Today I ran into a cluster error on our local instance using latest galaxy-dist and torque/pbs with the python-pbs binding.

Under heavy load of the galaxy process, it appears that the handler processes failed to contact the pbs-server, although the pbs_server was still up and running. after that, a lot of the following statements kept appearing in the handler.log file:

galaxy.jobs.runners.pbs DEBUG 2012-07-11 17:39:06,649 (11647/12788.pbs_master_address) Skipping state check because PBS server connection failed

After restarting the galaxy process (run.sh), everything worked again, with no changes to the pbs_server.

Would it be possible to setup some checks for this failure? Like:
 - contact system admin
 - restart galaxy
 - auto retry job submission after a while as to not crash workflows.

best regards,

Geert Vandeweyer
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to