#!/bin/bash -fe

# E3SM Coupled Model Group run_e3sm script template.
#
# Bash coding style inspired by:
# http://kfirlavi.herokuapp.com/blog/2012/11/14/defensive-bash-programming

main() {

# For debugging, uncomment libe below
#set -x

# --- Configuration flags ----

# Machine and project
readonly MACHINE=anvil
readonly PROJECT="condo"

# Simulation
readonly COMPSET="CMPASO-JRA1p4"
readonly RESOLUTION="TL319_IcoswISC30E3r5"
readonly CASE_NAME="test.CMPAS-JRA.TL319_IcoswISC30E3r5.anvil"  # MODIFY 
#readonly CASE_GROUP=""

# Code and compilation
readonly CHECKOUT="20240304"
readonly BRANCH="399d430"  # master as of 2024-03-04 E3Sm v3.0.0 tag
#readonly CHERRY=()
readonly DEBUG_COMPILE=false

# Run options
readonly MODEL_START_TYPE="initial"  # 'initial', 'continue', 'branch', 'hybrid'
readonly START_DATE="0001-01-01"

# Additional options for 'branch' and 'hybrid'
# readonly GET_REFCASE=TRUE
# readonly RUN_REFDIR=""
# readonly RUN_REFCASE=""
# readonly RUN_REFDATE="0301-01-01"

# Set paths
readonly CODE_ROOT="/lcrc/group/e3sm/${USER}/E3SM/code/${CHECKOUT}"
readonly CASE_ROOT="/lcrc/group/e3sm/${USER}/e3sm_scratch/${MACHINE}/${CASE_NAME}"

# Sub-directories
readonly CASE_BUILD_DIR=${CASE_ROOT}/build
readonly CASE_ARCHIVE_DIR=${CASE_ROOT}/archive

# Define type of run
#  short tests: 'S_2x5_ndays', 'M_1x10_ndays', 'M80_1x10_ndays'
#  or 'production' for full simulation

#readonly run='S_1x1_nmonth'
readonly run='production'
if [ "${run}" != "production" ]; then

  # Short test simulations
  tmp=($(echo $run | tr "_" " "))
  layout=${tmp[0]}
  units=${tmp[2]}
  resubmit=$(( ${tmp[1]%%x*} -1 ))
  length=${tmp[1]##*x}

  readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/tests/${run}/case_scripts
  readonly CASE_RUN_DIR=${CASE_ROOT}/tests/${run}/run
  readonly PELAYOUT=${layout}
  readonly WALLTIME="2:00:00"
  readonly STOP_OPTION=${units}
  readonly STOP_N=${length}
  readonly REST_OPTION=${STOP_OPTION}
  readonly REST_N=${STOP_N}
  readonly RESUBMIT=${resubmit}
  readonly DO_SHORT_TERM_ARCHIVING=false

else

  # Production simulation
  readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/case_scripts
  readonly CASE_RUN_DIR=${CASE_ROOT}/run
  readonly PELAYOUT="L"
  readonly WALLTIME="02:00:00"
  readonly STOP_OPTION="nmonths"
  readonly STOP_N="1"
  readonly REST_OPTION="nmonths"
  readonly REST_N="1"
  readonly RESUBMIT="0"
  readonly DO_SHORT_TERM_ARCHIVING=false
fi

# Coupler history 
readonly HIST_OPTION="nmonths"
readonly HIST_N="1"

# Leave empty (unless you understand what it does)
readonly OLD_EXECUTABLE=""

# --- Toggle flags for what to do ----
do_fetch_code=false
do_create_newcase=true
do_modify_pelayout=false
do_case_setup=true
do_case_build=true
do_case_submit=true

