[petsc-users] petsc4py f2py

[Aurelien Ponte]

there are indeed not petsc related mod files in 
/Users/aponte/.miniconda3/envs/petsc/include

I installed petsc4py via conda, may this be the issue?

aurélien


Le 19/01/2018 à 05:43, Smith, Barry F. a écrit :
> 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
>>

-- 
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