#! /usr/bin/bash #----------------------------------------------------------------------------- #SBATCH --account=bm1102 #SBATCH --job-name=exp.nib3505_r2b6.run #SBATCH --partition=compute #SBATCH --nodes=64 #SBATCH --chdir=/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/run #SBATCH --output=/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/run/LOG.exp.nib3505_r2b6.run.%j.o #SBATCH --time=03:00:00 #----------------------------------------------------------------------------- set +x set -o pipefail ulimit -s unlimited #----------------------------------------------------------------------------- # handle job cancellation. Usually slurm return exit code 0 in that case catchCancel() { echo "Job was canceled, setting non-zero exit code." exit 1 } trap catchCancel SIGTERM SIGINT SIGKILL #----------------------------------------------------------------------------- # ICON run script: # !ATTENTION! Do not change the format of the following lines. # They are evaluated by checksuite scripts. # created by ./make_target_runscript # target machine is bull_milan # target use_compiler is intel # with_mpi=yes # with_openmp=yes # memory_model=default # submit with sbatch # builder=bull_milan_intel with_openmp=yes #----------------------------------------------------------------------------- # # OpenMP environment variables # ---------------------------- export OMP_NUM_THREADS=4 export ICON_THREADS=4 export OMP_SCHEDULE=dynamic,1 export OMP_DYNAMIC="false" export OMP_STACKSIZE=200M # # MPI variables # ------------- proc0_shift=0 num_io_procs=1 : ${no_of_nodes:=${SLURM_JOB_NUM_NODES:=1}} ${mpi_procs_pernode:=$(( 128 * 1 / OMP_NUM_THREADS))} export no_of_nodes export mpi_procs_pernode ((mpi_total_procs=no_of_nodes * mpi_procs_pernode)) export no_of_nodes mpi_procs_pernode mpi_total_procs # # blocking length # --------------- : ${nproma:=32} ${nproma_sub:=32} ${nblocks_c:=0} export nproma nproma_sub nblocks_c # # Ecrad solver (0 for CPU/vector, 2 for GPU) # ------------------------------------------ radiation_ecrad_isolver=0 # #----------------------------------------------------------------------------- # load local setting, if existing # ------------------------------- if [ -a /home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/setting ] then echo "Load Setting" . /home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/setting fi # environment variables for the experiment and the target system # -------------------------------------------------------------- export EXPNAME="nib3505_r2b6" export MALLOC_TRIM_THRESHOLD_="-1" export SLURM_DIST_PLANESIZE="32" export KMP_AFFINITY="granularity=fine,scatter" export KMP_LIBRARY="turnaround" export MALLOC_TRIM_THRESHOLD_="-1" export MKL_DEBUG_CPU_TYPE="5" export MKL_ENABLE_INSTRUCTIONS="AVX2" export OMPI_MCA_btl="self" export OMPI_MCA_coll="^ml,hcoll" export OMPI_MCA_io="romio321" export OMPI_MCA_osc="ucx" export OMPI_MCA_pml="ucx" export UCX_HANDLE_ERRORS="bt" export UCX_TLS="shm,dc_mlx5,dc_x,self" export UCX_UNIFIED_MODE="y" # load profile # ------------ if [[ -a "/etc/profile" ]] then . /etc/profile fi #----------------------------------------------------------------------------- # load modules loadmodule="/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/etc/Modules/icon-levante" module load $loadmodule module list #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- # directories with absolute paths # ------------------------------- thisdir=$(pwd) export