[petsc-users] petsc4py f2py

[Aurelien Ponte]

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
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