That should be `systemctl restart pulsar.service` Marius
On Wed, 30 Jun 2021 at 17:05, Luc Cornet <luc.cor...@uliege.be> wrote: > 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.vandenb...@gmail.com> > À: "Luc Cornet" <luc.cor...@uliege.be> > Cc: "HelpGalaxy" <galaxy-dev@lists.galaxyproject.org>, "Baurain Denis" < > denis.baur...@uliege.be>, "Pierre Becker" <pierre.bec...@sciensano.be>, > "Colignon David" <david.colig...@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.cor...@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.vandenb...@gmail.com> > > À: "Luc Cornet" <luc.cor...@uliege.be> > > Cc: "HelpGalaxy" <galaxy-dev@lists.galaxyproject.org>, "Baurain Denis" < > > denis.baur...@uliege.be>, "Pierre Becker" <pierre.bec...@sciensano.be>, > > "Colignon David" <david.colig...@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.cor...@uliege.be > > | luc.cor...@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.vandenb...@gmail.com | > > m.vandenb...@gmail.com ] > > > À: "Luc Cornet" < [ mailto:luc.cor...@uliege.be | luc.cor...@uliege.be ] > > > > > Cc: "HelpGalaxy" < [ mailto:galaxy-dev@lists.galaxyproject.org | > > galaxy-dev@lists.galaxyproject.org ] >, "Baurain Denis" < [ mailto: > > denis.baur...@uliege.be | denis.baur...@uliege.be ] >, "Pierre Becker" < > > [ mailto:pierre.bec...@sciensano.be | pierre.bec...@sciensano.be ] >, > > "Colignon David" < [ mailto:david.colig...@uliege.be | > > david.colig...@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 > > > > > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > %(web_page_url)s > > > > To search Galaxy mailing lists use the unified search at: > > [ http://galaxyproject.org/search/ | http://galaxyproject.org/search/ ] > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > %(web_page_url)s > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/ > >
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