Re: [f2py] compilation appears successful
Pearu Peterson <[email protected]> Fri, 18 Mar 2011 07:12:26 +0200
| Newsgroups | gmane.comp.python.f2py.user |
|---|---|
| Message-ID | <[email protected]> |
Hi, What code defines translate_1d_periodic? It seems that spheresub.f95 does not define it. You should link f2py extension against a library or object code that defines translate_1d_periodic. HTH, Pearu On Thu, Mar 17, 2011 at 10:54 PM, Paul Anton Letnes < [email protected]> wrote: > ...but it is not (it seems), as you may have guessed. I am not sure how to > go about finding the error, so I attach the error message and compilation > output, and I hope that someone wiser than me can point me in the right > direction for further debugging! > > f2py is great, but sometimes I am still stumped by (my own) confusing > errors. > > Best regards, > Paul. > > +++ Python error +++ > >>> import spheresubpy > Traceback (most recent call last): > File "<input>", line 1, in <module> > ImportError: > dlopen(/Users/paulanto/Code/NanoSpheresSubstrate/spheresubpy.so, 2): Symbol > not found: _translate_1d_periodic_ > Referenced from: /Users/paulanto/Code/NanoSpheresSubstrate/spheresubpy.so > Expected in: flat namespace > in /Users/paulanto/Code/NanoSpheresSubstrate/spheresubpy.so > > +++ Compilation output +++ > % make clean && make > [21:49:17 on > 11-03-17] > rm -f spheresubpy.so spheresub.o spheresub.mod gmon.out a.out ftest > rm -f *.pyc > rm -f tags > gfortran -fPIC -c spheresub.f95 -g -pg -fbounds-check -ftrapv > -fno-automatic -Wall -Wuninitialized -O0 -pedantic -fimplicit-none > f2py -c -m spheresubpy spheresubpy.f95 spheresub.o --f90flags=' -g -pg > -fbounds-check -ftrapv -fno-automatic -Wall -Wuninitialized -O0 -pedantic > -fimplicit-none' --f90exec=gfortran > running build > running config_cc > unifing config_cc, config, build_clib, build_ext, build commands --compiler > options > running config_fc > unifing config_fc, config, build_clib, build_ext, build commands > --fcompiler options > running build_src > build_src > building extension "spheresubpy" sources > f2py options: [] > f2py:> > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpymodule.c > creating /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > Reading fortran codes... > Reading file 'spheresubpy.f95' (format:free) > Post-processing... > Block: spheresubpy > Block: spheresubpy > In: :spheresubpy:spheresubpy.f95:spheresubpy > get_parameters: got "name 'periodic' is not defined" on 'periodic' > In: :spheresubpy:spheresubpy.f95:spheresubpy > get_parameters: got "name 'periodic' is not defined" on 'periodic' > In: :spheresubpy:spheresubpy.f95:spheresubpy > get_parameters: got "name 'periodic' is not defined" on 'periodic' > In: :spheresubpy:spheresubpy.f95:spheresubpy > get_parameters: got "name 'nrhs' is not defined" on 'nrhs' > Block: w_hlm > Block: w_coeff_index > Block: w_coeff_index_b > Block: w_calc_psi > Block: w_calc_blm > Block: w_setup_rhs > Block: w_setup_lhs > Post-processing (stage 2)... > Block: spheresubpy > Block: unknown_interface > Block: spheresubpy > Block: w_hlm > Block: w_coeff_index > Block: w_coeff_index_b > Block: w_calc_psi > Block: w_calc_blm > Block: w_setup_rhs > Block: w_setup_lhs > Building modules... > Building module "spheresubpy"... > Constructing F90 module support for "spheresubpy"... > Variables: w_periodic_2d w_periodic_no w_periodic_1d > w_nrhs > Creating wrapper for Fortran function "w_hlm"("w_hlm")... > Constructing wrapper function "spheresubpy.w_hlm"... > w_hlm = w_hlm(lj,mj,li,mi) > Creating wrapper for Fortran function > "w_coeff_index"("w_coeff_index")... > Constructing wrapper function > "spheresubpy.w_coeff_index"... > w_coeff_index = w_coeff_index(lmax,i,l,m) > Creating wrapper for Fortran function > "w_coeff_index_b"("w_coeff_index_b")... > Constructing wrapper function > "spheresubpy.w_coeff_index_b"... > w_coeff_index_b = w_coeff_index_b(lmax,i,l,m) > Constructing wrapper function > "spheresubpy.w_calc_psi"... > psi = > w_calc_psi(xs,ys,zs,spheredata,epsilon_plus,epsilon_minus,lmax,buried,alm,blm,periodic,n_unit_cells,lattice_b1,lattice_b2,lattice_xi,k1,k2) > Constructing wrapper function > "spheresubpy.w_calc_blm"... > blm = > w_calc_blm(alm,beta,spheredata,lmax,epsilon_plus,epsilon_minus,buried,periodic,lattice_b1,lattice_b2,lattice_xi,k1,k2,n_unit_cells) > Constructing wrapper function > "spheresubpy.w_setup_rhs"... > blm_rhs = > w_setup_rhs(spheredata,lmax,epsilon_plus,epsilon_minus,buried) > Constructing wrapper function > "spheresubpy.w_setup_lhs"... > a = > w_setup_lhs(spheredata,epsilon_plus,epsilon_minus,lmax,buried,periodic,n_unit_cells,lattice_b1,lattice_b2,lattice_xi,k1,k2) > Wrote C/API