Re: setting up relax on mac -- August 10, 2013 - 23:28

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 <paul.schanda@xxxxxx> 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
> paul.schanda@xxxxxx
> http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en