Explain how SLURM variables work

[Adrien Le Guillou]

by default workflow steps use --export=NONE
this can be overridden in the sbatch_opts.

with --export=NONE, all SLURM_* vars are still passed.

note:

# in sh 
export ABC=10
export SLURM_ABC=20

# in sbatch
#SBATCH --export=NONE
echo $ABC               # gives ""
echo $SLURM_ABC # gives 20

# in sbatch
#SBATCH --export=ALL
echo $ABC               # gives 10
echo $SLURM_ABC # gives 20

# in sbatch
#SBATCH --export=ABC=30,SLURM_ABC=40
echo $ABC               # gives 30
echo $SLURM_ABC # gives 20

takeaway: SLURM_* cannot be overridden by --export, must actually be exported in the user ENV