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Describe the bug
Slurm is commonly configured to forward all environment variables. When defining env SNAKEMAKE_PROFILE then Slurm will by default forward this through sbatch. This causes the inner snakemake inside the job script to have args.profile set to a non-None value and subsequently snakemake existing with
Error: you need to specify the maximum number of jobs to be queued or executed at the same time with --jobs or -j.
* feat: cluster sidecar
* fix: do not pass SNAKEMAKE_PROFILE into cluster-submit (#1398)
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Snakemake version
v6.15.5
Describe the bug
Slurm is commonly configured to forward all environment variables. When defining env
SNAKEMAKE_PROFILE
then Slurm will by default forward this throughsbatch
. This causes the inner snakemake inside the job script to haveargs.profile
set to a non-None
value and subsequently snakemake existing withLogs
Minimal example
slurm-bih
profile)export SNAKEMAKE_PROFILE=$HOME/work/Development/slurm-bih ; snakemake -j1 f.2
.Additional context
Specifying
--profile=$HOME/work/Development/slurm-bih
works.The generated jobscript looks sane:
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