basedir="/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim" # experiments_dir can be predefined in a machine specific run_target_* header experiments_dir="${experiments_dir:=${basedir}/experiments}" export icon_data_rootFolder="/pool/data/ICON" export testingFolder_prefix="~/testingFolder" # how to start the icon model # --------------------------- export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --distribution=plane --hint=nomultithread --ntasks=$((no_of_nodes * mpi_procs_pernode)) --ntasks-per-node=${mpi_procs_pernode} --cpus-per-task=${OMP_NUM_THREADS}" export MODEL="/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/bin/icon" set | grep SLURM # how to submit the next job # -------------------------- submit="sbatch" job_name="exp.nib3505_r2b6.run" # cdo for post-processing # ----------------------- cdo="cdo" cdo_diff="cdo diffn" # export the python interpreter export PYTHON="/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/bin/python3" export PYTHONPATH=":/home/m/m300602/work/proj_vmix/icon/icon_35_zstar_tuning/icon-mpim/externals/mtime/build/python::/home/m/m300602/python/pytbx/mypy" # define script functions used in the experiment run script # --------------------------------------------------------- . ${basedir}/run/add_run_routines #----------------------------------------------------------------------------- ulimit -c 0 #!/bin/bash # ICON # # ------------------------------------------ # Copyright (C) 2004-2025, DWD, MPI-M, DKRZ, KIT, ETH, MeteoSwiss # Contact information: icon-model.org # See AUTHORS.TXT for a list of authors # See LICENSES/ for license information # SPDX-License-Identifier: BSD-3-Clause # ------------------------------------------ #============================================================================= #----------------------------------------------------------------------------- # the namelist filename ocean_namelist=NAMELIST_${EXPNAME} #----------------------------------------------------------------------------- # global timing start_date="2000-01-01T00:00:00Z" end_date="2500-01-01T00:00:00Z" # 201 years to ensure write of restart at end # restart=".true." #----------------------------------------------------------------------------- GRID=R2B6 LEV=L64 VERT_COR=0 DYN=1 if [ ${GRID} = R2B4 ] ; then grid_name="icon_grid_0036_R02B04_O" ocean_grids="R2B4_ocean-grid.nc" modelTimeStep="PT1H" restart_interval="P50Y" checkpoint_interval="P50Y" # ocean_GentMcWilliamsRedi_nml GMRedi_configuration=1 k_tracer_GM_kappa_parameter=1000.0 k_tracer_isoneutral_parameter=1000.0 elif [ ${GRID} == R2B6 ] ; then grid_name="OceanOnly_Global_IcosSymmetric_0039km_rotatedZ37d_BlackSea_Greenland_modified_srtm30_1min" ocean_grids="R2B6_ocean-grid.nc" modelTimeStep="PT1800S" restart_interval="P10Y" checkpoint_interval="P10Y" #ocean_GentMcWilliamsRedi_nml GMRedi_configuration=1 k_tracer_GM_kappa_parameter=400.0 k_tracer_isoneutral_parameter=400.0 elif [ ${GRID} == R2B7 ] ; then grid_name="OceanOnly_icon_grid_0023_R02B07_G_modified_srtm30_1min" ocean_grids="R2B7_ocean-grid.nc" modelTimeStep="PT1200S" restart_interval="P5Y" checkpoint_interval="P5Y" #ocean_GentMcWilliamsRedi_nml GMRedi_configuration=1 k_tracer_GM_kappa_parameter=400.0 k_tracer_isoneutral_parameter=400.0 elif [ ${GRID} == R2B8 ] ; then grid_name="OceanOnly_Global_IcosSymmetric_0010km_rotatedZ37d_modified_srtm30_1min" ocean_grids="R2B8_ocean-grid.nc" modelTimeStep="PT600S" restart_interval="P3M" checkpoint_interval="P3M" #ocean_GentMcWilliamsRedi_nml GMRedi_configuration=0 