Re,
This is the log of pulsar.
As pointed by Keith Superman, the pulsar don't restart since the step is skipped.
How can I force pulsar to restart ?
Thanks,
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 16:44:50
Objet: Re: [galaxy-dev] Re: Galaxy install problems
If you've set up pulsar to start as a systemd service you should get the
logs with journalctl.
I assume that's `journalctl -u pulsar.service`.
For a quickstart in journalctl check out
https://www.linode.com/docs/guides/how-to-use-journalctl/
On Wed, 30 Jun 2021 at 16:38, Luc Cornet <luc.cornet@uliege.be> wrote:
> OK,
>
> Sure but can you please tell me how to get these pulsar application logs ?
>
> Thanks
> 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 16:32:16
> Objet: [galaxy-dev] Re: Galaxy install problems
>
> Thanks, but these are not the pulsar application logs. Can you provide
> these please ?
>
> On Wed, 30 Jun 2021 at 16:30, Luc Cornet < [ mailto:luc.cornet@uliege.be
> | luc.cornet@uliege.be ] > wrote:
>
>
> Dear Marius,
>
> Many thank for your feedback.
>
> I join to this email: the playbook, the pulsarservers.yml file and the log
> of pulsar playbook.
>
> CLI plugin is for us the best solution since we have nothing to maintain.
> DRMAA is not actively developed for slurm, correct ?
>
>
> In the playbook, we use systemd which I think should restart pulsar but It
> might not be the case:
>
> TASK [galaxyproject.pulsar : systemd daemon-reload and enable/start
> service]
> ****************************************************************************
>
> ok: [HPC]
>
> RUNNING HANDLER [galaxyproject.pulsar : default restart pulsar handler]
> *********************************************************************************
>
> skipping: [HPC]
>
> 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" < [ mailto:m.vandenbeek@gmail.com |
> m.vandenbeek@gmail.com ] >
> À: "Luc Cornet" < [ mailto:luc.cornet@uliege.be | luc.cornet@uliege.be ]
> >
> Cc: "HelpGalaxy" < [ mailto:galaxy-dev@lists.galaxyproject.org |
> galaxy-dev@lists.galaxyproject.org ] >, "Baurain Denis" < [ mailto:
> Denis.Baurain@uliege.be | Denis.Baurain@uliege.be ] >, "Pierre Becker" <
> [ mailto:Pierre.Becker@sciensano.be | Pierre.Becker@sciensano.be ] >,
> "Colignon David" < [ mailto:David.Colignon@uliege.be |
> 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/ |
> http://usegalaxy.org/ ] | [ 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 ] | [
> 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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