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@@ -0,0 +1,1957 @@
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+#!/bin/bash
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+
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+#
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+# Job options
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+#
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+#SBATCH --job-name=EC00
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+#SBATCH --time=12:00:00
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+#SBATCH --account=ecearth
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+#
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+#SBATCH --nodes=4
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+#SBATCH --exclusive
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+#SBATCH --ntasks-per-node=102
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+#SBATCH --partition=batch
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+#
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+set -ueo pipefail
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+#
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+LOCAL_NODES=4
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+LOCAL_TASKS=408
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+#
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+stdout_file=${SLURM_SUBMIT_DIR-$PWD}/${SLURM_JOB_NAME-"local"}_${SLURM_JOB_ID-"id"}.log
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+exec > ${stdout_file}
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+echo "------------------ Job Info --------------------"
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+echo "jobid : ${SLURM_JOB_ID-"id"}"
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+echo "jobname : ${SLURM_JOB_NAME-"local"}"
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+echo "nodename : ${SLURMD_NODENAME-"local"}"
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+echo "# nodes : ${SLURM_JOB_NUM_NODES-$LOCAL_NODES}"
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+echo "# tasks : ${SLURM_NTASKS-$LOCAL_TASKS}"
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+echo "submit dir : ${SLURM_SUBMIT_DIR-$PWD}"
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+
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+set -ue
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+#
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+# Cluster variables
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+#
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+NB_CORES_PER_NODES=128
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+MAX_CORES_PER_NODES=100
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+LIST_CORES_SOCKET=`seq -s',' 0 $((NB_CORES_PER_NODES-1))`
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+#
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+# Directories
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+start_dir=${SLURM_SUBMIT_DIR-$PWD}
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+
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+# librunscript defines some helper functions
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+. ${start_dir}/librunscript.sh
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+
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+# =============================================================================
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+# *** BEGIN User configuration
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+# =============================================================================
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+
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+# -----------------------------------------------------------------------------
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+# *** General configuration
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+# -----------------------------------------------------------------------------
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+# Component configuration (for syntax of the $config variable, see librunscript.sh)
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+#
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+# Currently maintained:
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+# config="ifs amip oasis" # "GCM forced-SST" : IFS + AMIP
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+# config="ifs amip oasis lpjg:fdbck" # "Veg" : forced-GCM + LPJ-Guess
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+# config="ifs amip oasis tm5:chem,o3fb,ch4fb,aerfb" # "AerChem" : forced-GCM + TM5
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+#
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+# config="ifs nemo lim3 rnfmapper xios:detached oasis" # "GCM" : IFS+NEMO
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+# config="ifs nemo lim3 rnfmapper xios:detached oasis lpjg:fdbck" # "Veg" : GCM+LPJ-Guess
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+# config="ifs nemo lim3 rnfmapper xios:detached oasis pisces lpjg:fdbck tm5:co2,co2fb" # "C-cycle" : GCM+LPJG+TM5
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+# config="ifs nemo lim3 rnfmapper xios:detached oasis tm5:chem,o3fb,ch4fb,aerfb" # "AerChem" : GCM+TM5
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+#
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+# config="ifs nemo pisces lim3 rnfmapper xios:detached oasis" # "GCM" : IFS+NEMO+PISCES
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+#
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+
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+config="ifs nemo lim3 rnfmapper xios:detached oasis"
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+
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+# minimum sanity
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+has_config amip nemo && error "Cannot have both nemo and amip in config!!"
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+! has_config ifs && error "The ESM script requires ifs in config"
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+
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+# Experiment name (exactly 4 letters!)
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+export exp_name=EC00
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+
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+# Simulation start and end date. Use any (reasonable) syntax you want.
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+run_start_date="1850-01-01"
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+run_end_date="${run_start_date} + 10 years"
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+
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+# Set $force_run_from_scratch to 'true' if you want to force this run to start
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+# from scratch, possibly ignoring any restart files present in the run
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+# directory. Leave set to 'false' otherwise.
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+# NOTE: If set to 'true' the run directory $run_dir is cleaned!
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+force_run_from_scratch=true
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+special_restart=false
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+special_restart_from=ECE3
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+special_restart_date="1995-01-01"
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+
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+# Resolution (TM5 resolution is set at compilation)
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+ifs_grid=T255L91
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+nem_grid=ORCA1L75
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+
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+# Restart frequency. Use any (reasonable) number and time unit you want.
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+# For runs without restart, leave this variable empty
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+rst_freq="1 year"
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+
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+# Number of restart legs to be run in one go
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+run_num_legs=2
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+
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+# Coupling frequencies
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+has_config ifs tm5 && cpl_freq_atm_ctm_hrs=6
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+has_config ifs lpjg && cpl_freq_atm_lpjg_hrs=24
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+
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+# Don't change the coupling frequency because UPDCLIE (where SST and SIC
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+# are updated) is called every 24 hours (hardcoded in ifs-36r4/src/ifs/utility/updtim.F90)
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+has_config amip && cpl_freq_amip_sec=86400
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+
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+# Directories
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+#start_dir=${PWD}
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+ctrl_file_dir=${start_dir}/ctrl
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+output_control_files_dir=${start_dir}/ctrl
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+
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+# Architecture
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+build_arch=ecconf
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+use_machinefile=%USE_MACHINEFILE%
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+
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+# This file is used to store information about restarts
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+ece_info_file="ece.info"
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+
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+# -----------------------------------------------------------------------------
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+# *** Read platform dependent configuration
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+# -----------------------------------------------------------------------------
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+. ${start_dir}/ecconf.cfg
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+
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+configure
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+
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+# -----------------------------------------------------------------------------
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+# *** Time step settings
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+# -----------------------------------------------------------------------------
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+if has_config ifs
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+then
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+ case "${ifs_grid}" in
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+
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+ T159L*) ifs_time_step_sec=3600 ;;
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+ T255L*) ifs_time_step_sec=2700 ;;
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+ T511L*) ifs_time_step_sec=900 ;;
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+
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+ *) error "Can't set time steps for unknown horizontal grid: ${ifs_grid}"
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+ ;;
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+ esac
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+fi
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+
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+if has_config nemo
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+then
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+ case "${nem_grid}" in
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+
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+ ORCA1L*) nem_time_step_sec=2700; lim_time_step_sec=2700 ;;
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+ ORCA025L*) nem_time_step_sec=900 ; lim_time_step_sec=900 ;;
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+
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+ *) error "Can't set time steps for unknown horizontal grid: ${nem_grid}"
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+ ;;
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+ esac
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+fi
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+
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+if has_config ifs nemo
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+then
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+ case "${ifs_grid}--${nem_grid}" in
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+
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+ T159L*--ORCA1L*)
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+ ifs_time_step_sec=3600; nem_time_step_sec=2700; lim_time_step_sec=2700; cpl_freq_atm_oce_sec=10800
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+ ;;
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+ T255L*--ORCA1L*)
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+ ifs_time_step_sec=2700; nem_time_step_sec=2700; lim_time_step_sec=2700; cpl_freq_atm_oce_sec=2700
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+ ;;
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+ T511L*--ORCA025L*)
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+ ifs_time_step_sec=900 ; nem_time_step_sec=900 ; lim_time_step_sec=900 ; cpl_freq_atm_oce_sec=2700
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+ ;;
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+
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+ *) error "Can't set time steps for unknown combination of horizontal grids: ${ifs_grid}-${nem_grid}"
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+ ;;
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+ esac
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+fi
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+
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+# -----------------------------------------------------------------------------
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+# *** IFS configuration
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+# -----------------------------------------------------------------------------
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+
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+ifs_version=36r4
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+
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+ifs_di_freq=$(( 24 * 3600 / ifs_time_step_sec ))
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+ifs_ddh_freq=$(( 120 * 3600 / ifs_time_step_sec ))
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+
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+export ifs_res_hor=$(echo ${ifs_grid} | sed 's:T\([0-9]\+\)L\([0-9]\+\):\1:')
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+ifs_res_ver=$(echo ${ifs_grid} | sed 's:T\([0-9]\+\)L\([0-9]\+\):\2:')
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+
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+ifs_numproc=320
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+
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+ifs_exe_file=${ecearth_src_dir}/ifs-${ifs_version}/bin/ifsmaster-${build_arch}
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+
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+ifs_lastout=false
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+
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+# USE FORCING FROM CMIP5 (SOLAR, GHG, AEROSOL, O3)
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+ifs_cmip5=TRUE
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+# SWITCH FOR RCP AND HISTORICAL RUNS FOR CMIP5 (0=HISTO 1=RCP 3-PD, 2=RCP 4.5, 3=RCP 6.0, 4=RCP 8.5)
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+ifs_cmip5_rcp=0
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+# 1PCTCO2 and A4XCO2 should operate together with ifs_cmip_fixyear years, ie., the baseline GHGs level will use that for year ifs_cmip_fixyear
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+export ifs_cmip_fixyear=0
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+export ifs_cmip_fixyear_ch4=0
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+
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+# Repeat trap from ifs/suecrad.F90 for early catch
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+if ! has_config tm5:ch4fb && (( $ifs_cmip_fixyear != $ifs_cmip_fixyear_ch4 ))
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+then
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+ error 'CH4 in IFS is not provided by TM5, NCMIPFIXYR_CH4 should be set equal to NCMIPFIXYR'
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+fi
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+
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+# USE FORCING FROM CMIP6 (HAS PRIORITY OVER LCMIP5)
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+ifs_cmip6=TRUE
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+# MAC-SP anthropogenic simple plume model (parameterization of anthropogenic aerosol optical properties)
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+ifs_mac2sp=TRUE
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+# Use CMIP6 prescribed preindustrial aerosol
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+ifs_cmip6piaer=TRUE
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+
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+# !! scenario 'historical' max 2014
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+# 1850 (o3_pi)
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+# 1850 --> 2014 (o3_histo)
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+# !! other scenarios (> 2014), default: SSP3-7.0
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+# SSP1-1.9, SSP1-2.6, SSP1-2.6-Ext, SSP2-4.5, SSP3-7.0, SSP3-LowNTCF, SSP4-3.4, SSP5-3.4-OS, SSP4-6.0, SSP5-3.4-OS-Ext, SSP5-8.5, SSP5-8.5-Ext
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+ifs_cmip6_scenario=historical
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+
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+# Enable optional COVID-19 scenarios, will enforce ifs_cmip6_scenario=SSP2-4.5
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+ifs_covid19=FALSE
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+# Choose one scenario : Base TwoYearBlip ModerateGreen StrongGreen FossilFuel
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+ifs_covid19scen=Base
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+# Basic sanity checks
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+if [ ${ifs_covid19} == TRUE ] ; then
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+ [ ${ifs_cmip6_scenario} != SSP2-4.5 ] && echo "*WARNING* with ifs_covid19=TRUE IFS uses ifs_cmip6_scenario=SSP2-4.5 not ${ifs_cmip6_scenario}"
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+ has_config any lpjg pisces tm5 && error "ifs_covid19=TRUE is not supported with LPJ-GUESS, PISCES nor TM5"
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+fi
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+
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+# Read CMIP6 stratospheric aerosol data file, vertically integrated version
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+lcmip6_strataer_simp=FALSE
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+lcmip6_strataer_full=TRUE
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+lcmip6_strataer_bckgd=FALSE
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+
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+# for an abrupt increase of CO2 to 4x the starting year (ifs_cmip_fixyear)
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+export ifs_A4xCO2=FALSE
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+# for an 1% per year increase of CO2 until reaching 4x the starting year (ifs_cmip_fixyear)
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+export ifs_1PCTCO2=FALSE
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+export bgc_1PCTCO2=FALSE
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+
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+# Time-varying orbital forcing (Qiong Zhang, SU-2013-09)
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+# https://dev.ec-earth.org/projects/ecearth3/wiki/Orbital_forcing_in_EC-Earth_3
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+#
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+# ifs_orb_switch=false, no orbital calculations applied
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+# ifs_orb_switch=true, use orbital calculations according to ifs_orb_mode
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+# ifs_orb_mode="fixed_year", or "variable_year", or "fixed_parameters"
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+# fixed_year: calculate the orbital parameters at ifs_orb_iyear, e.g.,1850
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+# variable_year: calculate orbital parameters annually start from ifs_orb_iyear
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+# fixed_parameters: prescribe orbital parameters for given year
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+case "${ifs_grid}" in
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+ T159*) ifs_orb_switch=true ;;
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+ *) ifs_orb_switch=false ;;
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+esac
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+ifs_orb_mode="variable_year"
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+ifs_orb_iyear=$(date -u -d "${run_start_date}" +%Y)
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+
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+# Relaxation of soil moisture (Wilhelm May, LU; October 2017)
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+#
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+# LRXSM: Parameter indicating the levels to be nudged
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+#
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+# LRXSM = 0: no nudging
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+# LRXSM = 12: 4xdaily data and 3 levels (excluding level 1)
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+# LRXSM = 13: 4xdaily data and 4 levels
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+#
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+# LRXSMTx: time scale of the relaxation for level X (in hours)
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+#
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+# LRXSMTx = 0: actual values relpaced by external ones
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+# LRXSMTx = 24: 1 day
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+# LRXSMTx = 120: 5 days
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+#
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+# LRXSMS: indicates when the relaxation is done
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+#
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+# LRXSMS = 0: before the time step
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+# LRXSMS = 1: after the time step
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+#
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+has_config soilnudg && ifs_lrxsm=13 || ifs_lrxsm=0
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+ifs_lrxsmt1=96
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+ifs_lrxsmt2=72
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+ifs_lrxsmt3=48
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+ifs_lrxsmt4=24
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+ifs_lrxsms=1
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+
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+# IFS tuning parameters
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+variant=
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+has_config tm5:chem && variant=-AerChem
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+ifs_tuning_parameter_file=${ctrl_file_dir}/ifs-tuning-parameters-${ifs_grid}${variant}.sh
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+if [ -f ${ifs_tuning_parameter_file} ]
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+then
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+ source ${ifs_tuning_parameter_file}
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+else
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+ error "Sorry, ${ifs_tuning_parameter_file} not found, exiting."
