{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/175","repository_url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras","labels_url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/175/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/175/comments","events_url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/175/events","html_url":"https://github.com/galaxyproject/ansible-galaxy-extras/pull/175","id":271304196,"number":175,"title":"Adjust slurm.conf for Ubuntu 16.04 Xenial","user":{"login":"drosofff","id":11705625,"avatar_url":"https://avatars3.githubusercontent.com/u/11705625?v=4","gravatar_id":"","url":"https://api.github.com/users/drosofff","html_url":"https://github.com/drosofff","followers_url":"https://api.github.com/users/drosofff/followers","following_url":"https://api.github.com/users/drosofff/following{/other_user}","gists_url":"https://api.github.com/users/drosofff/gists{/gist_id}","starred_url":"https://api.github.com/users/drosofff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drosofff/subscriptions","organizations_url":"https://api.github.com/users/drosofff/orgs","repos_url":"https://api.github.com/users/drosofff/repos","events_url":"https://api.github.com/users/drosofff/events{/privacy}","received_events_url":"https://api.github.com/users/drosofff/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2017-11-05T18:54:49Z","updated_at":"2017-11-20T23:45:26Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/pulls/175","html_url":"https://github.com/galaxyproject/ansible-galaxy-extras/pull/175","diff_url":"https://github.com/galaxyproject/ansible-galaxy-extras/pull/175.diff","patch_url":"https://github.com/galaxyproject/ansible-galaxy-extras/pull/175.patch"},"body":"*Issue:*\r\n\r\nWhereas the role works fine with Ubuntu 14.04, queuing of jobs in slurm cluster is suboptimal in Ubuntu 16.04 Xenial.\r\n\r\nNamely, jobs are put in slurm wait queue with `Resources` in `NODELIST(REASON)` and are only launched one at a time, even if CPUs are available.\r\n\r\nThus, with two fastqc jobs launched under Galaxy + Ubuntu 14.04:\r\n\r\n```\r\n             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\r\n                 9     debug g12_fast   galaxy  R       0:15      1 ubuntu-14-04\r\n                10     debug g13_fast   galaxy  R       0:10      1 ubuntu-14-04\r\n```\r\n(OK)\r\n\r\nwith two fastqc jobs launched under Galaxy + Ubuntu 16.04:\r\n\r\n```\r\n             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\r\n                 3     debug g31_fast   galaxy PD       0:00      1 (Resources)\r\n                 2     debug g30_fast   galaxy  R       0:40      1 ubuntu-16-04\r\n```\r\n(Not OK, job 3 is unnecessarily stalled)\r\n\r\n*Fix:*\r\nReplace `SelectTypeParameters=CR_Core_Memory` with `SelectTypeParameters=CR_CPU`in `configure_slurm.py.j2`\r\n\r\nNow, with two fastqc jobs launched under Galaxy + Ubuntu 14.04:\r\n\r\n```\r\n             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\r\n                 9     debug g12_fast   galaxy  R       2:56      1 ubuntu-14-04\r\n                10     debug g13_fast   galaxy  R       2:51      1 ubuntu-14-04\r\n```\r\n(Still OK, parameter change does not impair the role)\r\n\r\nwith two fastqc jobs launched under Galaxy + Ubuntu 16.04:\r\n\r\n```\r\n             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\r\n                 2     debug g30_fast   galaxy  R       3:42      1 ubuntu-16-04\r\n                 3     debug g31_fast   galaxy  R       0:48      1 ubuntu-16-04\r\n```\r\n(Fixed, the job 3 is launched in parallel with job 2, using all CPUs available)\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/comments/345868927","html_url":"https://github.com/galaxyproject/ansible-galaxy-extras/pull/175#issuecomment-345868927","issue_url":"https://api.github.com/repos/galaxyproject/ansible-galaxy-extras/issues/175","id":345868927,"user":{"login":"drosofff","id":11705625,"avatar_url":"https://avatars3.githubusercontent.com/u/11705625?v=4","gravatar_id":"","url":"https://api.github.com/users/drosofff","html_url":"https://github.com/drosofff","followers_url":"https://api.github.com/users/drosofff/followers","following_url":"https://api.github.com/users/drosofff/following{/other_user}","gists_url":"https://api.github.com/users/drosofff/gists{/gist_id}","starred_url":"https://api.github.com/users/drosofff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drosofff/subscriptions","organizations_url":"https://api.github.com/users/drosofff/orgs","repos_url":"https://api.github.com/users/drosofff/repos","events_url":"https://api.github.com/users/drosofff/events{/privacy}","received_events_url":"https://api.github.com/users/drosofff/received_events","type":"User","site_admin":false},"created_at":"2017-11-20T23:45:26Z","updated_at":"2017-11-20T23:45:26Z","author_association":"MEMBER","body":"@natefoo More importantly, the config accommodates much better slurm v15 found in Ubuntu Xenial. Thanks a lot for the help !"}}
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