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@@ -0,0 +1,874 @@
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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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+
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+# Component configuration
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+# (for syntax of the $config variable, see librunscript.sh)
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+config="ifs nemo lim3 rnfmapper xios:detached oasis"
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+
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+# Experiment name (exactly 4 letters!)
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+exp_name=[[[MOD:GENERAL:EXP_NAME]]]
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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="[[[MOD:GENERAL:RUN_START_DATE]]]"
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+run_end_date="[[[MOD:GENERAL:RUN_END_DATE]]]"
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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 $run_dir is cleaned!
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+force_run_from_scratch=[[[MOD:GENERAL:FORCE_RUN_FROM_SCRATCH]]]
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+special_restart=false
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+special_restart_from=ECE3
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+special_restart_date="1995-01-01"
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+
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+# Resolution
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+ifs_grid=[[[MOD:IFS:GRID]]]
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+nem_grid=[[[MOD:NEM:GRID]]]
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+
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+# Restart frequency. Use any (reasonable) number and time unit you want.
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+# For runs without restart, leave this variable empty
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+rst_freq="[[[MOD:GENERAL:RST_FREQ]]]"
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+
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+# Number of restart legs to be run in one go
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+run_num_legs=[[[MOD:GENERAL:RUN_NUM_LEGS]]]
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+
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+# Coupling frequency between atmosphere and ocean (in seconds)
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+cpl_freq_atm_oce_sec=[[[MOD:OASIS:CPL_FREQ_ATM_OCE_SEC]]]
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+
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+# Directories
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+#start_dir=${PWD}
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+ctrl_file_dir=${start_dir}/ctrl
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+
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+# Architecture
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+build_arch=[[[PLT:ACTIVE:BUILD_ARCH]]]
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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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+. ${start_dir}/ecconf.cfg
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+
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+configure
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+
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+# -----------------------------------------------------------------------------
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+# *** Time step settings
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+# -----------------------------------------------------------------------------
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+case "${ifs_grid}--${nem_grid}" in
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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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+
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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_output_freq=$(( 6 * 3600 / ifs_time_step_sec ))
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+ifs_di_freq=$(( 24 * 3600 / ifs_time_step_sec ))
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+ifs_ddh_freq=$(( 120 * 3600 / ifs_time_step_sec ))
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+
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+ifs_res_hor=$(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=[[[MOD:IFS:NUMPROC]]]
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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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+ifs_cmip5=[[[MOD:IFS:CMIP5]]]
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+ifs_cmip5_rcp=[[[MOD:IFS:CMIP5_RCP]]]
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+ifs_cmip_fixyear=[[[MOD:IFS:CMIP_FIXYEAR]]]
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+ifs_mac2sp=[[[MOD:IFS:MAC2SP]]]
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+ifs_cmip6piaer=[[[MOD:IFS:CMIP6PIAER]]]
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+
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+ifs_cmip6=[[[MOD:IFS:CMIP6]]]
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+
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+lcmip6_strataer_simp=FALSE
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+lcmip6_strataer_full=[[[MOD:IFS:CMIP6]]]
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+lcmip6_strataer_bckgd=FALSE
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+
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+ifs_A4xCO2=[[[MOD:IFS:CMIP6_A4xCO2]]]
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+ifs_1PCTCO2=[[[MOD:IFS:CMIP6_1PCTCO2]]]
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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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+ifs_orb_switch=FALSE
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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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+# *** IFS tuning (the commented values are EC-Earth 3.2beta and IFS cy36r4)
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+# Default based on the v16 LPJG vegetation dataset discussed in #449-197 (jcn4)
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+# The default values are WITH 2nd indirect effect NCLOUDACT=2, NAERCLD=9
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+# jvg6 is the best alternative configuration found in #449 with NCLOUDACT=0
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+# jvg6 ECE32b IFS cy36r4
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+RPRCON=1.34E-3 # 1.52e-4 1.2E-3 1.4E-3
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+RVICE=0.137 # 0.126 0.13 0.15
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+RLCRITSNOW=4.0E-5 # 4.2e-5 3.0E-5 5.0E-5
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+RSNOWLIN2=0.035 # 0.035 0.035 0.025
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+ENTRORG=1.70E-4 # 1.58e-4 1.5E-4 1.8E-4
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+DETRPEN=0.75E-4 # 0.75e-4 0.75E-4 0.75E-4
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+ENTRDD=3.0E-4 # 3.5e-4 3.0E-4 2.0E-4
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+RMFDEPS=0.3 # 0.27 0.3 0.35
