Added PBS Pro support

* PBS Pro qsub does not have -d option
* Show error when qsub fails
* Only cache PBS modules when they have completed
* Fixed qstat logic
* Fixed pid caching issue (Timeout is now 5 seconds)

batch/commandline.py:
fixed pid caching issue
Sometimes qstat needed the fully qualified name when requesting job info

bin/functions:
qsub now returns error messages

contrib/vistrails/RemotePBS/init.py:
catch qsub errors
only cache when finished