Merge pull request #40 from benniel/fixes

Output fixes
Added a running queue.
Changed the way samples numbers are stored in the jobs queue to allow for easier replenishing.
Added a DyingMessage for workers to tell the server they wont be around anymore.
Added job replenishing code in the server.
Added socket timeout for result file transfers.
Changed exception logging in the server.
Removed some bad imports.
Merge pull request #41 from filinep/master

Changes
Fixed gathering results for simulations which have different number of iterations.
Removed dead code in the server.
Added stack trace to error email.
Merge pull request #42 from filinep/master

Gatherer fix
- Made single worker pool process which spawns workers
- Added progress collection to keep track of long running simulations
- Workers now send results via samba
- Workers always reconnect before sending a message
- Worker pool shows progress for all workers
- Added extensive logging
- Added lots of exception handling to try keep workers and server alive on disconnects
- Jobs get distributed fairly based on number of running sims for a user
Merge pull request #44 from filinep/master

Stability fixes, worker pool, logging and separate gatherer
Server and worker errors

- Changed the server to count only running jobs from the requesting ip.
  This makes workers dedicated to specific users not be counted towards the running count.
- Added a missing "send job request" in the worker when it times out
Merge pull request #45 from filinep/master

Server and worker errors
Various changes and bug fixes

-Added JAR hashing to prevent multiple copies of jar files in the database
-Added a node health status reporter (cpu, memory, disk space)
-Fixed a bug that prevented jar removal messages from being sent to workers
-Added a setting to control the progress update interval on workers
-XML files are now parsed on the client before the job upload process starts
-The upload no longer crashes when it receives invalid xml files
-Fixed an exception reporting bug in the worker

Signed-off-by: pleiades <pleiades@pleiades1.cs.up.ac.za>
Merge pull request #46 from benniel/changes

Various changes and bug fixes