postprocess.sh

#!/usr/bin/env bash

#SBATCH --partition=broadwl
#SBATCH --job-name=takeup_pp     # create a short name for your job
#SBATCH --nodes=1                # node count
#SBATCH --ntasks=1               # total number of tasks across all nodes
#SBATCH --cpus-per-task=1        # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=40G        # memory per cpu-core (4G is default)
#SBATCH --time=0-04:00:00        # maximum time needed (HH:MM:SS)
#SBATCH --mail-type=begin        # send email when job begins
#SBATCH --mail-type=end          # send email when job ends
#SBATCH --mail-user=karimn2.0@gmail.com
#SBATCH --output=temp/log/takeup_postprocess-%j.log
#SBATCH --error=temp/log/takeup_postprocess-%j.log
#SBATCH --export=IN_SLURM=1

LATEST_VERSION=62
VERSION=${1:-$LATEST_VERSION} # Get version from command line if provided
CMDSTAN_ARGS="--cmdstanr"
SLURM_INOUT_DIR=~/scratch-midway2

if [[ -v IN_SLURM ]]; then
  echo "Running in SLURM..."

  module load midway2 gdal/2.4.1 udunits cmake R/4.2.0

  OUTPUT_ARGS="--output-path=${SLURM_INOUT_DIR}"
  POSTPROCESS_INOUT_ARGS="--input-path=${SLURM_INOUT_DIR} --output-path=${SLURM_INOUT_DIR}"
  CORES=$SLURM_CPUS_PER_TASK

  echo "Running with ${CORES} cores."
  echo "INOUT ARGS: ${POSTPROCESS_INOUT_ARGS}."
else
  OUTPUT_ARGS="--output-path=data/stan_analysis_data"
  POSTPROCESS_INOUT_ARGS=
  CORES=12
fi

Rscript ./postprocess_dist_fit.R ${VERSION} ${POSTPROCESS_INOUT_ARGS} --cores=1 --load-from-csv