Galaxy IT Physicell: execution troubleshooting

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I seem to have a similar problem - my IT will not start. Here’s my shared History: Galaxy

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Hi @rheiland

I’m glad you asked! From what I can see, you have stale sessions across several histories for Physiocell and a few other interactive tools.

As you know, there is a limit on concurrent sessions for Interactive Environments at most UseGalaxy servers, and this can change dynamically over time in response to server load.

Quitting out of these under Activity bar → Interactive Tools may not be enough to reset an account’s concurrency listing. In practical use, this means that you may need to “delete” the executing tools within the history to fully quit out of a session.

Once this is done, the next queued IT session should start up, however I’ve sometimes needed to start the next session after the proceeding was fully closed out (no “executing IT datasets” remaining in any history).

Interactive tools queue in a special way, so I would be curious about how these end up working for you today! To clarify, the IT usage behavior space we are looking at is:

  1. Prefered session-end behavior: Does stopping an IT under Activity bar → Interactive Tools remove a session from the IT concurrency listing for an account.

    • Likely No, based on what I see in your account but I’ll also do some testing. I’ll also get some clarity about combinations of ITs (e.g. are Physiocell and RStudio in independent IT concurrency queues or the same queue).

  2. Alternative session-end behavior: Does stopping an IT by deleting it in a history remove a session from the IT listing under Activity bar → Interactive Tools and from the concurrency listing for an account.

    • Likely Yes, however this is not ideal. I’m mostly sharing so you can move forward!

  3. Concurrency and queueing behavior: Does stopping an IT by either 1 or 2 above allow queued IT sessions to move up in the concurrency queue and launch. Or are only new sessions started after picked up.

    • Uncertain. Your current account has what appears to be stale IT sessions left over from an A action.

Workaround Test (please try this): does a 2 action allow queued IT sessions to start up or are only newly launched sessions picked up.

Additional Tests (I’ll do this but your feedback is welcome too!): does 1 or 2 or Concurrency behavior vary by IT or combinations of ITs. Once the matrix is created, create a development request for more end-user clarity for these functions to layer on top of the technical WIPs.

Please try 2: deleting the yellow executing IT datasets to see if that is enough to get this at least moving forward for you. I’ll come back with an update once I know more too.

Thanks again for all of your feedback and help as we make the IT implementations within Galaxy more robust!! Additional comments are welcome, for example, is this behavior new or have you observed different behavior between different UseGalaxy servers?

More soon! :hammer_and_wrench:

Queued test case

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We had a stuck process on the backend that was preventing some jobs from being processed, this has been fixed now and your IT job is running now - please let us know if you run into more issues.