Cluster script with singularity

singularity_prepro_levels.slurm

#!/bin/bash
#
#SBATCH --job-name=prepro_levels
#SBATCH --ntasks=1
#SBATCH --exclusive
#SBATCH --partition=low
#SBATCH --time=48:00:00
#SBATCH --mail-user=fabien.maussion@uibk.ac.at
#SBATCH --mail-type=ALL

# Abort whenever a single step fails. Without this, bash will just continue on errors.
set -e

# Current RGI region
OGGM_RGI_REG=`printf "%02d" $SLURM_ARRAY_TASK_ID`
export OGGM_RGI_REG

# On every node, when slurm starts a job, it will make sure the directory
# /work/username exists and is writable by the jobs user.
# We create a sub-directory there for this job to store its runtime data at.
OGGM_WORKDIR="/work/$SLURM_JOB_USER/$SLURM_JOB_ID/rgi_reg_$RGI_REG"
mkdir -p "$OGGM_WORKDIR"
echo "RGI Region: $OGGM_RGI_REG"
echo "Workdir for this run: $OGGM_WORKDIR"

# Export the WORKDIR as environment variable so our script can use it to find its working directory.
export OGGM_WORKDIR

# Use the local data download cache
export OGGM_DOWNLOAD_CACHE=/home/data/download
export OGGM_DOWNLOAD_CACHE_RO=1
export OGGM_EXTRACT_DIR="/work/$SLURM_JOB_USER/$SLURM_JOB_ID/oggm_tmp"

# All commands in the EOF block run inside of the container
# Adjust container version to your needs, they are guaranteed to never change after their respective day has passed.
srun -n 1 -c "${SLURM_JOB_CPUS_PER_NODE}" singularity exec docker://oggm/oggm:20181123 bash -s <<EOF
  set -e
  # Setup a fake home dir inside of our workdir, so we don't clutter the actual shared homedir with potentially incompatible stuff.
  export HOME="$OGGM_WORKDIR/fake_home"
  mkdir "\$HOME"
  # Create a venv that _does_ use system-site-packages, since everything is already installed on the container.
  # We cannot work on the container itself, as the base system is immutable.
  python3 -m venv --system-site-packages "$OGGM_WORKDIR/oggm_env"
  source "$OGGM_WORKDIR/oggm_env/bin/activate"
  # Make sure latest pip is installed
  pip install --upgrade pip setuptools
  # Install a fixed OGGM version (20 Jan 2019)
  pip install --upgrade "git+https://github.com/OGGM/oggm.git@c0c81cb612d6c020647ca7262705349a097b606f"
  # Finally, the runs
  oggm_prepro --map-border 10
  oggm_prepro --map-border 80
  oggm_prepro --map-border 160
  oggm_prepro --map-border 250
EOF

# Print a final message so you can actually see it being done in the output log.
echo "SLURM DONE"