{"action":"created","issue":{"url":"https://api.github.com/repos/mschubert/clustermq/issues/157","repository_url":"https://api.github.com/repos/mschubert/clustermq","labels_url":"https://api.github.com/repos/mschubert/clustermq/issues/157/labels{/name}","comments_url":"https://api.github.com/repos/mschubert/clustermq/issues/157/comments","events_url":"https://api.github.com/repos/mschubert/clustermq/issues/157/events","html_url":"https://github.com/mschubert/clustermq/issues/157","id":465416834,"node_id":"MDU6SXNzdWU0NjU0MTY4MzQ=","number":157,"title":"Timeout when initializing SSH tunnel","user":{"login":"brendanf","id":16835777,"node_id":"MDQ6VXNlcjE2ODM1Nzc3","avatar_url":"https://avatars3.githubusercontent.com/u/16835777?v=4","gravatar_id":"","url":"https://api.github.com/users/brendanf","html_url":"https://github.com/brendanf","followers_url":"https://api.github.com/users/brendanf/followers","following_url":"https://api.github.com/users/brendanf/following{/other_user}","gists_url":"https://api.github.com/users/brendanf/gists{/gist_id}","starred_url":"https://api.github.com/users/brendanf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brendanf/subscriptions","organizations_url":"https://api.github.com/users/brendanf/orgs","repos_url":"https://api.github.com/users/brendanf/repos","events_url":"https://api.github.com/users/brendanf/events{/privacy}","received_events_url":"https://api.github.com/users/brendanf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2019-07-08T19:14:34Z","updated_at":"2019-07-10T12:33:46Z","closed_at":null,"author_association":"NONE","body":"I'm trying to submit jobs to my cluster (SLURM) via SSH in `drake` with the `clustermq` backend.  I need to load a conda environment on the cluster before running R.  I modified the template to activate the conda environment (and also set the R profile):\r\n\r\n```bash\r\n\"conda activate <my_environment> && \\\r\n        cd {{ project_dir | <my_directory> }} && \\\r\n        R_PROFILE={{ remote_profile | config/slurm.Rprofile }} R --no-save --no-restore -e \\\r\n        'clustermq:::ssh_proxy(ctl={{ ctl_port }}, job={{ job_port }})' \\\r\n        > {{ ssh_log | /dev/null }} 2>&1\"\r\n```\r\nThis failed with error message `Error in .subset2(public_bind_env, \"initialize\")(...) : \r\n  Remote R process did not respond after 5 seconds. Check your SSH server log.`\r\n\r\nChecking the SSH server log as suggested:\r\n```\r\nR version 3.5.1 (2018-07-02) -- \"Feather Spray\"\r\nCopyright (C) 2018 The R Foundation for Statistical Computing\r\nPlatform: x86_64-conda_cos6-linux-gnu (64-bit)\r\n\r\nR is free software and comes with ABSOLUTELY NO WARRANTY.\r\nYou are welcome to redistribute it under certain conditions.\r\nType 'license()' or 'licence()' for distribution details.\r\n\r\n  Natural language support but running in an English locale\r\n\r\nR is a collaborative project with many contributors.\r\nType 'contributors()' for more information and\r\n'citation()' on how to cite R or R packages in publications.\r\n\r\nType 'demo()' for some demos, 'help()' for on-line help, or\r\n'help.start()' for an HTML browser interface to help.\r\nType 'q()' to quit R.\r\n\r\n> clustermq:::ssh_proxy(ctl=54344, job=50552)\r\nmaster ctl listening at: tcp://localhost:54344\r\nforwarding local network from: tcp://rackham2:8266\r\nsent PROXY_UP to master ctl\r\n```\r\n\r\nI assume this is what the output should look like.  I'm guessing that the issue is that loading the conda environment and starting R is taking longer than 5 seconds, so the initialization is timing out locally.  Apparently this 5 second timeout is hardcoded.  Would it be possible to expose it as an option?"},"comment":{"url":"https://api.github.com/repos/mschubert/clustermq/issues/comments/510041666","html_url":"https://github.com/mschubert/clustermq/issues/157#issuecomment-510041666","issue_url":"https://api.github.com/repos/mschubert/clustermq/issues/157","id":510041666,"node_id":"MDEyOklzc3VlQ29tbWVudDUxMDA0MTY2Ng==","user":{"login":"mschubert","id":442360,"node_id":"MDQ6VXNlcjQ0MjM2MA==","avatar_url":"https://avatars0.githubusercontent.com/u/442360?v=4","gravatar_id":"","url":"https://api.github.com/users/mschubert","html_url":"https://github.com/mschubert","followers_url":"https://api.github.com/users/mschubert/followers","following_url":"https://api.github.com/users/mschubert/following{/other_user}","gists_url":"https://api.github.com/users/mschubert/gists{/gist_id}","starred_url":"https://api.github.com/users/mschubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mschubert/subscriptions","organizations_url":"https://api.github.com/users/mschubert/orgs","repos_url":"https://api.github.com/users/mschubert/repos","events_url":"https://api.github.com/users/mschubert/events{/privacy}","received_events_url":"https://api.github.com/users/mschubert/received_events","type":"User","site_admin":false},"created_at":"2019-07-10T12:33:46Z","updated_at":"2019-07-10T12:33:46Z","author_association":"OWNER","body":"Hi @brendanf :wave: ,\r\n\r\nThank you for spotting this!\r\n\r\nYour reasoning makes sense, there may just not be enough time to activate and environment and start R within the timeout given.\r\n\r\nDo you want to try and send a patch for this?"}}
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