> On Jan 18, 2018, at 10:48 PM, Aurelien Ponte <[email protected]> > wrote: > > 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?
I don't know. Does conda build the "Fortran" part of PETSc? If not that would explain the missing mod files. Barry > > 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 <[email protected]> >>> 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 >
