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(a)gmail.com>
> À: "Luc Cornet" <luc.cornet(a)uliege.be>
> Cc: "HelpGalaxy" <galaxy-dev(a)lists.galaxyproject.org>, "Baurain
Denis" <Denis.Baurain(a)uliege.be>, "Pierre Becker"
<Pierre.Becker(a)sciensano.be>, "Colignon David"
<David.Colignon(a)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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