Oh, those are the fat3 commands! I.e. the universal binaries I build for the relax DMG distribution archive. Try:
bash-3.2$ swig -I/sw/include/suitesparse/ -I/opt/local/include -python -o build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i Regards, Edward On 10 August 2013 23:28, Edward d'Auvergne <[email protected]> wrote: > Hi, > > The swig command might be back to front, try: > > bash-3.2$ /opt/local/bin/swig -I/opt/local/include/ > -I/sw/include/suitesparse/ -python -o > build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c > -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack > scipy/sparse/linalg/dsolve/umfpack/umfpack.i > > I'll look more into that one tomorrow. > > Regards, > > Edward > > > > On 10 August 2013 22:07, Paul Schanda <[email protected]> wrote: >> Hmm, not overly successful. >> I do have the umfpack*.h files in /opt/local/include/umfpack: >> >> [new-host-2:~] paul% ls /opt/local/include/umfpack*.h >> >> /opt/local/include/umfpack.h >> /opt/local/include/umfpack_col_to_triplet.h >> /opt/local/include/umfpack_defaults.h >> /opt/local/include/umfpack_free_numeric.h >> /opt/local/include/umfpack_free_symbolic.h >> /opt/local/include/umfpack_get_determinant.h >> /opt/local/include/umfpack_get_lunz.h >> /opt/local/include/umfpack_get_numeric.h >> /opt/local/include/umfpack_get_symbolic.h >> /opt/local/include/umfpack_global.h >> /opt/local/include/umfpack_load_numeric.h >> /opt/local/include/umfpack_load_symbolic.h >> /opt/local/include/umfpack_numeric.h >> /opt/local/include/umfpack_qsymbolic.h >> /opt/local/include/umfpack_report_control.h >> /opt/local/include/umfpack_report_info.h >> /opt/local/include/umfpack_report_matrix.h >> /opt/local/include/umfpack_report_numeric.h >> /opt/local/include/umfpack_report_perm.h >> /opt/local/include/umfpack_report_status.h >> /opt/local/include/umfpack_report_symbolic.h >> /opt/local/include/umfpack_report_triplet.h >> /opt/local/include/umfpack_report_vector.h >> /opt/local/include/umfpack_save_numeric.h >> /opt/local/include/umfpack_save_symbolic.h >> /opt/local/include/umfpack_scale.h >> /opt/local/include/umfpack_solve.h >> /opt/local/include/umfpack_symbolic.h >> /opt/local/include/umfpack_tictoc.h >> /opt/local/include/umfpack_timer.h >> /opt/local/include/umfpack_transpose.h >> /opt/local/include/umfpack_triplet_to_col.h >> /opt/local/include/umfpack_wsolve.h >> [new-host-2:~] paul% >> >> >> However, I tried using swig, and pointing to /opt/local/include as you >> suggest (trying some variations of the command), but was unsuccessful. >> >> bash-3.2$ /opt/local/bin/swig -I/sw/include/suitesparse/ -python -o >> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:192: Error: Unable to find >> 'umfpack.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:193: Error: Unable to find >> 'umfpack_solve.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:194: Error: Unable to find >> 'umfpack_defaults.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:195: Error: Unable to find >> 'umfpack_triplet_to_col.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:196: Error: Unable to find >> 'umfpack_col_to_triplet.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:197: Error: Unable to find >> 'umfpack_transpose.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:198: Error: Unable to find >> 'umfpack_scale.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:200: Error: Unable to find >> 'umfpack_report_symbolic.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:201: Error: Unable to find >> 'umfpack_report_numeric.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:202: Error: Unable to find >> 'umfpack_report_info.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:203: Error: Unable to find >> 'umfpack_report_control.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:215: Error: Unable to find >> 'umfpack_symbolic.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:216: Error: Unable to find >> 'umfpack_numeric.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:225: Error: Unable to find >> 'umfpack_free_symbolic.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:226: Error: Unable to find >> 'umfpack_free_numeric.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:248: Error: Unable to find >> 'umfpack_get_lunz.h' >> >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:272: Error: Unable to find >> 'umfpack_get_numeric.h' >> >> >> bash-3.2$ /opt/local/bin/swig -I/sw/include/suitesparse/ -python -o >> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i -I/opt/local/include/ >> >> swig error : Unrecognized option >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >> >> Use 'swig -help' for available options. >> >> >> bash-3.2$ /opt/local/bin/swig -I/opt/local/include/ -python -o >> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >> >> Unable to open file >> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c: >> No such file or directory >> >> bash-3.2$ >> >> >> In fact, I don't have build/src.macosx-10.5-fat3-2.7 >> >> I do have >> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/ but it >> is empty: >> >> bash-3.2$ ls >> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/ >> >> bash-3.2$ >> >> >> A long way to get it running... :-S >> >> paul >> >> >> >> On 10.08.13 09:39, Edward d'Auvergne wrote: >> >> Hi, >> >> Maybe the files in /opt would be sufficient. Try copying and pasting the >> swig command in my previous mail >> (http://thread.gmane.org/gmane.science.nmr.relax.devel/4339/focus=4351) and >> add -I/opt/local/include/ as that might just work. Note these compilation >> commands are for the 'sh' shell, so you need bash or sh to run them. >> >> Regards, >> >> Edward >> >> >> >> >> On Saturday, 10 August 2013, Paul Schanda wrote: >>> >>> Hi, >>> >>> I guess I'll get there. Eventually. >>> >>> In the meantime I don't find suitesparse on my system. At least not at >>> /sw/include/suitesparse. >>> >>> I have a few instances of SuiteSparse on the system, but none of them >>> contains umfpack files. >>> >>> I have a number of umfpack_*.h files, most of them at /opt/local/include: >>> /opt/local/include/umfpack.h >>> /opt/local/include/umfpack_col_to_triplet.h >>> /opt/local/include/umfpack_defaults.h >>> /opt/local/include/umfpack_free_numeric.h >>> /opt/local/include/umfpack_free_symbolic.h >>> /opt/local/include/umfpack_get_determinant.h >>> /opt/local/include/umfpack_get_lunz.h >>> /opt/local/include/umfpack_get_numeric.h >>> /opt/local/include/umfpack_get_symbolic.h >>> /opt/local/include/umfpack_global.h >>> /opt/local/include/umfpack_load_numeric.h >>> /opt/local/include/umfpack_load_symbolic.h >>> /opt/local/include/umfpack_numeric.h >>> /opt/local/include/umfpack_qsymbolic.h >>> /opt/local/include/umfpack_report_control.h >>> /opt/local/include/umfpack_report_info.h >>> /opt/local/include/umfpack_report_matrix.h >>> /opt/local/include/umfpack_report_numeric.h >>> /opt/local/include/umfpack_report_perm.h >>> /opt/local/include/umfpack_report_status.h >>> /opt/local/include/umfpack_report_symbolic.h >>> /opt/local/include/umfpack_report_triplet.h >>> /opt/local/include/umfpack_report_vector.h >>> /opt/local/include/umfpack_save_numeric.h >>> /opt/local/include/umfpack_save_symbolic.h >>> /opt/local/include/umfpack_scale.h >>> /opt/local/include/umfpack_solve.h >>> /opt/local/include/umfpack_symbolic.h >>> /opt/local/include/umfpack_tictoc.h >>> /opt/local/include/umfpack_timer.h >>> /opt/local/include/umfpack_transpose.h >>> /opt/local/include/umfpack_triplet_to_col.h >>> /opt/local/include/umfpack_wsolve.h >>> >>> >>> >>> Otherwise, I seem to have suitesparse installed via macports: >>> >>> [new-host-2:/Users/paul] root# port installed suitesparse >>> >>> The following ports are currently installed: >>> >>> SuiteSparse @3.4.0_0 >>> >>> SuiteSparse @3.4.0_3 >>> >>> SuiteSparse @4.0.0_0 >>> >>> SuiteSparse @4.1.0_0 (active) >>> >>> >>> In the suitesparse directory that is related to macports, there are no >>> umfpack files. >>> >>> [new-host-2:~] paul% ls >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/files/ >>> >>> UFconfig_UFconfig.mk-patch patch-CHOLMOD_Lib_Makefile.diff >>> >>> makefiles.patch >>> >>> [new-host-2:~] paul% ls >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/Portfile >>> >>> >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/Portfile >>> >>> >>> I could probably download SuiteSparse, but this of course comes at the >>> risk of downloading again something that does not talk to the other things >>> required... >>> As you say, it's tough with multiple python versions around... >>> >>> cheers - >>> >>> Paul >>> >>> On 09.08.13 16:30, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> You're actually almost there. That swig error with umfpack.i is >>> exactly the same problem I had yesterday when I was multiply >>> reinstalling everything on my Mac system. The problem was that it >>> could not find the suitesparse header *.h files. I found these on my >>> system at /sw/include/suitesparse - please make sure you have this >>> directory with umfpack_*.h files in it too - and that is what the >>> C_INCLUDE_PATH variable is for. The rest of the problems is due to >>> the C shell so, for avoiding a lot of pain, I would recommend >>> temporarily switching to bash. C shell issues caused the PATH error >>> message you saw. So please try the following: >>> >>> [gre:~/Downloads/scipy-0.12.0] % bash >>> gre:scipy-0.12.0 $ PATH=/usr/local/bin/:$PATH >>> C_INCLUDE_PATH=/sw/include/ >>> suitesparse/ ~/bin/python2.7 setup.py >>> install >>> >>> It is imperative to have the PATH and C_INCLUDE_PATH environmental >>> variables set this way before the Python command. Otherwise Scipy >>> will not be in a functional state and the import will give exactly the >>> error you saw. And /sw/include/suitesparse/ must exist and contain a >>> pile of umfpack_*.h files in it. We almost have it running now! Life >>> is tough having multiple Python versions around on a Mac! >>> >>> Regards, >>> >>> Edward >>> >>> >> >> >> -- >> Paul Schanda, Ph.D. >> Biomolecular NMR group >> Institut de Biologie Structurale Jean-Pierre Ebel (IBS) >> 41, rue Jules Horowitz >> F-38027 Grenoble >> France >> +33 438 78 95 55 >> [email protected] >> http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