# --- Now, do the work ---

# Make directories created by this script world-readable
umask 022

# Fetch code from Github
fetch_code

# Create case
create_newcase

# Custom PE layout
modify_pelayout

# Setup
case_setup

# Build
case_build

# Configure runtime options
runtime_options

# Copy script into case_script directory for provenance
copy_script

# Submit
case_submit

# All done
echo $'\n----- All done -----\n'

}

# =======================
# Custom user_nl settings
# =======================

user_nl() {

cat << EOF >> user_nl_eam
EOF

cat << EOF >> user_nl_elm
EOF

cat << EOF >> user_nl_mpaso
EOF

cat << EOF >> user_nl_mpassi
EOF

}

# =====================================
# Customize MPAS stream files if needed
# =====================================

patch_mpas_streams() {

echo

}

# =====================================================
# Custom PE layout: 
# =====================================================

modify_pelayout() {

    if [ "${do_modify_pelayout,,}" != "true" ]; then
        echo $'\n----- Skipping changing PE-layout -----\n'
        return
    fi

    echo $'\n----- changing PE layout to custom -----\n'
    pushd ${CASE_SCRIPTS_DIR}

    ./xmlchange MAX_MPITASKS_PER_NODE=32
    ./xmlchange MAX_TASKS_PER_NODE=256
    ./xmlchange NTASKS_ATM=1024
    ./xmlchange NTASKS_CPL=1024
    ./xmlchange NTASKS_OCN=1024
    ./xmlchange NTASKS_WAV=1024
    ./xmlchange NTASKS_GLC=1024
    ./xmlchange NTASKS_ICE=1024
    ./xmlchange NTASKS_ROF=1024
    ./xmlchange NTASKS_LND=1024
    ./xmlchange NTASKS_ESP=1
    ./xmlchange NTASKS_IAC=1

    ./xmlchange NTHRDS_ATM=8
    ./xmlchange NTHRDS_CPL=8
    ./xmlchange NTHRDS_OCN=8
    ./xmlchange NTHRDS_WAV=8
    ./xmlchange NTHRDS_GLC=1
    ./xmlchange NTHRDS_ICE=8
    ./xmlchange NTHRDS_ROF=8
    ./xmlchange NTHRDS_LND=8
    ./xmlchange NTHRDS_ESP=1
    ./xmlchange NTHRDS_IAC=1

    ./xmlchange ROOTPE_ATM=0
    ./xmlchange ROOTPE_CPL=0
    ./xmlchange ROOTPE_OCN=0
    ./xmlchange ROOTPE_WAV=0
    ./xmlchange ROOTPE_GLC=0
    ./xmlchange ROOTPE_ICE=0
    ./xmlchange ROOTPE_ROF=0
    ./xmlchange ROOTPE_LND=0
    ./xmlchange ROOTPE_ESP=0
    ./xmlchange ROOTPE_IAC=0

    popd

    }
######################################################
### Most users won't need to change anything below ###
######################################################

#-----------------------------------------------------
fetch_code() {

    if [ "${do_fetch_code,,}" != "true" ]; then
        echo $'\n----- Skipping fetch_code -----\n'
        return
    fi

    echo $'\n----- Starting fetch_code -----\n'
    local path=${CODE_ROOT}
    local repo=E3SM

    echo "Cloning $repo repository branch $BRANCH under $path"
    if [ -d "${path}" ]; then
        echo "ERROR: Directory already exists. Not overwriting"
        exit 20
    fi
    mkdir -p ${path}
    pushd ${path}

    # This will put repository, with all code
    git clone git@github.com:E3SM-Project/${repo}.git .

    # Check out desired branch
    git checkout ${BRANCH}

    # Custom addition
    if [ "${CHERRY}" != "" ]; then
        echo ----- WARNING: adding git cherry-pick -----
        for commit in "${CHERRY[@]}"
        do
            echo ${commit}
            git cherry-pick ${commit}
        done
        echo -------------------------------------------
    fi

