installing-snow-leopard.html

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         title="Permalink to Installing Snow Leopard">Installing Snow Leopard</a></h2>
 
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    <abbr class="published" title="2012-09-20T20:02:00-06:00">
      2012/09/20
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    <address class="vcard author">
      By <a class="url fn" href="https://keflavich.github.io/blog/author/adam-keflavichgmailcom.html">Adam (keflavich@gmail.com)</a>
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    <p>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):</p>
<ul class="simple">
<li>ipython</li>
<li>numpy</li>
<li>scipy</li>
<li>matplotlib</li>
<li>stsci-python</li>
<li>starlink</li>
<li>gfortran</li>
<li>latex</li>
<li>idl (check)</li>
</ul>
<p>Things that have happened:</p>
<ol class="arabic simple">
<li>Had to restart again (twice) to install additional updates</li>
<li>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
<a class="reference external" href="http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html">http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html</a>
that I had been using to set the tab title</li>
<li>My locate db broke. Needed repair: <tt class="docutils literal">sudo /usr/libexec/locate.updatedb</tt></li>
<li>numpy svn failed to build:
`` python setup.py buildRunning from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'F2PY Version 2_8111numpy/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 buildrunning config_ccunifing config_cc, config, build_clib, build_ext, build commands --compiler optionsrunning config_fcunifing config_fc, config, build_clib, build_ext, build commands --fcompiler optionsrunning build_srcbuild_srcbuilding py_modules sourcesbuilding library &quot;npymath&quot; sourcescustomize NAGFCompilerFound executable /usr/local/bin/f95customize AbsoftFCompilerCould not locate executable f90Found executable /usr/bin/f77absoft: no Fortran 90 compiler foundabsoft: no Fortran 90 compiler foundcustomize IBMFCompilerCould not locate executable xlf90Could not locate executable xlfcustomize IntelFCompilerCould not locate executable ifortCould not locate executable ifccustomize GnuFCompilerFound executable /usr/local/bin/g77gnu: no Fortran 90 compiler foundgnu: no Fortran 90 compiler foundcustomize Gnu95FCompilerFound executable /usr/local/bin/gfortrancustomize Gnu95FCompilercustomize Gnu95FCompiler using configC 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-prototypescompile 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.cgcc _configtest.o -o _configtestld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusfailure.removing: _configtest.c _configtest.oTraceback (most recent call last):  File &quot;setup.py&quot;, line 210, in     setup_package()  File &quot;setup.py&quot;, line 203, in setup_package    configuration=configuration )  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/core.py&quot;, line 186, in setup    return old_setup(<strong>new_attr)  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py&quot;, line 152, in setup    dist.run_commands()  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py&quot;, line 975, in run_commands    self.run_command(cmd)  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py&quot;, line 995, in run_command    cmd_obj.run()  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/command/build.py&quot;, line 37, in run    old_build.run(self)  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py&quot;, line 134, in run    self.run_command(cmd_name)  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py&quot;, line 333, in run_command    self.distribution.run_command(command)  File &quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py&quot;, line 995, in run_command    cmd_obj.run()  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py&quot;, line 152, in run    self.build_sources()  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py&quot;, line 163, in build_sources    self.build_library_sources(*libname_info)  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py&quot;, line 298, in build_library_sources    sources = self.generate_sources(sources, (lib_name, build_info))  File &quot;/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py&quot;, line 385, in generate_sources    source = func(extension, build_dir)  File &quot;numpy/core/setup.py&quot;, line 670, in get_mathlib_info    raise RuntimeError(&quot;Broken toolchain: cannot link a simple C program&quot;)RuntimeError: Broken toolchain: cannot link a simple C program``
**SOLUTION:</strong> Use the Mac OS X 10.6 python (/usr/bin/python). I will do this
until I run into another problem. Numpy build successfully</li>
<li>Build/install matplotlib - failed! Completely!</li>
<li>Acquired gcc/gfortran from <a class="reference external" href="http://hpc.sourceforge.net/">hpc</a></li>
<li>Followed instructions from <a class="reference external" href="http://blog.hyperjeff.net/?p=160">hyperjeff</a> on fortran install...</li>
<li>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``</li>
<li>Try to install scipy. Fail on missing umfpack, follow <a class="reference external" href="http://blog.hyperjeff.net/?p=160">hyperjeff</a>'s
instructions (but make sure to edit the site.cfg in scipy, not just the one in
numpy).
Had to add the following code:
<tt class="docutils literal">sudo cp AMD/Lib/libamd.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp UMFPACK/Lib/libumfpack.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp AMD/Include/amd.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp UFconfig/UFconfig.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp <span class="pre">UMFPACK/Include/*.h</span> /System/Library/Frameworks/Python.framework/Versions/2.6/include</tt></li>
<li>Installed fftw from <a class="reference external" href="http://www.fftw.org/">fftw.org</a> with simple ./configure, make, sudo
make install - no compiler opts as they killed the install</li>
<li>Get SoundSource from <a class="reference external" href="http://www.rogueamoeba.com/freebies/">rogueamoeba</a></li>
<li>Updated <a class="reference external" href="http://www.islayer.com/apps/istatmenus/">istatmenus</a></li>
</ol>

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