Hoffman2:Batch Mode: Difference between revisions
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export PATH=$HOME/.local/bin:$PATH | export PATH=$HOME/.local/bin:$PATH | ||
= Part 3: | = Part 3: Submit your job script = | ||
Make sure your job script has executive privileges by using chmod command | |||
chmod ug+x mycode.sh | |||
The rest is to submit your batch job script with qsub. | |||
For example: | |||
qsub mycode.sh | |||
= Other methods = | = Other methods = |
Revision as of 17:14, 30 September 2022
Here we show how you can submit your job with batch mode.
To use a batch job, you need to create a batch file with bash or tcsh. This file should have three parts:
- Part 1: List all the resources you want to reserve for your job
- Part 2: Load your modules, export the Linux environment that is needed for your script to run
- Part 3: Call your job script
Once you have your batch file, you can submit it using the qsub
command. For example (if your batch file is named as myjob.sh)
qsub myjob.sh
Job Submission Templates
Here are some batch file templates you can start with:
Part 1: Request Computing Resource
This example is based on code from the Submit Job template.
The first part of the batch file should let the Hoffman job scheduler know what resources you want to reserve for your job:
#!/bin/bash #$ -cwd #$ -o joblog.$JOB_ID #$ -j y #$ -pe shared 2 #$ -l h_rt=8:00:00,h_data=4G #$ -M $USER@mail #$ -m bea
Here's the meaning of each line:
#$ -cwd
- Use the current directory for the job
#$ -o joblog.$JOB_ID
- Write standard output to file joblog.$JOB_ID. $JOB_ID will be replaced by your job ID which is assigned once you submit your job.
#$ -j y
- Merge error log with standard output (in file joblog.$JOB_ID)
#$ -pe shared 2
- Request 2 processor cores
#$ -l h_rt=8:00:00,h_data=4G
- Use -l option to specify job running time length and reserve memory
h_rt=8:00:00
: reserve 8 hours for your job running timeh_data=4G
: reserve 4G per-core (since -pe 2 is used above, it will reserve 2 core x 4G memory = 8G total memory)
#$ -M $USER@mail
- Send notification to your user email address
#$ -m bea
- Specify the timing of the notification email to be sent out:
- b - when the job begins
- e - when the job ends
- a - when the job is aborted (ends in an error state)
Part 2: Setup the Environment
In the second part, you should setup your Unix environment for your code to run, which includes loading modules and export paths for libraries.
To use any module provided by Hoffman and CCN, you'll need the following two lines
# load the job environment: . /u/local/Modules/default/init/modules.sh module use /u/project/CCN/apps/modulefiles
For example, load FSL
# Load the FSL module module load fsl
Another example, export a FSL variable
# This is optional # More info here: https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:FSL export NO_FSL_JOBS=true
Or export an additional PATH for a custom installed library under your .local/ directory
export PATH=$HOME/.local/bin:$PATH
Part 3: Submit your job script
Make sure your job script has executive privileges by using chmod command
chmod ug+x mycode.sh
The rest is to submit your batch job script with qsub.
For example:
qsub mycode.sh
Other methods
- Use an interactive way to create your batch job file in Hoffman, read more about job.q
- Use qsub in one line command: examples
Job Array
Job Array is a type of batch mode. It is used to run the same processing job towards a large number of subjects on separate nodes in parallel. More about Job Array