Another SuperBuild failure on VM

Evgueni Ovtchinnikov

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May 9, 2017, 10:28:33 AM5/9/17

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SuperBuild failed on VM when building Gadgetron: look for lines in red below.

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 5.2.1

-- The CXX compiler identification is GNU 5.2.1

-- 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 :

-- Found Git: /usr/bin/git (found version "2.5.0")

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

CUDA_TOOLKIT_ROOT_DIR not found or specified

-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "5.5")

CUDA not found. CUDA components will not be compiled.

-- Found GTest: /home/stir/devel/SIRF-SuperBuild/INSTALL/lib/libgtest.a

-- Found Armadillo: /home/stir/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/stir/devel/SIRF-SuperBuild/INSTALL/include/armadillo_bits/config.hpp to link against the MKL ILP64 interface.

-- Found HDF5: /home/stir/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/stir/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/stir/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a/home/stir/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3.a

-- Found FFTW3: /home/stir/devel/SIRF-SuperBuild/INSTALL/lib/libfftw3f.a

MKL is NOT found ...

-- Looking for sgemm_

-- Looking for sgemm_ - 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 "2.7.10", minimum required is "2")

-- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.10")

-- Found NumPy: version "1.8.2" /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.

-- Could NOT find OpenGL (missing: OPENGL_gl_LIBRARY OPENGL_INCLUDE_DIR)

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 NOT found ...

CUDA not found, not compiling gpu fft toolbox

Compiling cpu based optical flow registration toolbox.

-- Boost version: 1.63.0

-- Found the following Boost libraries:

-- date_time

-- filesystem

-- system

-- thread

-- regex

-- chrono

-- atomic

-- 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 HDF5: /home/stir/devel/SIRF-SuperBuild/INSTALL/lib/libhdf5_cpp-shared.so;/home/stir/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.

Required dependencies for gadget compilation not found (ACE, ISMRMRD, FFTW3, HDF5).

-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)

Doxygen not found. Will not be able to build documentation

CPACK_PACKAGING_INSTALL_PREFIX: /home/stir/devel/SIRF-SuperBuild/INSTALL

-- Found CPack generators: DEB

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

Please set them or make sure they are set and tested correctly in the CMake files:

ACE_INCLUDE_DIR

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/mri_core

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/cmr

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/registration/optical_flow/cpu

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/image_io

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/python

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/python/example

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/apps/standalone/cpu/denoising/2d

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/apps/standalone/cpu/registration

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/apps/standalone/cpu/registration/2d

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/apps/standalone/cpu/registration/3d

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/test

used as include directory in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/test/integration

ACE_LIBRARY

linked by target "gadgetron_toolbox_cpureg" in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/registration/optical_flow/cpu

linked by target "gadgetron_toolbox_python" in directory /home/stir/devel/SIRF-SuperBuild/Gadgetron/toolboxes/python

-- Configuring incomplete, errors occurred!

See also "/home/stir/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

stir@ubuntu-stir:~/devel/SIRF-SuperBuild$

Evgueni Ovtchinnikov

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May 9, 2017, 11:36:40 AM5/9/17

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With libace-dev installed, SuperBuild completed the build successfully.

Running demos additionally required python-docopt and python-scipy.

From: Ovtchinnikov, Evgueni (STFC,RAL,SC)
Sent: 09 May 2017 15:42
To: Pasca, Edoardo (STFC,RAL,SC)
Subject: RE: Another SuperBuild failure on VM

No I did not have it. Now that it is installed, SuperBuild is building Gadgetron.

Should be in the list of pre-requisites then?

From: Pasca, Edoardo (STFC,RAL,SC)
Sent: 09 May 2017 15:36
To: Ovtchinnikov, Evgueni (STFC,RAL,SC)
Subject: RE: Another SuperBuild failure on VM

Do you have libace-dev installed?

Edo

Thielemans, Kris

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May 10, 2017, 5:53:21 AM5/10/17

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Hi Evgueni

Thanks for testing.

The dependencies that you mention are on

https://github.com/CCPPETMR/SIRF/wiki/SIRF-SuperBuild-Ubuntu-16.04

there it recommends to install matplotlib. Do we need python-scipy as well?

Can you or Edo update

https://github.com/CCPPETMR/SIRF/wiki/Installation-instructions

to explicitly refer to the Linux and MacOSX pages for more detail?

Thanks

Kris

Evgueni Ovtchinnikov

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May 10, 2017, 5:59:09 AM5/10/17

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Python-scipy is needed by the PET steepest ascent demo only (it calls scipy.optimize.fminbound).

I could actually put import scipy.optimize in the try: except brackets to make the installation of python-scipy optional.

Thielemans, Kris

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May 10, 2017, 6:15:06 AM5/10/17

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Ok

Can you add scipy to the wiki as a recommended package and put a line in the demo to tell users that this demo needs scipy? I don’t think complicating the code helps for a demo.

Kris

PS: this does say we cannot have any tests depending on scipy but I guess that’s ok

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