Re: setting up relax on mac -- August 13, 2013 - 15:12

And if you find any Python version which has minfx, bmrblib, numpy,
scipy, and wx installed, you can use that Python to run relax.  It
really doesn't matter which Python has all of these installed, as long
as one does.

Regards,

Edward



On 13 August 2013 14:47, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi Paul,
>
> I have updated a special script I use to manage all my Python versions
> (from 1.0 to 3.3 which I use for testing relax), and added it to the
> repository.  If you update your checked out relax code with 'svn up',
> have a look at the 'devel_scripts/python_seek.py' script.  This might
> help for sanity with all the Python versions you have on your Mac.
> This script will find all Python versions on the system using the
> 'locate' command and then print out all of the Python and module
> version information as used within relax.  It will help you determine
> what is installed and importantly where.
>
> Regards,
>
> Edward
>
>
>
> On 12 August 2013 11:46, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Hi,
> >
> > I'm not sure how that space got in there but it shouldn't be there.
> > I'm now going from the file 'docs/Mac_framework_build_3way' that comes
> > with relax:
> >
> > "Install the appropriate GNU fortran version to add to Xcode (for
> > example gfortran-42-5664.pkg from http://r.research.att.com/tools/).
> > Xcode does not come with a Fortran compiler and the fink version will
> > not be able to create Universal 3-way binaries."
> >
> > I find it a bit crazy that Xcode does not bundle gfortran when it has
> > all the other gcc compilation tools.  The link should provide the best
> > Fortan compiler for a Mac.  I hope this one finally solves the Scipy
> > problems!
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> >
> > On 11 August 2013 17:08, Paul Schanda <paul.schanda@xxxxxx> wrote:
> > > By the way, I guess in the command you suggested there should not be a 
> > > space
> > > in between include/ and suitesparse.
> > > That's at least how I understood it.
> > >
> > > paul
> > >
> > >
> > > On 11.08.13 15:35, Edward d'Auvergne wrote:
> > > > That is a stranger error.  It looks like it cannot find swig on the
> > > > $PATH environmental variable!  Weird.  For that problem, try adding
> > > > the directory with swig to the PATH variable with:
> > > >
> > > > bash gre:scipy-0.12.0 $ PATH=/opt/local/bin/:/usr/local/bin/:$PATH
> > > > C_INCLUDE_PATH=/sw/include/ suitesparse/ ~/bin/python2.7 setup.py
> > > > install
> > > >
> > > > Let's see if that helps the scipy setup along a little ;)
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > > On 11 August 2013 07:20, Paul Schanda <paul.schanda@xxxxxx> wrote:
> > > > > Well, there is possibly some progress. I have to admit that I have no
> > > > > clue
> > > > > what fat3 commands and swig exactly do, though.
> > > > >
> > > > > The following seemed to work (or at least not produce any error 
> > > > > message):
> > > > >
> > > > > bash-3.2$ 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
> > >
> > >
> > >
> > > --
> > > 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