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Commit 25bcbb4b authored by Aiko Voigt's avatar Aiko Voigt
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Adds icon-esm runscript to mimick ngc4008

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#! /bin/ksh
#=============================================================================
#SBATCH --account=p72044
#SBATCH --partition=skylake_0096
#SBATCH --qos=skylake_0096
###SBATCH --qos=skylake_0096_devel
#SBATCH --job-name=iesm-ngc4008
#SBATCH --nodes=3
###SBATCH --nodes=1
#SBATCH --ntasks-per-node=48
#SBATCH --ntasks-per-core=1
#SBATCH --output=/gpfs/data/fs72044/avoigt_teach/climlab_s2025/msc-climate-modeling-lab-s2025-code-4-students/runs/iesm-ngc4008/LOG.exp.iesm-ngc4008.run.%j.o
#SBATCH --error=/gpfs/data/fs72044/avoigt_teach/climlab_s2025/msc-climate-modeling-lab-s2025-code-4-students/runs/iesm-ngc4008/LOG.exp.iesm-ngc4008.run.%j.o
#SBATCH --exclusive
#SBATCH --time=02:30:00
###SBATCH --time=00:05:00
#SBATCH --mail-user=aiko.voigt@univie.ac.at
#SBATCH --mail-type=BEGIN,END,FAIL
set -x # debugging command: enables a mode of the shell where all executed commands are printed to the terminal
ulimit -s unlimited # unsets limits for RAM
# MPI variables
# -------------
no_of_nodes=3
mpi_procs_pernode=48
((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
# manual fix for mpi pinning with intel mpirun on vsc
# see https://wiki.vsc.ac.at/doku.php?id=doku:vsc5quickstart#intel_mpi
export I_MPI_PIN_RESPECT_CPUSET=0
#
# blocking length
# ---------------
nproma=16
#=============================================================================
# Input variables:
# SIMULATION NAME
EXP=iesm-ngc4008
ICONFOLDER=/gpfs/data/fs72044/avoigt_teach/climlab_s2025/icon-esm-univie # DIRECTORY OF ICON MODEL CODE
RUNSCRIPTDIR=/gpfs/data/fs72044/avoigt_teach/climlab_s2025/msc-climate-modeling-lab-s2025-code-4-students/runs/iesm-ngc4008/
basedir=$ICONFOLDER # icon base directory
. ${ICONFOLDER}/run/add_run_routines
# experiment directory, with plenty of space, create if new
EXPDIR=/gpfs/data/fs72044/avoigt_teach/experiments/s2025/${EXP}
if [ ! -d ${EXPDIR} ] ; then
mkdir -p ${EXPDIR}
fi
#
ls -ld ${EXPDIR}
if [ ! -d ${EXPDIR} ] ; then
mkdir ${EXPDIR}
fi
ls -ld ${EXPDIR}
cd $EXPDIR
#=================================================================================
#-----------------------------------------------------------------------------
# global timing
# NOTE: WE NEED TO START IN YEAR 2021 AS SST AND SIC START IN 2020, AND THE MODEL LOOKS 1 YEAR BACKWARD FOR THESE FIELDS
initial_date="2021-01-01"
final_date="2050-01-01"
start_date=$initial_date
end_date=$final_date
y0=${start_date%%-*}
yN=${end_date%%-*}
# restart intervals
restart_interval="P2Y"
checkpoint_interval="P1Y"
file_interval="P1Y"
############################################################
#
# NO FURTHER CHANGES TO THE DIRECTORIES AND SIMULATION NAME
# SHOULD BE NEEDED BELOW THIS LINE
#
############################################################
