Eclipse will throw GC overhead limit exceeded error when it runs out of memory, normally while performing memory-consuming operations such as building workspace on big projects.

Here's how the error looks like;

An internal error occurred during: "Building workspace".
GC overhead limit exceeded

To fix this problem, you'll need to allocate more memory to your Eclipse instance. To do this, go to the Eclipse installation directory, and locate the eclipse.ini file. The file might look like the following;

-startup
plugins/org.eclipse.equinox.launcher_1.1.1.R36x_v20101122_1400.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.gtk.linux.x86_64_1.1.2.R36x_v20101019_1345
-product
org.eclipse.epp.package.php.product
--launcher.defaultAction
openFile
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
-vmargs
-Dosgi.requiredJavaVersion=1.5
-XX:MaxPermSize=256m
-Xms40m
-Xmx384m

To increase the memory allocation for your Eclipse instance, edit the number in the following lines accordingly.

-Xms512m
-Xmx1024m

The number is the amount of memory, in Megabytes.

You can also increase the value of MaxPermSize, as the following;

-XX:MaxPermSize=1024m

Restart Eclipse for the changes to take effect.