Bug#895419: Acknowledgement (python3-dolfin: JIT compilation fails as python3-instant tries to includes petsc4py from python2)
I've had that issue in the past, but never bothered looking into it. Me, I'll hold out for 2018.1 (which kills Python 2 support) to fix these kind of bugs. Cheers, Nico On Fri, Apr 13, 2018 at 4:54 PM Fabrice Silva wrote: > Additional information from Johannes Ring (fenics dev) on > https://groups.google.com/d/topic/fenics-support/mfJdWYwq0-w/discussion > >The problem is that the path to petsc4py is included in >/usr/share/dolfin/cmake/DOLFINConfig.cmake and >/usr/share/dolfin/cmake/DOLFINTargets.cmake, while it should only >have been included in /usr/share/dolfin/cmake/DOLFINPython27.cmake >and /usr/share/dolfin/cmake/DOLFINPython36.cmake. > >The quick fix would be to either install python-petsc4py (the >petsc4py include files are the same for python2 and python3) or to >remove the path to petsc4py from DOLFINConfig.cmake and >DOLFINTargets.cmake. > > These recommendations solve the trouble (even if other errors are still > raised in the overly-simplified script). > > -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#895419: Acknowledgement (python3-dolfin: JIT compilation fails as python3-instant tries to includes petsc4py from python2)
Additional information from Johannes Ring (fenics dev) on https://groups.google.com/d/topic/fenics-support/mfJdWYwq0-w/discussion The problem is that the path to petsc4py is included in /usr/share/dolfin/cmake/DOLFINConfig.cmake and /usr/share/dolfin/cmake/DOLFINTargets.cmake, while it should only have been included in /usr/share/dolfin/cmake/DOLFINPython27.cmake and /usr/share/dolfin/cmake/DOLFINPython36.cmake. The quick fix would be to either install python-petsc4py (the petsc4py include files are the same for python2 and python3) or to remove the path to petsc4py from DOLFINConfig.cmake and DOLFINTargets.cmake. These recommendations solve the trouble (even if other errors are still raised in the overly-simplified script). --- /tmp/DOLFINConfig.cmake 2018-04-13 16:27:57.189842279 +0200 +++ /usr/share/dolfin/cmake/DOLFINConfig.cmake 2018-04-13 16:28:29.169796349 +0200 @@ -40,7 +40,7 @@ set(DOLFIN_INCLUDE_DIRS "/usr/include") # Third party include directories -set(DOLFIN_3RD_PARTY_INCLUDE_DIRS "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/python2.7/dist-packages/petsc4py/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real/include;/usr/include/superlu-dist;/usr/include/hypre;/usr/include/suitesparse;/usr/include/superlu;/usr/include/scotch;/usr/include/hdf5/openmpi;") +set(DOLFIN_3RD_PARTY_INCLUDE_DIRS "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real/include;/usr/include/superlu-dist;/usr/include/hypre;/usr/include/suitesparse;/usr/include/superlu;/usr/include/scotch;/usr/include/hdf5/openmpi;") # Python variables if ("ON" AND "TRUE") --- /tmp/DOLFINTargets.cmake 2018-04-13 16:40:19.260234464 +0200 +++ /usr/share/dolfin/cmake/DOLFINTargets.cmake 2018-04-13 16:37:52.096803585 +0200 @@ -55,9 +55,9 @@ set_target_properties(dolfin PROPERTIES INTERFACE_COMPILE_DEFINITIONS "NDEBUG;DOLFIN_SIZE_T=8;DOLFIN_LA_INDEX_SIZE=4;HAS_HDF5;_FORTIFY_SOURCE=2;HAS_SLEPC;HAS_PETSC;HAS_PETSC4PY;HAS_UMFPACK;HAS_CHOLMOD;HAS_SCOTCH;HAS_ZLIB;HAS_MPI;DOLFIN_VERSION=\"2017.2.0\"" - INTERFACE_INCLUDE_DIRECTORIES "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/python2.7/dist-packages/petsc4py/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include" + INTERFACE_INCLUDE_DIRECTORIES "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include" INTERFACE_LINK_LIBRARIES "Boost::boost;Boost::timer;/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;SLEPC::slepc;PETSC::petsc;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so" - INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/python2.7/dist-packages/petsc4py/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include" + INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "/usr/include;/usr/include/eigen3;/usr/include/hdf5/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include" ) if(CMAKE_VERSION VERSION_LESS 2.8.12) -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers