Learner Profiles

Three people this day is for. The exercises assume a terminal and a text editor. They do not assume a previous batch job.

Noor, first year, laptop only

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Noor writes Python on a laptop and has just been told the data set is on Snellius. Noor can use a terminal and has not seen a module or a queue. Noor needs episode 1 and episode 2 before any of the later material makes sense. The win for Noor is a single sbatch that runs pi_one.py and a clear rule about which directory holds the result.

Idris, SSH works, jobs do not

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Idris has logged in before and has a directory of scripts in /home. Jobs sit in the queue, or they die at the start because the module was loaded in a different order last time. Idris needs the header in the Slurm episode, module purge before module load, and the filesystem table. The array is the part Idris came to see.

Sam, a thousand short commands

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Sam already submits jobs and is now generating thousands of one-second tasks. The queue time is longer than the work. Sam can skim episodes 1 and 2, should still do the filesystem episode because the outputs are many small files, and should spend the afternoon on QCG-PilotJob and the one-page comparison with HyperQueue, Snakemake, and FireWorks. The timing episode is there so Sam can say whether more cores helped, with a number.

What you do not need

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You do not need to compile a program, write a workflow engine, or read an EasyBuild recipe. Those are real skills, and they are the book at https://hpceb.rgoswami.me/, not this day.