slurm_sing.sh

#!/bin/sh
#SBATCH --cluster=faculty
#SBATCH --qos=adamw
#SBATCH --partition=adamw
#SBATCH --job-name "EMMA model run slurm_sing.sh"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=60G
#SBATCH  -C INTEL
#SBATCH --time=2:00:00
#SBATCH --mail-user=bmaitner@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
#SBATCH -o singularity_test1.out


  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"

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

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

#this code works fine when executed interactively or by running this file, but fails when run with sbatch

  singularity run \
  --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
  --bind $APPTAINER_CACHEDIR/tmp:/tmp \
  --bind $APPTAINER_CACHEDIR/run:/run \
  $SIF_PATH/$SIF_FILE ./run.sh

  echo "v1"