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[Luc Scholtès <question685676@xxxxxxxxxxxxxxxxxxxxx>]

New question #685676 on Yade:
https://answers.launchpad.net/yade/+question/685676

Hi all,

I just downloaded the latest trunk from gitlab and got this error message at 97% compilation:

[ 97%] Linking CXX shared library lib/x86_64-linux-gnu/_packPredicates.so
/media/scholtes/sdb/yade/sources/trunk/trunk/py/wrapper/yadeWrapper.cpp: In member function ‘PyObject* yade::pyOmega::bufferFromIntrsct(const boost::shared_ptr<yade::Subdomain>&, unsigned int, unsigned int, bool)’:
/media/scholtes/sdb/yade/sources/trunk/trunk/py/wrapper/yadeWrapper.cpp:728:136: error: ‘PyMemoryView_FromMemory’ was not declared in this scope
    return PyMemoryView_FromMemory((char*) (subD->intersections[rank].data()), subD->intersections[rank].size()*sizeof(Body::id_t),PyBUF_WRITE);}
                                                                                                                                        ^
/media/scholtes/sdb/yade/sources/trunk/trunk/py/wrapper/yadeWrapper.cpp:731:145: error: ‘PyMemoryView_FromMemory’ was not declared in this scope
    return PyMemoryView_FromMemory((char*) &(subD->mirrorIntersections[rank][0]), subD->mirrorIntersections[rank].size()*sizeof(Body::id_t),PyBUF_WRITE);}
                                                                                                                                                 ^
[ 97%] Built target _packPredicates
py/CMakeFiles/wrapper.dir/build.make:62: recipe for target 'py/CMakeFiles/wrapper.dir/wrapper/yadeWrapper.cpp.o' failed

I am on Ubuntu 16.04.06 and here is what cmake returned:

-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Version is set to 2019-11-05.git-35899c7
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- 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 "2.7.12") 
-- Found PythonInterp: /usr/bin/python3.5 (found version "3.5.2") 
Python version 3.5.2 found, try to import dependencies...
-- Found NumPy: version "1.11.0" /usr/lib/python3/dist-packages/numpy/core/include
-- Found IPython: /usr/lib/python3/dist-packages/IPython  
-- Found matplotlib: /usr/lib/python3/dist-packages/matplotlib  
-- Found pygraphviz: /usr/lib/python3/dist-packages/pygraphviz  
-- Found Xlib: /usr/lib/python3/dist-packages/Xlib  
-- Found minieigen: /usr/lib/python3/dist-packages/minieigen.cpython-35m-x86_64-linux-gnu.so  
-- Could NOT find future (missing:  PY_future) 
Failed to import dependencies for Python version 3.5.2. NOT FOUND:future
-- Found PythonInterp: /usr/bin/python (found version "2.7.12") 
-- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.12") 
Python version 2.7.12 found, try to import dependencies...
-- Found NumPy: version "1.11.0" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found IPython: /usr/lib/python2.7/dist-packages/IPython  
-- Found matplotlib: /usr/lib/python2.7/dist-packages/matplotlib  
-- Found pygraphviz: /usr/lib/python2.7/dist-packages/pygraphviz  
-- Found Xlib: /usr/lib/python2.7/dist-packages/Xlib  
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so  
-- Found future: /usr/lib/python2.7/dist-packages/future  
-- Found past: /usr/lib/python2.7/dist-packages/past  
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc  
--   Boost_VERSION: 105800
--   Boost_LIB_VERSION: 1_58
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python-py27.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/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/usr/lib/x86_64-linux-gnu/libpthread.so
Found all python dependencies with version 2.7.12, will compile yade with that.
-- Chosen compiler flags are: CMAKE_CXX_FLAGS =  -fPIC -O2 --param=ssp-buffer-size=4  -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  -Wno-error=maybe-uninitialized -Wno-comment -Wno-float-conversion -Wno-unused-function -Wno-error=cpp -fdce 
-- Found Loki: /usr/include  
-- 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 "1.2.8") 
-- Found Eigen3, version: 3.2.92
-- Disable vectorization
-- The imported target "vtkRenderingPythonTkWidgets" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.2/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtk" references the file
   "/usr/bin/vtk"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.2/VTKTargets.cmake"
but not all the files it references.

-- Found VTK
-- 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  
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- 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
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.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
-- Found CGAL
-- Using typical suitesparse path /usr
-- SuiteSparse version 4.4.6 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so  
-- Found OpenBlas: /usr/lib/libopenblas.so  
-- BLAS_INCLUDE_DIR=/usr/include/openblas
-- Found Metis: /usr/include  
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so  
-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so  
-- Found MPI4PY: /usr/lib/python2.7/dist-packages/mpi4py/include  
-- MPI found
-- Found GL2PS: /usr/lib/libgl2ps.so  
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
-- BLAS_INCLUDE_DIR=/usr/include/openblas
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found Threads: TRUE  
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found OpenBlas
-- Found Lapack
-- CLP not found.
-- BLAS_INCLUDE_DIR=/usr/include/openblas
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- CLP NOT found
-- md5sum of freegult /usr/include/GL/freeglut_std.h is: 791a2febd8584ec530cdd7676191b6d5
-- freegult version is 2.8.1
Yade will be installed to /media/scholtes/sdb/yade/sources/trunk/install
-- Suffix is set to -2019-11-05.git-35899c7
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /media/scholtes/sdb/yade/sources/trunk/install
-- Found gts: /usr/lib/python2.7/dist-packages/gts  
-- Use system gts version
-- VTK version >5 and <8 is found
-- ===========================================================
-- Yade configured with following features: BoostLog Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING PotentialBlocks
-- Using MAX_LOG_LEVEL=5, ENABLE_LOGGER=ON
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /media/scholtes/sdb/yade/sources/trunk/build

Any suggestion?

Thanks 

Luc

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