{"id":241,"date":"2016-11-17T23:35:44","date_gmt":"2016-11-17T23:35:44","guid":{"rendered":"http:\/\/sites.sandiego.edu\/hpc\/?page_id=241"},"modified":"2017-05-17T16:21:19","modified_gmt":"2017-05-17T16:21:19","slug":"submit-jobs-hpc-saber1","status":"publish","type":"page","link":"https:\/\/sites.sandiego.edu\/hpc\/submit-jobs-hpc-saber1\/","title":{"rendered":"How to submit jobs on HPC saber1"},"content":{"rendered":"

Submitting jobs<\/span><\/h2>\n

PBS comes with very complete man pages. Therefore, for complete documentation of PBS commands you are encouraged to type man pbs<\/code> and go from there. Jobs are submitted using the qsub<\/code> command. Type man qsub<\/code> for information on the plethora of options that it offers.<\/p>\n

Let’s say I have an executable called “myprog”. Let me try and submit it to PBS:<\/p>\n

[username@launch ~]$ qsub myprog\r\nqsub:  file must be an ascii script\r\n<\/pre>\n
Oops… That didn’t work because qsub expects a shell script. Any shell should work, so use your favorite one. So I write a simple script called “myscript.sh”<\/p>\n
\n
#!\/bin\/bash<\/span>\r\ncd<\/span> $PBS_O_WORKDIR<\/span>\r\n.\/myprog argument1 argument2\r\n<\/pre>\n<\/div>\n
and then I submit it:<\/p>\n
[username@launch ~]$ qsub myscript.sh\r\n4681.mn01\r\n<\/pre>\n
That worked! Note the use of the $PBS_O_WORKDIR<\/code> environment variable. This is important, since by default PBS on our cluster will start executing the commands in your shell script from your home directory. To go to the directory in which you executed qsub<\/code>, cd<\/code> to $PBS_O_WORKDIR<\/code>. There are several other useful PBS environment variables that we will encounter later.<\/p>\n
Editing files<\/span><\/h3>\n
Editing files on the cluster can be done through a couple of different methods…<\/p>\n
Native Editors<\/span><\/h4>\n