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+RCLDIFF=3.E-6 # 3.6e-6 3.E-6
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+RCLDIFFC=5.0 # 5.0
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+RLCRIT_UPHYS=0.875e-5
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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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+#
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+ifs_veg_source="ifs"
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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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+* )
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+ error "Vegetation from ${ifs_veg_source} not implemented"
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+ ;;
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+esac
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+
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+# -----------------------------------------------------------------------------
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+# *** NEMO/LIM configuration
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+# -----------------------------------------------------------------------------
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+
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+# This is only needed if the experiment is started from an existing set of NEMO
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+# restart files
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+nem_restart_file_path=${start_dir}/nemo-rst
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+
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+nem_restart_offset=0
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+
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+nem_res_hor=$(echo ${nem_grid} | sed 's:ORCA\([0-9]\+\)L[0-9]\+:\1:')
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+
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+nem_exe_file=${ecearth_src_dir}/nemo-3.6/CONFIG/${nem_grid}_LIM3/BLD/bin/nemo.exe
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+
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+nem_numproc=[[[MOD:NEM:NUMPROC]]]
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+
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+# -----------------------------------------------------------------------------
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+# *** Runoff mapper configuration
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+# -----------------------------------------------------------------------------
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+
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+rnf_exe_file=${ecearth_src_dir}/runoff-mapper/bin/runoff-mapper.exe
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+rnf_numproc=1
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+
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+# -----------------------------------------------------------------------------
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+# *** OASIS configuration
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+# -----------------------------------------------------------------------------
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+
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+# Restart files for the coupling fields (note 8 character limit in OASIS)
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+# rstas.nc : atmoshpere single-category fields
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+# rstam.nc : atmoshpere multi-category fields
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+# rstos.nc : ocean single-category fields
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+# rstom.nc : ocean multi-category fields
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+oas_rst_files="rstas.nc rstos.nc"
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+
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+# Decide whether the OASIS weight files for interpolation should be linked from
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+# the setup directory (true) or not (false). In the latter case, the weights
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+# are re-computed at the start of the run.
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+oas_link_weights=true
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+
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+# Flux correction for runoff (not calving) sent from Oasis to ocean.
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+# 1.07945 is computed to compensate for a P-E=-0.016 mm/day
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+oas_mb_fluxcorr=1.07945
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+
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+# -----------------------------------------------------------------------------
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+# *** XIOS configuration
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+# -----------------------------------------------------------------------------
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+
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+xio_exe_file=${ecearth_src_dir}/xios-2/bin/xios_server.exe
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+
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+xio_numproc=[[[MOD:XIO:NUMPROC]]]
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+
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+# -----------------------------------------------------------------------------
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+# *** Extra initial conditions saved during the run
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+# -----------------------------------------------------------------------------
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+if has_config save_ic
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+then
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+ source ./libsave_ic.sh
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+ declare -a save_ic_date save_ic_date1 save_ic_sec save_ic_day save_ic_ppt_file save_ic_nemo_ts
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+fi
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+
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+# =============================================================================
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+# *** END of User configuration
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+# =============================================================================
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+
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+# =============================================================================
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+# *** This is where the code begins ...
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+# =============================================================================
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+
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+# -----------------------------------------------------------------------------
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+# *** Create the run dir if necessary and go there
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+# Everything is done from here.
