8000 f2py undefined symbol with PGI fortran compiler and MPI calls · Issue #16481 · numpy/numpy · GitHub
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danbeibei opened this issue Jun 2, 2020 · 1 comment · Fixed by #16730
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f2py undefined symbol with PGI fortran compiler and MPI calls #16481

danbeibei opened this issue Jun 2, 2020 · 1 comment · Fixed by #16730
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component: numpy.f2py

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@danbeibei
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danbeibei commented Jun 2, 2020 •
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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.
@danbeibei danbeibei mentioned this issue Jul 2, 2020
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@danbeibei
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An other possible workaround is to define LDSHARED environment variable:
LDSHARED=mpif90 CC=gcc f2py --verbose --f90exec=mpif90 --fcompiler=pg -c helloworld.f90 -m helloworld

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ENH: Use f90 compiler specified in f2py command line args for pgi compiler
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