[petsc-users] petsc4py f2py

[Smith, Barry F.]

Fatal Error: Can't open module file 'petsc.mod' for reading at (1): No such file or directory
error: Command "/opt/local/bin/gfortran -Wall -g -fno-second-underscore -DF2PY_REPORT_ON_ARRAY_COPY=1 -I/Users/aponte/.miniconda3/envs/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/"

Normally the module files like petsc.mod would be in the $PETSC_DIR/$PETSC_ARCH/include so in your case I'm guessing /Users/aponte/.miniconda3/envs/petsc/include 

so first do and ls and see if there are any *.mod files in that directory?

Barry


> On Jan 18, 2018, at 10:17 PM, Aurelien Ponte <aurelien.ponte at ifremer.fr> wrote:
> 
> Ok, I believe I made some progress.
> I found one more issue: PETSC_DIR was pointing toward an old macport install of petsc
> This is fixed now and here is what I have (without -E):
> 
> (petsc) barracuda:qgsolver aponte$ make PYTHON=~/.miniconda3/envs/petsc/bin/python PETSC_DIR=~/.miniconda3/envs/petsc build
> env \
>     F77="" F77FLAGS="" \
>     F90="" F90FLAGS="" \
>     LDSHARED="" \
>     /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.F90:11.6:
> 
>   use petsc
>       1
> Fatal Error: Can't open module file 'petsc.mod' for reading at (1): No such file or directory
> ./timestepper_adv.F90:11.6:
> 
>   use petsc
>       1
> Fatal Error: Can't open module file 'petsc.mod' for reading at (1): No such file or directory
> error: Command "/opt/local/bin/gfortran -Wall -g -fno-second-underscore -DF2PY_REPORT_ON_ARRAY_COPY=1 -I/Users/aponte/.miniconda3/envs/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
> 
> -- 
> 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
>