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facebookresearch / sumo-challenge

Scene Understanding and Modeling Challenge Library
https://sumochallenge.org/
MIT License
71 stars 15 forks source link

SUMO API build fails at PyMesh2 #64

Closed meder411 closed 5 years ago

meder411 commented 5 years ago

I've followed the installation instructions from the support website, but it consistently crashes when installing pymesh2 in the pip install --verbose -e . call. It seems this is a known issue with pip install pymesh2. Evidently it still isn't fixed properly, but you can install it directly from the wheel file. However, as all of this is built into the SUMO API, I'm not quite sure how to get around the install error. Is there an easy fix?

My build log is pasted below (forgive the length):

  Running setup.py install for pymesh2: started
    Running command /playpen/username/projects/sumo-challenge/sumo-api/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-6k9dk3c1/pymesh2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-0v5scnvh/install-record.txt --single-version-externally-managed --compile --install-headers /playpen/username/projects/sumo-challenge/sumo-api/venv/include/site/python3.7/pymesh2
    running install
    running build
    -- 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
    -- Found GMP: /playpen/username/libraries/anaconda3/include
    -- 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
    -- Boost version: 1.58.0
    -- Using system boost
    abort: repository /tmp/pip-install-6k9dk3c1/pymesh2/third_party not found!
    abort: repository /tmp/pip-install-6k9dk3c1/pymesh2/third_party not found!
    -- Performing Test standard_math_library_linked_to_automatically
    -- Performing Test standard_math_library_linked_to_automatically - Success
    -- Standard libraries to link to explicitly: none
    -- Performing Test COMPILER_SUPPORT_WERROR
    -- Performing Test COMPILER_SUPPORT_WERROR - Success
    -- Performing Test COMPILER_SUPPORT_pedantic
    -- Performing Test COMPILER_SUPPORT_pedantic - Success
    -- Performing Test COMPILER_SUPPORT_Wall
    -- Performing Test COMPILER_SUPPORT_Wall - Success
    -- Performing Test COMPILER_SUPPORT_Wextra
    -- Performing Test COMPILER_SUPPORT_Wextra - Success
    -- Performing Test COMPILER_SUPPORT_Wundef
    -- Performing Test COMPILER_SUPPORT_Wundef - Success
    -- Performing Test COMPILER_SUPPORT_Wcastalign
    -- Performing Test COMPILER_SUPPORT_Wcastalign - Success
    -- Performing Test COMPILER_SUPPORT_Wcharsubscripts
    -- Performing Test COMPILER_SUPPORT_Wcharsubscripts - Success
    -- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor
    -- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor - Success
    -- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs
    -- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs - Success
    -- Performing Test COMPILER_SUPPORT_Wpointerarith
    -- Performing Test COMPILER_SUPPORT_Wpointerarith - Success
    -- Performing Test COMPILER_SUPPORT_Wwritestrings
    -- Performing Test COMPILER_SUPPORT_Wwritestrings - Success
    -- Performing Test COMPILER_SUPPORT_Wformatsecurity
    -- Performing Test COMPILER_SUPPORT_Wformatsecurity - Success
    -- Performing Test COMPILER_SUPPORT_Wnopsabi
    -- Performing Test COMPILER_SUPPORT_Wnopsabi - Success
    -- Performing Test COMPILER_SUPPORT_Wnovariadicmacros
    -- Performing Test COMPILER_SUPPORT_Wnovariadicmacros - Success
    -- Performing Test COMPILER_SUPPORT_Wnolonglong
    -- Performing Test COMPILER_SUPPORT_Wnolonglong - Success
    -- Performing Test COMPILER_SUPPORT_fnochecknew
    -- Performing Test COMPILER_SUPPORT_fnochecknew - Success
    -- Performing Test COMPILER_SUPPORT_fnocommon
    -- Performing Test COMPILER_SUPPORT_fnocommon - Success
    -- Performing Test COMPILER_SUPPORT_fstrictaliasing
    -- Performing Test COMPILER_SUPPORT_fstrictaliasing - Success
    -- Performing Test COMPILER_SUPPORT_wd981
    -- Performing Test COMPILER_SUPPORT_wd981 - Failed
    -- Performing Test COMPILER_SUPPORT_wd2304
    -- Performing Test COMPILER_SUPPORT_wd2304 - Failed
    -- Performing Test COMPILER_SUPPORT_STRICTANSI
    -- Performing Test COMPILER_SUPPORT_STRICTANSI - Failed
