PrepareJob
From BIOcrunch
(Difference between revisions)
m |
|||
| Line 49: | Line 49: | ||
</source> | </source> | ||
| + | |||
| + | {{tutorial_bar}} | ||
Revision as of 15:38, 28 April 2015
To run your job on the cluster, prepare it on your local machine, then copy it to the cluster. Beside the datafiles you will need a jobfile containing all you setting.
Name your job file and your data files in a consistent way:
- Job file: myjobfile.sh
- User: Mustermann
- Email: max@mustermann.de
These jobfiles are written in a sort of "shell" command syntax of Linux systems.
Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards.
Lines starting with "#$" are commands for the job scheduler "qsub".
Lines starting not with "#" are commands to execute programs in this job.
Example (Beast)
you may use this as a template for Beast simply change all occurrences of "myjobfile" to your actual project name. also change User and email to your settings.
- #!/bin/csh
- #
- # Username (Which account to be charged cpu time)
- #$ -A Mustermann
- #
- #
- # If you want to make it queue now, get rid of the -a option by adding ## before $
- # If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
- ##$ -a 201407300600
- #
- #
- # Send mail to these users
- #$ -M max@mustermann.de
- #
- # Mail at beginning/end/on suspension
- #$ -m bes
- #
- # Export these environmental variables
- #$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
- #
- # The job is located in the current
- # working directory.
- #$ -cwd
- #$ -o myjobfile.out
- #$ -e myjobfile.err
- #
- env >./xenv
- /share/apps/beast180/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
- Step 1: Get an Account
- Step 2: Prepare you Job
- Step 3: Copy your Job to the cluster
- Step 4: Login on the cluster
- Step 5: Start the Job
- Step 6: Wait for the job to be finished
- Step 7: Get your results