    # Bring in all submodule components
    git submodule update --init --recursive

    popd
}

#-----------------------------------------------------
create_newcase() {

    if [ "${do_create_newcase,,}" != "true" ]; then
        echo $'\n----- Skipping create_newcase -----\n'
        return
    fi

    echo $'\n----- Starting create_newcase -----\n'

    if [[ ${PELAYOUT} == custom-* ]];
    then
        layout="M" # temporary placeholder for create_newcase
    else
        layout=${PELAYOUT}

    fi
    ${CODE_ROOT}/cime/scripts/create_newcase \
        --case ${CASE_NAME} \
        --output-root ${CASE_ROOT} \
        --script-root ${CASE_SCRIPTS_DIR} \
        --handle-preexisting-dirs u \
        --compset ${COMPSET} \
        --res ${RESOLUTION} \
        --machine ${MACHINE} ${COMPILER} \
        --project ${PROJECT} \
        --walltime ${WALLTIME} \
        --pecount ${layout} \

    if [ $? != 0 ]; then
      echo $'\nNote: if create_newcase failed because sub-directory already exists:'
      echo $'  * delete old case_script sub-directory'
      echo $'  * or set do_newcase=false\n'
      exit 35
    fi

}

#-----------------------------------------------------
case_setup() {

    if [ "${do_case_setup,,}" != "true" ]; then
        echo $'\n----- Skipping case_setup -----\n'
        return
    fi

    echo $'\n----- Starting case_setup -----\n'
    pushd ${CASE_SCRIPTS_DIR}

    # Setup some CIME directories
    ./xmlchange EXEROOT=${CASE_BUILD_DIR}
    ./xmlchange RUNDIR=${CASE_RUN_DIR}

    # Short term archiving
    ./xmlchange DOUT_S=${DO_SHORT_TERM_ARCHIVING^^}
    ./xmlchange DOUT_S_ROOT=${CASE_ARCHIVE_DIR}

    # Build with COSP, except for a data atmosphere (datm)
    if [ `./xmlquery --value COMP_ATM` == "datm"  ]; then 
      echo $'\nThe specified configuration uses a data atmosphere, so cannot activate COSP simulator\n'
    else
      echo $'\nConfiguring E3SM to use the COSP simulator\n'
      ./xmlchange --id CAM_CONFIG_OPTS --append --val='-cosp'
    fi

    # Extracts input_data_dir in case it is needed for user edits to the namelist later
    local input_data_dir=`./xmlquery DIN_LOC_ROOT --value`

    # Custom user_nl
    user_nl

    # Finally, run CIME case.setup
    ./case.setup --reset
    
    popd
}

#-----------------------------------------------------
case_build() {

    pushd ${CASE_SCRIPTS_DIR}

    # do_case_build = false
    if [ "${do_case_build,,}" != "true" ]; then

        echo $'\n----- case_build -----\n'

        if [ "${OLD_EXECUTABLE}" == "" ]; then
            # Ues previously built executable, make sure it exists
            if [ -x ${CASE_BUILD_DIR}/e3sm.exe ]; then
                echo 'Skipping build because $do_case_build = '${do_case_build}
            else
                echo 'ERROR: $do_case_build = '${do_case_build}' but no executable exists for this case.'
                exit 297
            fi
        else
            # If absolute pathname exists and is executable, reuse pre-exiting executable
            if [ -x ${OLD_EXECUTABLE} ]; then
                echo 'Using $OLD_EXECUTABLE = '${OLD_EXECUTABLE}
                cp -fp ${OLD_EXECUTABLE} ${CASE_BUILD_DIR}/
            else
                echo 'ERROR: $OLD_EXECUTABLE = '$OLD_EXECUTABLE' does not exist or is not an executable file.'
                exit 297
            fi
        fi
        echo 'WARNING: Setting BUILD_COMPLETE = TRUE.  This is a little risky, but trusting the user.'
        ./xmlchange BUILD_COMPLETE=TRUE

    # do_case_build = true
    else

        echo $'\n----- Starting case_build -----\n'