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+fi
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+
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+
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+# Select source of vegetation data:
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+# ifs climatology from IFS
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+# era20c vegetation from an off-line LPJ-Guess run forced with ERA20C
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+# (currently available only for T255 and T159)
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+# cmip6 vegetation from an EC-Earth3-Veg (interactive LPJ-Guess) run
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+# (currently available only for T255)
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+# custom_exp vegetation from any EC-Earth3-Veg run exp
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+# (must contain same variables as era20c & cmip6 and located in icmcl_exp folder)
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+# none don't create an ICMCL file with vegetation data (this is set
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+# automatically if LPJG is used with feedback)
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+#
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+ifs_veg_source="cmip6"
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+
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+has_config lpjg:fdbck && ifs_veg_source="none"
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+
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+case ${ifs_veg_source} in
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+"ifs" )
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+ # Use Lambert-Beer to compute effective vegetation cover
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+ n_compute_eff_veg_fraction=2
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+ ;;
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+"era20c" )
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+ # LPJG vegetation is provided as effective cover
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+ # Don't use Lambert-Beer
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+ n_compute_eff_veg_fraction=0
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+
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+ case "${ifs_grid}" in
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+ T159L*) veg_version=v29 ;;
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+ T255L*) veg_version=v16 ;;
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+ *) error "Vegetation from off-line LPJ-Guess not available for ${ifs_grid}" ;;
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+ esac
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+ ;;
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+"cmip6" )
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+ # LPJG vegetation is provided as effective cover
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+ # Don't use Lambert-Beer
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+ n_compute_eff_veg_fraction=0
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+
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+ case "${ifs_grid}" in
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+ T255L*) veg_version=v32 ;;
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+ *) error "Vegetation from CMIP6 EC-Earth3-Veg not available for ${ifs_grid}" ;;
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+ esac
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+ ;;
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+"custom_"* )
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+ # LPJG vegetation is provided as effective cover
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+ # Don't use Lambert-Beer
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+ n_compute_eff_veg_fraction=0
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+
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+ veg_version=${ifs_veg_source:7}
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+ if [ ! -d ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version} ]
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+ then
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+ error "requested IFS_VEG_SOURCE = ${ifs_veg_source} but not found in ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version}"
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+ fi
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+ ;;
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+"none" )
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+ # LPJG with feedback
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+ n_compute_eff_veg_fraction=0
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+ ! has_config lpjg:fdbck && error "IFS requires an offline source of vegetation"
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+ ;;
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+* )
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+ error "Vegetation from ${ifs_veg_source} not implemented"
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+ ;;
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+esac
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+
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+# use DMI land ice physics and varying snow albedo
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+case "${ifs_grid}" in
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+ T159*) ifs_landice=true ;;
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+ *) ifs_landice=false ;;
|
|
|
+esac
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** NEMO/LIM configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+# This is only needed if the experiment is started from an existing set of NEMO
|
|
|
+# restart files
|
|
|
+nem_restart_file_path=${start_dir}/nemo-rst
|
|
|
+
|
|
|
+nem_restart_offset=0
|
|
|
+
|
|
|
+nem_res_hor=$(echo ${nem_grid} | sed 's:ORCA\([0-9]\+\)L[0-9]\+:\1:')
|
|
|
+
|
|
|
+nem_config=${nem_grid}
|
|
|
+has_config lim3 && nem_config=${nem_config}_LIM3
|
|
|
+
|
|
|
+if has_config pisces tm5:co2
|
|
|
+then
|
|
|
+ nem_config=${nem_config}_CarbonCycle
|
|
|
+elif has_config pisces
|
|
|
+then
|
|
|
+ nem_config=${nem_config}_PISCES
|
|
|
+fi
|
|
|
+
|
|
|
+# TODO - nemo standalone configs are not accounted for in this script, but this would set the required nem_config
|
|
|
+! has_config ifs && nem_config=${nem_config}_standalone
|
|
|
+
|
|
|
+nem_exe_file=${ecearth_src_dir}/nemo-3.6/CONFIG/${nem_config}/BLD/bin/nemo.exe
|
|
|
+
|
|
|
+nem_numproc=86
|
|
|
+
|
|
|
+# Thermal conductivity of snow, see comment in ctrl/namelist.lim3.ref.sh
|
|
|
+case "${ifs_grid}" in
|
|
|
+ T159L* ) nem_rn_cdsn=0.25 ;;
|
|
|
+ * ) nem_rn_cdsn=0.27 ;;
|
|
|
+esac
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Runoff mapper configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+rnf_exe_file=${ecearth_src_dir}/runoff-mapper/bin/runoff-mapper.exe
|
|
|
+rnf_numproc=1
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** LPJ-GUESS configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+lpjg_time_step_sec=86400
|
|
|
+lpjg_numproc=32
|
|
|
+
|
|
|
+has_config lpjg && lpjg_on=1
|
|
|
+has_config lpjg:fdbck && lpjg_fdbck=1
|
|
|
+has_config tm5:co2 && lpjg_fdbck_tm5=1 || lpjg_fdbck_tm5=0
|
|
|
+
|
|
|
+export lpjg_fixNdepafter=-1
|
|
|
+export lpjg_fixLUafter=-1
|
|
|
+
|
|
|
+info '!!!! CMIP FIX YEAR SETTINGS:'
|
|
|
+info "ifs_cmip_fixyear: $ifs_cmip_fixyear"
|
|
|
+info "lpjg_fixNDepAfter: $lpjg_fixNdepafter"
|
|
|
+info "lpjg_fixLUAfter: $lpjg_fixLUafter"
|
|
|
+info '!!!!'
|
|
|
+
|
|
|
+lpjg_res=T${ifs_res_hor}
|
|
|
+lpjg_exe_file=${ecearth_src_dir}/lpjg/build/guess_${lpjg_res}
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** AMIP-reader configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+amip_exe_file=${ecearth_src_dir}/amip-forcing/bin/amip-forcing.exe
|
|
|
+amip_numproc=1
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** TM5 configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+if $(has_config tm5)
|
|
|
+then
|
|
|
+ # With TM5, NPRTRV is set to 1 in the namelist. To avoid some out-of-bound
|
|
|
+ # arrays in IFS, we must limit the number of cores for IFS
|
|
|
+ if (( ifs_numproc > (ifs_res_hor+1) ))
|
|
|
+ then
|
|
|
+ error "too much cores requested for IFS, max is $((ifs_res_hor+1))"
|
|
|
+ fi
|
|
|
+
|
|
|
+ # TM5 settings
|
|
|
+ has_config tm5:co2 && tmversion="co2" || tmversion="cb05"
|
|
|
+ has_config tm5:co2 && export tm5_co2=1 || export tm5_co2=0
|
|
|
+ export tm5_exch_nlevs=10
|
|
|
+ tm5_time_step_sec=3600
|
|
|
+ export tm5_numproc_x=2
|
|
|
+ export tm5_numproc_y=45
|
|
|
+ tm5_numproc=$(( tm5_numproc_x * tm5_numproc_y ))
|
|
|
+ export tm5_emiss_fixyear=0
|
|
|
+
|
|
|
+ # limited number of levels for feedback (aerosols, currently set to lmax_conv in TM5)
|
|
|
+ case ${tm5_exch_nlevs} in
|
|
|
+ 34) export tm5_exch_nlevs_cutoff=23 ;;
|
|
|
+ 10) export tm5_exch_nlevs_cutoff=10 ;;
|
|
|
+ 4) export tm5_exch_nlevs_cutoff=4 ;;
|
|
|
+ *) error "not supported number of levels for TM5"
|
|
|
+ esac
|
|
|
+
|
|
|
+ # executable
|
|
|
+ tm5_exe_file=${ecearth_src_dir}/tm5mp/build-${tmversion}-ml${tm5_exch_nlevs}/appl-tm5-${tmversion}.x
|
|
|
+
|
|
|
+ # path to initial conditions, modify as needed
|
|
|
+ tm5_restart_file_path=${ini_data_dir}/tm5/restart/${tmversion}-ml${tm5_exch_nlevs}
|
|
|
+
|
|
|
+ # fields sent back to IFS
|
|
|
+ has_config tm5:o3fb && tm5_to_ifs=O3 || tm5_to_ifs=
|
|
|
+ has_config tm5:ch4fb && tm5_to_ifs=${tm5_to_ifs},CH4
|
|
|
+ has_config tm5:aerfb && tm5_to_ifs=${tm5_to_ifs},"\
|
|
|
+N2,SU2,BC2,OC2,N3,SU3,BC3,OC3,SS3,DU3,\
|
|
|
+N4,SU4,BC4,OC4,SS4,DU4,N5,BC5,OC5,N6,DU6,N7,DU7,\
|
|
|
+NO3,MSA,\
|
|
|
+AOD_01,AOD_02,AOD_03,AOD_04,AOD_05,AOD_06,AOD_07,AOD_08,AOD_09,AOD_10,AOD_11,AOD_12,AOD_13,AOD_14,\
|
|
|
+SSA_01,SSA_02,SSA_03,SSA_04,SSA_05,SSA_06,SSA_07,SSA_08,SSA_09,SSA_10,SSA_11,SSA_12,SSA_13,SSA_14,\
|
|
|
+ASF_01,ASF_02,ASF_03,ASF_04,ASF_05,ASF_06,ASF_07,ASF_08,ASF_09,ASF_10,ASF_11,ASF_12,ASF_13,ASF_14"
|
|
|
+ has_config tm5:co2fb && tm5_to_ifs=${tm5_to_ifs},CO2
|
|
|
+
|
|
|
+ export tm5_to_ifs=$(echo ${tm5_to_ifs} | sed "s/^,//")
|
|
|
+
|
|
|
+ # coupled to LPJ-Guess and/or PISCES?