module "spheresubpy" to file > "/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpymodule.c" > Fortran 90 wrappers are saved to > "/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpy-f2pywrappers2.f90" > adding > '/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/fortranobject.c' > to sources. > adding > '/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7' > to include_dirs. > copying > /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c > -> > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > copying > /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.h > -> > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > adding > '/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpy-f2pywrappers2.f90' > to sources. > build_src: building npy-pkg config files > running build_ext > customize UnixCCompiler > customize UnixCCompiler using build_ext > customize NAGFCompiler > Found executable /opt/local/bin/gfortran > Could not locate executable f95 > nag: no Fortran 77 compiler found > nag: no Fortran 77 compiler found > customize AbsoftFCompiler > Could not locate executable f77 > absoft: no Fortran 77 compiler found > absoft: no Fortran 77 compiler found > customize IBMFCompiler > Could not locate executable xlf > ibm: no Fortran 77 compiler found > Could not locate executable xlf95 > ibm: no Fortran 77 compiler found > customize IntelFCompiler > Could not locate executable ifort > Could not locate executable ifc > customize GnuFCompiler > Found executable /opt/local/bin/gfortran-mp-4.4 > gnu: no Fortran 90 compiler found > gnu: no Fortran 90 compiler found > customize Gnu95FCompiler > customize Gnu95FCompiler > customize Gnu95FCompiler using build_ext > building 'spheresubpy' extension > compiling C sources > C compiler: /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic > -pipe -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes > > creating /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp- > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb > creating > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > compile options: > '-I/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > -c' > gcc-4.2: > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/fortranobject.c > gcc-4.2: > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpymodule.c > compiling Fortran 90 module sources > Fortran f77 compiler: /opt/local/bin/gfortran -Wall -ffixed-form > -fno-second-underscore -fPIC -O3 -funroll-loops > Fortran f90 compiler: gfortran -g -pg -fbounds-check -ftrapv -fno-automatic > -Wall -Wuninitialized -O0 -pedantic -fimplicit-none -fPIC -O3 -funroll-loops > Fortran fix compiler: gfortran -Wall -ffixed-form -fno-second-underscore -g > -pg -fbounds-check -ftrapv -fno-automatic -Wall -Wuninitialized -O0 > -pedantic -fimplicit-none -fPIC -O3 -funroll-loops > compile options: > '-I/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > -c' > extra options: > '-J/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/ > -I/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/' > gfortran:f90: spheresubpy.f95 > compiling Fortran sources > Fortran f77 compiler: /opt/local/bin/gfortran -Wall -ffixed-form > -fno-second-underscore -fPIC -O3 -funroll-loops > Fortran f90 compiler: gfortran -g -pg -fbounds-check -ftrapv -fno-automatic > -Wall -Wuninitialized -O0 -pedantic -fimplicit-none -fPIC -O3 -funroll-loops > Fortran fix compiler: gfortran -Wall -ffixed-form -fno-second-underscore -g > -pg -fbounds-check -ftrapv -fno-automatic -Wall -Wuninitialized -O0 > -pedantic -fimplicit-none -fPIC -O3 -funroll-loops > compile options: > '-I/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7 > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include > -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > -c' > extra options: > '-J/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/ > -I/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/' > gfortran:f90: > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpy-f2pywrappers2.f90 > /opt/local/bin/gfortran -Wall -Wall -undefined dynamic_lookup -bundle > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpymodule.o > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/fortranobject.o > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/spheresubpy.o > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb/src.macosx-10.6-x86_64-2.7/spheresubpy-f2pywrappers2.o > spheresub.o -L/opt/local/lib/gcc45/gcc/x86_64-apple-darwin10/4.5.2 > -lgfortran -o ./spheresubpy.so > running scons > Removing build directory > /var/folders/5A/5AGb4GQfEAKf-5kSrBqG+++++TI/-Tmp-/tmpZ2g_Bb > > > 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