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         title="Permalink to Rebuilding python from scratch again">Rebuilding python from scratch again</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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  <div class="entry-content">
    <p>I got scipy working a week or two ago, but doing so killed matplotib's
tkagg. So, I switched to the MacOSX backend, which worked ok until I
realized that the interactive (connect) features of macosx failed
miserably. This led me to try to get matplotlib working.... which broke
with those awful &quot;symbol not found&quot; errors in ft2font.so and _path.so,
which I've determined all have to do with linking to the wrong library
files.
The most worrisome part of this process was discovering that a full Time
Machine recovery of /usr and /Library/Frameworks and /Library/Python did
*not* restore python - it stayed dead with IDENTICAL errors. So there
are probably additional layers of hidden links.
The process below is based on <a class="reference external" href="http://blog.hyperjeff.net/?p=160">hyperjeff's blog post</a> but differs
substantially based on <a class="reference external" href="http://casa.colorado.edu/~skillman/research_and_codes/files/649710e82f85745eb65a90535f0f3098-5.html">Sam Skillman's recommendations</a> and the very
big issue I ran into that my /usr/local files appeared to be corrupted.
After this install, my path no longer includes /usr/local/bin and /sw
has been moved to /_sw... hopefully one of these days I'll be ballsy
enough to delete it.</p>
<ol class="arabic simple">
<li>Install python 2.6.4<ol class="arabic">
<li>Needed a clean terminal with no flags set at all. Don't know why -
all I had set were a bunch of -arch x86_64 flags.
<tt class="docutils literal">export <span class="pre">LD_LIBRARY_PATH=&quot;/usr/local/lib:/usr/X11/lib&quot;./configure</span> <span class="pre">--enable-framework=/Library/Frameworks</span> MACOSX_DEPLOYMENT_TARGET=10.6 make <span class="pre">-j</span> 17sudo make install</tt></li>
<li>Reset PYTHONPATH to blank</li>
<li>`` alias clearflags='export CFLAGS=&quot;&quot;; export CCFLAGS=&quot;&quot;; export CXXFLAGS=&quot;&quot;; export LDFLAGS=&quot;&quot;; export FFLAGS=&quot;&quot;;'``
to make sure</li>
</ol>
</li>
<li>Install FFTW
<tt class="docutils literal">cd ~/tmpcurl <span class="pre">-O</span> <span class="pre">http://www.fftw.org/fftw-3.2.2.tar.gztar</span> xf <span class="pre">fftw-3.2.2.tar.gzcd</span> <span class="pre">fftw-3.2.2clearflags./configure</span> <span class="pre">CC=&quot;gcc</span> <span class="pre">-arch</span> x86_64&quot; <span class="pre">CXX=&quot;g++</span> <span class="pre">-arch</span> x86_64&quot; <span class="pre">CPP=&quot;gcc</span> <span class="pre">-E&quot;</span> <span class="pre">CXXCPP=&quot;g++</span> <span class="pre">-E&quot;make</span> <span class="pre">-j</span> 17sudo make install</tt></li>
<li>Install UMFPACK
<tt class="docutils literal">cd ~/tmpcurl <span class="pre">-O</span> <span class="pre">http://www.cise.ufl.edu/research/sparse/umfpack/current/UMFPACK.tar.gzcurl</span> <span class="pre">-O</span> <span class="pre">http://www.cise.ufl.edu/research/sparse/UFconfig/current/UFconfig.tar.gzcurl</span> <span class="pre">-O</span> <span class="pre">http://www.cise.ufl.edu/research/sparse/amd/current/AMD.tar.gztar</span> xf AMD.tar.gztar xf UFconfig.tar.gztar xf UMFPACK.tar.gzsed <span class="pre">-ibck</span> 's/F77 = f77/F77 = gfortran/' UFconfig/UFconfig.mk sed <span class="pre">-ibck</span> '299,303s/# //' UFconfig/UFconfig.mkcp UFconfig/UFconfig.h AMD/Include/cp UFconfig/UFconfig.h UMFPACK/Include/cd UMFPACKmake <span class="pre">-j</span> 17make hbmake clean</tt></li>
<li>Install numpy<ol class="arabic">
<li>Set environment variables
<tt class="docutils literal">export MACOSX_DEPLOYMENT_TARGET=10.6export <span class="pre">CFLAGS=&quot;-arch</span> x86_64&quot;export <span class="pre">FFLAGS=&quot;-m64&quot;export</span> <span class="pre">LDFLAGS=&quot;-Wall</span> <span class="pre">-undefined</span> dynamic_lookup <span class="pre">-bundle</span> <span class="pre">-arch</span> x86_64&quot;export <span class="pre">PYTHONPATH=&quot;/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/&quot;echo</span> &quot;[amd]library_dirs = /Users/adam/tmp/AMD/Libinclude_dirs = /Users/adam/tmp/AMD/Includeamd_libs = amd[umfpack]library_dirs = /Users/adam/tmp/UMFPACK/Libinclude_dirs = /Users/adam/tmp/UMFPACK/Includeumfpack_libs = umfpack&quot; &gt; site.cfg</tt></li>
<li>Setup &amp; Install
<tt class="docutils literal">python setup.py build <span class="pre">--fcompiler=gnu95sudo</span> python setup.py install</tt></li>
<li>Test: python -c &quot;import numpy&quot;</li>
</ol>
</li>
<li>Install scipy. The important thing is to use g++-4.2 because g++-4.5
doesn't accept the -arch flag. Also, get rid of /sw if it's on your
computer at all.