|
|
|
+ has_config tm5:co2 lpjg && export cpl_tm_guess=T || export cpl_tm_guess=F
|
|
|
+ has_config tm5:co2 pisces && export cpl_tm_pisces=T || export cpl_tm_pisces=F
|
|
|
+fi
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** OASIS configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+# Restart files for the coupling fields (note 8 character limit in OASIS)
|
|
|
+# rstas.nc : atmosphere single-category fields
|
|
|
+# rstam.nc : atmosphere multi-category fields
|
|
|
+# rstos.nc : ocean single-category fields
|
|
|
+# rstom.nc : ocean multi-category fields
|
|
|
+oas_rst_ifs_nemo="rstas.nc rstos.nc"
|
|
|
+
|
|
|
+oas_rst_ifs_lpjg="vegin.nc lpjgv.nc"
|
|
|
+
|
|
|
+# Met fields from IFS to TM (always required)
|
|
|
+oas_rst_ifs_tm5="r_hum.nc r_g2d.nc r_udr.nc r_div.nc r_vor.nc \
|
|
|
+ r_ddr.nc r_tmp.nc r_dmf.nc r_s2d.nc r_umf.nc"
|
|
|
+
|
|
|
+has_config tm5:chem && \
|
|
|
+ oas_rst_ifs_tm5=${oas_rst_ifs_tm5}' r_cc_.nc r_clw.nc r_cco.nc r_ciw.nc r_ccu.nc'
|
|
|
+
|
|
|
+has_config tm5:o3fb || has_config tm5:ch4fb && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' o3ch4.nc'
|
|
|
+has_config tm5:aerfb && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' C???????'
|
|
|
+
|
|
|
+# C-cycle configuration
|
|
|
+has_config tm5:co2 lpjg && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' l_co2.nc rlpjg.nc'
|
|
|
+has_config tm5:co2 pisces && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' o_co2.nc pisce.nc'
|
|
|
+has_config tm5:co2fb && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' co2mx.nc'
|
|
|
+
|
|
|
+# final list of files depends on the activated components - this is used in save_ic as well
|
|
|
+#oas_rst_files="${oas_rst_ifs_nemo} ${oas_rst_ifs_tm5} vegin.nc lpjgv.nc"
|
|
|
+oas_rst_files=""
|
|
|
+has_config ifs nemo && oas_rst_files+=" ${oas_rst_ifs_nemo}"
|
|
|
+has_config ifs lpjg && oas_rst_files+=" ${oas_rst_ifs_lpjg}"
|
|
|
+has_config ifs tm5 && oas_rst_files+=" ${oas_rst_ifs_tm5}"
|
|
|
+
|
|
|
+# Decide whether the OASIS weight files for interpolation should be linked from
|
|
|
+# the setup directory (true) or not (false). In the latter case, the weights
|
|
|
+# are re-computed at the start of the run.
|
|
|
+oas_link_weights=true
|
|
|
+
|
|
|
+# Flux correction for runoff (not calving) sent from Oasis to ocean.
|
|
|
+# 1.07945 is computed to compensate for a P-E=-0.016 mm/day (valid for std res)
|
|
|
+case "${ifs_grid}" in
|
|
|
+ T159L* ) has_config nemo && oas_mb_fluxcorr=1.08652 ;;
|
|
|
+ * ) has_config nemo && oas_mb_fluxcorr=1.07945 ;;
|
|
|
+esac
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** XIOS configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+xio_exe_file=${ecearth_src_dir}/xios-2.5/bin/xios_server.exe
|
|
|
+
|
|
|
+xio_numproc=1
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Extra initial conditions saved during the run
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+if has_config save_ic
|
|
|
+then
|
|
|
+ source ./libsave_ic.sh
|
|
|
+ declare -a save_ic_date save_ic_date1 save_ic_sec save_ic_day save_ic_ppt_file save_ic_nemo_ts
|
|
|
+ oas_rst_files="${oas_rst_ifs_nemo} ${oas_rst_ifs_tm5} vegin.nc lpjgv.nc"
|
|
|
+fi
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Carbon cycle configuration
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# set to true to write co2 fluxes sent to TM5
|
|
|
+ccycle_debug_fluxes=true
|
|
|
+
|
|
|
+# =============================================================================
|
|
|
+# *** END of User configuration
|
|
|
+# =============================================================================
|
|
|
+
|
|
|
+# =============================================================================
|
|
|
+# *** This is where the code begins ...
|
|
|
+# =============================================================================
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Create the run dir if necessary and go there
|
|
|
+# Everything is done from here.
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+if [ ! -d ${run_dir} ]
|
|
|
+then
|
|
|
+ mkdir -p ${run_dir}
|
|
|
+ if $special_restart
|
|
|
+ then
|
|
|
+ force_run_from_scratch=false
|
|
|
+ echo 'rsync -av --delete ${run_dir}/../${special_restart_from}/ --exclude log --exclude output --exclude restart --exclude="${special_restart_from}_*" --exclude="srf*" --exclude="restart_*" --exclude="debug.*" --ex clude="output.*" ${run_dir}'
|
|
|
+ rsync -av --delete ${run_dir}/../${special_restart_from}/ --exclude log --exclude output --exclude restart --exclude="${special_restart_from}_*" --exclude="srf*" --exclude="restart_*" --exclude="debug.*" --exclude="output.*" ${run_dir}
|
|
|
+ cp -f ${nem_exe_file} ${run_dir}
|
|
|
+ cp -f ${ifs_exe_file} ${run_dir}
|
|
|
+ cp -f ${rnf_exe_file} ${run_dir}
|
|
|
+ cp -f ${xio_exe_file} ${run_dir}
|
|
|
+ special_year=${special_restart_date:0:4}
|
|
|
+ sed -i "/$special_year/q" ${run_dir}/ece.info
|
|
|
+ . ${run_dir}/ece.info
|
|
|
+ special_restart_leg=$(printf %03d $((leg_number+1)))
|
|
|
+ special_restart_leg_oasis=$(printf %03d $((leg_number+2)))
|
|
|
+ # PUT HERE THE INSTRUCTIONS TO COPY THE restart files
|
|
|
+ rsync -av ${run_dir}/../../archive/${special_restart_from}/restart/ifs/${special_restart_leg}/ ${run_dir}
|
|
|
+ rsync -av ${run_dir}/../../archive/${special_restart_from}/restart/oasis/${special_restart_leg_oasis}/ ${run_dir}
|
|
|
+ cd ${run_dir}/../../archive/${special_restart_from}/restart/nemo/${special_restart_leg}
|
|
|
+ for f in *.nc; do
|
|
|
+ nf=${exp_name}${f:4}
|
|
|
+ cp $f ${run_dir}/$nf
|
|
|
+ done
|
|
|
+ cd -
|
|
|
+ cd ${run_dir}
|
|
|
+ for f in ${exp_name}_????????_restart_???_????.nc; do
|
|
|
+ nf=${f:14}
|
|
|
+ ln -s $f $nf
|
|
|
+ done
|
|
|
+ cd -
|
|
|
+ rm -f ${run_dir}/ICMCL${special_restart_from}INIT
|
|
|
+ mv ${run_dir}/ICMGG${special_restart_from}INIUA ${run_dir}/ICMGG${exp_name}INIUA
|
|
|
+ mv ${run_dir}/ICMGG${special_restart_from}INIT ${run_dir}/ICMGG${exp_name}INIT
|
|
|
+ mv ${run_dir}/ICMSH${special_restart_from}INIT ${run_dir}/ICMSH${exp_name}INIT
|
|
|
+ fi
|
|
|
+else
|
|
|
+ force_run_from_scratch=false
|
|
|
+ special_restart=false
|
|
|
+fi
|
|
|
+cd ${run_dir}
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Determine the time span of this run and whether it's a restart leg
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+# Regularise the format of the start and end date of the simulation
|
|
|
+run_start_date=$(date -uR -d "${run_start_date}")
|
|
|
+run_end_date=$(date -uR -d "${run_end_date}")
|
|
|
+
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Set path to grib_set
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+
|
|
|
+grib_set=${GRIB_BIN_PATH}${GRIB_BIN_PATH:+/}grib_set
|
|
|
+
|
|
|
+# Loop over the number of legs
|
|
|
+for (( ; run_num_legs>0 ; run_num_legs-- ))
|
|
|
+do
|
|
|
+
|
|
|
+ # Check for restart information file and set the current leg start date
|
|
|
+ # Ignore restart information file if force_run_from_scratch is true
|
|
|
+ if ${force_run_from_scratch} || ! [ -r ${ece_info_file} ]
|
|
|
+ then
|
|
|
+ leg_is_restart=false
|
|
|
+ leg_start_date=${run_start_date}
|
|
|
+ leg_number=1
|
|
|
+ else
|
|
|
+ leg_is_restart=true
|
|
|
+ . ./${ece_info_file}
|
|
|
+ leg_start_date=${leg_end_date}
|
|
|
+ leg_number=$((leg_number+1))
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Compute the end date of the current leg
|
|
|
+ if [ -n "${rst_freq}" ]
|
|
|
+ then
|
|
|
+ leg_end_date=$(date -uR -d "${leg_start_date} + ${rst_freq}")
|
|
|
+ else
|
|
|
+ leg_end_date=${run_end_date}
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Check if legs are integer multiples of full years if LPJG is used
|
|
|
+ if has_config lpjg
|
|
|
+ then
|
|
|
+
|
|
|
+ if [[ $(date +%m%d%T -u -d "${leg_start_date}") != "010100:00:00" || \
|
|
|
+ $(date +%m%d%T -u -d "${leg_start_date} + ${rst_freq}") != "010100:00:00" ]]
|
|
|
+ then
|
|
|
+ error "LPJ-GUESS runs must start on Jan 1 and end on Dec 31. Multi-year legs are allowed."
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ if [ $(date -u -d "${leg_end_date}" +%s) -ge $(date -u -d "${run_end_date}" +%s) ]
|
|
|
+ then
|
|
|
+ leg_end_date=${run_end_date}
|
|
|
+ ifs_lastout=true
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Some time variables needed later
|
|
|
+ leg_length_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${leg_start_date}" +%s) ))
|
|
|
+ leg_start_sec=$(( $(date -u -d "${leg_start_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
|
|
|
+ leg_end_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
|
|
|
+ leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d)
|
|
|
+ leg_start_date_yyyy=$(date -u -d "${leg_start_date}" +%Y)
|
|
|
+ leg_end_date_yyyy=$(date -u -d "${leg_end_date}" +%Y)
|
|
|
+
|
|
|
+ # Check whether there's actually time left to simulate - exit otherwise
|
|
|
+ if [ ${leg_length_sec} -le 0 ]
|
|
|
+ then
|
|
|
+ info "Leg start date equal to or after end of simulation."
|
|
|
+ info "Nothing left to do. Exiting."
|
|
|
+ exit 0
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Initial conditions saved during the run
|
|
|
+ do_save_ic=false
|
|
|
+ has_config save_ic && save_ic_get_config
|
|
|
+ # if you do not use an option with save_ic, you must define 'do_save_ic' and
|
|
|
+ # 'save_ic_date_offset' here or in ../libsave_ic.sh/save_ic_get_config()
|
|
|
+ ${do_save_ic} && save_ic_define_vars
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Prepare the run directory for a run from scratch
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if ! $leg_is_restart
|
|
|
+ then
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Check if run dir is empty. If not, and if we are allowed to do so
|
|
|
+ # by ${force_run_from_scratch}, remove everything
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ if $(ls * >& /dev/null)
|
|
|
+ then
|
|
|
+ if ${force_run_from_scratch}
|
|
|
+ then
|
|
|
+ rm -fr ${run_dir}/*
|
|
|
+ else
|
|
|
+ error "Run directory not empty and \$force_run_from_scratch not set."
