{"action":"created","issue":{"url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/1","labels_url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/1/comments","events_url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/1/events","html_url":"https://github.com/CAMH-Scientific-Computing/SCC/issues/1","id":60129772,"number":1,"title":"FSL Script Issue","user":{"login":"djrotenberg","id":8863178,"avatar_url":"https://avatars.githubusercontent.com/u/8863178?v=3","gravatar_id":"","url":"https://api.github.com/users/djrotenberg","html_url":"https://github.com/djrotenberg","followers_url":"https://api.github.com/users/djrotenberg/followers","following_url":"https://api.github.com/users/djrotenberg/following{/other_user}","gists_url":"https://api.github.com/users/djrotenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/djrotenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djrotenberg/subscriptions","organizations_url":"https://api.github.com/users/djrotenberg/orgs","repos_url":"https://api.github.com/users/djrotenberg/repos","events_url":"https://api.github.com/users/djrotenberg/events{/privacy}","received_events_url":"https://api.github.com/users/djrotenberg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-06T17:07:29Z","updated_at":"2015-03-07T13:44:59Z","closed_at":null,"body":"Address FSL Issue:\r\n\r\nIn doing this I also found that the script I was using (which loops through a series of directories) was launching the feat command before the one in the previous loop had terminated (which is why I had so many processes running on the management node last week), I worked around this by inserting a sleep, but I have no idea why that was the case. I made up some test files and now it seems that I can run the script and it works, I can also submit it to the job queue but it I do that is doesn’t run. If someone could look into this that would be great!!\r\n\r\n\r\nJob submission script:\r\n/imaging/scratch/Hendershot/chendershto/data/analysis/cihr_infusion/scripts/analysis_scripts/batch_test.sh\r\n\r\nScript to launch FEAT:\r\n/imaging/scratch/Hendershot/chendershto/data/analysis/cihr_infusion/scripts/analysis_scripts/feat_test.sh\r\n"},"comment":{"url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/comments/77689824","html_url":"https://github.com/CAMH-Scientific-Computing/SCC/issues/1#issuecomment-77689824","issue_url":"https://api.github.com/repos/CAMH-Scientific-Computing/SCC/issues/1","id":77689824,"user":{"login":"pipitone","id":509382,"avatar_url":"https://avatars.githubusercontent.com/u/509382?v=3","gravatar_id":"","url":"https://api.github.com/users/pipitone","html_url":"https://github.com/pipitone","followers_url":"https://api.github.com/users/pipitone/followers","following_url":"https://api.github.com/users/pipitone/following{/other_user}","gists_url":"https://api.github.com/users/pipitone/gists{/gist_id}","starred_url":"https://api.github.com/users/pipitone/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pipitone/subscriptions","organizations_url":"https://api.github.com/users/pipitone/orgs","repos_url":"https://api.github.com/users/pipitone/repos","events_url":"https://api.github.com/users/pipitone/events{/privacy}","received_events_url":"https://api.github.com/users/pipitone/received_events","type":"User","site_admin":false},"created_at":"2015-03-07T13:44:59Z","updated_at":"2015-03-07T13:44:59Z","body":"This is not an FSL issue. The `feat_test.sh` command is basically this: \r\n\r\n```sh\r\ncmd=\"feat $subjectdir/1081/20130314/ATTN/ATTN1/design.fsf &\"\r\neval $cmd\r\n```\r\n\r\nThe trailing ampersand (`&`) on the `cmd` is causing the command to run in the background. If you were to be running several of these scripts on a node or in a loop, each command would fork off into the background immediately and not wait until the command terminated (that is what the `&` does). \r\n\r\nI'll have to see your full script to understand more about what you are trying to do and where you are running into trouble, but hopefully this helps you get started. "}}