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+# -----------------------------------------------------------------------------
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+if [ ! -d ${run_dir} ]
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+then
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+ mkdir -p ${run_dir}
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+ if $special_restart
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+ then
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+ force_run_from_scratch=false
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+ 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}
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+ cp -f ${nem_exe_file} ${run_dir}
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+ cp -f ${ifs_exe_file} ${run_dir}
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+ cp -f ${rnf_exe_file} ${run_dir}
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+ cp -f ${xio_exe_file} ${run_dir}
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+ special_year=${special_restart_date:0:4}
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+ sed -i "/$special_year/q" ${run_dir}/ece.info
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+ . ${run_dir}/ece.info
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+ special_restart_leg=$(printf %03d $((leg_number+1)))
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+ # PUT HERE THE INSTRUCTIONS TO COPY THE restart files
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+ rsync -av ${run_dir}/../${special_restart_from}/restart/ifs/${special_restart_leg}/ ${run_dir}
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+ rsync -av ${run_dir}/../${special_restart_from}/restart/oasis/${special_restart_leg}/ ${run_dir}
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+ cd ${run_dir}/../${special_restart_from}/restart/nemo/${special_restart_leg}
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+ for f in *.nc; do
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+ nf=${exp_name}${f:4}
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+ cp $f ${run_dir}/$nf
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+ done
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+ cd -
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+ cd ${run_dir}
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+ for f in ${exp_name}_????????_restart_???_????.nc; do
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+ nf=${f:14}
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+ ln -s $f $nf
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+ done
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+ cd -
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+ rm -f ${run_dir}/ICMCL${special_restart_from}INIT
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+ mv ${run_dir}/ICMGG${special_restart_from}INIUA ${run_dir}/ICMGG${exp_name}INIUA
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+ mv ${run_dir}/ICMGG${special_restart_from}INIT ${run_dir}/ICMGG${exp_name}INIT
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+ mv ${run_dir}/ICMSH${special_restart_from}INIT ${run_dir}/ICMSH${exp_name}INIT
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+ fi
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+else
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+ force_run_from_scratch=false
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+ special_restart=false
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+fi
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+cd ${run_dir}
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+
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+# -----------------------------------------------------------------------------
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+# *** Determine the time span of this run and whether it's a restart leg
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+# -----------------------------------------------------------------------------
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+
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+# Regularise the format of the start and end date of the simulation
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+run_start_date=$(date -uR -d "${run_start_date}")
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+run_end_date=$(date -uR -d "${run_end_date}")
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+
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+# -----------------------------------------------------------------------------
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+# *** Set path to grib_set
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+# -----------------------------------------------------------------------------
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+
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+grib_set=${GRIB_BIN_PATH}${GRIB_BIN_PATH:+/}grib_set
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+
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+# Loop over the number of legs
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+for (( ; run_num_legs>0 ; run_num_legs-- ))
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+do
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+
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+ # Check for restart information file and set the current leg start date
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+ # Ignore restart information file if force_run_from_scratch is true
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+ if ${force_run_from_scratch} || ! [ -r ${ece_info_file} ]
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+ then
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+ leg_is_restart=false
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+ leg_start_date=${run_start_date}
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+ leg_number=1
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+ else
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+ leg_is_restart=true
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+ . ./${ece_info_file}
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+ leg_start_date=${leg_end_date}
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+ leg_number=$((leg_number+1))
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+ fi
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+
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+ # Compute the end date of the current leg
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+ if [ -n "${rst_freq}" ]
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+ then
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+ leg_end_date=$(date -uR -d "${leg_start_date} + ${rst_freq}")
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+ else
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+ leg_end_date=${run_end_date}
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+ fi
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+
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+ if [ $(date -d "${leg_end_date}" +%s) -gt $(date -d "${run_end_date}" +%s) ]
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+ then
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+ leg_end_date=${run_end_date}
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+ fi
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+
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+ # Some time variables needed later
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+ leg_length_sec=$(( $(date -d "${leg_end_date}" +%s) - $(date -d "${leg_start_date}" +%s) ))
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+ leg_start_sec=$(( $(date -d "${leg_start_date}" +%s) - $(date -d "${run_start_date}" +%s) ))
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+ leg_end_sec=$(( $(date -d "${leg_end_date}" +%s) - $(date -d "${run_start_date}" +%s) ))
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+ leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d)
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+ leg_start_date_yyyy=$(date -u -d "${leg_start_date}" +%Y)
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+ leg_end_date_yyyy=$(date -u -d "${leg_end_date}" +%Y)
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+
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+ # Check whether there's actually time left to simulate - exit otherwise
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+ if [ ${leg_length_sec} -le 0 ]
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+ then
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+ info "Leg start date equal to or after end of simulation."
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+ info "Nothing left to do. Exiting."
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+ exit 0
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+ fi
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+
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+ # Initial conditions saved during the run
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+ do_save_ic=false
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+ has_config save_ic && save_ic_get_config
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+ # if you do not use an option with save_ic, you must define 'do_save_ic' and
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+ # 'save_ic_date_offset' here or in ../libsave_ic.sh/save_ic_get_config()
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+ ${do_save_ic} && save_ic_define_vars
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+
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+ # -------------------------------------------------------------------------
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+ # *** Prepare the run directory for a run from scratch
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+ # -------------------------------------------------------------------------
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+ if ! $leg_is_restart
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+ then
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+ # ---------------------------------------------------------------------
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+ # *** Check if run dir is empty. If not, and if we are allowed to do so
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+ # by ${force_run_from_scratch}, remove everything
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+ # ---------------------------------------------------------------------
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+ if $(ls * >& /dev/null)
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+ then
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+ if ${force_run_from_scratch}
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+ then
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+ rm -fr ${run_dir}/*
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|
|
+ 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
|
|
|
+
|
|
|
+ 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
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** 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}/${leg_start_date_yyyymmdd}/ICMGGECE3INIT \
|
|
|
+ ICMGG${exp_name}INIT
|
|
|
+ ln -s \
|
|
|
+ ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMSHECE3INIT \
|
|
|
+ ICMSH${exp_name}INIT
|
|
|
+ # Other stuff
|
|
|
+ ln -s ${ini_data_dir}/ifs/rtables/* .
|
|
|
+
|
|
|
+ # Output control (ppt files)
|
|
|
+ mkdir postins
|
|
|
+ cp ${ctrl_file_dir}/ppt* postins/
|
|
|
+ f_min=$(( ifs_output_freq * ifs_time_step_sec / 60 ))
|
|
|
+ for t in $(seq $f_min $f_min 1439)
|
|
|
+ do
|
|
|
+ hh=$(printf %02d $((t/60)) )
|
|
|
+ mm=$(printf %02d $((t%60)) )
|
|
|
+ ln -s pptdddddd0000 postins/pptdddddd$hh$mm
|
|
|
+ done
|
|
|
+ /bin/ls -1 postins/* > dirlist
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for NEMO (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ # 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
|
|
|
+ do
|
|
|
+ [ -f ${ini_data_dir}/nemo/initial/${nem_grid}/$f ] && ln -s ${ini_data_dir}/nemo/initial/${nem_grid}/$f
|
|
|
+ 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 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
|
|
|
+
|
|
|
+
|
|
|
+ # 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 ${ctrl_file_dir}/file_def_nemo-lim3.xml file_def_nemo-lim.xml
|
|
|
+ ln -s ${ctrl_file_dir}/file_def_nemo-opa.xml
|
|
|
+ ln -s ${ctrl_file_dir}/file_def_nemo-pisces.xml
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for the Runoff mapper (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ ln -s ${ini_data_dir}/runoff-mapper/runoff_maps.nc
|
|
|
+
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+ # *** Files needed for OASIS (linked)
|
|
|
+ # ---------------------------------------------------------------------
|
|
|
+
|
|
|
+ oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-ORCA${nem_res_hor}
|
|
|
+
|
|
|
+ # Name table file
|
|
|
+ ln -s ${ini_data_dir}/oasis/cf_name_table.txt
|
|
|
+
|
|
|
+ # Grid definition files
|
|
|
+ ln -s ${oas_grid_dir}/areas.nc
|
|
|
+ ln -s ${oas_grid_dir}/grids.nc
|
|
|
+ ln -s ${oas_grid_dir}/masks.nc
|
|
|
+
|
|
|
+ # 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
|
|
|
+
|
|
|
+ case ${nem_res_hor} in
|
|
|
+ 1) oas_ogrd=O1t0
|
|
|
+ ;;
|
|
|
+ 025) oas_ogrd=Ot25
|
|
|
+ ;;
|
|
|
+ *) error "Unsupported horizontal resolution (NEMO): ${nem_res_hor}"
|
|
|
+ ;;
|
|
|
+ esac
|
|
|
+
|
|
|
+ if ${oas_link_weights}
|
|
|
+ then
|
|
|
+ for f in ${oas_grid_dir}/rmp_????_to_????_GAUSWGT.nc
|
|
|
+ do
|
|
|
+ ln -s $f
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ for f in ${oas_rst_files}
|
|
|
+ do
|
|
|
+ cp ${oas_grid_dir}/rst/$f .