    -- Performing Test COMPILER_SUPPORT_Qunusedarguments
    -- Performing Test COMPILER_SUPPORT_Qunusedarguments - Failed
    -- Performing Test COMPILER_SUPPORT_ansi
    -- Performing Test COMPILER_SUPPORT_ansi - Success
    -- Performing Test COMPILER_SUPPORT_OPENMP
    -- Performing Test COMPILER_SUPPORT_OPENMP - Success
    -- searching for 'pkgconfig' directory in PKG_CONFIG_LIBDIR (  ), /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share, and /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/lib
    -- pkgconfig not found; installing in /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share
    -- Looking for Q_WS_X11
    -- Looking for Q_WS_X11 - found
    -- Looking for Q_WS_WIN
    -- Looking for Q_WS_WIN - not found
    -- Looking for Q_WS_QWS
    -- Looking for Q_WS_QWS - not found
    -- Looking for Q_WS_MAC
    -- Looking for Q_WS_MAC - not found
    -- Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.7")
    -- /tmp/pip-install-6k9dk3c1/pymesh2/third_party/build/eigen/test
    -- Found CHOLMOD: /usr/include/suitesparse
    -- Found UMFPACK: /usr/include/suitesparse
    -- Found SUPERLU: /usr/include/superlu
    -- Could NOT find PASTIX (missing:  PASTIX_INCLUDES PASTIX_LIBRARIES)
    -- Could NOT find SCOTCH (missing:  SCOTCH_INCLUDES SCOTCH_LIBRARIES)
    -- Could NOT find METIS (missing:  METIS_INCLUDES METIS_LIBRARIES)
    -- Found SPQR: /usr/include/suitesparse
    -- The Fortran compiler identification is GNU 5.4.0
    -- Check for working Fortran compiler: /usr/bin/gfortran
    -- Check for working Fortran compiler: /usr/bin/gfortran  -- works
    -- Detecting Fortran compiler ABI info
    -- Detecting Fortran compiler ABI info - done
    -- Checking whether /usr/bin/gfortran supports Fortran 90
    -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
    -- Could NOT find GOOGLEHASH (missing:  GOOGLEHASH_INCLUDES GOOGLEHASH_COMPILE)
    -- Could NOT find ADOLC (missing:  ADOLC_INCLUDES ADOLC_LIBRARIES)
    -- Found MPFR: /playpen/username/libraries/anaconda3/include (Required is at least version "2.3.0")
    -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
    -- Found FFTW: /usr/include
    -- Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.7")
    -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
    -- Could NOT find PASTIX (missing:  PASTIX_INCLUDES PASTIX_LIBRARIES)
    -- Could NOT find SCOTCH (missing:  SCOTCH_INCLUDES SCOTCH_LIBRARIES)
    -- Could NOT find METIS (missing:  METIS_INCLUDES METIS_LIBRARIES)
    -- ************************************************************
    -- ***    Eigen's unit tests configuration summary          ***
    -- ************************************************************
    --
    -- Build type:        Release
    -- Build site:        vision29.cs.unc.edu
    -- Build string:      linux-4.4.0-141-generic-_-5.4.0-sse2-64bit
    -- Enabled backends:  Cholmod,  UmfPack,  SuperLU,  SPQR,  Qt4 support,  MPFR C++,  fftw,
    -- Disabled backends: PaStiX,  METIS,  GoogleHash,  Adolc,  OpenGL,
    -- Default order:     Column-major
    -- Maximal matrix/vector size: 320
    -- SSE2:              Using architecture defaults
    -- SSE3:              Using architecture defaults
    -- SSSE3:             Using architecture defaults
    -- SSE4.1:            Using architecture defaults
    -- SSE4.2:            Using architecture defaults
    -- Altivec:           Using architecture defaults
    -- ARM NEON:          Using architecture defaults
    --
    CXX:               /usr/bin/c++
     CXX_VERSION:       c++ (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
     CXX_FLAGS:          -fexceptions -pedantic -Wall -Wextra -Wundef -Wcast-align -Wchar-subscripts -Wnon-virtual-dtor -Wunused-local-typedefs -Wpointer-arith -Wwrite-strings -Wformat-security -Wno-psabi -Wno-variadic-macros -Wno-long-long -fno-check-new -fno-common -fstrict-aliasing -ansi  -g2
     Sparse lib flags:   ;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;eigen_blas;eigen_lapack;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;eigen_blas;/usr/lib/x86_64-linux-gnu/libsuperlu.so;eigen_blas;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;eigen_lapack;eigen_blas

