{"action":"created","issue":{"url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/96","repository_url":"https://api.github.com/repos/FelixKrueger/Bismark","labels_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/96/labels{/name}","comments_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/96/comments","events_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/96/events","html_url":"https://github.com/FelixKrueger/Bismark/issues/96","id":214310459,"number":96,"title":"Optimal parallelisation: -p N / --multicore N with bowtie2","user":{"login":"sklages","id":1837422,"avatar_url":"https://avatars0.githubusercontent.com/u/1837422?v=3","gravatar_id":"","url":"https://api.github.com/users/sklages","html_url":"https://github.com/sklages","followers_url":"https://api.github.com/users/sklages/followers","following_url":"https://api.github.com/users/sklages/following{/other_user}","gists_url":"https://api.github.com/users/sklages/gists{/gist_id}","starred_url":"https://api.github.com/users/sklages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sklages/subscriptions","organizations_url":"https://api.github.com/users/sklages/orgs","repos_url":"https://api.github.com/users/sklages/repos","events_url":"https://api.github.com/users/sklages/events{/privacy}","received_events_url":"https://api.github.com/users/sklages/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2017-03-15T07:56:10Z","updated_at":"2017-03-15T15:00:46Z","closed_at":"2017-03-15T13:07:39Z","body":"Hi,\r\n\r\nI am playing around with bismark using a few large human WGBS datasets.\r\n\r\nSetup:\r\n- a few 80-core server, 1TB RAM\r\n- WGBS human datasets, Illumina PE125\r\n- Bismark Version: v0.17.1_dev\r\n- bowtie2 2.2.9\r\n\r\nI am wondering which is the \"optimal\" combination of `-p N / --multicore N`.\r\n\r\nNo matter which value for `-p` I use, bowtie2 always runs on a single core.\r\nUsing `--multicore N` spawns `N` (bowtie2) processes, just like it should.\r\n\r\nWhen I use `--multicore 8 -p 4` I would expect 8 bismark/bowtie2 processes each running on 4 cores (using 32 cores in total). But it runs 8 bowtie2 processes each running on one single core.\r\n\r\nSo obviously there is something wrong with my understanding of `-p N / --multicore N`.\r\n\r\nWhat about using `--multicore 70` together with `-p 1`? I could imagine that this way I/O becomes annoying with splitting/joining the data. \r\n\r\nAny ideas?\r\n\r\nbest,\r\nSven\r\n"},"comment":{"url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/comments/286769052","html_url":"https://github.com/FelixKrueger/Bismark/issues/96#issuecomment-286769052","issue_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/96","id":286769052,"user":{"login":"ewels","id":465550,"avatar_url":"https://avatars0.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"created_at":"2017-03-15T15:00:46Z","updated_at":"2017-03-15T15:00:46Z","body":"Brilliant, thanks for renaming it @FelixKrueger! 😁  The table would still be nice too 😉 "}}
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