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Re: [Question #693698]: Trouble when compiling with g++-9 or g++-7

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Sacha Duverger <question693698@xxxxxxxxxxxxxxxxxxxxx>
Date: Thu, 29 Oct 2020 17:40:55 -0000
Reply-to: question693698@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
Question #693698 on Yade changed:
https://answers.launchpad.net/yade/+question/693698

Sacha Duverger posted a new comment:
Thank you for your answers,

Before trying to compile with g++-7 I emptied the "build" and "install"
directories (with "rm -r build/* install/*"), this counts has a fresh
directory right? Anyway, I tried to start from a really fresh directory
(with another name) and had the same problem.

The g++-9 installed on my machine worked well when I used it to compile
another package (this package is the reason why I upgraded g++ in the
first place). Can there still be a problem with g++-9's necessary
packages while it already worked for another package than YADE?

I tried to compile YADE with clang but I don't see where I can identify
which package cause problems with g++. See [1] for the outputs of cmake
and make install.

I also tried to uninstall and reinstall all of my g++ versions, hoping
that it could fix problems on the necessary packages, but it still
doesn't work.

####################################################################################################################################################################################
[1] : Running cmake and make with clang

## cmake command

cmake -DENABLE_GUI=ON -DENABLE_MPI=OFF -DENABLE_PFVFLOW=OFF
-DENABLE_TWOPHASEFLOW=OFF -DENABLE_LBMFLOW=OFF
-DENABLE_POTENTIAL_BLOCKS=OFF -DCMAKE_CXX_COMPILER=clang
-DCMAKE_INSTALL_PREFIX=../install ../trunk

## cmake output

-- The C compiler identification is Clang 6.0.0
-- The CXX compiler identification is Clang 6.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - 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: /usr/bin/clang - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Version is set to 2020-10-20.git-427f64c
-- GCC Version >= 4.8. Adding -save-temps
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Log filtering: enabled
-- Enabling boost::log library and DEBUG=OFF. Logging will work nicely, backtraces will not have debug info, files will be small.
Loop on the following python versions and check available dependencies:3.8;3.7;3.6;3.5;3.4;3.3;3.2;3.1;3.0;2.7;2.6
-- Found PythonInterp: /usr/bin/python (found version "2.7.17") 
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.9") 
Python version 3.6.9 found, try to import dependencies...
-- Found NumPy: version "1.18.4" /home/sacha.duverger/.local/lib/python3.6/site-packages/numpy/core/include
-- Found IPython: /usr/lib/python3/dist-packages/IPython  
-- Found matplotlib: /home/sacha.duverger/.local/lib/python3.6/site-packages/matplotlib  
-- Found pygraphviz: /usr/lib/python3/dist-packages/pygraphviz  
-- Found Xlib: /usr/lib/python3/dist-packages/Xlib  
-- Found future: /usr/lib/python3/dist-packages/future  
-- Found past: /usr/lib/python3/dist-packages/past  
-- Found tkinter: /usr/lib/python3.6/tkinter  
--   Boost_VERSION: 106501
--   Boost_LIB_VERSION: 1_65_1
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python3-py36.so/usr/lib/x86_64-linux-gnu/libboost_thread.so-lpthread/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_log.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libboost_log_setup.so
Found all python dependencies with version 3.6.9, will compile yade with that.
-- Chosen compiler flags are: CMAKE_CXX_FLAGS =   -Werror -Wformat -Wformat-security -Wformat-nonliteral -Wall -Wextra -Wnarrowing -Wreturn-type -Wuninitialized -Wfloat-conversion -Wcast-align -Wdisabled-optimization -Wtrampolines -Wpointer-arith -Wswitch-bool -Wwrite-strings -Wnon-virtual-dtor -Wreturn-local-addr  -Wno-error=maybe-uninitialized -Wno-comment -Wno-error=cpp -fdce -fstack-protector-strong 
-- Determining preferred precision of Real numbers
-- Will now try to find python-mpmath using /usr/bin/python3.6
-- Disabling RealHP<N>, this compiler is too old to make this work.
-- mpfr disabled
-- Will use PrecisionDouble as Real type with 15 decimal places precision and use 64 bits of storage.
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkIOParallelXML' component is 'IOParallelXML'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkCommonCore' component is 'CommonCore'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkIOImage' component is 'IOImage'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkIOXML' component is 'IOXML'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkFiltersCore' component is 'FiltersCore'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkImagingCore' component is 'ImagingCore'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkRenderingCore' component is 'RenderingCore'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkImagingGeneral' component is 'ImagingGeneral'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


