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Re: [Question #688588]: Compilation error

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Lingran Zhang <question688588@xxxxxxxxxxxxxxxxxxxxx>
Date: Mon, 10 Feb 2020 13:12:51 -0000
Reply-to: question688588@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
Question #688588 on Yade changed:
https://answers.launchpad.net/yade/+question/688588

    Status: Answered => Open

Lingran Zhang is still having a problem:
Hi Robert,

Thank you for your suggestions.

Here is the feedback:

- manually compile the cgal (version 4.12.1 and 4.8): the same error
persists.

- download the newest trunk by git clone: errors are produced only when
DFNflow is compiled:

[ 89%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/Tenseur3.cpp.o
/home/zhang7/Documents/compareYade/trunk_download_dfn/pkg/pfv/DFNFlow.cpp: In member function ‘void yade::DFNBoundingSphere::saveVtk(const char*, bool)’:
/home/zhang7/Documents/compareYade/trunk_download_dfn/pkg/pfv/DFNFlow.cpp:59:41: error: unused parameter ‘withBoundaries’ [-Werror=unused-parameter]
   void saveVtk(const char* folder, bool withBoundaries) //FIXME: withBoundaries does nothing in DFNFlow right now. Needed for consistent templating.
                                    ~~~~~^~~~~~~~~~~~~~
[ 90%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/Timer.cpp.o
/home/zhang7/Documents/compareYade/trunk_download_dfn/pkg/pfv/DFNFlow.cpp: In member function ‘void yade::DFNFlowEngine::interpolateCrack(yade::TemplateFlowEngine_DFNFlowEngineT<yade::DFNCellInfo, yade::DFNVertexInfo, yade::CGT::_Tesselation<yade::CGT::TriangulationTypes<yade::DFNVertexInfo, yade::DFNCellInfo> >, yade::DFNBoundingSphere>::Tesselation&, yade::TemplateFlowEngine_DFNFlowEngineT<yade::DFNCellInfo, yade::DFNVertexInfo, yade::CGT::_Tesselation<yade::CGT::TriangulationTypes<yade::DFNVertexInfo, yade::DFNCellInfo> >, yade::DFNBoundingSphere>::Tesselation&)’:
/home/zhang7/Documents/compareYade/trunk_download_dfn/pkg/pfv/DFNFlow.cpp:208:22: error: variable ‘cellEnd’ set but not used [-Werror=unused-but-set-variable]
  FiniteCellsIterator cellEnd = newTri.finite_cells_end();
                      ^~~~~~~
[ 90%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/TriaxialState.cpp.o
[ 91%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/basicVTKwritter.cpp.o
[ 91%] Building CXX object CMakeFiles/yade.dir/lib/computational-geometry/MarchingCube.cpp.o
cc1plus: all warnings being treated as errors
make[2]: *** [CMakeFiles/yade.dir/build.make:1896: CMakeFiles/yade.dir/pkg/pfv/DFNFlow.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:143: CMakeFiles/yade.dir/all] Error 2
make: *** [Makefile:130: all] Error 2


Here is what cmake gives:
 
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- 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 2020-02-02.git-472f4cb
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- 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 "2.7.16") 
-- Found PythonInterp: /usr/bin/python3.7 (found version "3.7.3") 
Python version 3.7.3 found, try to import dependencies...
-- Found NumPy: version "1.16.2" /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-37m-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/python3.7/tkinter  
--   Boost_VERSION: 106700
--   Boost_LIB_VERSION: 1_67
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python37.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 3.7.3, 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-cast-function-type -Wshadow=compatible-local -Wno-error=cpp -fdce -fstack-protector-strong 
-- 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: 3.3.7
-- 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") 
-- 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-3.13/Modules/FindOpenGL.cmake:270 (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:424 (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
-- Found CGAL
-- Using typical suitesparse path /usr
-- SuiteSparse version 5.4.0 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/x86_64-linux-gnu/openmpi/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")  
-- Found MPI4PY: /usr/lib/python3/dist-packages/mpi4py/include  
-- 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_ - not found
-- Found Threads: TRUE  
-- 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
-- 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 LAPACK API found.
-- Found CLP version: 1.16.11, coinutils version: 2.10.14
-- WARNING: coinutils version older than 2.11.3. Falling back to C++14.
-- md5sum of freegult /usr/include/GL/freeglut_std.h is: 791a2febd8584ec530cdd7676191b6d5
-- freegult version is 2.8.1
Yade will be installed to /home/zhang7/Documents/compareYade/install
-- Suffix is set to -2020-02-02.git-472f4cb
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/zhang7/Documents/compareYade/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: BoostLog Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles PotentialBlocks
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING
-- 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/zhang7/Documents/compareYade/build

Can you have a look if there is a bug in DFNflow.cpp?

Many thanks!
Lingran

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