Tag Archives: NEURON

Installing NEURON, MPI, and Python on OS X Lion

I’ve recently run into the problem of trying to compile the source for NEURON 7.3a that includes support for parallel NEURON (using MPI) and Python on Mac OS X Lion. Using a number of helpful web resources, I wanted to cobble together an “as-of-this-writing” practice to get a kitchen sink working install for all components.

UPDATED 01-Sept-2012: Added instructions for mpi4py

Because I don’t have the resources to test many version combinations, etc., this assumes OS X 10.7.4 on a Retina MacBook Pro 10,1 (Mid 2012), with a working copy of XCode 4.4.1 installed (available for free from the Mac App Store). I suspect but cannot verify that this will work with many different versions of all of these components. Note: MacPorts is particularly sensitive to very new XCode and OS releases, so right after a new one, things don’t always work right away.

Finally this assumes you have admin access to the computer on which you are installing things and that you will use sudo for good and not evil.

And super-finally, this is basically an aggregate of web sources, some of which I had to modify to get it working. Sources are inline, below. Much is duplicated here because of the transience of web links.

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Installing XCode on OS X Lion and Mountain Lion

This is a series of posts leading toward a complete installation of NEURON neural simulation environment on OS X. All of this information is relevant for other purposes as well.

There are many places that have instructions on how to install XCode. For Lion and Mountain Lion, you go to the Mac App Store and download and install the XCode installer. If you previously had a version of XCode that installed in a directory called /Developer, excellent directions on how to use xcode-select are found on MacPorts.

Command line tools are now treated as a separate download. There are (at least) two ways of getting them.

1. Open Xcode. Go to the Xcode application menu and select Preferences. From there, go to Downloads and select the button for Command Line Tools.

2. Go to the Apple Developer website. You’ll need to be a free developer member to use this website. From there you will go to the Mac Developer downloads section, and you’ll have to find the relevant package for Command Line Tools for your OS. I’ve not tested whether or not you can install these without Xcode, but I’ve also heard that you may be able to either directly or with a little Homebrew hackery (note: I still recommend and use MacPorts to both Fink and Homebrew, but they all have strengths and weaknesses).