start_worker.slurm

#!/bin/bash
#SBATCH --account=pawsey0106
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=4G
#SBATCH --time=1:00:00
#SBATCH -J dask-worker   # name
#SBATCH -o dask-worker-%J.out

module load singularity

container=$1
scheduler_file=$2

#Set these to have singularity bind data locations
export SINGULARITY_BINDPATH=/group:/group,/scratch:/scratch,/run:/run,$HOME:$HOME

#This is needed to setup conda in the container correctly
export SINGULARITYENV_PREPEND_PATH=/srv/conda/envs/notebook/bin:/srv/conda/condabin:/srv/conda/bin
export SINGULARITYENV_XDG_RUNTIME_DIR=""

# calculate task memory limit
mempcpu=$SLURM_MEM_PER_CPU
memlim=$(echo $SLURM_CPUS_PER_TASK*$mempcpu*0.98 | bc)

echo Memory limit is $memlim

echo starting $SLURM_NTASKS workers with $SLURM_CPUS_PER_TASK CPUs each

srun --export=ALL -n $SLURM_NTASKS -c $SLURM_CPUS_PER_TASK \
singularity exec $container \
dask-worker --scheduler-file $scheduler_file --nthreads $SLURM_CPUS_PER_TASK --memory-limit ${memlim}M