- Running multiple similar jobs which only differ in terms of the input often is required in the context of parameter study / sensitivity analysis. Array jobs are recommended for this scenario.
- Long computations should be divided into shorter steps, creating a chain job.
- In order to avoid pitfalls and finding errors after waiting hours for a job to start, the following procedure for setting up batch jobs has been judged as useful:
- Avoid loading modules in your .zshrc or .bashrc.
- Test your application whether it starts as expected on a frontend node.
- Put all commands necessary for the program to start into a script file.
Don't forget the module commands and the shebang (#!) at the first line of the script:
- Use relative paths and ensure that you know the directory in which the job starts.
- Make the script executable (chmod 775 myscript.sh), run it (./myscript.sh) and make sure that everything works as expected.
- Put the memusage script in front of the executable name (e.g. r_memusage --vm who am i), run it for a minute and then kill the process (Ctrl+C). That way you can get an idea of how much memory the program uses.
- Ensure that you have configured your program's memory / stack limits when necessary.
- Put all job requests in the script file using the #SBATCH magic cookie.
- Pay attention to the limiting factors such as: memory, number of slots and job run time.
- Submit your script with a run time of 5 minutes so that it has greater chance of failing early. If everything starts as expected,
- Submit your final script.