slurm_verbose_1day.sbatch

#!/bin/bash
#
#SBATCH --cluster=faculty
#SBATCH --qos=adamw
#SBATCH --partition=adamw
#SBATCH --job-name "EMMA model slurm_verbose_1day.sbatch"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=160G
#SBATCH  -C INTEL
#SBATCH --time=24:00:00
#SBATCH --mail-user=bmaitner@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
#SBATCH -o emma_model_verbose.out


  # Specify directories needed and sif file

  echo "exporting directories"

  export PROJECT_FOLDER="/panasas/scratch/grp-adamw/"
  export APPTAINER_CACHEDIR="/panasas/scratch/grp-adamw/"$USER"/singularity"
  export SIF_PATH=$PROJECT_FOLDER"/"$USER"/singularity"
  export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"
  export EMMA_HOME="/projects/academic/adamw/users/"$USER"/emma_model"

  # make sure the sif file is in the correct location

  echo "copying sif"

  cp -r "/projects/academic/adamw/users/"$USER"/singularity/"$SIF_FILE $SIF_PATH/$SIF_FILE

  # make needed directories

  echo "making directories"

  mkdir -p "$APPTAINER_CACHEDIR/tmp"
  mkdir -p "$APPTAINER_CACHEDIR/run"

  # execute the function run_verbose.sh (which in turn runs the function run.R, which in turn calls tar_make())

  echo "executing run_verbose.sh"

  ## Commenting this out as it attempts to use my main home directory, instead of the current wd
  # singularity exec \
  # --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
  # --bind $APPTAINER_CACHEDIR/tmp:/tmp \
  # --bind $APPTAINER_CACHEDIR/run:/run \
  # $SIF_PATH/$SIF_FILE ./run_verbose.sh


  singularity exec \
  --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
  --bind $APPTAINER_CACHEDIR/tmp:/tmp \
  --bind $APPTAINER_CACHEDIR/run:/run \
  --home $EMMA_HOME \
  $SIF_PATH/$SIF_FILE ./run_verbose.sh