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Copy executables of model components
|
|
|
+ # *** Additionally, create symlinks to the original place for reference
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ cp ${ifs_exe_file} .
|
|
|
+ ln -s ${ifs_exe_file} $(basename ${ifs_exe_file}).lnk
|
|
|
+
|
|
|
+ if $(has_config amip)
|
|
|
+ then
|
|
|
+ cp ${amip_exe_file} .
|
|
|
+ ln -s ${amip_exe_file} $(basename ${amip_exe_file}).lnk
|
|
|
+ fi
|
|
|
+
|
|
|
+ if $(has_config nemo)
|
|
|
+ then
|
|
|
+ cp ${nem_exe_file} .
|
|
|
+ ln -s ${nem_exe_file} $(basename ${nem_exe_file}).lnk
|
|
|
+
|
|
|
+ cp ${rnf_exe_file} .
|
|
|
+ ln -s ${rnf_exe_file} $(basename ${rnf_exe_file}).lnk
|
|
|
+
|
|
|
+ cp ${xio_exe_file} .
|
|
|
+ ln -s ${xio_exe_file} $(basename ${xio_exe_file}).lnk
|
|
|
+ fi
|
|
|
+
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ cp ${lpjg_exe_file} .
|
|
|
+ ln -s ${lpjg_exe_file} $(basename ${lpjg_exe_file}).lnk
|
|
|
+ fi
|
|
|
+
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ cp ${tm5_exe_file} .
|
|
|
+ ln -s ${tm5_exe_file} $(basename ${tm5_exe_file}).lnk
|
|
|
+ fi
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for IFS (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Initial data
|
|
|
+ ln -s \
|
|
|
+ ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMGGECE3INIUA \
|
|
|
+ ICMGG${exp_name}INIUA
|
|
|
+ ln -s \
|
|
|
+ ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMSHECE3INIT \
|
|
|
+ ICMSH${exp_name}INIT
|
|
|
+ rm -f ICMGG${exp_name}INIT
|
|
|
+ cp ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMGGECE3INIT \
|
|
|
+ ICMGG${exp_name}INIT
|
|
|
+
|
|
|
+ # add bare_soil_albedo to ICMGG*INIT
|
|
|
+ tempfile=tmp.$$
|
|
|
+ ${grib_set} -s dataDate=$(date -u -d "$run_start_date" +%Y%m%d) \
|
|
|
+ ${ini_data_dir}/ifs/${ifs_grid}/climate/bare_soil_albedos.grb \
|
|
|
+ ${tempfile}
|
|
|
+
|
|
|
+ cat ${tempfile} >> ICMGG${exp_name}INIT
|
|
|
+ rm -f ${tempfile}
|
|
|
+
|
|
|
+ # add land ice mask if needed
|
|
|
+ if ${ifs_landice}
|
|
|
+ then
|
|
|
+ tempfile=tmp.$$
|
|
|
+ cdo divc,10 -setcode,82 -selcode,141 ICMGG${exp_name}INIT ${tempfile}
|
|
|
+ ${grib_set} -s gridType=reduced_gg ${tempfile} ${tempfile}
|
|
|
+ cat ${tempfile} >> ICMGG${exp_name}INIT
|
|
|
+ rm -f ${tempfile}
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Other stuff
|
|
|
+ ln -s ${ini_data_dir}/ifs/rtables/* .
|
|
|
+
|
|
|
+ # Output control (ppt files)
|
|
|
+ if [ ! -f ${output_control_files_dir}/pptdddddd0600 ] && [ ! -f ${output_control_files_dir}/pptdddddd0300 ];then
|
|
|
+ echo "Error from ece-esm.sh: Neither the file pptdddddd0600 or pptdddddd0300 exists in the directory:"
|
|
|
+ echo " " ${output_control_files_dir}
|
|
|
+ exit -1
|
|
|
+ fi
|
|
|
+ mkdir postins
|
|
|
+ cp ${output_control_files_dir}/ppt* postins/
|
|
|
+ if [ -f postins/pptdddddd0600 ];then
|
|
|
+ ln -s pptdddddd0600 postins/pptdddddd0000
|
|
|
+ ln -s pptdddddd0600 postins/pptdddddd1200
|
|
|
+ ln -s pptdddddd0600 postins/pptdddddd1800
|
|
|
+ fi
|
|
|
+ if [ -f postins/pptdddddd0300 ];then
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd0900
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd1500
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd2100
|
|
|
+ if [ ! -f postins/pptdddddd0600 ];then
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd0000
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd0600
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd1200
|
|
|
+ ln -s pptdddddd0300 postins/pptdddddd1800
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+ /bin/ls -1 postins/* > dirlist
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for LPJ-GUESS
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ # Check for valid grid
|
|
|
+ if [ $lpjg_res != "T255" -a $lpjg_res != "T159" ]
|
|
|
+ then
|
|
|
+ error "LPJG-gridlist doesn't exist for ifs-grid: ${ifs_grid}"
|
|
|
+ fi
|
|
|
+ # Initial data - saved state for LPJ-GUESS (.bin format)
|
|
|
+ lpjgstartdir=$(printf "lpjg_state_%04d" $leg_start_date_yyyy)
|
|
|
+ ln -sf ${ini_data_dir}/lpjg/ini_state/${lpjg_res}/${lpjgstartdir} ${run_dir}/${lpjgstartdir}
|
|
|
+
|
|
|
+ # Control files (i.e. .ins, landuse, N deposition, soil type files etc.)
|
|
|
+ cp -f ${ecearth_src_dir}/lpjg/data/ins/*.ins .
|
|
|
+ # activate the new litterfall scheme for C4MIP - for the coupled model this is done when both pisces and lpjg are activated
|
|
|
+ has_config pisces lpjg && echo -e "!override for EC-Earth-CC in runscript\nifpftlitterfall 1\ncalc_phen_after_restart 0" >> global.ins
|
|
|
+ mkdir -p ${run_dir}/landuse
|
|
|
+
|
|
|
+ fi
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for NEMO (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ if $(has_config nemo)
|
|
|
+ then
|
|
|
+ # Link initialisation files for matching ORCA grid
|
|
|
+ for f in \
|
|
|
+ bathy_meter.nc coordinates.nc \
|
|
|
+ ahmcoef.nc \
|
|
|
+ K1rowdrg.nc M2rowdrg.nc mask_itf.nc \
|
|
|
+ decay_scale_bot.nc decay_scale_cri.nc \
|
|
|
+ mixing_power_bot.nc mixing_power_cri.nc mixing_power_pyc.nc \
|
|
|
+ runoff_depth.nc subbasins.nc
|
|
|
+ do
|
|
|
+ [ -f ${ini_data_dir}/nemo/initial/${nem_grid}/$f ] && ln -s ${ini_data_dir}/nemo/initial/${nem_grid}/$f
|
|
|
+ done
|
|
|
+
|
|
|
+ # Copying the time independent NEMO files for the matching ORCA grid in order to facilitate cmorisation:
|
|
|
+ for f in \
|
|
|
+ bathy_meter.nc subbasins.nc
|
|
|
+ do
|
|
|
+ mkdir -p output/nemo/ofx-data
|
|
|
+ [ -f ${ini_data_dir}/nemo/initial/${nem_grid}/$f ] && cp -f ${ini_data_dir}/nemo/initial/${nem_grid}/$f output/nemo/ofx-data/
|
|
|
+ done
|
|
|
+
|
|
|
+ # Link geothermal heating file (independent of grid) and matching weight file
|
|
|
+ ln -s ${ini_data_dir}/nemo/initial/Goutorbe_ghflux.nc
|
|
|
+ ln -s ${ini_data_dir}/nemo/initial/weights_Goutorbe1_2_orca${nem_res_hor}_bilinear.nc
|
|
|
+
|
|
|
+ # Link the salinity climatology file (needed for diagnostics)
|
|
|
+ ln -s ${ini_data_dir}/nemo/climatology/${nem_grid}/sali_ref_clim_monthly.nc
|
|
|
+
|
|
|
+ # Link either restart files or climatology files for the initial state
|
|
|
+ if $(has_config nemo:start_from_restart)
|
|
|
+ then
|
|
|
+ # When linking restart files, we accept three options:
|
|
|
+ # (1) Merged files for ocean and ice, i.e.
|
|
|
+ # restart_oce.nc and restart_ice.nc
|
|
|
+ # (2) One-file-per-MPI-rank, i.e.
|
|
|
+ # restart_oce_????.nc and restart_ice_????.nc
|
|
|
+ # No check is done whether the number of restart files agrees
|
|
|
+ # with the number of MPI ranks for NEMO!
|
|
|
+ # (3) One-file-per-MPI-rank with a prefix, i.e.
|
|
|
+ # <exp_name>_<time_step>_restart_oce_????.nc (similar for the ice)
|
|
|
+ # The prefix is ignored.
|
|
|
+ # The code assumes that one of the options can be applied! If more
|
|
|
+ # options are applicable, the first is chosen. If none of the
|
|
|
+ # options apply, NEMO will crash with missing restart file.
|
|
|
+ if ls -U ${nem_restart_file_path}/restart_[oi]ce.nc > /dev/null 2>&1
|
|
|
+ then
|
|
|
+ ln -s ${nem_restart_file_path}/restart_[oi]ce.nc ./
|
|
|
+
|
|
|
+ elif ls -U ${nem_restart_file_path}/restart_[oi]ce_????.nc > /dev/null 2>&1
|
|
|
+ then
|
|
|
+ ln -s ${nem_restart_file_path}/restart_[oi]ce_????.nc ./
|
|
|
+
|
|
|
+ else
|
|
|
+ for f in ${nem_restart_file_path}/????_????????_restart_[oi]ce_????.nc
|
|
|
+ do
|
|
|
+ ln -s $f $(echo $f | sed 's/.*_\(restart_[oi]ce_....\.nc\)/\1/')
|
|
|
+ done
|
|
|
+ fi
|
|
|
+ else
|
|
|
+
|
|
|
+ # Temperature and salinity files for initialisation
|
|
|
+ ln -s ${ini_data_dir}/nemo/climatology/absolute_salinity_WOA13_decav_Reg1L75_clim.nc
|
|
|
+ ln -s ${ini_data_dir}/nemo/climatology/conservative_temperature_WOA13_decav_Reg1L75_clim.nc
|
|
|
+ ln -s ${ini_data_dir}/nemo/climatology/weights_WOA13d1_2_orca${nem_res_hor}_bilinear.nc
|
|
|
+
|
|
|
+ # Grid dependent runoff files
|
|
|
+ case ${nem_grid} in
|
|
|
+ ORCA1*) ln -s ${ini_data_dir}/nemo/climatology/runoff-icb_DaiTrenberth_Depoorter_ORCA1_JD.nc ;;
|
|
|
+ ORCA025*) ln -s ${ini_data_dir}/nemo/climatology/ORCA_R025_runoff_v1.1.nc ;;
|
|
|
+ esac
|
|
|
+ fi
|
|
|
+
|
|
|
+ # for ocean_nudging
|
|
|
+ if $(has_config nemo:ocenudg) ; then
|
|
|
+ ln -s ${ini_data_dir}/nemo/oce_nudg/resto.nc
|
|
|
+ fi
|
|
|
+
|
|
|
+ # XIOS files
|
|
|
+ . ${ctrl_file_dir}/iodef.xml.sh > iodef.xml
|
|
|
+ ln -s ${ctrl_file_dir}/context_nemo.xml
|
|
|
+ ln -s ${ctrl_file_dir}/domain_def_nemo.xml
|
|
|
+ ln -s ${ctrl_file_dir}/axis_def_nemo.xml
|
|
|
+ ln -s ${ctrl_file_dir}/grids_def_nemo.xml
|
|
|
+ ln -s ${ctrl_file_dir}/field_def_nemo-lim.xml
|
|
|
+ ln -s ${ctrl_file_dir}/field_def_nemo-opa.xml
|
|
|
+ ln -s ${ctrl_file_dir}/field_def_nemo-pisces.xml
|
|
|
+ ln -s ${ctrl_file_dir}/field_def_nemo-inerttrc.xml
|
|
|
+ ln -s ${output_control_files_dir}/file_def_nemo-lim3.xml file_def_nemo-lim.xml
|
|
|
+ ln -s ${output_control_files_dir}/file_def_nemo-opa.xml
|
|
|
+ ln -s ${output_control_files_dir}/file_def_nemo-pisces.xml
|
|
|
+
|
|
|
+ if [ -f ${ini_data_dir}/xios/ORCA${nem_res_hor}/coordinates_xios.nc ]
|
|
|
+ then
|
|
|
+ cp ${ini_data_dir}/xios/ORCA${nem_res_hor}/coordinates_xios.nc ./
|
|
|
+ else
|
|
|
+ info "File 'coordinates_xios.nc' not found. NEMO can not be run with land domain removal!"
