{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/551","repository_url":"https://api.github.com/repos/choderalab/yank","labels_url":"https://api.github.com/repos/choderalab/yank/issues/551/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/551/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/551/events","html_url":"https://github.com/choderalab/yank/pull/551","id":188360236,"number":551,"title":"[WIP] MPI fixes","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-09T21:44:18Z","updated_at":"2016-11-09T22:31:24Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/551","html_url":"https://github.com/choderalab/yank/pull/551","diff_url":"https://github.com/choderalab/yank/pull/551.diff","patch_url":"https://github.com/choderalab/yank/pull/551.patch"},"body":"Fixes issue noted in https://github.com/choderalab/yank-examples/pull/31#issuecomment-259518476 where error messages were not being printed before MPI Abort on error."},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/259545864","html_url":"https://github.com/choderalab/yank/pull/551#issuecomment-259545864","issue_url":"https://api.github.com/repos/choderalab/yank/issues/551","id":259545864,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-11-09T22:31:24Z","updated_at":"2016-11-09T22:31:24Z","body":"I've also added a band-aid fix for the issue noted [here](https://github.com/choderalab/yank-examples/pull/31#issuecomment-259535913) where `setup/molecules/*/` files generated last by rank 0 are not found by the other ranks if we immediately proceed through the MPI barrier after setup. This fix just adds a sleep of 5 seconds, but we might want to see if we can flush the disk buffers or improve the control logic in a longer-term fix."}}
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