ITK-SNAP (!66) · Merge requests · CIT HPC / Habrok / cit-hpc-easybuild

Aurel Istrate requested to merge ITK-SNAP into master May 16, 2024
Created by: Neves-P
Opening this PR to keep track of progress when building ITK-SNAP.
As of now, I tried using a newer toolchain, for which we have all the dependencies available already, but the build fails.
== 2024-05-16 14:37:32,488 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): cmd " cmake  -DCMAKE_INSTALL_PREFIX=/home1/f115372/.local/easybuild/software/ITK-SNAP/4.0.0-foss-2022b -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_POLICY_DEFAULT_CMP0094=NEW -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DENABLE_PRECOMPILED_HEADERS=OFF -DITK_DIR=$EBROOTITK -DVTK_DIR=$EBROOTVTK -DCMAKE_PREFIX_PATH=$EBROOTQT5/lib/cmake  /home1/f115372/.local/easybuild/build/ITKSNAP/4.0.0/foss-2022b/itksnap/" exited with exit code 1 and output:
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/GCCcore/12.2.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/GCCcore/12.2.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- ITK-SNAP Git Info:
CMake Deprecation Warning at CMakeLists.txt:16 (cmake_policy):
  The OLD behavior for policy CMP0026 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


-- ITK-SNAP Git Info:
--   Branch : HEAD
--   SHA    : 7a104c25401ce23599dc8d32ea80f3daae80f379
--   Date   : 2019-06-12 06:53:09 -0400
-- Found HDF5: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/HDF5/1.14.0-gompi-2022b/lib/libhdf5_cpp.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/HDF5/1.14.0-gompi-2022b/lib/libhdf5.so;/usr/lib64/libpthread.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Szip/2.1.1-GCCcore-12.2.0/lib/libsz.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/zlib/1.2.12-GCCcore-12.2.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/HDF5/1.14.0-gompi-2022b/lib/libhdf5.so;/usr/lib64/libpthread.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Szip/2.1.1-GCCcore-12.2.0/lib/libsz.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/zlib/1.2.12-GCCcore-12.2.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so (found version "1.14.0") found components: CXX C
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found OpenGL: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/libglvnd/1.6.0-GCCcore-12.2.0/lib/libOpenGL.so  found components: OpenGL GLX
-- Found Python3: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/Python/3.10.8-GCCcore-12.2.0/bin/python3.10 (found suitable version "3.10.8", minimum required is "3.10") found components: Interpreter Development.Module Development.Embed
-- Found MPI_C: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/OpenMPI/4.1.4-GCC-12.2.0/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C
-- Found X11: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/X11/20221110-GCCcore-12.2.0/include
-- Looking for XOpenDisplay in /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/X11/20221110-GCCcore-12.2.0/lib/libX11.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/X11/20221110-GCCcore-12.2.0/lib/libXext.so
-- Looking for XOpenDisplay in /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/X11/20221110-GCCcore-12.2.0/lib/libX11.so;/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/X11/20221110-GCCcore-12.2.0/lib/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
CMake Deprecation Warning at /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/VTK/9.2.6-foss-2022b/lib64/cmake/vtk-9.2/vtk-use-file-deprecated.cmake:1 (message):
  The `VTK_USE_FILE` is no longer used starting with 8.90.
Call Stack (most recent call first):
  CMake/standalone.cmake:11 (INCLUDE)
  CMakeLists.txt:153 (INCLUDE)


-- Found OpenGL: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/libglvnd/1.6.0-GCCcore-12.2.0/lib/libOpenGL.so
-- Found CURL: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/cURL/7.86.0-GCCcore-12.2.0/lib/libcurl.so (found version "7.86.0")
CMake Warning (dev) at Submodules/c3d/CMakeLists.txt:14 (OPTION):
  Policy CMP0077 is not set: option() honors normal variables.  Run "cmake
  --help-policy CMP0077" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  For compatibility with older versions of CMake, option is clearing the
  normal variable 'CONVERT3D_BUILD_AS_SUBPROJECT'.
This warning is for project developers.  Use -Wno-dev to suppress it.

--    CPACK_SYSTEM_NAME Linux-x86_64
--    CPACK_PACKAGE_FILE_NAME c3d-1.1.0-Linux-x86_64
-- GREEDY Version: 1.0.1 Released Mar 21, 2019
-- GIT Info:
--   Branch : HEAD
--   SHA    : 79e69e3d7b4d1e88cf87218ca99d6d373d323f9f
--   Date   : 2019-03-21 13:41:18 -0400
CMake Warning (dev) at Submodules/greedy/CMakeLists.txt:20 (OPTION):
  Policy CMP0077 is not set: option() honors normal variables.  Run "cmake
  --help-policy CMP0077" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  For compatibility with older versions of CMake, option is clearing the
  normal variable 'GREEDY_BUILD_AS_SUBPROJECT'.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/CMake/3.24.3-GCCcore-12.2.0/share/cmake-3.24/Modules/BundleUtilities.cmake:237 (message):
  Policy CMP0080 is not set: BundleUtilities cannot be included at configure
  time.  Run "cmake --help-policy CMP0080" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/CMake/3.24.3-GCCcore-12.2.0/share/cmake-3.24/Modules/BundleUtilities.cmake:246 (_warn_cmp0080)
  CMakeLists.txt:1160 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- === Installation Section ===
--    CMAKE_SYSTEM_PROCESSOR x86_64
--    CMAKE_SYSTEM_NAME Linux
CMake Warning (dev) at /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/CMake/3.24.3-GCCcore-12.2.0/share/cmake-3.24/Modules/BundleUtilities.cmake:237 (message):
  Policy CMP0080 is not set: BundleUtilities cannot be included at configure
  time.  Run "cmake --help-policy CMP0080" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/CMake/3.24.3-GCCcore-12.2.0/share/cmake-3.24/Modules/BundleUtilities.cmake:246 (_warn_cmp0080)
  CMake/DeployQt5.cmake:114 (include)
  CMakeLists.txt:1476 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Error at CMakeLists.txt:1487 (get_property):
  get_property could not find TARGET Qt5::QXcbEglIntegrationPlugin.  Perhaps
  it has not yet been created.


-- Configuring incomplete, errors occurred!
It seems like we actually get further in the build with foss/2021b.
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