Adam Ginsburg's blog

As you might expect from numerous blog posts and the general difficulty people have always experienced upgrading mac OS versions, Mavericks caused some truly hideous issues.

The only really "new" issues specifically for Mavericks relate to app nap. The main solution is minrk's appnope. Otherwise, command line options like defaults write <app domain name> NSAppSleepDisabled -bool YES are required if the button is missing from Mac's Get Info pane.

I tried installing the conda stack to get python running quickly. This worked to an extremely limited degree: the TkAgg shipped with anaconda links to XQuartz, which is highly undesirable for a number of reasons. This meant that matplotlib plots showed up as X11 plots. With the Mac OS X backend, the windows failed to show up in the Dock and therefore were totally unusable (though they did look OK).

I am still using conda to maintain multiple parallel versions of python for testing. However, I went back to my typical install-from-source approach.

To get the matplotlib backends to interact nicely with apple, you need to install them using the /Library version of python

# this had to happen sometime early:
$ xcode-select --install

$ wget https://pypi.python.org/pypi/pip#downloads
$ tar -xzvf ~/Downloads/pip-1.5.2.tar.gz
$ cd pip-1.5.2
$ /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install
$ /Library/Frameworks/Python.framework/Versions/2.7/bin/pip install virtualenv
$ cd
$ /Library/Frameworks/Python.framework/Versions/2.7/bin/virtualenv virtual-python

After this, I was surprisingly able to install everything in the python stack with no hitches. Obviously, that could not possibly last.

While matplotlib and numpy worked fine, scipy had problems.

ImportError: dlopen(/Users/adam/virtual-python/lib/python2.7/site-packages/scipy/integrate/_odepack.so, 2): Symbol not found: __gfortran_internal_free
Referenced from: /Users/adam/virtual-python/lib/python2.7/site-packages/scipy/integrate/_odepack.so
Expected in: flat namespace
   in /Users/adam/virtual-python/lib/python2.7/site-packages/scipy/integrate/_odepack.so

This terrible error led me back to re-compiling scipy. I tried installing with hpc gfortran, but that didn't work at all, first apparently because of linking errors in numpy. When I investigated numpy, I found that the compilers apparently don't work at all:

C compiler: /usr/local/bin/gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64
...
RuntimeError: Broken toolchain: cannot link a simple C program

I had to give up on that, and then googling returned no results at all, which I thought was a bit weird. Scipy seems to want gcc and g++ 4.2, even though they're years old. I had to find those and gfortran-4.2 somehow, but the old site that used to serve them seems to have lost the files! They had an older version, though, which appears to work. Scipy is a scary install.