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Files needed for TOP/PISCES
|
|
|
+ if $(has_config pisces)
|
|
|
+ then
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/dust_INCA_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/ndeposition_Duce_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/pmarge_etopo_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/river_global_news_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/Solubility_T62_Mahowald_ORCA_R1.nc
|
|
|
+
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/par_fraction_gewex_clim90s00s_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/DIC_GLODAP_annual_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/Alkalini_GLODAP_annual_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/O2_WOA2009_monthly_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/PO4_WOA2009_monthly_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/Si_WOA2009_monthly_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/DOC_PISCES_monthly_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/Fer_PISCES_monthly_ORCA_R1.nc
|
|
|
+ ln -fs ${ini_data_dir}/nemo/pisces/NO3_WOA2009_monthly_ORCA_R1.nc
|
|
|
+
|
|
|
+ # create co2 concentration file atcco2.txt if required
|
|
|
+ if { [ $ifs_cmip_fixyear -gt 0 ] || [[ "${ifs_A4xCO2}" = "TRUE" ]]; } && [[ "${bgc_1PCTCO2}" = "FALSE" ]]
|
|
|
+ then
|
|
|
+ rm -f atcco2.txt
|
|
|
+ elif [[ "${bgc_1PCTCO2}" = "TRUE" ]]
|
|
|
+ then
|
|
|
+ cp -f ${ini_data_dir}/nemo/pisces/mole-fraction-of-carbon-dioxide-in-air_1pctCO2_1849-2016.txt atcco2.txt
|
|
|
+ else
|
|
|
+ # determine scenario-name and co2-file middle-fix
|
|
|
+ case $(echo ${ifs_cmip6_scenario} | tr '[:upper:]' '[:lower:]') in
|
|
|
+ hist*) pis_scen="ssp585"; pis_sco2_mfix="REMIND-MAGPIE-ssp585-1-2-1";;
|
|
|
+ ssp2-4.5*) pis_scen="ssp245"; pis_sco2_mfix="MESSAGE-GLOBIOM-ssp245-1-2-1";;
|
|
|
+ ssp5-3.4*) pis_scen="ssp534os"; pis_sco2_mfix="REMIND-MAGPIE-ssp534-over-1-2-1";;
|
|
|
+ ssp5-8.5*) pis_scen="ssp585"; pis_sco2_mfix="REMIND-MAGPIE-ssp585-1-2-1";;
|
|
|
+ *) error "Scenario ${ifs_cmip6_scenario} not defined for PISCES" ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ # concatenate historic and scenario (2015+) co2 concentration file
|
|
|
+ pis_sco2_pfix="${ini_data_dir}/nemo/pisces/mole-fraction-of-carbon-dioxide-in-air_input4MIPs_GHGConcentrations"
|
|
|
+ cat ${pis_sco2_pfix}_CMIP_UoM-CMIP-1-2-0_gr1-GMNHSH_1849-2014.txt ${pis_sco2_pfix}_ScenarioMIP_UoM-${pis_sco2_mfix}_gr1-GMNHSH_2015-2500.txt > atcco2.txt
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ #linking surface boundary conditions for CFCs (even if CFCs are not included)
|
|
|
+ ln -fs ${ini_data_dir}/nemo/cfc/CFCs_CDIAC_extension_1637_2019.dat CFCs_CDIAC.dat
|
|
|
+
|
|
|
+ if $(has_config pisces:start_from_restart)
|
|
|
+ then
|
|
|
+ # Same three options as for nemo:start_from_restart
|
|
|
+ if ls -U ${nem_restart_file_path}/restart_trc.nc > /dev/null 2>&1
|
|
|
+ then
|
|
|
+ ln -s ${nem_restart_file_path}/restart_trc.nc ./
|
|
|
+
|
|
|
+ elif ls -U ${nem_restart_file_path}/restart_trc_????.nc > /dev/null 2>&1
|
|
|
+ then
|
|
|
+ ln -s ${nem_restart_file_path}/restart_trc_????.nc ./
|
|
|
+
|
|
|
+ else
|
|
|
+ for f in ${nem_restart_file_path}/????_????????_restart_trc_????.nc
|
|
|
+ do
|
|
|
+ ln -s $f $(echo $f | sed 's/.*_\(restart_trc_....\.nc\)/\1/')
|
|
|
+ done
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ fi
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for the Runoff mapper (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ has_config rnfmapper && \
|
|
|
+ ln -s ${ini_data_dir}/runoff-mapper/runoff_maps.nc
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** File and dir needed for TM5
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ tm5_istart=9
|
|
|
+
|
|
|
+ case ${tm5_istart} in
|
|
|
+ 33|32) ln -s \
|
|
|
+ ${tm5_restart_file_path}/TM5_restart_${leg_start_date_yyyymmdd}_0000_glb300x200.nc
|
|
|
+ ;;
|
|
|
+ 31) ln -s ${tm5_restart_file_path}/tm5_save.hdf
|
|
|
+ ;;
|
|
|
+ 5) ln -s ${tm5_restart_file_path}/tm5_mmix.hdf
|
|
|
+ ;;
|
|
|
+ 2|9)
|
|
|
+ ;;
|
|
|
+ *) error "Unsupported initial fields option (TM5): ${tm5_istart}"
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ # spectral info
|
|
|
+ ln -s ${ini_data_dir}/tm5/TM5_INPUT/T${ifs_res_hor}_info.txt
|
|
|
+
|
|
|
+ # Profiling dir for TM5
|
|
|
+ mkdir -p ${run_dir}/tm5_profile
|
|
|
+ fi
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for OASIS (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Name table file
|
|
|
+ ln -s ${ini_data_dir}/oasis/cf_name_table.txt
|
|
|
+
|
|
|
+ # -- Get grid definition and weight files for IFS/NEMO or IFS/AMIP coupling
|
|
|
+ has_config nemo && \
|
|
|
+ oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-ORCA${nem_res_hor} && \
|
|
|
+ mycp='cp'
|
|
|
+
|
|
|
+ has_config amip && \
|
|
|
+ oas_grid_dir=${ini_data_dir}/oasis/AMIP && \
|
|
|
+ mycp='cdo -f nc copy' # to enforce nc format, needed for 'cdo merge' to work (have nc4c with Primavera files)
|
|
|
+
|
|
|
+ # Grid definition files
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ ${mycp} ${oas_grid_dir}/areas.nc gcm_areas.nc
|
|
|
+ ${mycp} ${oas_grid_dir}/grids.nc gcm_grids.nc
|
|
|
+ ${mycp} ${oas_grid_dir}/masks.nc gcm_masks.nc
|
|
|
+ else
|
|
|
+ ln -s ${oas_grid_dir}/areas.nc
|
|
|
+ ln -s ${oas_grid_dir}/grids.nc
|
|
|
+ ln -s ${oas_grid_dir}/masks.nc
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Weight files
|
|
|
+ case ${ifs_res_hor} in
|
|
|
+ 159) oas_agrd=080
|
|
|
+ ;;
|
|
|
+ 255) oas_agrd=128
|
|
|
+ ;;
|
|
|
+ 511) oas_agrd=256
|
|
|
+ ;;
|
|
|
+ 799) oas_agrd=400
|
|
|
+ ;;
|
|
|
+ *) error "Unsupported horizontal resolution (IFS): ${ifs_res_hor}"
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ if $(has_config nemo)
|
|
|
+ then
|
|
|
+ case ${nem_res_hor} in
|
|
|
+ 1) oas_ogrd=O1t0
|
|
|
+ ;;
|
|
|
+ 025) oas_ogrd=Ot25
|
|
|
+ ;;
|
|
|
+ *) error "Unsupported horizontal resolution (NEMO): ${nem_res_hor}"
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+ fi
|
|
|
+
|
|
|
+ if ${oas_link_weights}
|
|
|
+ then
|
|
|
+ for f in ${oas_grid_dir}/rmp_????_to_????_GAUSWGT.nc
|
|
|
+ do
|
|
|
+ ln -s $f
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ if $(has_config ifs nemo)
|
|
|
+ then
|
|
|
+ for f in ${oas_rst_ifs_nemo}
|
|
|
+ do
|
|
|
+ cp ${oas_grid_dir}/rst/$f .
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -- Get grid definition, weight and restart files for TM5 coupling
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-TM5-LPJG
|
|
|
+
|
|
|
+ cp ${oas_grid_dir}/tm5_areas.nc .
|
|
|
+ cp ${oas_grid_dir}/tm5_grids.nc .
|
|
|
+ cp ${oas_grid_dir}/tm5_masks.nc .
|
|
|
+
|
|
|
+ if ${oas_link_weights}
|
|
|
+ then
|
|
|
+ for f in ${oas_grid_dir}/rmp_????_to_????_*.nc
|
|
|
+ do
|
|
|
+ ln -s $f
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -- Get restart files for TM5-IFS/LPJG/PISCES
|
|
|
+ for f in ${oas_rst_ifs_tm5}
|
|
|
+ do
|
|
|
+ cp ${oas_grid_dir}/rst/${tm5_exch_nlevs}-levels/$f .
|
|
|
+ done
|
|
|
+
|
|
|
+ # -- Merge grid definition files
|
|
|
+ cdo merge gcm_areas.nc tm5_areas.nc areas.nc
|
|
|
+ cdo merge gcm_grids.nc tm5_grids.nc grids.nc
|
|
|
+ cdo merge gcm_masks.nc tm5_masks.nc masks.nc
|
|
|
+ fi
|
|
|
+
|
|
|
+ else # i.e. $leg_is_restart == true
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Remove all leftover output files from previous legs
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ # IFS files
|
|
|
+ rm -f ICM{SH,GG}${exp_name}+??????
|
|
|
+
|
|
|
+ # NEMO files
|
|
|
+ rm -f ${exp_name}_??_????????_????????_{grid_U,grid_V,grid_W,grid_T,icemod,SBC,scalar,SBC_scalar,diad_T}.nc
|
|
|
+
|
|
|
+ # TM5 restart file type
|
|
|
+ tm5_istart=33
|
|
|
+
|
|
|
+ if [ $tm5_istart -eq 31 ] && $(has_config tm5)
|
|
|
+ then
|
|
|
+ ln -sf save_${leg_start_date_yyyymmdd}00_glb300x200.hdf tm5_save.hdf
|
|
|
+ fi
|
|
|
+
|
|
|
+ fi # ! $leg_is_restart
|
|
|
+
|
|
|
+ #--------------------------------------------------------------------------
|
|
|
+ # *** Surface restoring and ocean nudging options
|
|
|
+ #--------------------------------------------------------------------------
|
|
|
+ if $(has_config nemo:ocenudg) ; then
|
|
|
+ ln -fs ${ini_data_dir}/nemo/oce_nudg/temp_sal*.nc ./
|
|
|
+ fi
|
|
|
+
|
|
|
+ if $(has_config nemo:surfresto) ; then
|
|
|
+ ln -fs ${ini_data_dir}/nemo/surface_restoring/sss_restore_data*.nc ./
|
|
|
+ ln -fs ${ini_data_dir}/nemo/surface_restoring/sst_restore_data*.nc ./
|
|
|
+ ln -fs ${ini_data_dir}/nemo/surface_restoring/mask_restore*.nc ./
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Remove land grid-points
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config nemo:elpin)
|
|
|
+ then
|
|
|
+ if [ ! -f coordinates_xios.nc ]
|
|
|
+ then
|
|
|
+ error "ELpIN requested, but file 'coordinates_xios.nc' was not found"
|
|
|
+ fi
|
|
|
+ jpns=($(${ecearth_src_dir}/util/ELPiN/ELPiNv2.cmd ${nem_numproc}))
|
|
|
+ info "nemo domain decompostion from ELpIN: ${jpns[@]}"
|
|
|
+ nem_numproc=${jpns[0]}
|
|
|
+ nem_jpni=${jpns[1]}
|
|
|
+ nem_jpnj=${jpns[2]}
|
|
|
+ elif has_config nemo
|
|
|
+ then
|
|
|
+ info "nemo original domain decomposition (not using ELPiN)"
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Initial conditions saved during the run
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ ${do_save_ic} && save_ic_prepare_output
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Create some control files
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Create TM5 runtime rcfile
|
|
|
+ tm5_start_date=$(date -u -d "${leg_start_date}" +%F\ %T)
|
|
|
+ tm5_end_date=$(date -u -d "${leg_end_date}" +%F\ %T)
|
|
|
+
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ cp -f ${ctrl_file_dir}/tm5-config-run.rc ${run_dir}
|
|
|
+ ${ecearth_src_dir}/tm5mp/setup_tm5 --no-compile \
|
|
|
+ --time-start="${tm5_start_date}" --time-final="${tm5_end_date}" \
|
|
|
+ --istart=${tm5_istart} ${run_dir}/tm5-config-run.rc
|
|
|
+ fi
|
|
|
+
|
|
|
+ # IFS frequency output for namelist
|
|
|
+ if [ -f postins/pptdddddd0300 ]
|
|
|
+ then
|
|
|
+ ifs_output_freq=$(( 3 * 3600 / ifs_time_step_sec ))
|
|
|
+ elif [ -f postins/pptdddddd0600 ]
|
|
|
+ then
|
|
|
+ ifs_output_freq=$(( 6 * 3600 / ifs_time_step_sec ))
|
|
|
+ else
|
|
|
+ error "IFS output frequency undefined."
