![]() ![]() You can add any switch to qsub to your submission script this way. Instead of remembering to use the -cwd switch everytime you submit a job with qsub, you can add the switch to your submission script by putting it on a line prefixed with a "#$": rw- 1 prentice admin 77 Feb 12 11:31 bash_hello.sh Your job 2304 ("bash_hello.sh") has been submitted You can specify this behavior with the -cwd switch to qsub (see the qsub man page for a full list of all the qsub options): This is also desirable for programs that read/write data from/to files so you can have all the input and output files in the same directory. Normally, it's more convenient to have the program run in the directory you submit it from, so that it will put it's output files in that same directory. That's good - that means there were no errors running this job. Notice that the standard error file, bash_hello.sh.e2302 has a size of 0. rw-r-r- 1 prentice admin 0 Feb 12 11:34 /home/prentice/bash_hello.sh.e2302 ![]() The "o" file is for standard output, and the "e" file is for standard error: It also names the job with the name of the submission script by default. By default, SGE runs the job in your home directory and writes the standard output and standard error of jobs to files in your home directory. You may also see "qw", which means the job is queued and waiting to run. The "r" in the state column means the job is running. Job-ID prior name user state submit/start at queue slots ja-task-IDĢ302 0.55500 bash_hello prentice r 11:23:09 1 Once the job is submitted, you can check the status of it using the qstat command: In the in above output, the "2302" is the job-ID, and the string in parenthesis ("bash_hello") is the job name. Your job 2302 ("bash_hello") has been submitted This script can how be submitted to sge using the qsub command: The "sleep 30" line is there just to keep this short script to run a little longer for demonstration purposes. For example, this simple BASH shell script can be a job submission script: Job submission scripts are nothing more than shell scripts that can have some additional "comment" lines added that specify options for SGE. It may be helpful to read the man pages for these commands:Īll of the SGE man pages should be in your MANPATH by default, so you can access all of them using the 'man' command. ![]() The first step to taking advantage of the Hyperion cluster is understanding how to submit jobs to the cluster using SGE. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |