Hi,
I just wanted to jump in and point out real quick:
Did you restart pulsar after rolling out the new config ?
to which you've answered that you re-ran the playbook, but that's not a sufficient answer.
RUNNING HANDLER [galaxyproject.pulsar : default restart pulsar handler] ********************************************************************************* skipping: [HPC]
The "restart Pulsar" step in the playbook is being skipped, so it looks like the Pulsar server has not, in fact, been restarted.
Cheers, Keith
Currently, we never used DRMAA. The job were executed immediately on the cluster with CLI or DRMAA. We had this part in pulsarservers.yml, to activate CLI: managers: _default_: type: queued_cli job_plugin: slurm native_specification: "-p batch --tasks=1 --cpus-per-task=2 --mem-per-cpu=1000 -t 10:00" min_polling_interval: 0.5 amqp_publish_retry: True amqp_publish_retry_max_retries: 5 amqp_publish_retry_interval_start: 10 amqp_publish_retry_interval_step: 10 amqp_publish_retry_interval_max: 60
Thanks for your help, Luc
Luc Cornet, PhD Bio-informatician Mycology and Aerobiology Sciensano
----- Mail original ----- De: "Marius van den Beek" m.vandenbeek@gmail.com À: "Luc Cornet" luc.cornet@uliege.be Cc: "HelpGalaxy" galaxy-dev@lists.galaxyproject.org, "Baurain Denis" Denis.Baurain@uliege.be, "Pierre Becker" Pierre.Becker@sciensano.be, "Colignon David" David.Colignon@uliege.be Envoyé: Mercredi 30 Juin 2021 16:02:04 Objet: [galaxy-dev] Re: Galaxy install problems
Hi Luc,
I'm sorry to hear that you're struggling to set up Galaxy to your liking. Let me start by pointing out that [ http://usegalaxy.org/ | usegalaxy.org ] uses slurm with DRMAA, this is certainly going to be more performant and reliable than the CLI plugin. There is little maintenance necessary, so maybe that is why activity on slurm-drmaa is low (See also [ https://github.com/natefoo/slurm-drmaa | https://github.com/natefoo/slurm-drmaa ] ). I would be curious to know how you came to the conclusion that there is some incompatibility between DRMAA and slurm Note that one of the setups we teach during the training submits via DRMAA to slurm.
Then I'd like to point out that there are a huge variety of different ways in which you can configure Galaxy and the job submission. We teach the most common ones during the training week, with the aim that you understand how these things work together, as well as giving you a handle on how you can manage these different settings and services using a configuration management system. We cannot tailor a solution to your infrastructure during this week.
About your problem specifically, I had asked this on gitter before:
Did you restart pulsar after rolling out the new config ?
to which you've answered that you re-ran the playbook, but that's not a sufficient answer.
Every playbook is different, and we cannot know if this includes a restarter service for pulsar. Also please don't assume that everyone that could potentially help you knows ansible and the playbooks that are being taught intimately, and in what ways you have customized your playbook. It is much more helpful to write up the relevant settings you've changed and the logs that go with it.
You've also been asked to provide logs of the restart, which as far as I can tell you haven't provided. You had mentioned on gitter that pulsar continues to use DRMAA to submit jobs, so you'll want to double check whether you've really restarted pulsar after the config changes, and look at the startup logs for pulsar, and find out how it is possible for pulsar to submit jobs via drmaa if it is not set up to do so.
Best, Marius
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