PETSc_api.h error when installing dolfinx main branch python from source

General
1

~/dolfinx/python/pip install .

      Testing: /home/prusso/.local/lib/python3.10/site-packages/basix
      -- 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 Boost 1.74.0 at /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0
      --   Requested configuration: QUIET REQUIRED COMPONENTS timer;filesystem
      -- Found boost_headers 1.74.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_headers-1.74.0
      -- Found boost_timer 1.74.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_timer-1.74.0
      --   [x] libboost_timer.so.1.74.0
      --   [ ] libboost_timer.a
      -- Adding boost_timer dependencies: chrono;headers
      -- Found boost_chrono 1.74.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_chrono-1.74.0
      --   [x] libboost_chrono.so.1.74.0
      --   [ ] libboost_chrono.a
      -- Adding boost_chrono dependencies: headers
      -- Found boost_filesystem 1.74.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_filesystem-1.74.0
      --   [x] libboost_filesystem.so.1.74.0
      --   [ ] libboost_filesystem.a
      -- Adding boost_filesystem dependencies: headers
      -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.70") found components: timer filesystem
      -- Found Python3: /usr/bin/python3 (found version "3.10.12") found components: Interpreter
      -- Adding /home/prusso/.local/lib/python3.10/site-packages/basix to Basix search hints
      -- HDF5: Using hdf5 compiler wrapper to determine C configuration
      -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.7") found components: C
      -- HDF5_DIR: HDF5_DIR-NOTFOUND
      -- HDF5_DEFINITIONS:
      -- HDF5_INCLUDE_DIRS: /usr/include/hdf5/openmpi
      -- HDF5_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so
      -- HDF5_HL_LIBRARIES:
      -- HDF5_C_DEFINITIONS:
      -- HDF5_C_INCLUDE_DIR:
      -- HDF5_C_INCLUDE_DIRS: /usr/include/hdf5/openmpi
      -- HDF5_C_LIBRARY:
      -- HDF5_C_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so
      -- HDF5_C_HL_LIBRARY:
      -- HDF5_C_HL_LIBRARIES:
      -- Defined targets (if any):
      -- ... hdf5::hdf5
      -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
      -- Checking for one of the modules 'PETSc;petsc'
      -- Performing Test HAVE_PEDANTIC
      -- Performing Test HAVE_PEDANTIC - Success
      -- Found petsc4py include directory at /home/prusso/.local/lib/python3.10/site-packages/petsc4py/include
      -- Found mpi4py include directory at /home/prusso/.local/lib/python3.10/site-packages/mpi4py/include
      -- Configuring done
      -- Generating done
      CMake Warning:
        Manually-specified variables were not used by the project:
      
          Python3_LIBRARIES
      
      
      -- Build files have been written to: /home/prusso/dolfinx/python/build/temp.linux-x86_64-3.10
      [ 23%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/assemble.cpp.o
      [ 23%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/dolfinx.cpp.o
      [ 23%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/common.cpp.o
      [ 30%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/fem.cpp.o
      [ 38%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/geometry.cpp.o
      [ 46%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/graph.cpp.o
      [ 53%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/io.cpp.o
      [ 61%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/la.cpp.o
      [ 69%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/log.cpp.o
      [ 76%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/mesh.cpp.o
      [ 84%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/petsc.cpp.o
      [ 92%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/refinement.cpp.o
      In file included from /home/prusso/.local/lib/python3.10/site-packages/petsc4py/include/petsc4py/../../PETSc_api.h:9,
                       from /home/prusso/.local/lib/python3.10/site-packages/petsc4py/include/petsc4py/petsc4py.h:10,
                       from /home/prusso/dolfinx/python/dolfinx/wrappers/caster_petsc.h:9,
                       from /home/prusso/dolfinx/python/dolfinx/wrappers/petsc.cpp:9:
      /home/prusso/.local/lib/python3.10/site-packages/petsc4py/include/petsc4py/../../PETSc.h:105:3: error: ‘PetscDevice’ does not name a type; did you mean ‘PetscDefined’?

For the current main branch the cpp compiled and installed. For some reason just for main branch I have this PETSc.h error. The v0.6.0’s python does work with pip install .

Anyone maybe know how to resolve this for Ubuntu jammy desktop?

2

What version of petsc4py and petsc are you running?

It doesn’t seem like there is anything that has changed Since the 0.6 release History for python/dolfinx/wrappers/caster_petsc.h - FEniCS/dolfinx · GitHub

3

So what I did to solve this problem is:

pip uninstall mpi4py, petsc4py and remove petsc stuff from ~/.local/lib/…/site-packages/petsc*

Then I used spack to install main branch and activated the environment in the terminal. The main branch needs I think a version of petsc4py not available from apt at the current time…