{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2428","repository_url":"https://api.github.com/repos/openmicroscopy/bioformats","labels_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2428/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2428/comments","events_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2428/events","html_url":"https://github.com/openmicroscopy/bioformats/pull/2428","id":156011493,"number":2428,"title":"FileStitcher: avoid re-initializing underlying readers","user":{"login":"simleo","id":1183171,"avatar_url":"https://avatars.githubusercontent.com/u/1183171?v=3","gravatar_id":"","url":"https://api.github.com/users/simleo","html_url":"https://github.com/simleo","followers_url":"https://api.github.com/users/simleo/followers","following_url":"https://api.github.com/users/simleo/following{/other_user}","gists_url":"https://api.github.com/users/simleo/gists{/gist_id}","starred_url":"https://api.github.com/users/simleo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simleo/subscriptions","organizations_url":"https://api.github.com/users/simleo/orgs","repos_url":"https://api.github.com/users/simleo/repos","events_url":"https://api.github.com/users/simleo/events{/privacy}","received_events_url":"https://api.github.com/users/simleo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openmicroscopy/bioformats/labels/exclude","name":"exclude","color":"e10c02"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-05-20T17:21:56Z","updated_at":"2016-05-22T09:22:11Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/pulls/2428","html_url":"https://github.com/openmicroscopy/bioformats/pull/2428","diff_url":"https://github.com/openmicroscopy/bioformats/pull/2428.diff","patch_url":"https://github.com/openmicroscopy/bioformats/pull/2428.patch"},"body":"Keep individual readers from `ExternalSeries` open and don't re-initialize them in `initReader`."},"comment":{"url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/comments/220822462","html_url":"https://github.com/openmicroscopy/bioformats/pull/2428#issuecomment-220822462","issue_url":"https://api.github.com/repos/openmicroscopy/bioformats/issues/2428","id":220822462,"user":{"login":"joshmoore","id":88113,"avatar_url":"https://avatars.githubusercontent.com/u/88113?v=3","gravatar_id":"","url":"https://api.github.com/users/joshmoore","html_url":"https://github.com/joshmoore","followers_url":"https://api.github.com/users/joshmoore/followers","following_url":"https://api.github.com/users/joshmoore/following{/other_user}","gists_url":"https://api.github.com/users/joshmoore/gists{/gist_id}","starred_url":"https://api.github.com/users/joshmoore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joshmoore/subscriptions","organizations_url":"https://api.github.com/users/joshmoore/orgs","repos_url":"https://api.github.com/users/joshmoore/repos","events_url":"https://api.github.com/users/joshmoore/events{/privacy}","received_events_url":"https://api.github.com/users/joshmoore/received_events","type":"User","site_admin":false},"created_at":"2016-05-22T09:22:11Z","updated_at":"2016-05-22T09:22:11Z","body":"> \"Too many open files\" is what @melissalinkert said might happen with this PR. But why is it happening without it?\r\n\r\nI don't know, though it's pretty clear that there's a leak in the other 2 PRs. After one double-click in OMERO.web on one of the images I see hours later this in the `lsof` output:\r\n\r\n```\r\njava    55914 omero  204r      REG               0,52  278145101  974777713 /uod/idr/filesets/idr0010-doil-dnadamage/20150501-original/Restored GW screen/1-23/001-23 dapi.stk\r\njava    55914 omero  205r      REG               0,52  278145101  974777713 /uod/idr/filesets/idr0010-doil-dnadamage/20150501-original/Restored GW screen/1-23/001-23 dapi.stk\r\n```\r\n\r\n> And how did you manage to import six plates without it if setId alone takes more than eight hours? \r\n\r\nI don't know. build 115 with this PR and build 116 without this PR seem to have similar times! For comparison, the times for *with* this PR:\r\n\r\n```\r\n[jamoore@minke import]$ find 1_to_0053/rslt/ -name stderr -exec grep uploaded {} +\r\n1_to_0053/rslt/1/0001.sh/stderr:3 files uploaded, 1 fileset, 1 plate created, 384 images imported, 0 errors in 1:43:19.622\r\n1_to_0053/rslt/1/0002.sh/stderr:3 files uploaded, 1 fileset, 1 plate created, 384 images imported, 0 errors in 1:44:47.801\r\n1_to_0053/rslt/1/0003.sh/stderr:3 files uploaded, 1 fileset, 1 plate created, 384 images imported, 0 errors in 1:52:49.478\r\n1_to_0053/rslt/1/0004.sh/stderr:3 files uploaded, 1 fileset, 1 plate created, 384 images imported, 0 errors in 1:41:06.111\r\n1_to_0053/rslt/1/0005.sh/stderr:3 files uploaded, 1 fileset, 1 plate created, 384 images imported, 0 errors in 1:40:38.703\r\n1_to_0053/rslt/1/0006.sh/stderr:3 files uploaded, 0 filesets created, 0 images imported, 1 error in 1:37:20.623\r\n1_to_0053/rslt/1/0007.sh/stderr:3 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:15:33.067\r\n```\r\n\r\n> Also, seems weird to hit 16384 open files when there's only two per plate.\r\n\r\nI can try another import if you want, but I assume as the import progresses (perhaps during thumbnailing) the file is opened again and again leading to the exhaustion."}}
{"actor":{"display_login":"joshmoore"}}