{"action":"created","issue":{"url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/519","labels_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/519/labels{/name}","comments_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/519/comments","events_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/519/events","html_url":"https://github.com/radical-cybertools/radical.pilot/issues/519","id":64356205,"number":519,"title":"blue waters: stdout/stderr behavior and cleaned pilot directory","user":{"login":"marksantcroos","id":383387,"avatar_url":"https://avatars.githubusercontent.com/u/383387?v=3","gravatar_id":"","url":"https://api.github.com/users/marksantcroos","html_url":"https://github.com/marksantcroos","followers_url":"https://api.github.com/users/marksantcroos/followers","following_url":"https://api.github.com/users/marksantcroos/following{/other_user}","gists_url":"https://api.github.com/users/marksantcroos/gists{/gist_id}","starred_url":"https://api.github.com/users/marksantcroos/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marksantcroos/subscriptions","organizations_url":"https://api.github.com/users/marksantcroos/orgs","repos_url":"https://api.github.com/users/marksantcroos/repos","events_url":"https://api.github.com/users/marksantcroos/events{/privacy}","received_events_url":"https://api.github.com/users/marksantcroos/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"marksantcroos","id":383387,"avatar_url":"https://avatars.githubusercontent.com/u/383387?v=3","gravatar_id":"","url":"https://api.github.com/users/marksantcroos","html_url":"https://github.com/marksantcroos","followers_url":"https://api.github.com/users/marksantcroos/followers","following_url":"https://api.github.com/users/marksantcroos/following{/other_user}","gists_url":"https://api.github.com/users/marksantcroos/gists{/gist_id}","starred_url":"https://api.github.com/users/marksantcroos/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marksantcroos/subscriptions","organizations_url":"https://api.github.com/users/marksantcroos/orgs","repos_url":"https://api.github.com/users/marksantcroos/repos","events_url":"https://api.github.com/users/marksantcroos/events{/privacy}","received_events_url":"https://api.github.com/users/marksantcroos/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2015-03-25T19:45:06Z","updated_at":"2015-04-26T11:42:49Z","closed_at":null,"body":"From email:\r\n```\r\nBW Job ID: 1488389.nid11293 \r\nJob Name: SAGA-Python-PBSJobScript.PdQ4fK \r\nExec host list suppressed in email \r\nAn error has occurred processing your job, see below. \r\nrequest to copy stageout files failed on node '26209' for job 1488389.nid11293\r\n\r\nUnable to copy file /mnt/a/u/sciteam/marksant/1488389.nid11293.OU to marksant@h2ologin2:/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.out, error 1\r\n*** error from copy\r\n/bin/mv: cannot move `/mnt/a/u/sciteam/marksant/1488389.nid11293.OU' to `/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.out': No such file or directory\r\ntouch: cannot touch `/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.out': No such file or directory\r\n*** end error output\r\n\r\nUnable to copy file /mnt/a/u/sciteam/marksant/1488389.nid11293.ER to marksant@h2ologin2:/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.err, error 1\r\n*** error from copy\r\n/bin/mv: cannot move `/mnt/a/u/sciteam/marksant/1488389.nid11293.ER' to `/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.err': No such file or directory\r\ntouch: cannot touch `/scratch/sciteam/marksant/radical.pilot.sandbox/rp.session.netbook.mark.016519.0015-pilot.0000/agent.err': No such file or directory\r\n*** end error output\r\n```"},"comment":{"url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/comments/96368302","html_url":"https://github.com/radical-cybertools/radical.pilot/issues/519#issuecomment-96368302","issue_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/519","id":96368302,"user":{"login":"andre-merzky","id":1319674,"avatar_url":"https://avatars.githubusercontent.com/u/1319674?v=3","gravatar_id":"","url":"https://api.github.com/users/andre-merzky","html_url":"https://github.com/andre-merzky","followers_url":"https://api.github.com/users/andre-merzky/followers","following_url":"https://api.github.com/users/andre-merzky/following{/other_user}","gists_url":"https://api.github.com/users/andre-merzky/gists{/gist_id}","starred_url":"https://api.github.com/users/andre-merzky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andre-merzky/subscriptions","organizations_url":"https://api.github.com/users/andre-merzky/orgs","repos_url":"https://api.github.com/users/andre-merzky/repos","events_url":"https://api.github.com/users/andre-merzky/events{/privacy}","received_events_url":"https://api.github.com/users/andre-merzky/received_events","type":"User","site_admin":false},"created_at":"2015-04-26T11:42:49Z","updated_at":"2015-04-26T11:42:49Z","body":"For the first problem, wouldn't the fix be to honor the workdir in our qsub script?  I would be uncomfortable *not* doing this, because of cleanup, race conditions, non-shared FS for the staging area, etc.\r\n\r\nFor the second problem, do we need to rely on PBS for catching stdout/stderr of the agent?  We handle stdout/stderr on our own for units, I don't see why handling it for the bootstrapper and pilot should be any more difficult?"}}