|
|
|
+ done
|
|
|
+
|
|
|
+ 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}.nc
|
|
|
+
|
|
|
+ fi # ! $leg_is_restart
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Remove land grid-points
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $(has_config nemo:elpin)
|
|
|
+ then
|
|
|
+ jpns=($(${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]}
|
|
|
+ else
|
|
|
+ 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
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # IFS, NEMO, LIM namelist and OASIS namcouple files
|
|
|
+ . ${ctrl_file_dir}/namelist.ifs.sh > fort.4
|
|
|
+ . ${ctrl_file_dir}/namelist.nemo.ref.sh > namelist_ref
|
|
|
+ . ${ctrl_file_dir}/namelist.nemo-${nem_grid}-coupled.cfg.sh > namelist_cfg
|
|
|
+ . ${ctrl_file_dir}/namelist.lim3.ref.sh > namelist_ice_ref
|
|
|
+ . ${ctrl_file_dir}/namelist.lim3-${nem_grid}.cfg.sh > namelist_ice_cfg
|
|
|
+
|
|
|
+ . ${ctrl_file_dir}/namelist.runoffmapper.sh > namelist.runoffmapper
|
|
|
+
|
|
|
+ . ${ctrl_file_dir}/namcouple.sh > namcouple
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Create ICMCL file with vegetation fields
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ 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" )
|
|
|
+ # Vegetation from an off-line LPJG run forced with ERA20C (v16)
|
|
|
+
|
|
|
+ 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
|
|
|
+ if [ $ifs_cmip_fixyear -le 0 ]
|
|
|
+ then
|
|
|
+ cat ${ini_data_dir}/ifs/${ifs_grid}/icmcl_v16/icmcl_$yr.grb >> ICMCL${exp_name}INIT
|
|
|
+ else
|
|
|
+ # Fixed year forcing, requires cdo!
|
|
|
+ # 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_v16/icmcl_${ifs_cmip_fixyear}.grb ${tempfile}
|
|
|
+ cat ${tempfile} >> ICMCL${exp_name}INIT
|
|
|
+ fi
|
|
|
+ done
|
|
|
+ ;;
|
|
|
+ * )
|
|
|
+ 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 $leg_is_restart
|
|
|
+ then
|
|
|
+ ns=$(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
|
|
|
+ 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
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Remove some OASIS files of the previous leg
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ rm -f anaisout_*
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Start the run
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ export DR_HOOK_IGNORE_SIGNALS='-1'
|
|
|
+
|
|
|
+ export CPLNG='active'
|
|
|
+
|
|
|
+ # Use the launch function from the platform configuration file
|
|
|
+ t1=$(date +%s)
|
|
|
+ launch \
|
|
|
+ ${xio_numproc} ${xio_exe_file} -- \
|
|
|
+ ${nem_numproc} ${nem_exe_file} -- \
|
|
|
+ ${rnf_numproc} ${rnf_exe_file} -- \
|
|
|
+ ${ifs_numproc} ${ifs_exe_file} -v ecmwf -e ${exp_name}
|
|
|
+ t2=$(date +%s)
|
|
|
+
|
|
|
+ tr=$(date -d "0 -$t1 sec + $t2 sec" +%T)
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Check for signs of success
|
|
|
+ # Note the tests provide no guarantee that things went fine! They are
|
|
|
+ # just based on the IFS and NEMO log files. More tests (e.g. checking
|
|
|
+ # restart files) could be implemented.