|
|
|
+ fi
|
|
|
+
|
|
|
+ # IFS, NEMO, LIM, AMIP namelist and OASIS namcouple files
|
|
|
+ has_config ifs && . ${ctrl_file_dir}/namelist.ifs.sh > fort.4
|
|
|
+ has_config nemo && . ${ctrl_file_dir}/namelist.nemo.ref.sh > namelist_ref
|
|
|
+ has_config ifs nemo && . ${ctrl_file_dir}/namelist.nemo-${nem_grid}-coupled.cfg.sh > namelist_cfg
|
|
|
+ has_config lim3 && . ${ctrl_file_dir}/namelist.lim3.ref.sh > namelist_ice_ref
|
|
|
+ has_config lim3 && . ${ctrl_file_dir}/namelist.lim3-${nem_grid}.cfg.sh > namelist_ice_cfg
|
|
|
+ has_config rnfmapper && . ${ctrl_file_dir}/namelist.runoffmapper.sh > namelist.runoffmapper
|
|
|
+ has_config amip && . ${ctrl_file_dir}/namelist.amip.sh > namelist.amip
|
|
|
+ has_config pisces && . ${ctrl_file_dir}/namelist.nemo.top.ref.sh > namelist_top_ref
|
|
|
+ has_config pisces && . ${ctrl_file_dir}/namelist.nemo.top.cfg.sh > namelist_top_cfg
|
|
|
+ has_config pisces && . ${ctrl_file_dir}/namelist.nemo.pisces.ref.sh > namelist_pisces_ref
|
|
|
+ has_config pisces && . ${ctrl_file_dir}/namelist.nemo.pisces.cfg.sh > namelist_pisces_cfg
|
|
|
+ has_config nemo && . ${ctrl_file_dir}/namelist.nemo.age.ref.sh > namelist_age_ref
|
|
|
+ has_config nemo && . ${ctrl_file_dir}/namelist.nemo.age.cfg.sh > namelist_age_cfg
|
|
|
+ #include CFCs namelist even if CFCs are not included
|
|
|
+ has_config nemo && . ${ctrl_file_dir}/namelist.nemo.cfc.ref.sh > namelist_cfc_ref
|
|
|
+ has_config nemo && . ${ctrl_file_dir}/namelist.nemo.cfc.cfg.sh > namelist_cfc_cfg
|
|
|
+ # C-cycle - overwrite coupled nemo namelist
|
|
|
+ has_config pisces tm5:co2 && \
|
|
|
+ . ${ctrl_file_dir}/namelist.nemo-${nem_grid}-carboncycle.cfg.sh > namelist_cfg
|
|
|
+
|
|
|
+ lucia=0
|
|
|
+ . ${ctrl_file_dir}/namcouple.sh > namcouple
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** LPJ-GUESS initial data
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ # LPJG runtime rcfile - update with leg dates
|
|
|
+ . ${ctrl_file_dir}/namelist.lpjg.sh > lpjg_steps.rc
|
|
|
+
|
|
|
+ # determine lpjg scenario-name and co2-file middle-fix
|
|
|
+ case $(echo ${ifs_cmip6_scenario} | tr '[:upper:]' '[:lower:]') in
|
|
|
+ hist*) lpjg_scen="ssp370"; lu_src="AIM" ; lpjg_sco2_mfix="AIM-ssp370-1-2-1" ; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ ssp1-1.9*) lpjg_scen="ssp119"; lu_src="IMAGE" ; lpjg_sco2_mfix="IMAGE-ssp119-1-2-1" ; lu_file_posfix="2019_03_13.txt";;
|
|
|
+ ssp1-2.6*) lpjg_scen="ssp126"; lu_src="IMAGE" ; lpjg_sco2_mfix="IMAGE-ssp126-1-2-1" ; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ ssp2-4.5*) lpjg_scen="ssp245"; lu_src="MESSAGE"; lpjg_sco2_mfix="MESSAGE-GLOBIOM-ssp245-1-2-1"; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ ssp3-7.0*) lpjg_scen="ssp370"; lu_src="AIM" ; lpjg_sco2_mfix="AIM-ssp370-1-2-1" ; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ ssp4-3.4*) lpjg_scen="ssp434"; lu_src="GCAM" ; lpjg_sco2_mfix="GCAM4-ssp434-1-2-1" ; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ ssp5-3.4*) lpjg_scen="ssp534os"; lu_src="MAGPIE"; lpjg_sco2_mfix="REMIND-MAGPIE-ssp534-over-1-2-1" ; lu_file_posfix="2019_05_10.txt";;
|
|
|
+ ssp5-8.5*) lpjg_scen="ssp585"; lu_src="MAGPIE" ; lpjg_sco2_mfix="REMIND-MAGPIE-ssp585-1-2-1" ; lu_file_posfix="2018_10_08.txt";;
|
|
|
+ *) error "Scenario ${ifs_cmip6_scenario} not defined for LPJ-GUESS" ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ lpjg_scenario_new="historical + $lpjg_sco2_mfix"
|
|
|
+ lpjg_scenario_info=${run_dir}/lpjg_scenario.info
|
|
|
+
|
|
|
+ if [ -f $lpjg_scenario_info ]
|
|
|
+ then
|
|
|
+ source $lpjg_scenario_info
|
|
|
+ if [ "$lpjg_scenario_new" = "$lpjg_scenario" ]
|
|
|
+ then
|
|
|
+ lpjg_copy_rte=false
|
|
|
+ else
|
|
|
+ lpjg_copy_rte=true
|
|
|
+ fi
|
|
|
+ else
|
|
|
+ lpjg_copy_rte=true
|
|
|
+ fi
|
|
|
+
|
|
|
+ # copy RTE only if necessary (at beginning of a run or when scenario changes)
|
|
|
+ if $lpjg_copy_rte
|
|
|
+ then
|
|
|
+ # write info about installed scenarios to file
|
|
|
+ echo "lpjg_scenario=\"historical + $lpjg_sco2_mfix\"" > $lpjg_scenario_info
|
|
|
+ # set file prefixes depending on scenario
|
|
|
+ lu_file_prefix="1850_2100_luh2_Hist_ScenarioMIP_UofMD"
|
|
|
+ lu_file_midfix="2_1_f"
|
|
|
+
|
|
|
+ lu_path="${ini_data_dir}/lpjg/landuse/${lpjg_res}/${lpjg_scen}"
|
|
|
+
|
|
|
+ # copy and reference-link landuse, gross transitions, crops, n-fertilisation
|
|
|
+ for inp in lu gross crop nfert
|
|
|
+ do
|
|
|
+ if [ $inp == "crop" -o $inp == "nfert" ]
|
|
|
+ then
|
|
|
+ lu_src_file="${lu_path}/${inp}_rfirr_${lu_file_prefix}_${lu_src}_${lpjg_scen}_${lu_file_midfix}_${lpjg_res}_${lu_file_posfix}"
|
|
|
+ else
|
|
|
+ lu_src_file="${lu_path}/${inp}_${lu_file_prefix}_${lu_src}_${lpjg_scen}_${lu_file_midfix}_${lpjg_res}_${lu_file_posfix}"
|
|
|
+ fi
|
|
|
+ cp -f $lu_src_file ${run_dir}/landuse/${inp}_luh2.txt
|
|
|
+ ln -fs $lu_src_file ${run_dir}/landuse/${inp}_luh2.txt.lnk
|
|
|
+ done
|
|
|
+
|
|
|
+ # nitrogen deposition files
|
|
|
+ mkdir -p ${run_dir}/ndep
|
|
|
+ for inp in drynhx2 drynoy2 wetnhx2 wetnoy2
|
|
|
+ do
|
|
|
+ ndep_src_file="${ini_data_dir}/lpjg/ndep/${lpjg_res}/${lpjg_scen}/${lpjg_scen}_${lpjg_res}_${inp}.nc"
|
|
|
+ cp -f $ndep_src_file ${run_dir}/ndep/${inp}.nc
|
|
|
+ ln -fs $ndep_src_file ${run_dir}/ndep/${inp}.nc.lnk
|
|
|
+ done
|
|
|
+
|
|
|
+ # concatenate historic and scenario (2015+) co2 concentration file
|
|
|
+ # hist co2 file
|
|
|
+ lpjg_hco2_file="${ini_data_dir}/ifs/cmip6-data/mole-fraction-of-carbon-dioxide-in-air_input4MIPs_GHGConcentrations_CMIP_UoM-CMIP-1-2-0_gr1-GMNHSH_0000-2014.nc"
|
|
|
+ # scenario co2 file
|
|
|
+ lpjg_sco2_file="${ini_data_dir}/ifs/cmip6-data/mole-fraction-of-carbon-dioxide-in-air_input4MIPs_GHGConcentrations_ScenarioMIP_UoM-${lpjg_sco2_mfix}_gr1-GMNHSH_2015-2500.nc"
|
|
|
+ # combined file
|
|
|
+ lpjg_co2_file="${run_dir}/mole_fraction_of_carbon_dioxide_in_air_input4MIPs_lpjg.nc"
|
|
|
+ rm -f $lpjg_co2_file
|
|
|
+ cdo mergetime $lpjg_hco2_file $lpjg_sco2_file $lpjg_co2_file
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Populate or update LPJG run directories
|
|
|
+ for (( n=1; n<=${lpjg_numproc}; n++ ))
|
|
|
+ do
|
|
|
+ # if run from scratch or number of procs has been extended
|
|
|
+ if ! $leg_is_restart || [ ! -d ${run_dir}/run${n} ]
|
|
|
+ then
|
|
|
+ # Make output directories
|
|
|
+ mkdir -p ${run_dir}/run${n}/output
|
|
|
+
|
|
|
+ # Copy *.ins, lpjg_steps.rc and OASIS-MCT restart files
|
|
|
+ cp ${run_dir}/*.ins ${run_dir}/run${n}
|
|
|
+
|
|
|
+ # Copy output control files
|
|
|
+ cp ${output_control_files_dir}/lpjg_cmip6_output.ins ${run_dir}/run${n}
|
|
|
+ ln -s ${output_control_files_dir}/lpjg_cmip6_output.ins ${run_dir}/run${n}/lpjg_cmip6_output.ins.lnk
|
|
|
+
|
|
|
+ cp ${ini_data_dir}/lpjg/oasismct/ghg*.txt ${run_dir}/run${n}
|
|
|
+ cp ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/ece_gridlist_${lpjg_res}.txt ${run_dir}/run${n}/ece_gridlist.txt
|
|
|
+ ln -s ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/ece_gridlist_${lpjg_res}.txt ${run_dir}/run${n}/ece_gridlist.txt.lnk
|
|
|
+
|
|
|
+ # Data only needed by master
|
|
|
+ if [ $n == 1 ]
|
|
|
+ then
|
|
|
+ cp ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/*.nc ${run_dir}
|
|
|
+ cp ${ini_data_dir}/lpjg/oasismct/lpjgv.txt ${run_dir}/run${n}
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+ # Refresh output-dirs after they hav been removed at end of the last leg
|
|
|
+ mkdir -p ${run_dir}/run${n}/output/CMIP6
|
|
|
+ mkdir -p ${run_dir}/run${n}/output/CRESCENDO
|
|
|
+ done
|
|
|
+
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ lpjg_restart_dir="restart/lpjg/$(printf %03d $((leg_number-1)))"
|
|
|
+ lpjg_rst_state="${lpjg_restart_dir}/lpjg_state_${leg_start_date_yyyy}"
|
|
|
+ if [ -d "$lpjg_rst_state" ]
|
|
|
+ then
|
|
|
+ ln -sf $lpjg_rst_state
|
|
|
+ else
|
|
|
+ echo "lpjg restart dir $lpjg_rst_state not available"
|
|
|
+ exit -1
|
|
|
+ fi
|
|
|
+ # get oasis restart files
|
|
|
+ oasis_restart_dir="restart/oasis/$(printf %03d $((leg_number)))"
|
|
|
+ cp -f ${oasis_restart_dir}/*.nc ${run_dir}/
|
|
|
+
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Create ICMCL file with vegetation fields
|
|
|
+ # not needed if LPJG is used with feedback
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ tempfile=tmp.$$
|
|
|
+
|
|
|
+ case ${ifs_veg_source} in
|
|
|
+ "ifs" )
|
|
|
+ # Vegetation from IFS (climatology)