    -- ************************************************************
    --
    -- Configured Eigen 3.2.7
    --
    -- Some things you can do now:
    -- --------------+--------------------------------------------------------------
    -- Command       |   Description
    -- --------------+--------------------------------------------------------------
    -- make install  | Install to /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party. To change that:
    --               |     cmake . -DCMAKE_INSTALL_PREFIX=yourpath
    --               |   Eigen headers will then be installed to:
    --               |     /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/eigen3
    --               |   To install Eigen headers to a separate location, do:
    --               |     cmake . -DEIGEN_INCLUDE_INSTALL_DIR=yourpath
    -- make doc      | Generate the API documentation, requires Doxygen & LaTeX
    -- make check    | Build and run the unit-tests. Read this page:
    --               |   http://eigen.tuxfamily.org/index.php?title=Tests
    -- make blas     | Build BLAS library (not the same thing as Eigen)
    -- --------------+--------------------------------------------------------------
    --
    -- Looking for sys/types.h
    -- Looking for sys/types.h - found
    -- Looking for inttypes.h
    -- Looking for inttypes.h - found
    -- Looking for stddef.h
    -- Looking for stddef.h - found
    -- Looking for stdint.h
    -- Looking for stdint.h - found
    -- Check size of off_t
    -- Check size of off_t - done
    -- Looking for fseeko
    -- Looking for fseeko - found
    -- Looking for ftello
    -- Looking for ftello - found
    -- Looking for PRIdMAX
    -- Looking for PRIdMAX - found
    --
    -- ========== qhull Build Information ==========
    -- Build Version:                             7.2.0
    -- Install Prefix (CMAKE_INSTALL_PREFIX):     /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party
    -- Binary Directory (BIN_INSTALL_DIR):        /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/bin
    -- Library Directory (LIB_INSTALL_DIR):       /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/lib
    -- Include Directory (INCLUDE_INSTALL_DIR):   /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include
    -- Documentation Directory (DOC_INSTALL_DIR): /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull
    -- Man Pages Directory (MAN_INSTALL_DIR):     /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/man/man1
    -- Build Type (CMAKE_BUILD_TYPE):
    -- To override these options, add -D{OPTION_NAME}=... to the cmake command
    --   Build the debug targets                  -DCMAKE_BUILD_TYPE=Debug
    --
    -- To build and install qhull, enter "make" and "make install"
    -- To smoketest qhull, enter "ctest"
    --
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/build
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    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/eigen3/Eigen/src/Eigenvalues/HessenbergDecomposition.h
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    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/eigen3/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
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    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullLinkedList.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullPoint.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullPoints.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullPointSet.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullQh.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullRidge.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullSet.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullSets.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullStat.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullVertex.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/QhullVertexSet.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/RboxPoints.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/RoadError.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/RoadLogEvent.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/libqhullcpp/RoadTest.h
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/man/man1/qhull.1
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/man/man1/rbox.1
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/README.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/REGISTER.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/Announce.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/COPYING.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/index.htm
    -- Up-to-date: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qhull.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optc.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--cone.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qhalf.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-get.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/rbox.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--4d.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-quick.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optp.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qvoronoi.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--dt.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--geom.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optg.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--half.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-opto.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/rbox.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-impre.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qhull.man