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Checking for IFS success
|
|
|
+ if [ -f ifs.stat ]
|
|
|
+ then
|
|
|
+ if [ "$(awk 'END{print $3}' ifs.stat)" == "CNT0" ]
|
|
|
+ then
|
|
|
+ info "Leg successfully completed according to IFS log file 'ifs.stat'."
|
|
|
+ else
|
|
|
+ error "Leg not completed according to IFS log file 'ifs.stat'."
|
|
|
+ fi
|
|
|
+ else
|
|
|
+ error "IFS log file 'ifs.stat' not found after run."
|
|
|
+ fi
|
|
|
+
|
|
|
+ # Check for NEMO success
|
|
|
+ if [ -f ocean.output ]
|
|
|
+ then
|
|
|
+ if [ "$(awk '/New day/{d=$10}END{print d}' ocean.output)" == "$(date -d "${leg_end_date} - 1 day" +%Y/%m/%d)" ]
|
|
|
+ then
|
|
|
+ info "Leg successfully completed according to NEMO log file 'ocean.output'."
|
|
|
+ else
|
|
|
+ error "Leg not completed according to NEMO log file 'ocean.output'."
|
|
|
+ fi
|
|
|
+
|
|
|
+ else
|
|
|
+ error "NEMO log file 'ocean.output' not found after run."
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move IFS output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${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} ${outdir}
|
|
|
+ fi
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Move NEMO output files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${archive_dir}/output/nemo/$(printf %03d $((leg_number)))"
|
|
|
+ mkdir -p ${outdir}
|
|
|
+
|
|
|
+ for f in ${exp_name}_??_????????_????????_*.nc ; do mv $f $outdir/ ; done
|
|
|
+ #for v in grid_U grid_V grid_W grid_T icemod SBC scalar SBC_scalar
|
|
|
+ #do
|
|
|
+ # for f in ${exp_name}_??_????????_????????_${v}.nc
|
|
|
+ # do
|
|
|
+ # test -f $f && mv $f $outdir/
|
|
|
+ # done
|
|
|
+ #done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** 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 NEMO restart files to archive directory
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ if $leg_is_restart
|
|
|
+ then
|
|
|
+ outdir="${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 ${outdir}
|
|
|
+ done
|
|
|
+ fi
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Copy OASIS restart files to archive directory
|
|
|
+ # NOTE: These files are copied and not moved as they are used in the
|
|
|
+ # next leg!
|
|
|
+ # Note also that the OASIS restart files present at the end of
|
|
|
+ # the leg correspond to the start of the next leg!
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ outdir="${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 \
|
|
|
+ nout.000000 debug.??.?????? A*_??.nc O*_??.nc
|
|
|
+ do
|
|
|
+ test -f ${f} && mv ${f} ${outdir}
|
|
|
+ done
|
|
|
+
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+ # *** Write the restart control file
|
|
|
+ # -------------------------------------------------------------------------
|
|
|
+
|
|
|
+ # Compute CPMIP performance
|
|
|
+ sypd="$(cpmip_sypd $leg_length_sec $(($t2 - $t1)))"
|
|
|
+ chpsy="$(cpmip_chpsy $leg_length_sec $(($t2 - $t1)) $(($ifs_numproc + $nem_numproc + $rnf_numproc + $xio_numproc)))"
|
|
|
+
|
|
|
+ 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
|
