pythonpipanacondampi4pypetsc

Issue installing petsc4py with Anaconda using pip, to indicate external PETSc directory

I) The issue

I cannot install petsc4py in my Anaconda environment using pip.

Installing with conda doesn't work because it won't check my predefined PETSC_DIR and PETSC_ARCH environment variables during installation. numpy and cython are installed.

The error output by pip install is shown in section IV, below.

II) Versions

I have Ananconda 2020.02, installed with Python 3.7. My OS is Ubuntu 18.04.

III) Reproducing the issue

1) Make a user installation of OpenMPI 4.0.3

Configured using

--prefix="/home/$USER/.openmpi" CC=gcc FC=gfortran

Then make and make install.

Add .openmpi/bin file to PATH and add .openmpi/lib to LD_LIBRARY_PATH:

export PATH=/home/$USER/.openmpi/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/$USER/.openmpi/lib/

2) Install PETSc 3.13

Configured indicating mpicc and mpifort from /home/$USER/.openmpi/bin and downloading blas/lapack, scalapack, MUMPS, METIS, PARMETIS and PTSCOTCH, with -O2 compiler optimization (Note: I used MKL for blas/lapack and scalapack). Also indicate PETSC_DIR folder location and PETSC_ARCH name in ./configure. I chose the option of no C++ compilers.

Then make all and make check. I also did a make test, which took quite a while. There were no failures, only success, skip and to do.

export PETSC_DIR and PETSC_ARCH (important for pets4py).

3) Install mpi4py using pip

I installed this using pip, because mpi4py cannot be installed using conda while indicating a custom mpicc path, according to the answer to my question provided by Iliev in this link in Stack Overflow.

4) Try to install petsc4py using pip

I wrote using --no-cache-dir:

pip install --no-cache-dir petsc4py

The build failed. The information displayed in the terminal is shown in the next section.

IV) The errors

The errors are shown below.

(Bonus meta question: is there a way to set automatic line break in the code fences in Stack Overflow?)

