{"action":"opened","number":41,"pull_request":{"url":"https://api.github.com/repos/marshallward/payu/pulls/41","id":39553516,"html_url":"https://github.com/marshallward/payu/pull/41","diff_url":"https://github.com/marshallward/payu/pull/41.diff","patch_url":"https://github.com/marshallward/payu/pull/41.patch","issue_url":"https://api.github.com/repos/marshallward/payu/issues/41","number":41,"state":"open","locked":false,"title":"Made payu-collate respect collate_ncpus from config. Fixed bug introduced in last commit: referencing unknown variable","user":{"login":"aidanheerdegen","id":6063709,"avatar_url":"https://avatars.githubusercontent.com/u/6063709?v=3","gravatar_id":"","url":"https://api.github.com/users/aidanheerdegen","html_url":"https://github.com/aidanheerdegen","followers_url":"https://api.github.com/users/aidanheerdegen/followers","following_url":"https://api.github.com/users/aidanheerdegen/following{/other_user}","gists_url":"https://api.github.com/users/aidanheerdegen/gists{/gist_id}","starred_url":"https://api.github.com/users/aidanheerdegen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aidanheerdegen/subscriptions","organizations_url":"https://api.github.com/users/aidanheerdegen/orgs","repos_url":"https://api.github.com/users/aidanheerdegen/repos","events_url":"https://api.github.com/users/aidanheerdegen/events{/privacy}","received_events_url":"https://api.github.com/users/aidanheerdegen/received_events","type":"User","site_admin":false},"body":"Previous version didn't work when submitted as a batch job because of a dumb error I introduced. Should have checked that.\r\n\r\nThe only substantial revision is to make fms.collate respect the collate_ncpus setting from config. This wasn't the case in the previous version. That config was only used in the batch version, which sets up the number of CPUs for the job and fms.collate just grabbed the number of CPUs from the environment.\r\n\r\nSo now payu-collate does (collate_cmd.py) does a (slightly bodgy) test to see if we're in a PBS environment (not strictly necessary I guess ... ) and then sets an environment variable to pass this information on to fms.collate.\r\n\r\nMarshall, maybe you'd prefer not to do that bodgy test and just set the environment variable? I tried looking in the run command to find an analogous example, but couldn't see anything. If there is a standard/usual/better way of doing this I'm happy to change 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