Major Description
I encountered a case where the JVM of a Tasktracker child did not exit after the main thread returned; a thread dump showed only the threads named STDOUT and STDERR from CommandRunner as non-daemon threads, and both were doing a read().
CommandRunner usually works correctly when the subprocess is expected to be finished before the timeout or when no timeout is used. By usually, I mean in the absence of external thread interrupts. The busy loop that waits for the process to finish has a sleep that is skipped over by an exception; this causes the waiting main thread to compete with the subprocess in a tight loop and effectively reduces the available cpu by 50%.