Well, there is possibly some progress. I have to admit that I have no
clue
what fat3 commands and swig exactly do, though.
The following seemed to work (or at least not produce any error
message):
bash-3.2$ pwd
/Users/paul/Downloads/scipy-0.12.0
bash-3.2$ /opt/local/bin/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
bash-3.2$
However, this does not really solve the swig problem when installing
scipy.
I guess there is still some problem with the path.
(Note that I slightly modified your command, that you suggested:
[gre:~/Downloads/scipy-0.12.0] % bash
gre:scipy-0.12.0 $ PATH=/usr/local/bin/:$PATH
C_INCLUDE_PATH=/sw/include/
suitesparse/ ~/bin/python2.7 setup.py
install
as my pythone2.7 is somewhere else)
Here is what I get.
bash-3.2$ PATH=/usr/local/bin/:$PATH
C_INCLUDE_PATH=/sw/include/suitesparse
/usr/bin/python2.7 setup.py install
Running from scipy source directory.
blas_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3',
'-I/System/Library/Frameworks/vecLib.framework/Headers']
lapack_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3']
umfpack_info:
libraries umfpack not found in
/System/Library/Frameworks/Python.framework/Versions/2.7/lib
libraries umfpack not found in /usr/local/lib
libraries umfpack not found in /usr/lib
amd_info:
libraries amd not found in
/System/Library/Frameworks/Python.framework/Versions/2.7/lib
libraries amd not found in /usr/local/lib
libraries amd not found in /usr/lib
FOUND:
libraries = ['amd']
library_dirs = ['/opt/local/lib']
swig_opts = ['-I/opt/local/include']
define_macros = [('SCIPY_AMD_H', None)]
include_dirs = ['/opt/local/include']
FOUND:
libraries = ['umfpack', 'amd']
library_dirs = ['/opt/local/lib']
swig_opts = ['-I/opt/local/include', '-I/opt/local/include']
define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
include_dirs = ['/opt/local/include']
running install
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 py_modules sources
building library "dfftpack" sources
building library "fftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" sources
building library "fitpack" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack_scipy" sources
building library "sc_c_misc" sources
building library "sc_cephes" sources
building library "sc_mach" sources
building library "sc_amos" sources
building library "sc_cdf" sources
building library "sc_specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.cluster._hierarchy_wrap" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.integrate.lsoda" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.interpolate.interpnd" sources
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
adding
'build/src.macosx-10.8-intel-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f'
to sources.
building extension "scipy.interpolate._interpolate" sources
building extension "scipy.io.matlab.streams" sources
building extension "scipy.io.matlab.mio_utils" sources
building extension "scipy.io.matlab.mio5_utils" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
adding
'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/lib/blas/fblas-f2pywrappers.f'
to sources.
building extension "scipy.lib.blas.cblas" sources
adding 'build/src.macosx-10.8-intel-2.7/scipy/lib/blas/cblas.pyf' to
sources.
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
adding 'build/src.macosx-10.8-intel-2.7/scipy/lib/lapack/clapack.pyf'
to
sources.
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.linalg._fblas" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
adding
'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/linalg/_fblas-f2pywrappers.f'
to sources.
building extension "scipy.linalg._flapack" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
adding
'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/linalg/_flapack-f2pywrappers.f'
to sources.
building extension "scipy.linalg._flinalg" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal._spectral" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.8-intel-2.7' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._superlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack"
sources
adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.
swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i
swig -python -I/opt/local/include -I/opt/local/include
-I/opt/local/include
-o
build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c
-outdir
build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack
scipy/sparse/linalg/dsolve/umfpack/umfpack.i
unable to execute swig: No such file or directory
error: command 'swig' failed with exit status 1
bash-3.2$
paul
On 10.08.13 23:33, Edward d'Auvergne wrote:
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 <edward.dauvergne@xxxxxxxxx>
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 <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
--
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