Snakemake executor plugin: slurm-gustave-roussy
Snakemake plugin executor designed to match Gustave Roussy computing cluster specificities : automatic partition seleciton, and default resources value.
Installation
Install this plugin by installing it with pip or mamba, e.g.:
pip install snakemake-executor-plugin-slurm-gustave-roussy
Usage
In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:
snakemake --executor slurm-gustave-roussy ...
with ... being any additional arguments you want to use.
The executor plugin has the following settings:
CLI argument |
Description |
Default |
Choices |
Required |
Type |
|---|---|---|---|---|---|
|
Optional arguments passed to slurm |
|
✗ |
Further details
Automatic partition selection
This executor automatically selects the best queue on Flamingo computing
cluster at Gustave Roussy.
In order not to break pipelines running on Colibri, and other (old) clusters,
this executor selects the best queue if, and only if the host name startswith
“flamingo“.
GPU queue is automatically selected once job.resources.gres is not null.
One can find examples in official Snakemake documentation and expecially about
gpu resources
Default values
By default, according to Flamingo defaults behavior, --mem is set to
1024 bytes, and --time to 6 hours.
As described in offcial Snakemake documentation, one can change these
values, respectively through job.resources.mem_mb as
described here,
and through job.threads as described in
there.
Additional arguments
Additional Slurm arguments can be provided through Snakemake command line,
using --slurm_gustave_roussy_args "..."