[galaxy-dev] Re: Galaxy install problems

Hi, I just wanted to jump in and point out real quick: 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&gt; > À: "Luc Cornet" <luc.cornet(a)uliege.be&gt; > Cc: "HelpGalaxy" <galaxy-dev(a)lists.galaxyproject.org&gt;, "Baurain Denis" <Denis.Baurain(a)uliege.be&gt;, "Pierre Becker" <Pierre.Becker(a)sciensano.be&gt;, "Colignon David" <David.Colignon(a)uliege.be&gt; > 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: > > > 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/<pulsarservers.yml><pulsar.yml&g... > 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/