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Re: [Question #682504]: error in running an example. showing 3D error

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: ehsan benabbas <question682504@xxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 02 Aug 2019 20:37:27 -0000
Reply-to: question682504@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
Question #682504 on Yade changed:
https://answers.launchpad.net/yade/+question/682504

    Status: Needs information => Open

ehsan benabbas gave more information on the question:
Thank you. Ok, I did what you said and here it is the output:

ehsan@ehsan:~$ cd ~/yade-cmake-test
ehsan@ehsan:~/yade-cmake-test$ cmake -DCMAKE_INSTALL_PREFIX=/home/ehsan/myYade/install /home/ehsan/trunk
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- 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 2019-07-08.git-e27605e
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
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 "2.7.15") 
-- Found PythonInterp: /usr/local/bin/python3.7 (found version "3.7.4") 
Python version 3.7.4 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)


CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python3-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)


CMake Warning (dev) at /usr/share/cmake-3.10/Modules/FindBoost.cmake:911 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "chrono" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  cMake/YadePythonHelpers.cmake:68 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py3; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:68 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)


Failed to import dependencies for Python version 3.7.4. NOT FOUND:libboost-python
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.8") 
Python version 3.6.8 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py36; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)


-- Found NumPy: version "1.17.0" /home/ehsan/.local/lib/python3.6/site-packages/numpy/core/include
-- Found IPython: /usr/local/lib/python3.6/dist-packages/IPython  
-- Found matplotlib: /usr/local/lib/python3.6/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-36m-x86_64-linux-gnu.so  
-- 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_python-py36.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_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libpthread.so
Found all python dependencies with version 3.6.8, will compile yade with that.
-- Found Loki: /usr/include  
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- 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
-- 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-6.3/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-6.3/VTKTargets.cmake"
but not all the files it references.

-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 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/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
-- Found CGAL
-- SuiteSparse version 5.1.2 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so  
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so  
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Found Metis: /usr/include  
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found MPI_C: /usr/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- MPI found
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so  
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- 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
-- Found CLP: /usr/include/coin, /usr/lib/x86_64-linux-gnu/libClp.so
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Found CLP
Yade will be installed to /home/ehsan/myYade/install
-- Suffix is set to -2019-07-08.git-e27605e
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/ehsan/myYade/install
-- Could NOT find gts (missing: PY_gts) 
-- Use embedded version of gts. Please, consider installing the corresponding package
-- VTK version >5 and <8 is found
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW LINSOLV MPI TWOPHASEFLOW GL2PS LBMFLOW PotentialParticles PotentialBlocks
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY THERMAL PROFILING
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ehsan/yade-cmake-test

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