|
|
|
+
|
|
|
+ icmclfile=${ini_data_dir}/ifs/${ifs_grid}/climate/ICMCL_ONLY_VEG_PD
|
|
|
+
|
|
|
+ # Create data for december, the year before the leg starts
|
|
|
+ ${grib_set} \
|
|
|
+ -s dataDate=$(printf "%04d" $((leg_start_date_yyyy-1)))1215 \
|
|
|
+ ${icmclfile}-12 ICMCL${exp_name}INIT
|
|
|
+
|
|
|
+ # Create data for all month in the years of the leg
|
|
|
+ for (( y=${leg_start_date_yyyy} ; y<=${leg_end_date_yyyy} ; y++ ))
|
|
|
+ do
|
|
|
+ yy=$(printf "%04d" $y)
|
|
|
+ for m in {1..12}
|
|
|
+ do
|
|
|
+ mm=$(printf "%02d" $m)
|
|
|
+ ${grib_set} -s dataDate=${yy}${mm}15 ${icmclfile}-${mm} ${tempfile}
|
|
|
+ cat ${tempfile} >> ICMCL${exp_name}INIT
|
|
|
+ done
|
|
|
+ done
|
|
|
+
|
|
|
+ # Create data for january, the year after the leg ends
|
|
|
+ ${grib_set} \
|
|
|
+ -s dataDate=$(printf "%04d" $((leg_end_date_yyyy+1)))0115 \
|
|
|
+ ${icmclfile}-01 ${tempfile}
|
|
|
+ cat ${tempfile} >> ICMCL${exp_name}INIT
|
|
|
+ ;;
|
|
|
+ "era20c"|"cmip6"|"custom_"* )
|
|
|
+ # Vegetation from a LPJG run (off-line or EC-Earth3-Veg)
|
|
|
+
|
|
|
+ rm -f ICMCL${exp_name}INIT
|
|
|
+
|
|
|
+ # Create data for all years of the leg, including one year
|
|
|
+ # before and one year after
|
|
|
+ for (( yr=leg_start_date_yyyy-1 ; yr<=leg_end_date_yyyy+1 ; yr+=1 ))
|
|
|
+ do
|
|
|
+
|
|
|
+ case ${ifs_veg_source} in
|
|
|
+ 'era20c' )
|
|
|
+ # no scenario needed with era20c
|
|
|
+ icmcl_scenario="" ;;
|
|
|
+ 'custom_'* )
|
|
|
+ # no scenario implemented yet with custom_dir
|
|
|
+ icmcl_scenario="" ;;
|
|
|
+ 'cmip6' )
|
|
|
+ # select scenario, use SSP3-7.0 as default
|
|
|
+ # if not otherwise specified
|
|
|
+ icmcl_scenario="historical"
|
|
|
+ if ( [ $ifs_cmip_fixyear -le 0 ] && [ $yr -ge 2015 ] ) || \
|
|
|
+ [ $ifs_cmip_fixyear -ge 2015 ]
|
|
|
+ then
|
|
|
+ [[ ${ifs_cmip6_scenario} =~ ^SSP ]] \
|
|
|
+ && icmcl_scenario=${ifs_cmip6_scenario} \
|
|
|
+ || if [ ${ifs_covid19^^} == TRUE ]
|
|
|
+ then
|
|
|
+ icmcl_scenario='SSP2-4.5'
|
|
|
+ else
|
|
|
+ icmcl_scenario='SSP3-7.0'
|
|
|
+ fi
|
|
|
+ fi ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ if [ $ifs_cmip_fixyear -le 0 ] || [[ ${ifs_veg_source} == custom_* ]]
|
|
|
+ then
|
|
|
+ cat ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version}/${icmcl_scenario}/icmcl_$yr.grb >> ICMCL${exp_name}INIT
|
|
|
+ else
|
|
|
+ # Fixed year forcing, requires cdo! (only when not using ifs_veg_source=custom_exp*)
|
|
|
+ # If cdo is not available at runtime you need to fix proper
|
|
|
+ # icmcl files beforehand and use them here
|
|
|
+ cdo setyear,$yr ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version}/${icmcl_scenario}/icmcl_${ifs_cmip_fixyear}.grb ${tempfile}
|
|
|
+ cat ${tempfile} >> ICMCL${exp_name}INIT
|
|
|
+ fi
|
|
|
+ done
|
|
|
+ ;;
|
|
|
+ "none" )
|
|
|
+ info "no ICMCL file is created"
|
|
|
+ ;;
|
|
|
+ * )
|
|
|
+ error "Vegetation from ${ifs_veg_source} not implemented"
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ # Clean up
|
|
|
+ rm -f ${tempfile}
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Link the appropriate NEMO restart files of the previous leg
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart && $(has_config nemo) && ! $special_restart
|
|
|
+ then
|
|
|
+ ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec - nem_restart_offset )))
|
|
|
+ for (( n=0 ; n<nem_numproc ; n++ ))
|
|
|
+ do
|
|
|
+ np=$(printf %04d ${n})
|
|
|
+ ln -fs ${exp_name}_${ns}_restart_oce_${np}.nc restart_oce_${np}.nc
|
|
|
+ ln -fs ${exp_name}_${ns}_restart_ice_${np}.nc restart_ice_${np}.nc
|
|
|
+ has_config pisces && \
|
|
|
+ ln -fs ${exp_name}_${ns}_restart_trc_${np}.nc restart_trc_${np}.nc
|
|
|
+ done
|
|
|
+
|
|
|
+ # Make sure there are no global restart files
|
|
|
+ # If links are found, they will be removed. We are cautious and do
|
|
|
+ # _not_ remove real files! However, if real global restart files are
|
|
|
+ # present, NEMO/LIM will stop because time stamps will not match.
|
|
|
+ [ -h restart_oce.nc ] && rm restart_oce.nc
|
|
|
+ [ -h restart_ice.nc ] && rm restart_ice.nc
|
|
|
+ [ -h restart_trc.nc ] && rm restart_trc.nc
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Remove some OASIS files of the previous leg
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ rm -f anaisout_*
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Remove any ccycle debug output files
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if ${ccycle_debug_fluxes} && $leg_is_restart && $(has_config tm5:co2)
|
|
|
+ then
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ rm -f GUE_{CNAT,CANT,CNPP}_*.nc run1/GUE_{CNAT,CANT,CNPP}_*.nc
|
|
|
+ rm -f TM5_Land{CNAT,CANT,CNPP}_*.nc
|
|
|
+ fi
|
|
|
+ if $(has_config pisces)
|
|
|
+ then
|
|
|
+ rm -f O_CO2FLX_*.nc
|
|
|
+ rm -f TM5_OceCFLX_*.nc
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Check consistency of OASIS restarts and IFS rcf with ece_info_file
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ info "Check OASIS restarts and IFS rcf before launch"
|
|
|
+ leg_nb_3d=$(printf %03d $((leg_number)))
|
|
|
+
|
|
|
+ for oasis_restart_file in restart/oasis/${leg_nb_3d}/*
|
|
|
+ do
|
|
|
+ [ ! -f "${oasis_restart_file}" ] && break
|
|
|
+
|
|
|
+ if ! diff -q $(basename ${oasis_restart_file}) ${oasis_restart_file} >/dev/null
|
|
|
+ then
|
|
|
+ echo "*WARNING* Overwriting OASIS restart (${oasis_restart_file})"
|
|
|
+ cp -f ${oasis_restart_file} .
|
|
|
+ fi
|
|
|
+ done
|
|
|
+
|
|
|
+ rcf_restart_file=restart/ifs/${leg_nb_3d}/rcf
|
|
|
+ if [ -f "${rcf_restart_file}" ]
|
|
|
+ then
|
|
|
+ if ! diff -q rcf ${rcf_restart_file} >/dev/null
|
|
|
+ then
|
|
|
+ echo "*WARNING* Overwriting IFS rcf file (${rcf_restart_file})"
|
|
|
+ cp -f ${rcf_restart_file} .
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Start the run
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ export DR_HOOK_IGNORE_SIGNALS='-1'
|
|
|
+ export CPLNG='active'
|
|
|
+
|
|
|
+ # Use the launch function from the platform configuration file
|
|
|
+ has_config nemo && \
|
|
|
+ cmd="${xio_numproc} ${xio_exe_file} -- \
|
|
|
+ ${nem_numproc} ${nem_exe_file} -- \
|
|
|
+ ${ifs_numproc} ${ifs_exe_file} -v ecmwf -e ${exp_name}" || \
|
|
|
+ cmd="${ifs_numproc} ${ifs_exe_file} -v ecmwf -e ${exp_name}"
|
|
|
+
|
|
|
+ has_config lpjg && cmd=${cmd}" -- ${lpjg_numproc} ${lpjg_exe_file} guess.ins -parallel"
|
|
|
+ has_config tm5 && cmd=${cmd}" -- ${tm5_numproc} ${tm5_exe_file} tm5-run.rc"
|
|
|
+ has_config amip && cmd=${cmd}" -- ${amip_numproc} ${amip_exe_file}"
|
|
|
+ has_config nemo && cmd=${cmd}" -- ${rnf_numproc} ${rnf_exe_file}"
|
|
|
+
|
|
|
+ t1=$(date +%s)
|
|
|
+ launch $cmd
|
|
|
+ t2=$(date +%s)
|
|
|
+
|
|
|
+ tr=$(date -d "0 -$t1 sec + $t2 sec" +%T)
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Check for signs of success
|
|
|
+ # Note the tests provide no guarantee that things went fine! They are
|
|
|
+ # just based on the IFS, NEMO and TM5 log files. More tests (e.g. checking
|
|
|
+ # restart files) could be implemented.
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Checking for IFS success
|
|
|
+ if [ -f ifs.stat ]
|
|
|
+ then
|
|
|
+ if [ "$(awk 'END{print $3}' ifs.stat)" == "CNT0" ]
|
|
|
+ then
|
|
|
+ info "Leg successfully completed according to IFS log file 'ifs.stat'."
|
|
|
+ else
|
|
|
+ error "Leg not completed according to IFS log file 'ifs.stat'."
|
|
|
+ fi
|
|
|
+ else
|
|
|
+ error "IFS log file 'ifs.stat' not found after run."
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Check for NEMO success
|
|
|
+ if $(has_config nemo)
|
|
|
+ then
|
|
|
+ if [ -f ocean.output ]
|
|
|
+ then
|
|
|
+ if [ "$(sed -n '/New day/h; ${g;s:.*\([0-9/]\{10\}\).*:\1:;p;}' ocean.output)" == "$(date -u -d "${leg_end_date} - 1 day" +%Y/%m/%d)" ]
|
|
|
+ then
|
|
|
+ info "Leg successfully completed according to NEMO log file 'ocean.output'."
|
|
|
+ else
|
|
|
+ error "Leg not completed according to NEMO log file 'ocean.output'."
|
|
|
+ fi
|
|
|
+ else
|
|
|
+ error "NEMO log file 'ocean.output' not found after run."
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Check for TM5 success
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ if [ -f tm5.ok ]
|
|
|
+ then
|
|
|
+ info "Leg successfully completed according to existing TM5 file 'tm5.ok'."
|
|
|
+ else
|
|
|
+ error "Leg not completed according to non-existing TM5 file 'tm5.ok'."
