Description
I am trying to wrap fortran code with f2py. The fortran code includes some MPI calls and is compiled with the PGI compiler.
When importing the wrapped module in python I get this error: undefined symbol: mpi_comm_rank_
Reproducing code example:
1 ! file: helloworld.f90
2 subroutine sayhello(comm)
3 use mpi
4 implicit none
5 integer :: comm, rank, size, ierr
6 call MPI_Comm_size(comm, size, ierr)
7 call MPI_Comm_rank(comm, rank, ierr)
8 print *, 'Hello, World! I am process ',rank,' of ',size,'.'
9 end subroutine sayhello
Compilation
CC=gcc f2py --verbose --f90exec=mpif90 --fcompiler=pg -c helloworld.f90 -m helloworld
Partial output
[...]
<class 'numpy.distutils.fcompiler.pg.PGroupFCompiler'>
version_cmd = ['***/pgi/linuxpower/19.9/bin/pgfortran', '-V']
compiler_f77 = ['***/pgi/linuxpower/19.9/bin/pgfortran', '-fpic', '-Minform=inform', '-Mnosecond_underscore', '-fast']
compiler_fix = ['***/spectrum_mpi/10.03.00.01rtm3-rh7_20190611/bin/mpif90', '-Mfixed', '-fpic', '-Minform=inform', '-Mnosecond_underscore', '-fast']
compiler_f90 = ['***/spectrum_mpi/10.03.00.01rtm3-rh7_20190611/bin/mpif90', '-fpic', '-Minform=inform', '-Mnosecond_underscore', '-fast']
linker_so = ['***/pgi/linuxpower/19.9/bin/pgfortran', '-shared', '-fpic']
archiver = None
ranlib = None
linker_exe = None
version = LooseVersion ('19.9-0')
libraries = []
library_dirs = []
object_switch = '-o '
compile_switch = '-c'
include_dirs = ['***/python_venv/python_numpy_pgi_reproducer/include', '***/anaconda3/2019.03/include/python3.7m']
[...]
***/pgi/linuxpower/19.9/bin/pgfortran -shared -fpic /tmp/tmpfy731xy8/tmp/tmpfy731xy8/src.linux-ppc64le-3.7/helloworldmodule.o /tmp/tmpfy731xy8/tmp/tmpfy731xy8/src.linux-ppc64le-3.7/fortranobject.o /tmp/tmpfy731xy8/helloworld.o -o ./helloworld.cpython-37m-powerpc64le-linux-gnu.so
Removing build directory /tmp/tmpfy731xy8
The "linker_so" executable is chosen to be the pgfortran executable, whereas I would like to use the mpif90 executable instead.
This leads to the following error when importing the wrapped module from python:
$ python -c "import helloworld"
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: ***/helloworld.cpython-37m-powerpc64le-linux-gnu.so: undefined symbol: mpi_comm_rank_
System informations
$ mpif90 --version
pgf90 19.9-0 linuxpower target on Linuxpower
$ python --version
Python 3.7.3
$ python -c "import sys, numpy; print(numpy.__version__, sys.version)"
1.18.4 3.7.3 (default, Mar 27 2019, 22:31:02)
[GCC 7.3.0]
Workarround
This solves the problem in my case:
In file numpy/distutils/fcompiler/pg.py - line 36 (numpy installed version)
-'linker_so': ["pgfortran"],
+'linker_so': ["<F90>"],
The executable supplied with the --f90exec option is then the one picked to be the linker executable and the ImportError does not occur.