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qhull.txt
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qhull-cpp.xml
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qdelaun.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/normal_voronoi_knauss_oesterle.jpg
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optf.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optt.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qvoron_f.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/rbox.man
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh--rand.gif
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-eg.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/index.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qconvex.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-optq.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-faq.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qdelau_f.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/doc/qhull/qh-code.htm
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/include/polyclipping/clipper.hpp
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/lib/libpolyclipping.so.19.0.0
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/lib/libpolyclipping.so.19
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/lib/libpolyclipping.so
    -- Installing: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/../python/pymesh/third_party/share/pkgconfig/polyclipping.pc
    -- 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
    -- Performing Test IS_SUPPORTED_-Wno-deprecated-declarations
    -- Performing Test IS_SUPPORTED_-Wno-deprecated-declarations - Success
    -- Found Eigen: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include/eigen3
    -- Found PythonInterp: /playpen/username/projects/sumo-challenge/sumo-api/venv/bin/python (found version "3.7.2")
    -- Found Python: /playpen/username/libraries/anaconda3/envs/mapped-conv/include/python3.7m
    -- Found NumPy: version "1.16.1" /playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/numpy/core/include
    -- Found SWIG: /usr/bin/swig3.0 (found version "3.0.8")
    -- Found OpenCL: /usr/lib/x86_64-linux-gnu/libOpenCL.so
    -- SparseHash not found, consider set $SPARSEHASH_PATH environment variable (missing:  SPARSEHASH_INCLUDE_DIRS)
    -- Boost version: 1.58.0
    -- Build type: Release
    -- USING CXXFLAGS = ' -std=c++11 -Wno-deprecated-declarations -O3 -DNDEBUG -Os'
    -- USING EXEFLAGS = ' '
    -- Targetting Unix Makefiles
    -- Using /usr/bin/c++ compiler.
    -- Requested component: MPFR
    -- Requested component: GMP
    -- Found Qhull: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/lib/libqhull.so
    -- Found Quartet: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include/quartet
    -- Found Triangle: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/lib/libtriangle.a
    -- Found Tetgen: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include
    -- Found Cork: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include
    -- Found Clipper: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include/polyclipping
    -- Found LIBIGL: /tmp/pip-install-6k9dk3c1/pymesh2/third_party/libigl/include
    -- Found CARVE: /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/include
    -- BSP library cannot be found.  Consider set BSP_PATH environment variable (missing:  BSP_INCLUDE_DIRS BSP_LIBRARIES)
    -- Looking for sgemm_
    -- Looking for sgemm_ - found
    -- A library with BLAS API found.
    -- Found UMFPACK: /usr/include/suitesparse
    -- Found CHOLMOD: /usr/include/suitesparse
    -- METIS library cannot be found.  Consider set METIS_PATH environment variable (missing:  METIS_INCLUDE_DIRS METIS_LIBRARIES)
    -- tinyxml2 library cannot be found.  Consider set TINYXML2_PATH environment variable (missing:  TINYXML2_INCLUDE_DIRS TINYXML2_LIBRARIES)
    -- Looking for cheev_
    -- Looking for cheev_ - not found
    -- Looking for cheev
    -- Looking for cheev - not found
    -- Looking for cheev_
    -- Looking for cheev_ - found
    -- A library with LAPACK API found.
    -- GeoGram library cannot be found.  Consider set GEOGRAM_PATH environment variable (missing:  GEOGRAM_INCLUDE_DIRS GEOGRAM_LIBRARIES)
    -- CMAKE_INSTALL_RPATH: /usr/local/pymesh-0.1.14-py3.7.egg/pymesh/lib;/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pymesh-0.1.14-py3.7.egg/pymesh/lib;/home/username/.local/lib/python3.7/site-packages/pymesh-0.1.14-py3.7.egg/pymesh/lib;/usr/local/pymesh-0.1.14-py3.7.egg/pymesh/third_party/lib;/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pymesh-0.1.14-py3.7.egg/pymesh/third_party/lib;/home/username/.local/lib/python3.7/site-packages/pymesh-0.1.14-py3.7.egg/pymesh/third_party/lib;/usr/local/pymesh/lib;/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pymesh/lib;/home/username/.local/lib/python3.7/site-packages/pymesh/lib;/usr/local/pymesh/third_party/lib;/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pymesh/third_party/lib;/home/username/.local/lib/python3.7/site-packages/pymesh/third_party/lib;/tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/lib;/tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/third_party/lib
    CMake Warning at tools/CMakeLists.txt:103 (MESSAGE):
      SparseSolver module is not built because Metis is missing