        # Turn on debug compilation option if requested
        if [ "${DEBUG_COMPILE^^}" == "TRUE" ]; then
            ./xmlchange DEBUG=${DEBUG_COMPILE^^}
        fi

        # Run CIME case.build
        ./case.build

    fi

    # Some user_nl settings won't be updated to *_in files under the run directory
    # Call preview_namelists to make sure *_in and user_nl files are consistent.
    echo $'\n----- Preview namelists -----\n'
    ./preview_namelists

    popd
}

#-----------------------------------------------------
runtime_options() {

    echo $'\n----- Starting runtime_options -----\n'
    pushd ${CASE_SCRIPTS_DIR}

    # Set simulation start date
    ./xmlchange RUN_STARTDATE=${START_DATE}

    # Segment length
    ./xmlchange STOP_OPTION=${STOP_OPTION,,},STOP_N=${STOP_N}

    # Restart frequency
    ./xmlchange REST_OPTION=${REST_OPTION,,},REST_N=${REST_N}

    # Coupler history
    ./xmlchange HIST_OPTION=${HIST_OPTION,,},HIST_N=${HIST_N}

    # Coupler budgets (always on)
    ./xmlchange BUDGETS=TRUE

    # Set resubmissions
    if (( RESUBMIT > 0 )); then
        ./xmlchange RESUBMIT=${RESUBMIT}
    fi

    # Run type
    # Start from default of user-specified initial conditions
    if [ "${MODEL_START_TYPE,,}" == "initial" ]; then
        ./xmlchange RUN_TYPE="startup"
        ./xmlchange CONTINUE_RUN="FALSE"

    # Continue existing run
    elif [ "${MODEL_START_TYPE,,}" == "continue" ]; then
        ./xmlchange CONTINUE_RUN="TRUE"

    elif [ "${MODEL_START_TYPE,,}" == "branch" ] || [ "${MODEL_START_TYPE,,}" == "hybrid" ]; then
        ./xmlchange RUN_TYPE=${MODEL_START_TYPE,,}
        ./xmlchange GET_REFCASE=${GET_REFCASE}
        ./xmlchange RUN_REFDIR=${RUN_REFDIR}
        ./xmlchange RUN_REFCASE=${RUN_REFCASE}
        ./xmlchange RUN_REFDATE=${RUN_REFDATE}
        echo 'Warning: $MODEL_START_TYPE = '${MODEL_START_TYPE} 
        echo '$RUN_REFDIR = '${RUN_REFDIR}
        echo '$RUN_REFCASE = '${RUN_REFCASE}
        echo '$RUN_REFDATE = '${START_DATE}
    else
        echo 'ERROR: $MODEL_START_TYPE = '${MODEL_START_TYPE}' is unrecognized. Exiting.'
        exit 380
    fi

    # Patch mpas streams files
    patch_mpas_streams

    popd
}

#-----------------------------------------------------
case_submit() {

    if [ "${do_case_submit,,}" != "true" ]; then
        echo $'\n----- Skipping case_submit -----\n'
        return
    fi

    echo $'\n----- Starting case_submit -----\n'
    pushd ${CASE_SCRIPTS_DIR}
    
    # Run CIME case.submit
    ./case.submit

    popd
}

#-----------------------------------------------------
copy_script() {

    echo $'\n----- Saving run script for provenance -----\n'

    local script_provenance_dir=${CASE_SCRIPTS_DIR}/run_script_provenance
    mkdir -p ${script_provenance_dir}
    local this_script_name=`basename $0`
    local script_provenance_name=${this_script_name}.`date +%Y%m%d-%H%M%S`
    cp -vp ${this_script_name} ${script_provenance_dir}/${script_provenance_name}

}

#-----------------------------------------------------
# Silent versions of popd and pushd
pushd() {
    command pushd "$@" > /dev/null
}
popd() {
    command popd "$@" > /dev/null
}

# Now, actually run the script
#-----------------------------------------------------
main