#-----------------------------------------------------------------------------
# Provide input files
# $Id: format.tmpl 9264 2021-06-21 21:24:57Z m221078 $
#
# [files]
# [files.atmosphere]
data_dir=/gpfs/data/fs72044/avoigt_teach/ICON-inputdata/amip-VSC4
data_dir_ngc4008=/gpfs/data/fs72044/avoigt_teach/ICON-inputdata/ngc4008_for_iconesm
# [files.atmosphere.mapped]
grid_dir=$data_dir/grid
ln -sfv $grid_dir/icon_grid_0013_R02B04_G.nc icon_grid_G.nc
# [files.atmosphere.mapped.initial]
initial_dir=$data_dir/initial_condition
ln -sfv $initial_dir/ifs2icon_1979010100_R02B04_G.nc ifs2icon.nc
# [files.atmosphere.mapped.ozone]
ozone_dir=$data_dir_ngc4008/ozone
for((yr = y0 + -1; yr <= yN + 1; ++yr))
do
ln -sfv $ozone_dir/bc_ozone_ssp370_${yr}.remapcon_grid_0013_R02B04_G.nc bc_ozone_${yr}.nc
done
# [files.atmosphere.mapped.ocean_surface]
ocean_surface_dir=$data_dir_ngc4008/sst_and_seaice
ln -sfv $ocean_surface_dir/siconcbcs.ngc4008.2020-2050.r2b4.nc bc_sic.nc
ln -sfv $ocean_surface_dir/tosbcs.ngc4008.2020-2050.r2b4.nc bc_sst.nc
# [files.atmosphere.mapped.aerosols]
aerosols_dir=$data_dir/aerosol
ln -sfv $aerosols_dir/bc_aeropt_kinne_lw_b16_coa.nc .
ln -sfv $aerosols_dir/bc_aeropt_kinne_sw_b14_coa.nc .
ln -sfv $aerosols_dir/bc_aeropt_kinne_sw_b14_fin_1850.nc bc_aeropt_kinne_sw_b14_fin.nc
# [files.atmosphere.model]
model_dir=/gpfs/data/fs72044/avoigt_teach/climlab_s2025/icon-esm-univie
# [files.atmosphere.model.data]
ln -sfv $model_dir/data/lsdata.nc .
ln -sfv $model_dir/data/ECHAM6_CldOptProps.nc .
cp $data_dir_ngc4008/aerosols/MACv2.0-SP-merged-historical-and-SSP3-70_v1.nc MACv2.0-SP_v1.nc
# [files.atmosphere.model.run]
run_dir=$model_dir/run
cp -fv $run_dir/dict.iconam.mpim dict.txt
# [files.atmosphere.independent]
ln -sfv $data_dir_ngc4008/greenhouse_gases/greenhouse_ssp370.nc bc_greenhouse_gases.nc
# [files.atmosphere.independent.volcano_aerosols]
for((yr = y0 + -1; yr <= yN + 1; ++yr))
do
label=${yr}
((yr >= 2015)) && label=2014
volcano_aerosols_dir=$data_dir/aerosol
ln -sfv $volcano_aerosols_dir/bc_aeropt_cmip6_volc_lw_b16_sw_b14_${label}.nc \
bc_aeropt_cmip6_volc_lw_b16_sw_b14_${yr}.nc
done # offsets
# [files.atmosphere.independent.solar_irradiance]
solar_irradiance_dir=$data_dir/solar_radiation
ln -sfv $solar_irradiance_dir/swflux_14band_cmip6_1850-2299-v3.2.nc \
bc_solar_irradiance_sw_b14.nc
# [files.land]
land_dir=$data_dir/land
# [files.land.mapped]
ln -sfv $land_dir/ic_land_soil_1976.nc ic_land_soil.nc
ln -sfv $land_dir/bc_land_frac_11pfts_1976.nc bc_land_frac.nc
ln -sfv $land_dir/bc_land_phys_1976.nc bc_land_phys.nc
ln -sfv $land_dir/bc_land_soil_1976.nc bc_land_soil.nc
ln -sfv $land_dir/bc_land_sso_1976.nc bc_land_sso.nc
# [files.land.hydro]
hydro_dir=$land_dir
# preliminary test version
ln -sfv $hydro_dir/hdpara_r2b4_0013_0035_v3.nc bc_land_hd.nc
# [files.land.model]
model_dir=$basedir/externals/jsbach/data
ln -sfv $model_dir/lctlib_nlct21.def .
