{"action":"created","issue":{"url":"https://api.github.com/repos/BD2KGenomics/toil/issues/718","repository_url":"https://api.github.com/repos/BD2KGenomics/toil","labels_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/718/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/718/comments","events_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/718/events","html_url":"https://github.com/BD2KGenomics/toil/pull/718","id":141679428,"number":718,"title":"Support for Slurm batchSystem (resolves #682)","user":{"login":"dleehr","id":2752599,"avatar_url":"https://avatars.githubusercontent.com/u/2752599?v=3","gravatar_id":"","url":"https://api.github.com/users/dleehr","html_url":"https://github.com/dleehr","followers_url":"https://api.github.com/users/dleehr/followers","following_url":"https://api.github.com/users/dleehr/following{/other_user}","gists_url":"https://api.github.com/users/dleehr/gists{/gist_id}","starred_url":"https://api.github.com/users/dleehr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dleehr/subscriptions","organizations_url":"https://api.github.com/users/dleehr/orgs","repos_url":"https://api.github.com/users/dleehr/repos","events_url":"https://api.github.com/users/dleehr/events{/privacy}","received_events_url":"https://api.github.com/users/dleehr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2016-03-17T19:09:55Z","updated_at":"2016-03-24T16:03:46Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BD2KGenomics/toil/pulls/718","html_url":"https://github.com/BD2KGenomics/toil/pull/718","diff_url":"https://github.com/BD2KGenomics/toil/pull/718.diff","patch_url":"https://github.com/BD2KGenomics/toil/pull/718.patch"},"body":"Implements support for slurm scheduler\r\n\r\n- SlurmBatchSystem class is modeled after GridengineBatchSystem\r\n- Maps AbstractBatchSystem methods to sbatch, squeue, scancel, sacct, sinfo subprocess calls\r\n- Includes SlurmBatchSystemTest for testing system"},"comment":{"url":"https://api.github.com/repos/BD2KGenomics/toil/issues/comments/200902890","html_url":"https://github.com/BD2KGenomics/toil/pull/718#issuecomment-200902890","issue_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/718","id":200902890,"user":{"login":"dleehr","id":2752599,"avatar_url":"https://avatars.githubusercontent.com/u/2752599?v=3","gravatar_id":"","url":"https://api.github.com/users/dleehr","html_url":"https://github.com/dleehr","followers_url":"https://api.github.com/users/dleehr/followers","following_url":"https://api.github.com/users/dleehr/following{/other_user}","gists_url":"https://api.github.com/users/dleehr/gists{/gist_id}","starred_url":"https://api.github.com/users/dleehr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dleehr/subscriptions","organizations_url":"https://api.github.com/users/dleehr/orgs","repos_url":"https://api.github.com/users/dleehr/repos","events_url":"https://api.github.com/users/dleehr/events{/privacy}","received_events_url":"https://api.github.com/users/dleehr/received_events","type":"User","site_admin":false},"created_at":"2016-03-24T16:03:46Z","updated_at":"2016-03-24T16:03:46Z","body":"The issue was that the slurm config on the jenkins slave did not set the CPU and memory per node. The batchSystemTests do submit jobs with memory and CPU requirements, and slurm was not able to handle these requests. I've fixed the config in https://github.com/BD2KGenomics/cgcloud/pull/137 but we'll need to rebuild the jenkins slave image from that before this can be retried."}}