    -- Looking for pthread.h
    -- Looking for pthread.h - found
    -- Looking for pthread_create
    -- Looking for pthread_create - not found
    -- Looking for pthread_create in pthreads
    -- Looking for pthread_create in pthreads - not found
    -- Looking for pthread_create in pthread
    -- Looking for pthread_create in pthread - found
    -- Found Threads: TRUE
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /tmp/pip-install-6k9dk3c1/pymesh2/build
    Scanning dependencies of target Mesh
    [  0%] Building CXX object src/CMakeFiles/Mesh.dir/Misc/HashGrid.cpp.o
    [  0%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/FaceCentroidAttribute.cpp.o
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    [  5%] Building CXX object src/CMakeFiles/Mesh.dir/Geometry/MeshGeometry.cpp.o
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    [ 16%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexMeanCurvatureAttribute.cpp.o
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    [ 27%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexGaussianCurvatureAttribute.cpp.o
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    [ 27%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/FaceCircumCenterAttribute.cpp.o
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    [ 33%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/FaceAreaAttribute.cpp.o
    [ 33%] Building CXX object src/CMakeFiles/Mesh.dir/MeshFactory.cpp.o
    [ 38%] Building CXX object src/CMakeFiles/Mesh.dir/Connectivity/MeshConnectivity.cpp.o
    [ 38%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VoxelVolumeAttribute.cpp.o
    [ 38%] Building CXX object src/CMakeFiles/Mesh.dir/IO/NodeWriter.cpp.o
    [ 44%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexLaplacianAttribute.cpp.o
    [ 44%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/FaceIncircleRadiusAttribute.cpp.o
    [ 44%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexValanceAttribute.cpp.o
    [ 44%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexIndexAttribute.cpp.o
    [ 44%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MeshParser.cpp.o
    [ 50%] Building CXX object src/CMakeFiles/Mesh.dir/IO/PLYParser.cpp.o
    [ 55%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MSHParser.cpp.o
    [ 61%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/VertexVolumeAttribute.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/FaceCircumRadiusAttribute.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/IO/POLYWriter.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/IO/PLYWriter.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/IO/NodeParser.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/Attributes/MeshAttributeFactory.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/Math/ZSparseMatrix.cpp.o
    [ 66%] Building CXX object src/CMakeFiles/Mesh.dir/IO/POLYParser.cpp.o
    [ 72%] Building CXX object src/CMakeFiles/Mesh.dir/IO/STLWriter.cpp.o
    [ 72%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MEDITParser.cpp.o
    [ 72%] Building CXX object src/CMakeFiles/Mesh.dir/IO/OFFParser.cpp.o
    [ 77%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MEDITWriter.cpp.o
    [ 77%] Building CXX object src/CMakeFiles/Mesh.dir/IO/OBJWriter.cpp.o
    [ 77%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MeshWriter.cpp.o
    [ 83%] Building CXX object src/CMakeFiles/Mesh.dir/IO/OBJParser.cpp.o
    [ 83%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MshLoader.cpp.o
    [ 83%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MshSaver.cpp.o
    [ 83%] Building CXX object src/CMakeFiles/Mesh.dir/IO/MSHWriter.cpp.o
    [ 88%] Building CXX object src/CMakeFiles/Mesh.dir/IO/IOUtils.cpp.o
    [ 88%] Building CXX object src/CMakeFiles/Mesh.dir/IO/STLParser.cpp.o
    [ 94%] Building C object src/CMakeFiles/Mesh.dir/IO/rply.c.o
    [ 94%] Building CXX object src/CMakeFiles/Mesh.dir/IO/OFFWriter.cpp.o
    [ 94%] Linking CXX shared library ../../python/pymesh/lib/libMesh.so
    [ 94%] Built target Mesh
    [ 94%] Swig source
    /tmp/pip-install-6k9dk3c1/pymesh2/src/Mesh.h:47: Warning 362: operator= ignored
    /tmp/pip-install-6k9dk3c1/pymesh2/src/Math/ZSparseMatrix.h:20: Warning 362: operator= ignored
    /tmp/pip-install-6k9dk3c1/pymesh2/src/Math/ZSparseMatrix.h:10: Warning 401: Nothing known about base class 'Eigen::SparseMatrix< Float,Eigen::ColMajor,int >'. Ignored.
    /tmp/pip-install-6k9dk3c1/pymesh2/src/Math/ZSparseMatrix.h:10: Warning 401: Maybe you forgot to instantiate 'Eigen::SparseMatrix< Float,Eigen::ColMajor,int >' using %template.
    Scanning dependencies of target _PyMesh
