Re: setting up relax on macRe: setting up relax on mac|
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/:$PATH C_INCLUDE_PATH=/sw/include/ suitesparse/ ~/bin/python2.7 setup.py installas my pythone2.7 is somewhere else) Here is what I get. bash-3.2$ 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 |