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SLURM

SLURM#

The template.sh file#

When using SLURM as backend, the soopervisor add {env-name} command wil create an {env-name}/template.sh file.

Under the hood, Soopervisor uses the template.sh for all tasks in your pipeline and executes a sbatch job.sh command for each one.

template.sh contains two placeholders {{name}} and {{command}}, these placeholders are mandatory and should not be removed, at runtime Soopervisor will replace them with the name of the task and the command execute, one per task in your pipeline. However, you may add other commands to template.sh to customize execution. Typically, you’ll have to add any preparation steps, like activating a virtual environment:

#!/bin/bash
#SBATCH --job-name={{name}}
#SBATCH --output=result.out
#

# activate conda environment
conda activate myenv
# execute task
srun {{command}}

Customizing task execution#

You may want to use different settings for each task in your pipeline in some scenarios. To achieve that, you can add more files next to the template.sh file, and Soopervisor will choose which one to use depending on the task’s name.

The resolution logic is as follows. Say you have a task named fit-gpu:

  1. Look for an exact match (i.e., fit-gpu.sh)

  2. Look for a file with a double underscore placeholder (e.g., fit-__.sh, or __-gpu.sh)

  3. If no matches, use template.sh

You can use this templating feature to customize the submitted jobs, for example to pass custom parameters to the srun command.

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