If you open very many projects at once in the IDE, it is possible for all file descriptors available to the Java process to be consumed. In Linux the limit is set to 1024 by default; you can check this by typing in a shell:

ulimit -n

If the IDE consumes all the file descriptors you will get many exceptions and the IDE will not function properly. (If this happens, shut down the IDE, delete $userdir/var/cache/ and $userdir/config/Services/org-netbeans-modules-project-ui-OpenProjectList.settings, and restart.)

You may find out the number of file descriptors you are currenty using by running

ls -1 /proc/`jps -l | fgrep org.netbeans.Main | cut -d' ' -f1 | head -1`/fd | wc -l

You can work around the problem by increasing the number of file descriptors allowed for processes of the given user. You need to edit the file /etc/security/limits.conf as root, adding the following two lines there:

 USERNAME           soft    nofile          2048
 USERNAME           hard    nofile          2048

where USERNAME is the Unix username. Then you need to log out and log back in as the user USERNAME.

Source: NetBeans User FAQ