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Post-process initial conditions saved during the run if requested
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ ${do_save_ic} && save_ic_postproc
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move IFS output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${archive_dir}/output/ifs/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ prv_leg=$(printf %03d $((leg_number-1)))
|
|
|
+
|
|
|
+ # This takes care of a special IFS feature: The output for the last time
|
|
|
+ # step of each leg is written at the first time step of the new leg. The
|
|
|
+ # following code makes sure that the output is appended to the appropriate
|
|
|
+ # file. Since GRIB files are just streams, its done with a simple cat
|
|
|
+ # command.
|
|
|
+ for f in ICMSH${exp_name}+?????? ICMGG${exp_name}+??????
|
|
|
+ do
|
|
|
+ if [ -f output/ifs/${prv_leg}/${f} ]
|
|
|
+ then
|
|
|
+ cat ${f} >> output/ifs/${prv_leg}/${f}
|
|
|
+ rm -f ${f}
|
|
|
+ else
|
|
|
+ mv ${f} ${outdir}
|
|
|
+ fi
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move NEMO output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config nemo)
|
|
|
+ then
|
|
|
+ outdir="${archive_dir}/output/nemo/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for v in grid_U grid_V grid_W grid_T icemod SBC scalar SBC_scalar diad_T ptrc_T bioscalar \
|
|
|
+ grid_T_2D grid_U_2D grid_V_2D grid_W_2D grid_T_3D grid_U_3D grid_V_3D grid_W_3D \
|
|
|
+ grid_T_SFC grid_1point grid_T_3D_ncatice vert_sum \
|
|
|
+ grid_ptr_W_3basin_3D grid_ptr_T_3basin_2D grid_ptr_T_2D \
|
|
|
+ zoom_700_sum zoom_300_sum zoom_2000_sum
|
|
|
+ do
|
|
|
+ for f in ${exp_name}_*_????????_????????_*${v}.nc
|
|
|
+ do
|
|
|
+ test -f $f && mv $f $outdir/
|
|
|
+ done
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move LPJ-GUESS output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ outdir="output/lpjg/$(printf %03d $((leg_number)))"
|
|
|
+ if [ -d ${outdir} ]
|
|
|
+ then
|
|
|
+ rm -rf ${outdir}
|
|
|
+ fi
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ # LPJG run directories
|
|
|
+ # concatenate *.out (or compressed *.out.gz) files from each run* into output dir
|
|
|
+ flist=$(cd ${run_dir}/run1/output && find *.out.gz -type f 2>/dev/null || true)
|
|
|
+ if [ "$flist" = "" ]
|
|
|
+ then
|
|
|
+ lpjg_compress_output=false
|
|
|
+ flist=$(cd ${run_dir}/run1/output && find *.out -type f 2>/dev/null)
|
|
|
+ else
|
|
|
+ lpjg_compress_output=true
|
|
|
+ fi
|
|
|
+
|
|
|
+ mkdir ${outdir}/CMIP6
|
|
|
+
|
|
|
+ for (( n=1; n<=${lpjg_numproc}; n++ ))
|
|
|
+ do
|
|
|
+ for ofile in $flist
|
|
|
+ do
|
|
|
+ if $lpjg_compress_output
|
|
|
+ then
|
|
|
+ [ $n == 1 ] && gzip -c ${run_dir}/run${n}/output/`basename ${ofile} .gz`.hdr > ${outdir}/$ofile
|
|
|
+ cat ${run_dir}/run${n}/output/${ofile} >> ${outdir}/$ofile
|
|
|
+ else
|
|
|
+ if (( n == 1 ))
|
|
|
+ then
|
|
|
+ cat ${run_dir}/run${n}/output/${ofile} > ${outdir}/$ofile
|
|
|
+ else
|
|
|
+ awk '(FNR!=1){print $0}' ${run_dir}/run${n}/output/${ofile} >> ${outdir}/$ofile
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+ done
|
|
|
+ rm -rf ${run_dir}/run${n}/output
|
|
|
+ done
|
|
|
+
|
|
|
+ # move monthly file if available
|
|
|
+ if [ -f ${run_dir}/LPJ-GUESS_monthlyoutput.txt ]
|
|
|
+ then
|
|
|
+ mv ${run_dir}/LPJ-GUESS_monthlyoutput.txt ${outdir}
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move TM5 output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config tm5)
|
|
|
+ then
|
|
|
+ outdir="output/tm5/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ set +e
|
|
|
+ mv budget_??????????_??????????_global.hdf ${outdir}
|
|
|
+ mv j_statistics_??????????_??????????.hdf ${outdir}
|
|
|
+ mv mmix_??????????_??????????_glb???x???.hdf ${outdir}
|
|
|
+ mv aerocom?_TM5_*_????????_daily.nc ${outdir}
|
|
|
+ mv aerocom?_TM5_*_??????_monthly.nc ${outdir}
|
|
|
+ mv AOD_????_??_??.nc ${outdir}
|
|
|
+ mv -f TM5MP_${exp_name}_griddef.nc ${outdir}
|
|
|
+ mv TM5MP_${exp_name}_TP_????_??_??.nc ${outdir}
|
|
|
+ mv TM5MP_${exp_name}_vmr3_????_??_??.nc ${outdir}
|
|
|
+ mv general_TM5_${exp_name}_??????????_hourly.nc ${outdir}
|
|
|
+ mv general_TM5_${exp_name}_??????_monthly.nc ${outdir}
|
|
|
+ mv *EC-Earth3-*_${exp_name}_*.nc ${outdir}
|
|
|
+ set -e
|
|
|
+
|
|
|
+ # move profiling files if any
|
|
|
+ if [ "$(ls -A ${run_dir}/tm5_profile)" ]
|
|
|
+ then
|
|
|
+ outdir="output/tm5/profile_$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for f in ${run_dir}/tm5_profile/*
|
|
|
+ do
|
|
|
+ test -f ${f} && mv $f ${outdir}
|
|
|
+ done
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move IFS restart files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ outdir="${archive_dir}/restart/ifs/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ # Figure out the time part of the restart files (cf. CTIME on rcf files)
|
|
|
+ # NOTE: Assuming that restarts are at full days (time=0000) only!
|
|
|
+ nd="$(printf %06d $((leg_start_sec/(24*3600))))0000"
|
|
|
+
|
|
|
+ mv srf${nd}.???? ${outdir}
|
|
|
+
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move ccycle debug output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if ${ccycle_debug_fluxes} && $(has_config tm5:co2)
|
|
|
+ then
|
|
|
+ outdir="output/tm5/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ for f in CNAT CANT CNPP ; do
|
|
|
+ mv TM5_Land${f}_*.nc ${outdir}
|
|
|
+ rm -f GUE_${f}_*.nc run1/GUE_${f}_*.nc
|
|
|
+ #gf=`ls -1 GUE_${f}_*.nc | head -n 1`
|
|
|
+ #cdo mergetime ${gf} run1/${gf} ${outdir}/${gf}
|
|
|
+ done
|
|
|
+ fi
|
|
|
+ if $(has_config pisces)
|
|
|
+ then
|
|
|
+ mv TM5_OceCFLX_*.nc ${outdir}
|
|
|
+ rm -f O_CO2FLX_*.nc
|
|
|
+ #mv O_CO2FLX_*.nc ${outdir}
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move LPJ-GUESS restart files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config lpjg)
|
|
|
+ then
|
|
|
+ outdir="restart/lpjg/$(printf %03d $((leg_number)))"
|
|
|
+ if [ -d ${outdir} ]
|
|
|
+ then
|
|
|
+ rm -rf ${outdir}
|
|
|
+ fi
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ state_dir="./lpjg_state_$(printf %04d $((leg_end_date_yyyy)))"
|
|
|
+ mv ${state_dir} ${outdir}
|
|
|
+ # LPJG writes into run1 dir, so mv to main rundir
|
|
|
+ mv -f run1/lpjgv.nc .
|
|
|
+ has_config tm5:co2 lpjg && mv -f run1/rlpjg.nc .
|
|
|
+
|
|
|
+ # remove restart link
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ old_state_dir="./lpjg_state_$(printf %04d $((leg_start_date_yyyy)))"
|
|
|
+ if [ -L $old_state_dir ]
|
|
|
+ then
|
|
|
+ rm -f "$old_state_dir"
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move NEMO restart files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart && $(has_config nemo)
|
|
|
+ then
|
|
|
+ outdir="${archive_dir}/restart/nemo/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec - nem_restart_offset )))
|
|
|
+ for f in oce ice
|
|
|
+ do
|
|
|
+ mv ${exp_name}_${ns}_restart_${f}_????.nc ${outdir}
|
|
|
+ done
|
|
|
+
|
|
|
+ if has_config pisces
|
|
|
+ then
|
|
|
+ mv ${exp_name}_${ns}_restart_trc_????.nc ${outdir}
|
|
|
+ fi
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move TM5 restart file to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart && $(has_config tm5)
|
|
|
+ then
|
|
|
+ outdir="restart/tm5/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ case ${tm5_istart} in
|
|
|
+ 33|32) f=TM5_restart_${leg_start_date_yyyymmdd}_0000_glb300x200.nc
|
|
|
+ ;;
|
|
|
+ 31) f=save_${leg_start_date_yyyymmdd}00_glb300x200.hdf
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ mv $f ${outdir}
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Copy OASIS restart files to archive directory
|
|
|
+ # NOTE: These files are copied and not moved as they are used in the
|
|
|
+ # next leg!
|
|
|
+ # Note also that the OASIS restart files present at the end of
|
|
|
+ # the leg correspond to the start of the next leg!
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${archive_dir}/restart/oasis/$(printf %03d $((leg_number+1)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for f in ${oas_rst_files}
|
|
|
+ do
|
|
|
+ test -f ${f} && cp ${f} ${outdir}
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Copy rcf files to the archive directory (of the next leg!)
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${archive_dir}/restart/ifs/$(printf %03d $((leg_number+1)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for f in rcf
|
|
|
+ do
|
|
|
+ test -f ${f} && cp ${f} ${outdir}
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move log files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${archive_dir}/log/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for f in \
|
|
|
+ ifs.log ifs.stat fort.4 ocean.output \
|
|
|
+ time.step solver.stat guess.log run1/guess0.log \
|
|
|
+ amip.log namelist.amip \
|
|
|
+ nout.000000 debug.root.?? \
|
|
|
+ ctm.tm5.log.0
|
|
|
+ do
|
|
|
+ test -f ${f} && mv ${f} ${outdir}
|
|
|
+ done
|
|
|
+ has_config pisces && cp ocean.carbon ${outdir}
|
|
|
+
|
|
|
+ for f in ctm.tm5.log.*
|
|
|
+ do
|
|
|
+ if [[ -f ${f} ]]
|
|
|
+ then
|
|
|
+ [[ -s ${f} ]] && mv ${f} ${outdir} || \rm -f ${f}
|
|
|
+ fi
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Write the restart control file
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Compute CPMIP performance
|
|
|
+ sypd="$(cpmip_sypd $leg_length_sec $(($t2 - $t1)))"
|
|
|
+ ncores=0
|
|
|
+ has_config nemo && (( ncores+=${nem_numproc} )) || :
|
|
|
+ has_config ifs && (( ncores+=${ifs_numproc} )) || :
|
|
|
+ has_config xios && (( ncores+=${xio_numproc} )) || :
|
|
|
+ has_config rnfmapper && (( ncores+=${rnf_numproc} )) || :
|
|
|
+ has_config lpjg && (( ncores+=${lpjg_numproc} )) || :
|
|
|
+ has_config tm5 && (( ncores+=${tm5_numproc} )) || :
|
|
|
+ has_config amip && (( ncores+=${amip_numproc} )) || :
|
|
|
+ chpsy="$(cpmip_chpsy $leg_length_sec $(($t2 - $t1)) $ncores)"
|
|
|
+
|
|
|
+ echo "#" | tee -a ${ece_info_file}
|
|
|
+ echo "# Finished leg at `date '+%F %T'` after ${tr} (hh:mm:ss)" \
|
|
|
+ | tee -a ${ece_info_file}
|
|
|
+ echo "# CPMIP performance: $sypd SYPD $chpsy CHPSY"| tee -a ${ece_info_file}
|
|
|
+ echo "leg_number=${leg_number}" | tee -a ${ece_info_file}
|
|
|
+ echo "leg_start_date=\"${leg_start_date}\"" | tee -a ${ece_info_file}
|
|
|
+ echo "leg_end_date=\"${leg_end_date}\"" | tee -a ${ece_info_file}
|
|
|
+
|
|
|
+ # Need to reset force_run_from_scratch in order to avoid destroying the next leg
|
|
|
+ force_run_from_scratch=false
|
|
|
+ special_restart=false
|
|
|
+
|
|
|
+done # loop over legs
|
|
|
+
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+# *** Platform dependent finalising of the run
|
|
|
+# -----------------------------------------------------------------------------
|
|
|
+finalise
|
|
|
+
|
|
|
+exit 0
|
