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/
<http://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 <http://rsync.macports.org/release/ports/math/SuiteSparse/Portfile>
/opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/Portfile
<http://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
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