k_tracer_GM_kappa_parameter=0.0 k_tracer_isoneutral_parameter=0.0 elif [ ${GRID} == R2B9 ] ; then grid_name="OceanOnly_IcosSymmetric_4932m_rotatedZ37d_modified_srtm30_1min" ocean_grids="R2B9_ocean-grid.nc" modelTimeStep="PT300S" restart_interval="P1M" checkpoint_interval="P1M" #ocean_GentMcWilliamsRedi_nml GMRedi_configuration=0 k_tracer_GM_kappa_parameter=0.0 k_tracer_isoneutral_parameter=0.0 elif [ ${GRID} == R2B10 ] ; then grid_name="OceanOnly_Global_IcosSymmetric_2466m_rotatedZ37d_GEBCO_2023" ocean_grids="R2B10_ocean-grid.nc" modelTimeStep="PT120S" restart_interval="P1M" checkpoint_interval="P1M" #ocean_GentMcWilliamsRedi_nml GMRedi_configuration=0 k_tracer_GM_kappa_parameter=0.0 k_tracer_isoneutral_parameter=0.0 fi if [ ${LEV} == L40 ] ; then n_zlev=40 dzlev_m="12.,10.,10.,10.,10.,10.,13.,15.,20.,25.,30.,35.,40.,45.,50.,55.,60.,70.,80.,90., 100.,110.,120.,130.,140.,150.,170.,180.,190.,200.,220.,250.,270.,300.,350.,400., 450.,500.,500.,600." levidx_100m=9 levidx_200m=12 levidx_2000m=30 minVerticalLevels=2 elif [ ${LEV} == L64 ] ; then n_zlev=64 dzlev_m="12.,10.,10.,10.,10.,10.,10.,10.,10.,10.,11.,12.,13.,14.,15.,16.,17.,18.,20.,22., 24.,26.,28.,30.,32.,35.,38.,41.,45.,49.,53.,58.,62.,66.,71.,75.,80.,85.,91.,97., 104.,111.,118.,125.,132.,138.,145.,152.,160.,167.,175.,182.,188.,195.,201.,208., 213.,219.,224.,230.,235.,241.,250.,260." levidx_100m=10 levidx_200m=17 levidx_2000m=46 minVerticalLevels=2 elif [ ${LEV} == L72 ] ; then n_zlev=72 dzlev_m="2.0,2.2,2.5,2.8,3.1,3.5,3.9,4.4,4.9,5.4,5.9,6.4,7.1,7.7,8.4,9.2,10.1,11.0, 12.0,13.2,14.4,15.7,17.1,18.7,20.4,22.3,24.3,26.5,28.9,31.5,34.3,37.3,40.6, 43.1,45.3,46.8,48.4,50.0,51.7,53.4,55.2,57.0,58.9,60.8,62.9,66.6,72.6,80.6, 90.6,100.2,110.0,120.3,128.7,137.4,146.4,155.7,165.2,174.8,184.4,194.1,203.6, 212.9,221.9,230.5,238.5,245.9,252.4,258.1,262.8,266.4,268.9,270.1" levidx_100m=15 levidx_200m=25 levidx_2000m=55 minVerticalLevels=10 elif [ ${LEV} == L128 ] ; then n_zlev=128 dzlev_m="2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 3.0, 3.1, 3.2,\ 3.4, 3.5, 3.7, 3.9, 4.0, 4.2, 4.4, 4.6, 4.8, 5.0, 5.3, 5.5,\ 5.8, 6.0, 6.3, 6.6, 6.9, 7.2, 7.5, 7.8, 8.2, 8.5, 8.9, 9.3,\ 9.8, 10.2, 10.7, 11.1, 11.5, 11.9, 12.3, 12.7, 13.1, 13.5,\ 14.0, 14.5, 14.9, 15.4, 15.9, 16.5, 17.0, 17.6, 18.2, 18.8,\ 19.4, 20.0, 20.7, 21.4, 22.1, 22.8, 23.6, 24.4, 25.2, 26.0,\ 26.9, 27.8, 28.7, 29.7, 30.6, 31.7, 32.7, 33.8, 34.9, 36.1,\ 37.3, 38.5, 39.8, 41.1, 42.5, 43.9, 45.3, 46.8, 48.4, 50.0,\ 51.7, 53.4, 55.2, 57.0, 58.9, 60.8, 62.9, 64.9, 67.1, 69.3,\ 71.6, 74.0, 76.5, 79.0, 81.6, 84.3, 87.1, 90.0, 93.0, 96.1,\ 99.3, 102.6, 106.0, 109.5, 113.2, 116.9, 120.8, 124.8, 128.9,\ 133.2, 137.6, 142.2, 146.9, 151.8, 156.9, 162.1, 167.4, 173.0,\ 178.7, 184.7, 190.8, 197.1" levidx_100m=27 levidx_200m=37 levidx_2000m=96 minVerticalLevels=12 fi # #----------------------------------------------------------------------------- # calculate model timesteps using $days_data output_interval="P1M" # ocean model output interval in days daily="P1D" monthly="P1M" file_interval="${restart_interval}" output="long" #minimum,cmip6,cmip6full,long fx_date="${start_date}" num_io_procs=1 # #----------------------------------------------------------------------------- #set the vertical mixing scheme vert_mix="TKE" #PP, TKE, TKEIDEMIX # #----------------------------------------------------------------------------- #set the vertical coordinate : 0=zlev, 1=zstar if [ ${VERT_COR} = 0 ] ; then vert_cor_type=0 select_lhs=2 