SLURM Examples¶
nohup \
snakemake \
--snakefile $IMPUTATION_SNAKEFILE \
--configfile $IMPUTATION_CONFIG \
--rerun-incomplete \
--jobs 48 \
--use-singularity \
--restart-times 2 \
--keep-going \
--cluster \
"sbatch \
--qos debug \
-N 1 \
--ntasks 1 \
--cpus-per-task 48 \
-o $LOG/%{rule}.out \
--export ALL" \
> $LOG/nohup_`date +%Y-%m-%d.%H:%M:%S`.log &
Another SLURM example where file latency causes issues with snakemakes ability to detect if a job is completed (note the --latency-wait
parameter):
nohup
snakemake \
--snakefile $IMPUTATION_SNAKEFILE \
--configfile $IMPUTATION_CONFIG \
--rerun-incomplete \
--jobs 1 \
--use-singularity \
--restart-times 2 \
--keep-going \
--latency-wait 30 \
--cluster \
"sbatch \
--qos regular \
-N {threads} \
--mem={resources.mem_per_thread_gb}G \
--tmp={resources.disk_per_thread_gb}G \
-o $LOG/{rule}.out \
--export ALL \
--time=05:59:59" \
> $LOG/nohup_`date +%Y-%m-%d.%H:%M:%S`.log &