Hi Paul, I've made a few improvements to the 'devel_scripts/python_seek.py' script. This should now better find all Python versions on the system so you can find one suitable for relax. Any progress with building a suitable Python environment?
Regards, Edward On 13 August 2013 14:47, Edward d'Auvergne <[email protected]> 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 <[email protected]> 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 <[email protected]> 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/:$PATH >>>> C_INCLUDE_PATH=/sw/include/ suitesparse/ ~/bin/python2.7 setup.py >>>> install >>>> >>>> Let's see if that helps the scipy setup along a little ;) >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 11 August 2013 07:20, Paul Schanda <[email protected]> wrote: >>>>> >>>>> Well, there is possibly some progress. I have to admit that I have no >>>>> clue >>>>> what fat3 commands and swig exactly do, though. >>>>> >>>>> The following seemed to work (or at least not produce any error message): >>>>> >>>>> bash-3.2$ 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 <[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 >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>> >>> >>> >>> -- >>> 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