CMake Deprecation Warning at /usr/local/lib/cmake/vtk-9.0/vtk-config.cmake:71 (message):
  The new name for the 'vtkImagingHybrid' component is 'ImagingHybrid'
Call Stack (most recent call first):
  CMakeLists.txt:642 (FIND_PACKAGE)


-- Found Threads: TRUE  
-- Found VTK
-- Found OpenMP_C: -fopenmp=libomp (found version "3.1") 
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) 
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (found version "3.1")
-- OpenMP NOT found
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message):
  The package name passed to `find_package_handle_standard_args` (PkgConfig)
  does not match the name of the calling package (glib2).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  /usr/share/cmake-3.18/Modules/FindPkgConfig.cmake:59 (find_package_handle_standard_args)
  cMake/Findglib2.cmake:30 (INCLUDE)
  CMakeLists.txt:675 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindOpenGL.cmake:305 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/lib/x86_64-linux-gnu/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/lib/x86_64-linux-gnu/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/lib/x86_64-linux-gnu/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  CMakeLists.txt:693 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so   
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so  
-- USE QT5
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer  
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu  
-- Found CGAL: /usr/include, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- CGAL NOT found
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so  
-- Found GL2PS
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so  
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/x86_64-linux-gnu/libopenblas.so  
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found OpenBlas
-- Found Lapack
-- md5sum of freegult /usr/include/GL/freeglut_std.h is: 791a2febd8584ec530cdd7676191b6d5
-- freegult version is 2.8.1
Yade will be installed to /home/sacha.duverger/packages/yade/install
-- Suffix is set to -2020-10-20.git-427f64c
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/sacha.duverger/packages/yade/install
-- Could NOT find gts (missing: PY_gts) 
-- Use embedded version of gts. Please, consider installing the corresponding package
-- linking -lquadmath skipped
-- VTK version >7 is found
-- ===========================================================
-- Yade configured with following features: BoostLog PrecisionDouble Odeint VTK GTS GUI-Qt5 FEMLIKE GL2PS PotentialParticles
-- Disabled features: RealHP mpmath MPFR OPENMP CGAL PFVFLOW LINSOLV MPI TWOPHASEFLOW SPH DEFORM LIQMIGRATION LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialBlocks
-- Using MAX_LOG_LEVEL=5, ENABLE_LOGGER=ON
-- Optimized build
-- C++ standard version: 14
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/sacha.duverger/packages/yade/build

## make install output

Scanning dependencies of target _GLViewer_autogen
[  0%] Automatic MOC for target _GLViewer
Scanning dependencies of target _gts
Scanning dependencies of target _packObb
[  0%] Building CXX object py/CMakeFiles/_gts.dir/3rd-party/pygts-0.3.1/cleanup.cpp.o
[  1%] Building CXX object py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o
Scanning dependencies of target _polyhedra_utils
[  1%] Building CXX object py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o
clang: error: unknown argument: '-fdce'
py/CMakeFiles/_gts.dir/build.make:81: recipe for target 'py/CMakeFiles/_gts.dir/3rd-party/pygts-0.3.1/cleanup.cpp.o' failed
make[2]: *** [py/CMakeFiles/_gts.dir/3rd-party/pygts-0.3.1/cleanup.cpp.o] Error 1
CMakeFiles/Makefile2:355: recipe for target 'py/CMakeFiles/_gts.dir/all' failed
make[1]: *** [py/CMakeFiles/_gts.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
clang: error: unknown argument: '-fdce'
py/CMakeFiles/_packObb.dir/build.make:81: recipe for target 'py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o' failed
make[2]: *** [py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o] Error 1
CMakeFiles/Makefile2:437: recipe for target 'py/CMakeFiles/_packObb.dir/all' failed
make[1]: *** [py/CMakeFiles/_packObb.dir/all] Error 2
clang: error: unknown argument: '-fdce'
py/CMakeFiles/_polyhedra_utils.dir/build.make:81: recipe for target 'py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o' failed
make[2]: *** [py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o] Error 1
CMakeFiles/Makefile2:410: recipe for target 'py/CMakeFiles/_polyhedra_utils.dir/all' failed
make[1]: *** [py/CMakeFiles/_polyhedra_utils.dir/all] Error 2
[  1%] Built target _GLViewer_autogen
Makefile:148: recipe for target 'all' failed
make: *** [all] Error 2

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