    [ 94%] Building CXX object src/CMakeFiles/_PyMesh.dir/__/python/pymesh/swig/PyMeshPYTHON_wrap.cxx.o
    In file included from /playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                     from /playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from /tmp/pip-install-6k9dk3c1/pymesh2/python/pymesh/swig/PyMeshPYTHON_wrap.cxx:3175:
    /playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it with " \
      ^
    [100%] Linking CXX shared module ../../python/pymesh/lib/_PyMesh.so
    lto1: fatal error: bytecode stream generated with LTO version 6.0 instead of the expected 4.1
    compilation terminated.
    lto-wrapper: fatal error: /usr/bin/c++ returned 1 exit status
    compilation terminated.
    /usr/bin/ld: error: lto-wrapper failed
    collect2: error: ld returned 1 exit status
    src/CMakeFiles/_PyMesh.dir/build.make:116: recipe for target '../python/pymesh/lib/_PyMesh.so' failed
    make[2]: *** [../python/pymesh/lib/_PyMesh.so] Error 1
    CMakeFiles/Makefile2:87: recipe for target 'src/CMakeFiles/_PyMesh.dir/all' failed
    make[1]: *** [src/CMakeFiles/_PyMesh.dir/all] Error 2
    Makefile:83: recipe for target 'all' failed
    make: *** [all] Error 2
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-6k9dk3c1/pymesh2/setup.py", line 147, in <module>
        distclass=BinaryDistribution,
      File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup
        return distutils.core.setup(**attrs)
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-6k9dk3c1/pymesh2/setup.py", line 81, in run
        self.build_pymesh();
      File "/tmp/pip-install-6k9dk3c1/pymesh2/setup.py", line 73, in build_pymesh
        check_call(command.split());
      File "/playpen/username/libraries/anaconda3/envs/mapped-conv/lib/python3.7/subprocess.py", line 347, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['make', '-j', '47']' returned non-zero exit status 2.
    Running setup.py install for pymesh2: finished with status 'error'
Cleaning up...
  Removing source in /tmp/pip-install-6k9dk3c1/pymesh2
  Removing source in /tmp/pip-install-6k9dk3c1/sklearn
  Removing source in /tmp/pip-install-6k9dk3c1/sympy
  Removing source in /tmp/pip-install-6k9dk3c1/transforms3d
Removed build tracker '/tmp/pip-req-tracker-04ux47ru'
Exception information:
Traceback (most recent call last):
  File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 179, in main
    status = self.run(options, args)
  File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 393, in run
    use_user_site=options.use_user_site,
  File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pip/_internal/req/__init__.py", line 57, in install_given_reqs
    **kwargs
  File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 945, in install
    spinner=spinner,
  File "/playpen/username/projects/sumo-challenge/sumo-api/venv/lib/python3.7/site-packages/pip/_internal/utils/misc.py", line 761, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip._internal.exceptions.InstallationError: Command "/playpen/username/projects/sumo-challenge/sumo-api/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-6k9dk3c1/pymesh2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-0v5scnvh/install-record.txt --single-version-externally-managed --compile --install-headers /playpen/username/projects/sumo-challenge/sumo-api/venv/include/site/python3.7/pymesh2" failed with error code 1 in /tmp/pip-install-6k9dk3c1/pymesh2/
dhuber23b commented 5 years ago

I tested the install of pymesh2 standalone as well as the entire sumo install instructions on Ubuntu 16.04, which is the linux version that is currently supported, and it is working. What operating system is causing this problem?

meder411 commented 5 years ago

Hm. I'm using Ubuntu 16.04.5 LTS (GNU/Linux 4.4.0-141-generic x86_64). Must be some other issue on my system. Some other folks I know have been having trouble with install pymesh2 independently from SUMO also, so it might be our servers. I will investigate further. Thanks for checking on this.

dhuber23b commented 5 years ago

Ok, I will close this issue then.

meder411 commented 5 years ago

@dhuber23b Just a heads up that I identified the problem as being due to the use of Anaconda python. The key error was: 

lto1: fatal error: bytecode stream generated with LTO version 6.0 instead of the expected 4.1 compilation terminated.

It showed up in some unrelated issue here and the solution there was to only use the conda installer. That's not quite possible here, but it might be worth mentioning in the docs that users should use the system python (or avoid conda for this). When I switched to system python everything installed fine.