{"action":"opened","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/40","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/40/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/40/events","html_url":"https://github.com/marbl/canu/issues/40","id":130849705,"number":40,"title":"SGE general settings","user":{"login":"dcopetti","id":13842014,"avatar_url":"https://avatars.githubusercontent.com/u/13842014?v=3","gravatar_id":"","url":"https://api.github.com/users/dcopetti","html_url":"https://github.com/dcopetti","followers_url":"https://api.github.com/users/dcopetti/followers","following_url":"https://api.github.com/users/dcopetti/following{/other_user}","gists_url":"https://api.github.com/users/dcopetti/gists{/gist_id}","starred_url":"https://api.github.com/users/dcopetti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcopetti/subscriptions","organizations_url":"https://api.github.com/users/dcopetti/orgs","repos_url":"https://api.github.com/users/dcopetti/repos","events_url":"https://api.github.com/users/dcopetti/events{/privacy}","received_events_url":"https://api.github.com/users/dcopetti/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-02-02T23:13:45Z","updated_at":"2016-02-02T23:13:45Z","closed_at":null,"body":"Hello,\r\nWe are having issues on running Canu on our cluster, the error says:\r\ncanu failed with 'can't configure for SGE'.\r\n\r\nThe command is: /opt/canu/Linux-amd64/bin/canu -d /home/../250k_assembly -p test250k genomeSize=380m corMinCoverage=2 errorRate=0.18 -pacbio-raw input_subreads.fa\r\nand we have a PSSC cluster with 4 nodes, each with 12 core and 32 GB Ram, so a total of 48 cores and 128GB Ram. The SGE is GE 6.2u5p3 and it has CentOS release 6.5 (Final).\r\n\r\nFollowing the documentation, we tested all the 6x2 options at Grid Engine Configuration (here one example)\r\n 754     $global{\"gridEngineThreadsOption\"}              =\"-pe make THREADS\";\r\n 755     $global{\"gridEngineMemoryOption\"}               =\"-l h_vmem=MEMORY\";\r\nbut always got the same error.\r\n\r\nHow do we set up the assembler to run on our cluster?\r\nWill we then be able to modulate the resources (cores, cpus, memory), so that we can have other processes running at the same time?\r\nThanks"}}