Monthly Archives: December 2015

Gephi on Mac OS X El Capitan

Background

Short version: Upgrade to El Capitan broke Gephi

Long version:

For some of my research I use Gephi for graph visualizations. It’s not great, but every time I go looking for something better I’m unimpressed with the competition as well.

Unfortunately, the current version of Gephi requires Java 6 and is not compatible with the latest versions of Java.

In order to get it to work, I had perviously installed the 1.6 JDK on my Mac, and then updated the Gephi configuration file to point to that runtime.

This last week when I upgraded to the Mac OS El Capitan, it broke this (among other things…).

How I fixed it

I am mostly posting this for myself for future reference, in case I need to address this again in the future, but here is what I did to get it to work.

  1. I tried installing this hotfix: http://support.apple.com/kb/DL1572  This installs the legacy java runtime.
  2. I restarted my machine and still no luck. I’m not sure if the above did anything new, as I had previously installed this when I got it working originally.
  3. I found and updated the Gephi configuration file found at:

    /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf

  4. From my last battled, I had previously edited this to point to the correct (1.6) runtime. I had added this line:

    jdkhome="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

  5. Apparently, with the upgrade this directory has now moved outside the /System directory to make /Library directly under the root. So I had to change it to:
    jdkhome="/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"
  6. After that, Gephi started up just fine.