Problems starting VNC on OOD with LSF manager

[cjh (Chris)]

Rotaugenlaubfrosch,

This sounds similar to an issue I had when setting up OOD with LSF, in my case it was a race condition, if LSF didn’t show a submitted job via ‘bjobs’ immediately after submission, the startup procedure would never continue.

My solution was to make a wrapper script for the bjobs command to have it sleep for a few seconds before running the actual ‘bjobs’ command, then pointed to it in cluster.yml:

job:
  bin_overrides:
    bjobs: "/path/to/bjobs/wrapper"

The delay was enough so that the launched job was found, and the startup worked afterwards:

Jupyter interactive app question - launching, but not providing link to

Thank you for the response. We’re running LSF 9.1.3 currently (and working on migrating to 10.x). It looks like the problem is a delay between when bsub returns the jobid for a new job, and when the bjobs command starts returning that jobid’s status. I’d been aware of this gap, though it’s usually less than a second and can run longer, obviously it’s too long, and OnDemand considers the job to have failed since it doesn’t return for that id immediately. I made a wrapper script for the bjobs …