Oh, just to be sure that you do know this, but the scipy library is optional for relax. It is currently only needed for the frame order analysis in relax. Therefore you don't need it for the relaxation dispersion analysis. In the future this might change if we add matplotlib support.
Regards, Edward On 22 August 2013 11:28, Paul Schanda <[email protected]> wrote: > Hi Edward, > > Thanks for your e-mails. I was absent lately. > I searched for the Fortran version, but hesitated about which one to take. > I am using OS X 10.8.4, but on the site you gave me > (http://r.research.att.com/tools/) I found only 10.7 or below. > > I tend to compile scipy anyways, as I surely have all the required modules > (minfx, scipy, numpy, bmrblib) somewhere (e.g. in > /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python) but > not in /usr/bin/python2.7 > > paul > > > > 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 >>>>> > > > -- > 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
