specify time

[smilesun]

in sbatch, one could specify

#!/bin/bash
#SBATCH -p gpu_p
#SBATCH --qos=gpu
#SBATCH --gres=gpu:1
#SBATCH -c 1
#SBATCH --mem=32G
#SBATCH -t 48:00:00
#SBATCH --nice=10000 

where -t specify the time, is there an option to do that as well using yaml here with snakemake?

Since I constantly got out-of-memory error running my GPU job, i wonder if that is a time out error?

[jdblischak]

You can update this profile to pass any valid sbatch argument. The --time flag is explicitly used as a demonstration in the README:

https://github.com/jdblischak/smk-simple-slurm#a-variable-argument-to-sbatch-eg---time

[jdblischak]

Also note that you can define time as an integer or a string. There are existing examples for both strategies: time-integer and time-string