Collecting petsc4py
  Downloading petsc4py-3.12.0.tar.gz (1.8 MB)
     |████████████████████████████████| 1.8 MB 2.8 MB/s 
Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from petsc4py) (1.18.1)
Building wheels for collected packages: petsc4py
  Building wheel for petsc4py (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-khk8pv9d
       cwd: /tmp/pip-install-5qdqmoex/petsc4py/
  Complete output (97 lines):
  running bdist_wheel
  running build
  running build_src
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/petsc4py
  copying src/PETSc.py -> build/lib.linux-x86_64-3.7/petsc4py
  copying src/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py
  copying src/__main__.py -> build/lib.linux-x86_64-3.7/petsc4py
  creating build/lib.linux-x86_64-3.7/petsc4py/lib
  copying src/lib/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py/lib
  creating build/lib.linux-x86_64-3.7/petsc4py/include
  creating build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
  copying src/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py
  copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.7/petsc4py/lib
  running build_ext
  PETSC_DIR:    /home/breno/Documents/petsc
  PETSC_ARCH:   MUMPS-mkl-real-opt
  version:      3.13.0 release
  integer-size: 32-bit
  scalar-type:  real
  precision:    double
  language:     CONLY
  compiler:     /home/breno/.openmpi/bin/mpicc
  linker:       /home/breno/.openmpi/bin/mpicc
  building 'PETSc' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt
  creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src
  /home/breno/.openmpi/bin/mpicc -pthread -B /home/breno/anaconda3/compiler_compat -Wl,--sysroot=/ -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -O2 -march=native -mtune=native -fPIC -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/breno/Documents/petsc/MUMPS-mkl-real-opt/include -I/home/breno/Documents/petsc/include -Isrc/include -I/home/breno/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/breno/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src/PETSc.o
  In file included from src/PETSc.c:4:0:
  src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Sys_28infoAllow’:
  src/petsc4py.PETSc.c:65427:47: error: too many arguments to function ‘PetscInfoAllow’
     __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(PetscInfoAllow(__pyx_v_tval, NULL)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(27, 163, __pyx_L1_error)
                                                 ^~~~~~~~~~~~~~
  In file included from /home/breno/Documents/petsc/include/petscsys.h:1474:0,
                   from /home/breno/Documents/petsc/include/petscbag.h:4,
                   from /home/breno/Documents/petsc/include/petsc.h:5,
                   from src/petsc4py.PETSc.c:596,
                   from src/PETSc.c:4:
  /home/breno/Documents/petsc/include/petsclog.h:56:29: note: declared here
   PETSC_EXTERN PetscErrorCode PetscInfoAllow(PetscBool);
                               ^~~~~~~~~~~~~~
  In file included from src/PETSc.c:4:0:
  src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_304matMultSymbolic’:
  src/petsc4py.PETSc.c:148044:47: warning: implicit declaration of function ‘MatMatMultSymbolic’; did you mean ‘MatProductSymbolic’? [-Wimplicit-function-declaration]
     __pyx_t_5 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultSymbolic(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_rval, (&__pyx_v_result->mat))); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(36, 1309, __pyx_L1_error)
                                                 ^~~~~~~~~~~~~~~~~~
                                                 MatProductSymbolic
  src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_306matMultNumeric’:
  src/petsc4py.PETSc.c:148235:47: warning: implicit declaration of function ‘MatMatMultNumeric’; did you mean ‘MatProductNumeric’? [-Wimplicit-function-declaration]
     __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultNumeric(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_result->mat)); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(36, 1317, __pyx_L1_error)
                                                 ^~~~~~~~~~~~~~~~~
                                                 MatProductNumeric
  src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_6DMStag_54get1DCoordinateLocationSlot’:
  src/petsc4py.PETSc.c:265960:3: warning: ‘DMStagGet1dCoordinateLocationSlot’ is deprecated [-Wdeprecated-declarations]
     __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMStagGet1dCoordinateLocationSlot(__pyx_v_self->__pyx_base.dm, __pyx_v_sloc, (&__pyx_v_slot))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(47, 274, __pyx_L1_error)
     ^~~~~~~~~
  In file included from /home/breno/Documents/petsc/include/petsc.h:22:0,
                   from src/petsc4py.PETSc.c:596,
                   from src/PETSc.c:4:
  /home/breno/Documents/petsc/include/petscdmstag.h:127:130: note: declared here
   PETSC_DEPRECATED_FUNCTION("Use DMStagGetProductCoordinateLocationSlot() (since version 3.13") PETSC_STATIC_INLINE PetscErrorCode DMStagGet1dCoordinateLocationSlot(DM dm,DMStagStencilLocation loc,PetscInt *s) {return DMStagGetProductCoordinateLocationSlot(dm,loc,s);}
                                                                                                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from src/PETSc.c:4:0:
  src/petsc4py.PETSc.c: In function ‘__pyx_pymod_exec_PETSc’:
  src/petsc4py.PETSc.c:309773:43: error: ‘MATLMVMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBROYDEN’?
     __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 78, __pyx_L1_error)
                                             ^~~~~~~~~~~
                                             MATLMVMBROYDEN
  src/petsc4py.PETSc.c:309773:43: note: each undeclared identifier is reported only once for each function it appears in
  src/petsc4py.PETSc.c:309785:43: error: ‘MATLMVMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBRDN’?
     __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 79, __pyx_L1_error)
                                             ^~~~~~~~~~~~~~
                                             MATLMVMBRDN
  src/petsc4py.PETSc.c:309797:43: error: ‘MATLMVMSYMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’?
     __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 80, __pyx_L1_error)
                                             ^~~~~~~~~~~~~~
                                             MATLMVMBADBRDN
  src/petsc4py.PETSc.c:309809:43: error: ‘MATLMVMSYMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMSYMBRDN’?
     __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 81, __pyx_L1_error)
                                             ^~~~~~~~~~~~~~~~~
                                             MATLMVMSYMBRDN
  src/petsc4py.PETSc.c:309821:43: error: ‘MATLMVMDIAGBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’?
     __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMDIAGBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 82, __pyx_L1_error)
                                             ^~~~~~~~~~~~~~~
                                             MATLMVMBADBRDN
  error: command '/home/breno/.openmpi/bin/mpicc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for petsc4py
  Running setup.py clean for petsc4py
Failed to build petsc4py
Installing collected packages: petsc4py
    Running setup.py install for petsc4py ... error
    ERROR: Command errored out with exit status 1:
     command: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/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-_npojm20/install-record.txt --single-version-externally-managed --compile --install-headers /home/breno/anaconda3/include/python3.7m/petsc4py
         cwd: /tmp/pip-install-5qdqmoex/petsc4py/
    Complete output (97 lines):
