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Sunday, February 14, 2010

Installing Snow Leopard

I'm going to attempt to install snow leopard today. This post will serve as a record of the difficulties I run into.

Things to install (and ensure they are 64-bit):

  • ipython
  • numpy
  • scipy
  • matplotlib
  • stsci-python
  • starlink
  • gfortran
  • latex
  • idl (check)


Things that have happened:

  1. Had to restart again (twice) to install additional updates
  2. My bash command line looked funny - something about bash changed, but I don't know what. The fix was easy: commented out some code from http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html that I had been using to set the tab title
  3. My locate db broke. Needed repair: sudo /usr/libexec/locate.updatedb
  4. numpy svn failed to build:
    python setup.py build
    Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'
    F2PY Version 2_8111
    numpy/core/setup_common.py:86: MismatchCAPIWarning: API mismatch detected, the C API version numbers have to be updated. Current C api version is 4, with checksum 59750b518272c8987f02d66445afd3f1, but recorded checksum for C API version 4 in codegen_dir/cversions.txt is 3d8940bf7b0d2a4e25be4338c14c3c85. If functions were added in the C API, you have to update C_API_VERSION in numpy/core/setup_common.pyc.
    MismatchCAPIWarning)
    blas_opt_info:
    FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-faltivec', '-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 = ['-faltivec']

    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 "npymath" sources
    customize NAGFCompiler
    Found executable /usr/local/bin/f95
    customize AbsoftFCompiler
    Could not locate executable f90
    Found executable /usr/bin/f77
    absoft: no Fortran 90 compiler found
    absoft: no Fortran 90 compiler found
    customize IBMFCompiler
    Could not locate executable xlf90
    Could not locate executable xlf
    customize IntelFCompiler
    Could not locate executable ifort
    Could not locate executable ifc
    customize GnuFCompiler
    Found executable /usr/local/bin/g77
    gnu: no Fortran 90 compiler found
    gnu: no Fortran 90 compiler found
    customize Gnu95FCompiler
    Found executable /usr/local/bin/gfortran
    customize Gnu95FCompiler
    customize Gnu95FCompiler using config
    C compiler: gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

    compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
    gcc: _configtest.c
    gcc _configtest.o -o _configtest
    ld: library not found for -lcrt1.10.5.o
    collect2: ld returned 1 exit status
    ld: library not found for -lcrt1.10.5.o
    collect2: ld returned 1 exit status
    failure.
    removing: _configtest.c _configtest.o
    Traceback (most recent call last):
    File "setup.py", line 210, in
    setup_package()
    File "setup.py", line 203, in setup_package
    configuration=configuration )
    File "/Users/adam/repos/numpy-svn/numpy/distutils/core.py", line 186, in setup
    return old_setup(**new_attr)
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
    File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
    File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
    File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 152, in run
    self.build_sources()
    File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 163, in build_sources
    self.build_library_sources(*libname_info)
    File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 298, in build_library_sources
    sources = self.generate_sources(sources, (lib_name, build_info))
    File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 385, in generate_sources
    source = func(extension, build_dir)
    File "numpy/core/setup.py", line 670, in get_mathlib_info
    raise RuntimeError("Broken toolchain: cannot link a simple C program")
    RuntimeError: Broken toolchain: cannot link a simple C program


    SOLUTION: Use the Mac OS X 10.6 python (/usr/bin/python). I will do this until I run into another problem. Numpy build successfully
  5. Build/install matplotlib - failed! Completely!
  6. Acquired gcc/gfortran from hpc
  7. Followed instructions from hyperjeff on fortran install...
  8. Get rid of numpy 1.2.1: mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/.not_numpy.bak
  9. Try to install scipy. Fail on missing umfpack, follow hyperjeff's instructions (but make sure to edit the site.cfg in scipy, not just the one in numpy)

    Had to add the following code:

    sudo cp AMD/Lib/libamd.a /System/Library/Frameworks/Python.framework/Versions/2.6/lib
    sudo cp UMFPACK/Lib/libumfpack.a /System/Library/Frameworks/Python.framework/Versions/2.6/lib
    sudo cp AMD/Include/amd.h /System/Library/Frameworks/Python.framework/Versions/2.6/include
    sudo cp UFconfig/UFconfig.h /System/Library/Frameworks/Python.framework/Versions/2.6/include
    sudo cp UMFPACK/Include/*.h /System/Library/Frameworks/Python.framework/Versions/2.6/include

  10. Installed fftw from fftw.org with simple ./configure, make, sudo make install - no compiler opts as they killed the install
  11. Get SoundSource from rogueamoeba
  12. Updated istatmenus

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