[petsc-users] petsc4py f2py

[Smith, Barry F.]

  Maybe it is not processing the 

#include <petsc/finclude/petscdm.h>

as expected? Could you run with the -E option to see what it puts in for the include file?

  Barry

> On Jan 18, 2018, at 9:56 AM, Aurelien Ponte <aurelien.ponte at ifremer.fr> wrote:
> 
> Hi,
> I am trying to speed up with f2py part of a python code that depends on petsc4py
> and cannot compile the fortran library.
> The error message are at the end of this message.
> The code is found here:
> https://github.com/apatlpo/qgsolver/tree/fwrapping/qgsolver
> This attempt borrows heavily from petsc4py/demo/wrap-f2py.
> The error 'Unexpected MODULE statement' does not get lot's of replies on google unfortunately
> Would you have any suggestions?
> 
> thanks
> aurélien
> 
> 
> (petsc) br146-244:qgsolver aponte$ make PYTHON=/Users/aponte/.miniconda3/envs/petsc/bin/python build
> /Users/aponte/.miniconda3/envs/petsc/bin:/opt/local/bin:/opt/local/sbin:/Users/aponte/.miniconda3/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin:/usr/local/bin:/Users/aponte/Installed/f90tohtml:/usr/local/mysql/bin:/Users/aponte/Tools/ftagshtml-0.520/bin:/usr/local/ferret/bin:/usr/local/bin:/Users/aponte/Installed/f90tohtml:/usr/local/mysql/bin:/Users/aponte/Tools/ftagshtml-0.520/bin:/usr/local/ferret/bin
> /Users/aponte/.miniconda3/envs/petsc/bin/python
> /bin/sh
> env \
>         F77="/opt/local/bin/mpif90-openmpi-gcc49" F77FLAGS="-Os -Os  -I/opt/local/include" \
>         F90="/opt/local/bin/mpif90-openmpi-gcc49" F90FLAGS="-Os -Os  -I/opt/local/include" \
>         LDSHARED="/opt/local/bin/mpif90-openmpi-gcc49" \
>     /Users/aponte/.miniconda3/envs/petsc/bin/python setup.py -q build_ext --inplace
> Reading .f2py_f2cmap ...
>     Mapping "integer(kind=HANDLE_KIND)" to "long"
>     Mapping "integer(kind=handle_kind)" to "long"
> Successfully applied user defined changes from .f2py_f2cmap
> In file included from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
>                  from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
>                  from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from build/src.macosx-10.9-x86_64-3.6/./fortranobject.h:13,
>                  from ./timestepper_advmodule.c:18:
> /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>  #warning "Using deprecated NumPy API, disable it by " \
>   ^
> In file included from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
>                  from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
>                  from /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from build/src.macosx-10.9-x86_64-3.6/./fortranobject.h:13,
>                  from build/src.macosx-10.9-x86_64-3.6/./fortranobject.c:2:
> /Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>  #warning "Using deprecated NumPy API, disable it by " \
>   ^
> build/src.macosx-10.9-x86_64-3.6/./fortranobject.c: In function 'format_def':
> build/src.macosx-10.9-x86_64-3.6/./fortranobject.c:138:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>          if (size < sizeof(notalloc)) {
>                   ^
> ./timestepper_adv.F90:9.22:
> 
> module timestepper_adv
>                       1
> Error: Unexpected MODULE statement at (1)
> ./timestepper_adv.F90:11.11:
> 
>   use petsc
>            1
> Error: Unexpected USE statement at (1)
> ./timestepper_adv.F90:12.15:
> 
>   implicit none
>                1
> Error: Unexpected IMPLICIT NONE statement at (1)
> ./timestepper_adv.F90:14.15:
> 
>   type gridinfo
>                1
> 
> ...
> 
> Error: Symbol 'grd' at (1) has no IMPLICIT type
> ./timestepper_adv.F90:59.18:
> 
>     type(gridinfo) grd
>                   1
> Error: Derived type 'gridinfo' at (1) is being used before it is defined
> Fatal Error: Error count reached limit of 25.
> error: Command "/opt/local/bin/mpif90-openmpi-gcc49 -Os -Os -I/opt/local/include -arch x86_64 -fPIC -O3 -funroll-loops -DF2PY_REPORT_ON_ARRAY_COPY=1 -I/opt/local/lib/petsc/include -I/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/petsc4py/include -I. -Ibuild/src.macosx-10.9-x86_64-3.6/. -I/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include -I/Users/aponte/.miniconda3/envs/petsc/include/python3.6m -c -c ./timestepper_adv.F90 -o build/temp.macosx-10.9-x86_64-3.6/timestepper_adv.o -Jbuild/temp.macosx-10.9-x86_64-3.6/ -Ibuild/temp.macosx-10.9-x86_64-3.6/" failed with exit status 1
> make: *** [timestepper_adv.so] Error 1
> 
> -- 
> Aurélien Ponte
> Tel: (+33) 2 98 22 40 73
> Fax: (+33) 2 98 22 44 96
> UMR 6523, IFREMER
> ZI de la Pointe du Diable
> CS 10070
> 29280 Plouzané
>