetron-prefix/src/Gadgetron-build/CMakeFiles/CMakeOutput.log".
CMakeFiles/Gadgetron.dir/build.make:111: recipe for target 'Gadgetron-prefix/src/Gadgetron-stamp/Gadgetron-configure' failed
make[2]: *** [Gadgetron-prefix/src/Gadgetron-stamp/Gadgetron-configure] Error 1
CMakeFiles/Makefile2:338: recipe for target 'CMakeFiles/Gadgetron.dir/all' failed
make[1]: *** [CMakeFiles/Gadgetron.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
Any suggestions ?
Regards
Evan
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Kris Thielemans
This is an upstream problem. New issue created. gadgetron/gadgetron#524
Kris Thielemans
I've attempted to fix this. Can you please try to build with
cmake -DGadgetron_TAG=chroot_fixes
(in addition to any other settings you need).
Kris Thielemans
Closed #27.
Kris Thielemans
fixed with updates accepted by Gadgetron