    running install
    running build
    running build_src
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/petsc4py
    copying src/PETSc.py -> build/lib.linux-x86_64-3.7/petsc4py
    copying src/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py
    copying src/__main__.py -> build/lib.linux-x86_64-3.7/petsc4py
    creating build/lib.linux-x86_64-3.7/petsc4py/lib
    copying src/lib/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py/lib
    creating build/lib.linux-x86_64-3.7/petsc4py/include
    creating build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py
    copying src/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py
    copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.7/petsc4py/lib
    running build_ext
    PETSC_DIR:    /home/breno/Documents/petsc
    PETSC_ARCH:   MUMPS-mkl-real-opt
    version:      3.13.0 release
    integer-size: 32-bit
    scalar-type:  real
    precision:    double
    language:     CONLY
    compiler:     /home/breno/.openmpi/bin/mpicc
    linker:       /home/breno/.openmpi/bin/mpicc
    building 'PETSc' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt
    creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src
    /home/breno/.openmpi/bin/mpicc -pthread -B /home/breno/anaconda3/compiler_compat -Wl,--sysroot=/ -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -O2 -march=native -mtune=native -fPIC -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/breno/Documents/petsc/MUMPS-mkl-real-opt/include -I/home/breno/Documents/petsc/include -Isrc/include -I/home/breno/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/breno/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src/PETSc.o
    In file included from src/PETSc.c:4:0:
    src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Sys_28infoAllow’:
    src/petsc4py.PETSc.c:65427:47: error: too many arguments to function ‘PetscInfoAllow’
       __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(PetscInfoAllow(__pyx_v_tval, NULL)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(27, 163, __pyx_L1_error)
                                                   ^~~~~~~~~~~~~~
    In file included from /home/breno/Documents/petsc/include/petscsys.h:1474:0,
                     from /home/breno/Documents/petsc/include/petscbag.h:4,
                     from /home/breno/Documents/petsc/include/petsc.h:5,
                     from src/petsc4py.PETSc.c:596,
                     from src/PETSc.c:4:
    /home/breno/Documents/petsc/include/petsclog.h:56:29: note: declared here
     PETSC_EXTERN PetscErrorCode PetscInfoAllow(PetscBool);
                                 ^~~~~~~~~~~~~~
    In file included from src/PETSc.c:4:0:
    src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_304matMultSymbolic’:
    src/petsc4py.PETSc.c:148044:47: warning: implicit declaration of function ‘MatMatMultSymbolic’; did you mean ‘MatProductSymbolic’? [-Wimplicit-function-declaration]
       __pyx_t_5 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultSymbolic(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_rval, (&__pyx_v_result->mat))); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(36, 1309, __pyx_L1_error)
                                                   ^~~~~~~~~~~~~~~~~~
                                                   MatProductSymbolic
    src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_306matMultNumeric’:
    src/petsc4py.PETSc.c:148235:47: warning: implicit declaration of function ‘MatMatMultNumeric’; did you mean ‘MatProductNumeric’? [-Wimplicit-function-declaration]
       __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultNumeric(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_result->mat)); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(36, 1317, __pyx_L1_error)
                                                   ^~~~~~~~~~~~~~~~~
                                                   MatProductNumeric
    src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_6DMStag_54get1DCoordinateLocationSlot’:
    src/petsc4py.PETSc.c:265960:3: warning: ‘DMStagGet1dCoordinateLocationSlot’ is deprecated [-Wdeprecated-declarations]
       __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMStagGet1dCoordinateLocationSlot(__pyx_v_self->__pyx_base.dm, __pyx_v_sloc, (&__pyx_v_slot))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(47, 274, __pyx_L1_error)
       ^~~~~~~~~
    In file included from /home/breno/Documents/petsc/include/petsc.h:22:0,
                     from src/petsc4py.PETSc.c:596,
                     from src/PETSc.c:4:
    /home/breno/Documents/petsc/include/petscdmstag.h:127:130: note: declared here
     PETSC_DEPRECATED_FUNCTION("Use DMStagGetProductCoordinateLocationSlot() (since version 3.13") PETSC_STATIC_INLINE PetscErrorCode DMStagGet1dCoordinateLocationSlot(DM dm,DMStagStencilLocation loc,PetscInt *s) {return DMStagGetProductCoordinateLocationSlot(dm,loc,s);}
                                                                                                                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    In file included from src/PETSc.c:4:0:
    src/petsc4py.PETSc.c: In function ‘__pyx_pymod_exec_PETSc’:
    src/petsc4py.PETSc.c:309773:43: error: ‘MATLMVMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBROYDEN’?
       __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 78, __pyx_L1_error)
                                               ^~~~~~~~~~~
                                               MATLMVMBROYDEN
    src/petsc4py.PETSc.c:309773:43: note: each undeclared identifier is reported only once for each function it appears in
    src/petsc4py.PETSc.c:309785:43: error: ‘MATLMVMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBRDN’?
       __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 79, __pyx_L1_error)
                                               ^~~~~~~~~~~~~~
                                               MATLMVMBRDN
    src/petsc4py.PETSc.c:309797:43: error: ‘MATLMVMSYMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’?
       __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 80, __pyx_L1_error)
                                               ^~~~~~~~~~~~~~
                                               MATLMVMBADBRDN
    src/petsc4py.PETSc.c:309809:43: error: ‘MATLMVMSYMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMSYMBRDN’?
       __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 81, __pyx_L1_error)
                                               ^~~~~~~~~~~~~~~~~
                                               MATLMVMSYMBRDN
    src/petsc4py.PETSc.c:309821:43: error: ‘MATLMVMDIAGBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’?
       __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMDIAGBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 82, __pyx_L1_error)
                                               ^~~~~~~~~~~~~~~
                                               MATLMVMBADBRDN
    error: command '/home/breno/.openmpi/bin/mpicc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/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-_npojm20/install-record.txt --single-version-externally-managed --compile --install-headers /home/breno/anaconda3/include/python3.7m/petsc4py Check the logs for full command output.
Solution

  • I was trying to install petsc4py with the then latest released version 3.12.0 while having installed and configured PETSc version 3.13.0. This now seems quite obvious that it wouldn't work, but there wasn't a clear mention of this in the documentation.

    You can either install the none-released version using pip install https://bitbucket.org/petsc/petsc4py/issues/137/error-installing-in-anaconda-environment OR wait for it to be released officially!

    Important conclusion

    Make sure that your version of PETSc is the same as petsc4py!