First, make sure that debugger is slow with any project. It may be caused by method breakpoints. If so, try removing the method breakpoints.

If the problem remains, then it's caused by the changes in the Linux kernel, for details please check this Sun bug.

For the problem background read this bug report in our tracker.

Also check this Kernel bug.

It's a Kernel/JDK problem that affects not only IntelliJ IDEA, but other IDEs and debuggers as well.

Check for workarounds in JetBrains/Sun/Kernel trackers.

The known solution is running sudo sysctl -w net.ipv4.tcp_abc=0 before starting IntelliJ IDEA.