How to compute/Batch jobs
|Examining job's output|
Batch jobs are a non-interactive type of jobs. You must prepare a startup script (=batch script) for your job, submit the job, wait until it is finished and after that you can check its results.
Prepare a startup script
|Working with data in a job||
A startup script is collection of commands with given order, which are executed by your requested resources. You can specify requested resources outside (via qsub options) or inside your startup script. Both ways are absolutely correct, choose what you personally prefer.
Specify requested resources
You can specify resources inside the startup script via #PBS line prefix + an option. Create a text file in any editor (vim, pico, nano..) with following lines:
#!/bin/bash #PBS -N myFirstJob #PBS -l select=1:ncpus=4:mem=4gb:scratch_local=10gb #PBS -l walltime=1:00:00 #Options above for scheduling system: job will run 1 hour at maximum, 1 machine with 4 processors + 4gb RAM memory + 10gb scratch memory are requested module add g03 #loads the Gaussian's application modules, version 03 trap 'clean_scratch' TERM EXIT # setup SCRATCH cleaning in case of an error cd $SCRATCHDIR || exit 1 # enters user's scratch directory cp /software/testData/gaussian_test.com $SCRATCHDIR # gets job's input data g03 <gaussian_test.com >results.out # starts the Gaussian application and saves output into results.out cp results.out /home/$USER || export CLEAN_SCRATCH=false # moves the produced (output) data to user's home directory or leave it in SCRATCH if an error occured
Submit the job
You can submit your job via qsub command. For example:
In case you want to specify requested resources outside batch script, move the PBS options to the submitting command:
qsub -l select=1:ncpus=4:mem=4gb:scratch_local=10gb -l walltime=1:00:00 myJob.sh
Qsub returns jobID (10583298 in this example) which you can use to track your job.
If you specify requested resources inside your startup script, run just qsub command with name of the script.
Examine job's output
You can find information about this topic here.