#-----------------------------------------------------------------------------
# automatic restart setup
# set some default values and derive some run parameteres
restart=${restart:=".false."}
restartSemaphoreFilename='isRestartRun.sem'
#AUTOMATIC_RESTART_SETUP:
if [ -f ${restartSemaphoreFilename} ]; then
restart=.true.
# do not delete switch-file, to enable restart after unintended abort
#[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
fi
#END AUTOMATIC_RESTART_SETUP
# wait 5min to let GPFS finish the write operations
if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
sleep 10;
fi
fi
#
# create ICON master, coupling and model namelists
# ------------------------------------------------
# For a complete list see Namelist_overview and Namelist_overview.pdf
#
cat > icon_master.namelist << EOF
&master_nml
lrestart = ${restart}
/
&master_time_control_nml
calendar = 'proleptic gregorian'
checkpointtimeintval = '$checkpoint_interval'
restarttimeintval = '$restart_interval'
experimentstartdate = '2021-01-01' ! TODO: hack to reproduce result, NOTE: WE NEED TO START IN YEAR 2021 AS SST AND SIC START IN 2020, AND THE MODEL LOOKS 1 YEAR BACKWARD FOR THESE FIELDS
experimentstopdate = '$final_date'
/
&master_model_nml ! 'atmo'
model_name = 'atmo'
model_namelist_filename = 'NAMELIST_atm'
model_type = 1
/
&jsb_control_nml
is_standalone = .false.
/
&jsb_model_nml
model_id = 1
model_name = 'JSBACH'
model_shortname = 'jsb'
model_description = 'JSBACH land surface model'
model_namelist_filename = 'NAMELIST_lnd'
/
EOF
#-----------------------------------------------------------------------------
# II. ATMOSPHERE and LAND
#-----------------------------------------------------------------------------
#
# atmosphere namelist
# -------------------
cat > NAMELIST_atm << EOF
&parallel_nml
nproma = $nproma
num_io_procs = 0
num_prefetch_proc = 0
pio_type = 1 !1=default, assync I/O, 2=experimental CDI, 0=nothing?
/
&grid_nml
dynamics_grid_filename = 'icon_grid_G.nc'
/
&run_nml
num_lev = 47 ! number of full levels
modeltimestep = 'PT15M'
ltestcase = .false. ! run testcase
ldynamics = .true. ! dynamics
ltransport = .true. ! transport
iforcing = 2 ! 0: none, 1: HS, 2: ECHAM, 3: NWP
output = 'nml'
msg_level = 8 ! level of details report during integration
restart_filename = 'AMIP-VSC4_restart_atm_<rsttime>.nc'
activate_sync_timers = .true.
/
&extpar_nml
itopo = 1 ! 1: read topography from the grid file
itype_lwemiss = 0
/
&initicon_nml
init_mode = 2 ! 2: initialize from IFS analysis
ifs2icon_filename = 'ifs2icon.nc'
/
&nonhydrostatic_nml
ndyn_substeps = 8 ! dtime/dt_dyn
damp_height = 50000. ! [m]
rayleigh_coeff = 0.1000 ! set to 0.1001 for rerun with little change
vwind_offctr = 0.2
divdamp_fac = 0.004
/
&interpol_nml
rbf_scale_mode_ll = 1
/
&sleve_nml
min_lay_thckn = 40. ! [m]
top_height = 83000. ! [m]
stretch_fac = 0.9
decay_scale_1 = 4000. ! [m]
decay_scale_2 = 2500. ! [m]
decay_exp = 1.2
flat_height = 16000. ! [m]
/
&diffusion_nml
/
&transport_nml
ihadv_tracer = 52, 2, 2
itype_hlimit = 3, 4, 4
ivadv_tracer = 3, 3, 3
tracer_names = 'hus', 'clw', 'cli'
/
&echam_phy_nml
! domain 1
! atmospheric physics ("" = never)
echam_phy_config(1)%dt_rad = 'PT90M'
echam_phy_config(1)%dt_vdf = 'PT15M'
echam_phy_config(1)%dt_cnv = 'PT15M'
echam_phy_config(1)%dt_cld = 'PT15M'
echam_phy_config(1)%dt_gwd = 'PT15M'
echam_phy_config(1)%dt_sso = 'PT15M'
! atmospheric chemistry ("" = never)
echam_phy_config(1)%dt_mox = 'PT15M'
! surface (true or false)
echam_phy_config(1)%ljsb = .true.
echam_phy_config(1)%lamip = .true.
echam_phy_config(1)%lice = .true.
echam_phy_config(1)%lmlo = .false.
echam_phy_config(1)%llake = .true.
