{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51","labels_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/comments","events_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/events","html_url":"https://github.com/pcingola/BigDataScript/issues/51","id":52470703,"number":51,"title":"SGE: qsub: command required for a binary job","user":{"login":"floerhard","id":10242442,"avatar_url":"https://avatars.githubusercontent.com/u/10242442?v=3","gravatar_id":"","url":"https://api.github.com/users/floerhard","html_url":"https://github.com/floerhard","followers_url":"https://api.github.com/users/floerhard/followers","following_url":"https://api.github.com/users/floerhard/following{/other_user}","gists_url":"https://api.github.com/users/floerhard/gists{/gist_id}","starred_url":"https://api.github.com/users/floerhard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/floerhard/subscriptions","organizations_url":"https://api.github.com/users/floerhard/orgs","repos_url":"https://api.github.com/users/floerhard/repos","events_url":"https://api.github.com/users/floerhard/events{/privacy}","received_events_url":"https://api.github.com/users/floerhard/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/pcingola/BigDataScript/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":15,"created_at":"2014-12-19T10:54:43Z","updated_at":"2015-01-09T17:48:16Z","closed_at":null,"body":"Dear Pablo,\r\n\r\nfirst of all, nice work, bds looks like a really nice platform to build pipelines on!\r\n\r\nI wanted to try a minimal example (Hello World with 'task') on our SGE cluster using BigDataScript 0.99c (build 2014-12-15)\r\n\r\n```\r\n#!/usr/bin/env bds\r\ntask echo Hello world\r\n```\r\n\r\n```\r\nbds -system sge -debug -l -v hello_world.bds\r\n```\r\n\r\nThe output is\r\n```\r\n00:00:00.214\tExecutioner: ExecutionerClusterSge, task hello_world.bds.20141219_114332_240/task.line_3.id_1\r\n00:00:00.214\tRunning command: echo \"bds exec 86400 '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.exitCode' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.sh' \" | qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\n00:00:00.215\tCommand (CmdCluster): CmdCluster: qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\n00:00:00.216\tCmdCluster 'hello_world.bds.20141219_114332_240/task.line_3.id_1': Start\r\n00:00:00.216\tExecutionerClusterSge 'ClusterSge[11]': Queue: No task to run.\r\n00:00:00.216\tCmdLocal: Executing  qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster\r\nWARNING: Process closed stdout prematurely. Could not read PID\r\nCmdCluster: qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\nqsub: command required for a binary job\r\n```\r\n\r\nIs the shell script is missing from the qsub call?\r\n\r\nBest,\r\nFlorian"},"comment":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/comments/69370510","html_url":"https://github.com/pcingola/BigDataScript/issues/51#issuecomment-69370510","issue_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51","id":69370510,"user":{"login":"golharam","id":671079,"avatar_url":"https://avatars.githubusercontent.com/u/671079?v=3","gravatar_id":"","url":"https://api.github.com/users/golharam","html_url":"https://github.com/golharam","followers_url":"https://api.github.com/users/golharam/followers","following_url":"https://api.github.com/users/golharam/following{/other_user}","gists_url":"https://api.github.com/users/golharam/gists{/gist_id}","starred_url":"https://api.github.com/users/golharam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/golharam/subscriptions","organizations_url":"https://api.github.com/users/golharam/orgs","repos_url":"https://api.github.com/users/golharam/repos","events_url":"https://api.github.com/users/golharam/events{/privacy}","received_events_url":"https://api.github.com/users/golharam/received_events","type":"User","site_admin":false},"created_at":"2015-01-09T17:48:16Z","updated_at":"2015-01-09T17:48:16Z","body":"No, there is no .exit file.  Here's what I have:\r\n\r\n[golharr@kraken examples]$ ll\r\ntotal 24\r\n-rw------- 1 golharr bioinfo   13 Jan  9 12:45 bds.pid.44039\r\n-rwxr-xr-x 1 golharr bioinfo  152 Jan  9 12:19 test.bds\r\ndrwxr-xr-x 2 golharr bioinfo 1024 Jan  9 12:45 test.bds.20150109_124519_400\r\n\r\n[golharr@kraken examples]$ ll test.bds.20150109_124519_400/\r\ntotal 16\r\n-rwxr--r-- 1 golharr bioinfo  36 Jan  9 12:45 task.line_7.id_2.sh\r\n-rw-r--r-- 1 golharr bioinfo   0 Jan  9 12:45\r\ntask.line_7.id_2.stderr.cluster\r\n-rw-r--r-- 1 golharr bioinfo 135 Jan  9 12:45\r\ntask.line_7.id_2.stdout.cluster\r\n\r\n\r\n\r\nOn Fri, Jan 9, 2015 at 12:41 PM, Pablo Cingolani <notifications@github.com>\r\nwrote:\r\n\r\n> @golharam <https://github.com/golharam>\r\n> When the task is completed in the slave node, bds-exec creates an 'exit'\r\n> file.\r\n> In you case the file was\r\n>\r\n> /home/golharr/workspace/BigDataScript/examples/test.bds.20150109_122430_716/task.line_7.id_2.exit\r\n>\r\n> Was the file created successfully and visible from the head node (where\r\n> you are running bds)? Try using the \"-log\" option to see if the files are\r\n> created (if you don't use \"-log\" bds deletes them when execution finishes).\r\n>\r\n> Another question: Is your cluster using NFS? I was told that some slow NFS\r\n> systems take a few seconds to update file status...(as opposed to\r\n> infiniband or other options).\r\n>\r\n> —\r\n> Reply to this email directly or view it on GitHub\r\n> <https://github.com/pcingola/BigDataScript/issues/51#issuecomment-69369551>\r\n> .\r\n>"}}