{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1426","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1426/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1426/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1426/events","html_url":"https://github.com/galaxyproject/galaxy/issues/1426","id":125044898,"number":1426,"title":"Improve SLURM stderr parsing and filtering","user":{"login":"natefoo","id":286969,"avatar_url":"https://avatars.githubusercontent.com/u/286969?v=3","gravatar_id":"","url":"https://api.github.com/users/natefoo","html_url":"https://github.com/natefoo","followers_url":"https://api.github.com/users/natefoo/followers","following_url":"https://api.github.com/users/natefoo/following{/other_user}","gists_url":"https://api.github.com/users/natefoo/gists{/gist_id}","starred_url":"https://api.github.com/users/natefoo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/natefoo/subscriptions","organizations_url":"https://api.github.com/users/natefoo/orgs","repos_url":"https://api.github.com/users/natefoo/repos","events_url":"https://api.github.com/users/natefoo/events{/privacy}","received_events_url":"https://api.github.com/users/natefoo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/area/jobs","name":"area/jobs","color":"006b75"},{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/kind/bug","name":"kind/bug","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-01-05T20:30:59Z","updated_at":"2016-07-12T16:04:35Z","closed_at":null,"body":"Currently we look for this message to detect if a job was killed for exceeding the memory CR:\r\n\r\n```\r\nslurmstepd: error: Exceeded job memory limit\r\n```\r\n\r\nHowever, in some versions, the following may be displayed:\r\n\r\n```\r\nslurmstepd: Exceeded job memory limit\r\n```\r\n\r\nAdditionally, SLURM will sometimes log this message even if the job is not killed. This should be stripped from the stderr of successful jobs (and appended to stdout??) to prevent them from failing:\r\n\r\n```\r\nslurmstepd: error: Exceeded step memory limit at some point. Step may have been partially swapped out to disk.\r\n```\r\n\r\nRelated: http://bugs.schedmd.com/show_bug.cgi?id=1682"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/232095486","html_url":"https://github.com/galaxyproject/galaxy/issues/1426#issuecomment-232095486","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1426","id":232095486,"user":{"login":"ericenns","id":492127,"avatar_url":"https://avatars.githubusercontent.com/u/492127?v=3","gravatar_id":"","url":"https://api.github.com/users/ericenns","html_url":"https://github.com/ericenns","followers_url":"https://api.github.com/users/ericenns/followers","following_url":"https://api.github.com/users/ericenns/following{/other_user}","gists_url":"https://api.github.com/users/ericenns/gists{/gist_id}","starred_url":"https://api.github.com/users/ericenns/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ericenns/subscriptions","organizations_url":"https://api.github.com/users/ericenns/orgs","repos_url":"https://api.github.com/users/ericenns/repos","events_url":"https://api.github.com/users/ericenns/events{/privacy}","received_events_url":"https://api.github.com/users/ericenns/received_events","type":"User","site_admin":false},"created_at":"2016-07-12T16:04:35Z","updated_at":"2016-07-12T16:04:35Z","body":"@natefoo \r\n\r\nI see the following:\r\n\r\n    slurmstepd: Job 976744 exceeded virtual memory limit (20144560 > 18454937), being killed"}}
{"actor":{"display_login":"ericenns"}}