/
&echam_rad_nml
! domain 1
echam_rad_config(1)%isolrad = 1
echam_rad_config(1)%irad_h2o = 1
echam_rad_config(1)%irad_co2 = 4
echam_rad_config(1)%irad_ch4 = 4
echam_rad_config(1)%irad_n2o = 4
echam_rad_config(1)%irad_o3 = 8
echam_rad_config(1)%irad_o2 = 2
echam_rad_config(1)%irad_cfc11 = 4
echam_rad_config(1)%irad_cfc12 = 4
echam_rad_config(1)%irad_aero = 18
/
&echam_gwd_nml
/
&echam_sso_nml
/
&echam_vdf_nml
/
&echam_cnv_nml
/
&echam_cld_nml
/
&echam_cov_nml
/
&ccycle_nml
/
&sea_ice_nml
/
! Parameters for all output files
! -------------------------------
&io_nml
output_nml_dict = 'dict.txt'
netcdf_dict = 'dict.txt'
itype_pres_msl = 4
! restart_file_type = 5
! restart_write_mode = 'joint procs multifile' ! not useful in r2b4 setup
! lnetcdf_flt64_output = .true. ! 64 bit output in all files
! lkeep_in_sync = .true. ! sync after each timestep
write_initial_state = .false.
/
&dbg_index_nml
idbg_mxmn = 0 ! initialize MIN/MAX debug output
idbg_val = 0 ! initialize one cell debug output
idbg_slev = 1 ! initialize start level for debug output
idbg_elev = 2 ! initialize end level for debug output
dbg_lat_in = 30.0 ! latitude location of one cell debug output
dbg_lon_in = -30.0 ! longitude location of one cell debug output
str_mod_tst = 'InterFaceOce' ! define modules to print out in debug mode
/
! Define output files
! -------------------
!
! 3-dimensional files include 'ps' and 'pfull' to allow the vertical
! interpolation to pressure levels by cdo ap2pl.
/
! Standard AMIP output...
&output_nml ! 'atm_3d'
output_filename = '${EXP}_atm_3d'
filename_format = '<output_filename>_<levtype_l>_<datetime2>'
filetype = 5
remap = 0
operation = 'mean'
output_grid = .TRUE.
output_start = '${initial_date}'
output_end = '${final_date}'
output_interval = 'P1M'
file_interval = '$file_interval' !'P10YT1S'
include_last = .false.
ml_varlist = 'zg', 'ps', 'pfull', 'rho', 'ta', 'ua', 'va', 'wap', 'hus',
'clw', 'cli', 'hur', 'cl'
/
! Standard AMIP output...
&output_nml ! 'atm_2d'
output_filename = '${EXP}_atm_2d'
filename_format = '<output_filename>_<levtype_l>_<datetime2>'
filetype = 5
remap = 0
operation = 'mean'
output_grid = .TRUE.
output_start = '${initial_date}'
output_end = '${final_date}'
output_interval = 'P1M'
file_interval = '$file_interval' !'P10YT1S'
include_last = .false.
ml_varlist = 'orog', 'ps', 'psl', 'cosmu0', 'rsdt', 'rsut', 'rsutcs',
'rlut', 'rlutcs', 'rsds', 'rsdscs', 'rlds', 'rldscs', 'rsus',
'rsuscs', 'rlus', 'ts', 'sic', 'sit', 'albedo', 'clt', 'prlr',
'prls', 'prcr', 'prcs', 'pr', 'prw', 'cllvi', 'clivi', 'hfls',
'hfss', 'evspsbl', 'tauu', 'tauv', 'tauu_sso', 'tauv_sso',
'diss_sso', 'sfcwind', 'uas', 'vas', 'tas', 'dew2', 'ptp'
/
! As an example, included output for rsdt on lat-lon grid for every time step for January 1979
&output_nml ! 'rsdt_latlon_everytimestep'
output_filename = '${EXP}_rsdt_latlon_everytimestep'
filename_format = '<output_filename>_<levtype_l>_<datetime2>'
filetype = 5
remap = 1 ! 1: latlon, 0: native grid
reg_lat_def = -90.0,0.5,90.0
reg_lon_def = -180.0,0.5,180.0
operation = 'false'
output_grid = .TRUE.
