setup

#!/bin/bash

WD=$PWD

SYSTEM=Anemone

BRANCH=branch_4.2
#COMMIT=b1b3d9e142670c8358f240a8eeb13979600d8039
TAG=4.2.2

NEMODIR=${WD}/nemo
STOP=0

# Handle arguments
usage() { echo "Usage: $0 [-b branch] [-c commit | -t tag] [-d directory] [-s system] [-x stop_after_download]" 1>&2; exit 1; }
while getopts ":b:c:t:d:s:x" o; do
    case "${o}" in
        b)
            BRANCH=${OPTARG}
            ;;
        c)
            COMMIT=${OPTARG}
            ;;
        t)
            TAG=${OPTARG}
            ;;
        d)
            NEMODIR=$(realpath "${OPTARG}")
            ;;
        s)
            SYSTEM=${OPTARG}
            ;;
        x)
            STOP=1
            ;;
        *)
            usage
            ;;
    esac
done
shift $((OPTIND-1))

# Check only one of "-c" or "-t" is specified
if [ -n "${COMMIT}" ] && [ -n "${TAG}" ]; then
    echo "Specify only one of "-c" or "-t"."
    exit
fi

# Check system is supported and ensure 'correct' case of $SYSTEM
if [[ "$SYSTEM" =~ ^([aA][nN][eE][mM][oO][nN][eE])$ ]]; then
      SYSTEM=Anemone
    elif [[ "$SYSTEM" =~ ^([aA][rR][cC][hH][eE][rR][2])$ ]]; then
      SYSTEM=Archer2
    else
      echo "System not recognised. Options are: Anemone, Archer2"
    exit
fi


# Download NEMO
echo "Downloading NEMO"

# Checking out from NEMO GitLab
git clone https://forge.nemo-ocean.eu/nemo/nemo.git -b "$BRANCH" "$NEMODIR" || exit

if [ -n "${COMMIT}" ]; then
    cd "$NEMODIR" || exit
    git reset --hard "$COMMIT" || exit
    cd "$WD" || exit
fi

if [ -n "${TAG}" ]; then
    cd "$NEMODIR" || exit
    git reset --hard "$TAG" || exit
    cd "$WD" || exit
fi

if [[ "$STOP" == 1 ]]; then
    exit
fi

###########################################
# SYSTEM
###########################################
# System specific options
echo "Setting up configuration and scripts for ${SYSTEM}"

echo $PWD

ln -sfT compile_nemo_${SYSTEM} scripts/compile_nemo
ln -sfT compile_tools_${SYSTEM} scripts/compile_tools
ln -sfT mkslurm_NPD_${SYSTEM} scripts/python/mkslurm_NPD

ln -sfT INPUT_eORCA025_${SYSTEM} data/INPUT_eORCA025
ln -sfT INPUT_eORCA12_${SYSTEM} data/INPUT_eORCA12
ln -sfT INPUT_RAPID12_${SYSTEM} data/INPUT_RAPID12
ln -sfT INPUT_RAPID12_${SYSTEM} data/INPUT_RAPID12
ln -sfT INPUT_RAPID36_${SYSTEM} data/INPUT_RAPID36
ln -sfT INPUT_RAPID36_${SYSTEM} data/INPUT_RAPID36


# Copy
echo "Copying customized files into ${NEMODIR}"
cp -r "${WD}"/{arch,cfgs,data,ext,scripts,tools} "$NEMODIR"/. || exit

cp -r "${WD}"/scripts/TIDY "$NEMODIR"/cfgs/GLOBAL_QCO/eORCA025/.
cp -r "${WD}"/scripts/TIDY "$NEMODIR"/cfgs/GLOBAL_QCO/eORCA12/.

cp -r "${WD}"/scripts/TIDY "$NEMODIR"/cfgs/AGRIF_QCO/eORCA025-RAPID12/.
cp -r "${WD}"/scripts/TIDY "$NEMODIR"/cfgs/AGRIF_QCO/eORCA025-RAPID12-RAPID36/.

###########################################
# TOOLS
###########################################
# # Compile tools
# echo "Compiling tools"
# cd "$NEMODIR"/tools || exit
# ../scripts/compile_tools || exit
# 
# 
# # Submit DOMAINcfg
# echo "Submitting scripts to create domain files"
# for DIR in "${WD}"/tools/DOMAINcfg/*/; do
#     DIR=$(basename "$DIR")
#     echo "$DIR"
#     cd "$NEMODIR"/tools/DOMAINcfg/"$DIR"/ || exit
#     if [ "$DIR" == "eORCA025-RAPID12" ] ; then
#         DOMAIN_JOBID12=$(sbatch --parsable build_domains.slurm) || exit
#     elif [ "$DIR" == "eORCA025-RAPID12-RAPID36" ] ; then
#         DOMAIN_JOBID36=$(sbatch --parsable build_domains.slurm) || exit
#     else
#         sbatch build_domains.slurm || exit
#     fi
# done
# 
# 
# # TO CHECK - note dependency of weights submission on completion of domain building.
# 
# # Submit WEIGHTS
# echo "Submitting scripts to create weights"
# for DIR in "${WD}"/tools/WEIGHTS/*/; do
#     DIR=$(basename "$DIR")
#     echo "$DIR"
#     cd "$NEMODIR"/tools/WEIGHTS/"$DIR"/ || exit
#     if [ -e build_weights_R36.slurm ] ; then
#         sbatch --dependency=afterok:"$DOMAIN_JOBID36" build_weights_R36.slurm || exit
#     else
#         sbatch --dependency=afterok:"$DOMAIN_JOBID12" build_weights.slurm || exit
#     fi
# done


###########################################
# CONFIGURATIONS
###########################################

# Add and compile cfgs
echo "Compiling NEMO"
cd "$NEMODIR" || exit
./scripts/compile_nemo || exit

# Bye-Bye
squeue -u "$USER"
cd "$WD" || exit