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 >
