Compilation error - yadeWrapperAny idea

Hi,

> return PyMemoryView_FromMemory ... is from python3[1], using python3
instead of 2.7 should fix it it.

[1]https://docs.python.org/3/c-api/memoryview.html

On Thu, Nov 7, 2019 at 10:18 AM Luc Scholtès <
<email address hidden>> wrote:

> 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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>
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Hey Luc,

I am not sure about it, the pipeline on gitlab for 16.04 seems to pass [1]. Could be worth following the docker exactly [2]. Have you tried compiling with -DENABLE_MPI=OFF?
Cheers,

Robert

[1]https://gitlab.com/yade-dev/trunk/-/jobs/344010835
[2]https://gitlab.com/yade-dev/docker-yade/blob/ubuntu16-py3/Dockerfile

Ah deepak is right. Copying and pasting the apt-get install from the docker link should install all your python3 dependecies.

Thank you guys

I had an uncomplete python3 installed alongside python2...

I reinstalled everything and I can now compile and run YADE.

Nonetheless, I have this at cmake:

-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package

while I got this before:

-- Found GTS

probably not a big deal... until it becomes one :)

Hi all,

I'm facing the same problem.
@Luc can you be more precise on how you solved the problem?

I copied and pasted the apt-get install from the link but I'm still not able to compile.
thanks for your help

Hi Antonio,
What's the meaning of "same problem"?
For the record, the answer was already contained in the original question (which hasn't been mentioned yet apparently):
-- Could NOT find future (missing: PY_future)

I doubt the above problem can occur if one follows "yade installation" section strictly (no need to go search
gitlab pipelines!), but if it the case let us know, it means a dependency needs to be added.

Bruno

Hi Bruno,

I started the compilation from zero (erasing old folders and following the "yade installation" section) and everything went well, so problem solved.
I don't know why before I couldn't compile the code successfully, maybe I had some wrong stuff in the build folder.
thanks