Faster Computing - HPC - jargon explained

[marknovak]

https://stackoverflow.com/questions/65603381/slurm-nodes-tasks-cores-and-cpus

[marknovak]

one single job (with 8 tasks)

#!/bin/bash
#SBATCH --ntasks=8
## more options
srun echo hello

Slurm will start the 8 tasks at the same time, so it will need 8 CPUS to become available at the same time. This is typically only used with parallel jobs where processes need to communicate with each others, for instance using an Message Passing Interface library.

[marknovak]

8 distinct jobs (each with one task)

#!/bin/bash
#SBATCH --job-name=arrayJob
#SBATCH --output=arrayJob_%A_%a.out
#SBATCH --error=arrayJob_%A_%a.err
#SBATCH --array=1-8
#SBATCH --time=01:00:00
#SBATCH --ntasks=1

if 8 CPUs become available at once, they will all start at the same time, but if only 4 CPUs become available at first, 4 tasks will run, the other 4 remaining pending. When the initial 4 are done, the other 4 are started. It is typically used in the case of embarrassingly parallel jobs, where the processes do not need to communicate or synchronise, like for applying the same program to a list of files

[marknovak]

nodes vs tasks vs cpus vs cores
https://login.scg.stanford.edu/faqs/cores/

[marknovak]

There are other operations available to tasks, such as specifying the array task ID more granularly.
If you wanted to specify each array task ID, you could do so with the below:

#SBATCH --array 1,2,6,8,13,52

If you wanted to specify some interval of a set, you could use something like the below. The below would have four task IDs: 1, 3, 5, and 7.

#SBATCH --array 1-7:2

If you want to bottleneck yourself, you could limit how many array tasks are running at a time with the below, which has 100 array tasks created but only five can run at a time.

#SBATCH --array 1-100%5

[marknovak]

https://researchcomputing.princeton.edu/support/knowledge-base/slurm