{"action":"created","issue":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/246","labels_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/246/labels{/name}","comments_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/246/comments","events_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/246/events","html_url":"https://github.com/cBio/cbio-cluster/issues/246","id":69018320,"number":246,"title":"Python submitted DRMAA jobs are not running on the worker nodes","user":{"login":"vipints","id":1714549,"avatar_url":"https://avatars.githubusercontent.com/u/1714549?v=3","gravatar_id":"","url":"https://api.github.com/users/vipints","html_url":"https://github.com/vipints","followers_url":"https://api.github.com/users/vipints/followers","following_url":"https://api.github.com/users/vipints/following{/other_user}","gists_url":"https://api.github.com/users/vipints/gists{/gist_id}","starred_url":"https://api.github.com/users/vipints/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vipints/subscriptions","organizations_url":"https://api.github.com/users/vipints/orgs","repos_url":"https://api.github.com/users/vipints/repos","events_url":"https://api.github.com/users/vipints/events{/privacy}","received_events_url":"https://api.github.com/users/vipints/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cBio/cbio-cluster/labels/Torque/Moab%20scheduler","name":"Torque/Moab scheduler","color":"009800"},{"url":"https://api.github.com/repos/cBio/cbio-cluster/labels/vendorticket","name":"vendorticket","color":"5319e7"}],"state":"open","locked":false,"assignee":{"login":"tatarsky","id":6439722,"avatar_url":"https://avatars.githubusercontent.com/u/6439722?v=3","gravatar_id":"","url":"https://api.github.com/users/tatarsky","html_url":"https://github.com/tatarsky","followers_url":"https://api.github.com/users/tatarsky/followers","following_url":"https://api.github.com/users/tatarsky/following{/other_user}","gists_url":"https://api.github.com/users/tatarsky/gists{/gist_id}","starred_url":"https://api.github.com/users/tatarsky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tatarsky/subscriptions","organizations_url":"https://api.github.com/users/tatarsky/orgs","repos_url":"https://api.github.com/users/tatarsky/repos","events_url":"https://api.github.com/users/tatarsky/events{/privacy}","received_events_url":"https://api.github.com/users/tatarsky/received_events","type":"User","site_admin":false},"milestone":null,"comments":71,"created_at":"2015-04-16T21:57:58Z","updated_at":"2015-08-05T15:51:34Z","closed_at":null,"body":"Since yesterday, I am struggling to debug an error caused by running python scripts via drmaa module. My compute jobs are failing with `Exit_status=127`, here is one such event, `tracejob -slm -n 2 3025874`. drmaa module is able to dispatch the job to the worker node with all necessary PATH variables but it fails just after that (only using a single second). The log file didn't give much information. \r\n\r\n`-bash: module: line 1: syntax error: unexpected end of file`\r\n`-bash: error importing function definition for BASH_FUNC_module'`\r\n`-bash: line 1: /var/spool/torque/mom_priv/jobs/3025874.mskcc-fe1.local.SC: No such file or directory`\r\n\r\nI am able to run this python script without Torque on the login machine and a worker node (with qlogin). \r\n\r\nDid anybody use drmaa, python combination in cluster computing? \r\n\r\nI checked the drmaa job environment, all env PATH variables are loaded correctly. I am not sure why the worker node is kicking out my job. \r\n\r\nI am not quite sure, how I proceed the debugging/where to look, any suggestions/help :)"},"comment":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/comments/128047089","html_url":"https://github.com/cBio/cbio-cluster/issues/246#issuecomment-128047089","issue_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/246","id":128047089,"user":{"login":"tatarsky","id":6439722,"avatar_url":"https://avatars.githubusercontent.com/u/6439722?v=3","gravatar_id":"","url":"https://api.github.com/users/tatarsky","html_url":"https://github.com/tatarsky","followers_url":"https://api.github.com/users/tatarsky/followers","following_url":"https://api.github.com/users/tatarsky/following{/other_user}","gists_url":"https://api.github.com/users/tatarsky/gists{/gist_id}","starred_url":"https://api.github.com/users/tatarsky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tatarsky/subscriptions","organizations_url":"https://api.github.com/users/tatarsky/orgs","repos_url":"https://api.github.com/users/tatarsky/repos","events_url":"https://api.github.com/users/tatarsky/events{/privacy}","received_events_url":"https://api.github.com/users/tatarsky/received_events","type":"User","site_admin":false},"created_at":"2015-08-05T15:51:34Z","updated_at":"2015-08-05T15:51:34Z","body":"Interesting on a) and noted before on b). Somewhere in our emails we discuss why that configure fails and it appeared to boil down to the config test program being unable to locate pbs_submit_hash even though its right there in the library. Felt like another c++ name mangling problem IIRC. Will scan emails. "}}