A lot can go wrong in the process of submitting and running Hadoop job:

• Hadoop::Runner.pm module not found: The Perl Hadoop package is not configured, see Setting the environment.
• ipc.Client: Retrying connect to server: IP_ADDRESS:PORT. Already tried ? time(s): The jobtracker cannot be contacted. If using -jt jobtracker:port flag, check, that the jobtracker address is correct.
• /net/projects/hadoop/bin/hadoop-cluster fails to start a cluster: Look where the jobtracker was scheduled by SGE using qstat. Login to that machine and investigate logs in /var/log/hadoop/$USER/$SGE_JOBID/.