<tt class="docutils literal">sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyXcd <span class="pre">~/repos/scipy-0.7.1python</span> setup.py cleanrm <span class="pre">-rf</span> <span class="pre">buildclearflagsFFLAGS=&quot;-m64&quot;</span> <span class="pre">CFLAGS=&quot;-arch</span> x86_64 <span class="pre">-I/usr/local/include/freetype2</span> <span class="pre">-I/usr/X11/include</span> <span class="pre">-L/usr/X11/lib&quot;</span>&nbsp; <span class="pre">LDFLAGS=&quot;-Wall</span> <span class="pre">-undefined</span> dynamic_lookup <span class="pre">-bundle</span>&nbsp; <span class="pre">-lpng</span> <span class="pre">-arch</span> x86_64&quot; <span class="pre">CXX=&quot;/usr/bin/g++-4.2&quot;</span> <span class="pre">CC=&quot;/usr/bin/gcc-4.2&quot;</span> python setup.py buildpython setup.py install</tt>
Test the install:
<tt class="docutils literal">python <span class="pre">-c</span> &quot;import scipy, scipy.fftpack, scipy.interpolate&quot;</tt></li>
<li><ol class="first arabic">
<li>Install matplotlib. MAKE SURE /usr/bin/texbin is in front of
/usr/local/bin and /sw/bin so that dvipng comes from MacTEX. I
also ended up having to remove /usr/local/bin from my path
completely
<tt class="docutils literal">sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyXcd <span class="pre">~/repos/matplotlib-svnpython</span> setup.py cleanrm <span class="pre">-rf</span> buildclearflags</tt></li>
<li>Do hyperjeff's recommended edits except don't use /usr/local
because it's f'd:
make.osx:
<tt class="docutils literal"><span class="pre">MACOSX_DEPLOYMENT_TARGET=10.6PREFIX=/usrPYTHON=/Library/Frameworks/Python.framework/Versions/Current/bin/python##</span> You shouldn't need to configure past this point (and <span class="pre">yet…)PKG_CONFIG_PATH=&quot;${PREFIX}/lib/pkgconfig&quot;CFLAGS=&quot;-arch</span> i386 <span class="pre">-arch</span> x86_64 <span class="pre">-I${PREFIX}/include</span> <span class="pre">-I${PREFIX}/include/freetype2</span> <span class="pre">-isysroot</span> <span class="pre">/Developer/SDKs/MacOSX10.6.sdk&quot;LDFLAGS=&quot;-arch</span> i386 <span class="pre">-arch</span> x86_64 <span class="pre">-L${PREFIX}/lib</span> <span class="pre">-syslibroot,/Developer/SDKs/MacOSX10.6.sdk&quot;FFLAGS=&quot;-arch</span> i386 <span class="pre">-arch</span> x86_64&quot;</tt>
setup.cfg:
<tt class="docutils literal">wxagg = False</tt></li>
<li>Do the install (different from hyperjeff b/c I don't want root)
`` sudo make -f make.osx fetch deps make -f mpl_build mpl_installpython setup.py install``</li>
</ol>
</li>
<li>Install setuptools</li>
<li>easy_install ipython</li>
<li>install everything else pythonically</li>
</ol>
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