output_start = '1979-01-01'
output_end = '1979-02-01'
output_interval = 'PT15M'
file_interval = 'P1D'
include_last = .false.
ml_varlist = 'rsdt'
/
EOF
# jsbach namelist
# ---------------
cat > NAMELIST_lnd << EOF
&jsb_model_nml
usecase = 'jsbach_pfts'
use_lakes = .true.
/
&jsb_seb_nml
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_rad_nml
use_alb_veg_simple = .false. ! if jsbach_lite
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_turb_nml
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_sse_nml
l_heat_cap_map = .false.
l_heat_cond_map = .false.
l_heat_cap_dyn = .false.
l_heat_cond_dyn = .false.
l_snow = .true.
l_dynsnow = .true.
l_freeze = .true.
l_supercool = .true.
bc_filename = 'bc_land_soil.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_hydro_nml
l_organic = .false.
bc_filename = 'bc_land_soil.nc'
ic_filename = 'ic_land_soil.nc'
bc_sso_filename = 'bc_land_sso.nc'
/
&jsb_assimi_nml
active = .true. ! if jsbach_pfts
/
&jsb_pheno_nml
scheme = 'logrop' ! 'climatology' if jsbach_lite
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_carbon_nml
active = .true.
bc_filename = 'bc_land_carbon.nc'
ic_filename = 'ic_land_carbon.nc'
read_cpools = .false.
/
&jsb_fuel_nml
active = .true.
fuel_algorithm = 1
/
&jsb_disturb_nml
active = .false.
ic_filename = 'ic_land_soil.nc'
bc_filename = 'bc_land_phys.nc'
fire_algorithm = 1
windbreak_algorithm = 1
lburn_pasture = .false.
/
EOF
## setup for status check & restart
final_status_file=${EXPDIR}/${EXP}.final_status
## Copy icon executable to working directory
cp -p $ICONFOLDER/bin/icon ./icon.exe
##
## Start model
date
ulimit -s unlimited
ldd icon.exe
START="/gpfs/opt/sw/skylake/spack-0.19.0/opt/spack/linux-almalinux8-skylake_avx512/intel-2021.7.1/intel-oneapi-mpi-2021.7.1-fzg6q4xcj7efjmce3cuqa2b7cum5d3po/mpi/2021.7.1/bin/mpiexec -n $mpi_total_procs"
MODEL=${EXPDIR}/icon.exe
rm -f finish.status
${START} ${MODEL}
if [ -r finish.status ] ; then
check_final_status 0 "${START} ${MODEL}"
else
check_final_status -1 "${START} ${MODEL}"
fi
#-----------------------------------------------------------------------------
finish_status=`cat finish.status`
echo $finish_status
#-----------------------------------------------------------------------------
namelist_list=""
#-----------------------------------------------------------------------------
# check if we have to restart, ie resubmit
# Note: this is a different mechanism from checking the restart
if [ $finish_status = "RESTART" ]; then
echo "restart next experiment..."
this_script="${RUNSCRIPTDIR}/exp.${EXP}.run"
echo 'this_script: ' "$this_script"
# note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
touch ${restartSemaphoreFilename}
cd ${RUNSCRIPTDIR}
sbatch exp.${EXP}.run
else
[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
fi
#-----------------------------------------------------------------------------
cd ${RUNSCRIPTDIR}
#-----------------------------------------------------------------------------
#
echo "============================"
echo "Script run successfully: ${finish_status}"
echo "============================"
#-----------------------------------------------------------------------------
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