l_lhs_direct=".TRUE." STRETCH_C='' LIMIT="0.8" else vert_cor_type=1 select_lhs=1 l_lhs_direct=".FALSE." STRETCH_C=",'stretch_c'" LIMIT="6.0" fi #----------------------------------------------------------------------------- autoPostProcessing="false" # submit postprocessing job #----------------------------------------------------------------------------- # global resolution iforc=12 forcing_timescale=365 # length of OMIP/NCEP dataset: 1 = annual; 12 = monthly data; 365/else = daily data init_relax=1 ocean_data_InputFolder="/pool/data/ICON/oes/input/r0006/${grid_name}" grids_folder=${ocean_data_InputFolder} #----------------------------------------------------------------------------- #icon_data_rootFolder=/pool/data/ICON # # write namelist parameters # ------------------------- if [ x${output} = xcmip6full ] ; then num_io_procs=14 cat > ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_PT3H_inst" output_start = "${start_date}" output_end = "${end_date}" output_interval = "PT3H" filename_format = "_" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1" ml_varlist = 'to'${STRETCH_C} / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_2d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1" ml_varlist = 'zos','to','so','u','v','mlotst','hi','hs','conc','ice_u', 'ice_v'${STRETCH_C} / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_3d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1...${levidx_200m}" ml_varlist = 'to' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_max" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "max" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'mlotst' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_sqr" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "square" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1" ml_varlist = 'to','so' / EOF fi if [ x${output} = xcmip6 ] || [ x${output} = xcmip6full ] ; then cat >> ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_kin" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1,${levidx_100m},${levidx_2000m}" ml_varlist = 'zos','mlotst','hi','hs','conc','ice_u','ice_v','u','v','to','so', 'kin','vort' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_3d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'to','so','u','v','w','A_veloc_v','A_tracer_v_to','A_tracer_v_so', 'normal_velocity','rho','rhopot','mass_flux', 'heat_content_liquid_water','swrab','rsdoabsorb' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_2d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1" ml_varlist = 'to','so','zos','hi','hs','conc','ice_u','ice_v','heat_content_seaice', 'heat_content_snow','heat_content_total','atmos_fluxes_stress_xw', 'atmos_fluxes_stress_yw','atmos_fluxes_stress_x','atmos_fluxes_stress_y', 'sea_level_pressure','Wind_Speed_10m','Qtop','Qbot','Qbot_slow', 'ice_vn','mld','condep','draftave','mlotst','zHeatOceI','heatOceI', 'heatOceW','zUnderIce','HeatFlux_Total','HeatFlux_ShortWave', 'HeatFlux_LongWave','HeatFlux_Sensible','HeatFlux_Latent', 'FrshFlux_Runoff','FrshFlux_Precipitation','FrshFlux_Evaporation', 'FrshFlux_TotalOcean','FrshFlux_VolumeIce','totalsnowfall', 'FrshFlux_VolumeTotal','swsum','heatabs'${STRETCH_C} / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_min" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "min" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'mlotst' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_max" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'mlotst' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_sqr" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "square" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1" ml_varlist = 'mlotst','so','to','zos' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_mon" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:ocean_monitor' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_moc" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:ocean_moc' / EOF if [ x${vert_mix} = xTKE ] ; then cat >> ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_tke" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:oce_vmix_tke' / EOF fi cat >> ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_fx" output_start = "${fx_date}" output_end = "${fx_date} " output_interval = "P1000Y" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'lsm_ctr_c','lsm_c','lsm_e','surface_cell_sea_land_mask', 'surface_edge_sea_land_mask','surface_vertex_sea_land_mask', 'vertex_bottomLevel','basin_c','regio_c','bottom_thick_c', 'bottom_thick_e','column_thick_c','column_thick_e','wet_c','wet_e', 'wet_halo_zero_c','wet_halo_zero_e','prism_thick_c', 'invConstantPrismThickness','prism_volume','prism_thick_e', 'prism_thick_flat_sfc_c','prism_thick_flat_sfc_e', 'inverse prism_thick_c','prism_center_dist_c', 'constantPrismCenters_Zdistance','constantPrismCenters_invZdistance', 'inv_prism_thick_e','inv_prism_center_dist_c', 'inv_prism_center_dist_e','depth_CellMiddle' / EOF elif [ x${output} = xminimum ] ; then num_io_procs=1 cat >> ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_kin" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = "1,${levidx_200m},${levidx_2000m}" ml_varlist = 'zos','mlotst','hi','hs','conc','ice_u','ice_v','u','v','to','so', 'kin','vort' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1D_ice" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1D" filename_format = "_" ! operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'hi','hs','conc','ice_u','ice_v','s11','s12','s22','delta','e11','e12','e22','sigma_i','sigma_ii' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_mon" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:ocean_monitor' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_qps" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'to', 'so', 'tke', 'u', 'v', 'zos', 'hi', 'hs', 'conc', 'mlotst', 'verticallyTotal_mass_flux_e', 'ice_u', 'ice_v', 'zos_square', 'HeatFlux_Total', 'FrshFlux_Runoff', 'FrshFlux_Precipitation', 'FrshFlux_Evaporation', 'FrshFlux_TotalOcean', 'FrshFlux_VolumeIce', 'totalsnowfall', 'FrshFlux_VolumeTotal', 'group:ocean_moc' / &output_nml filetype = 5 output_filename = "${EXPNAME}_fx" output_start = "${fx_date}" output_end = "${fx_date}" output_interval = "P1000Y" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'lsm_ctr_c','lsm_c','lsm_e','surface_cell_sea_land_mask', 'surface_edge_sea_land_mask','surface_vertex_sea_land_mask', 'vertex_bottomLevel','basin_c','regio_c','bottom_thick_c', 'bottom_thick_e','column_thick_c','column_thick_e','wet_c','wet_e', 'wet_halo_zero_c','wet_halo_zero_e','prism_thick_c', 'invConstantPrismThickness','prism_volume','prism_thick_e', 'prism_thick_flat_sfc_c','prism_thick_flat_sfc_e', 'inverse prism_thick_c','prism_center_dist_c', 'constantPrismCenters_Zdistance','constantPrismCenters_invZdistance', 'inv_prism_thick_e','inv_prism_center_dist_c', 'inv_prism_center_dist_e','depth_CellMiddle' / EOF elif [ x${output} = xlong ] ; then num_io_procs=1 cat >> ${ocean_namelist} << EOF &output_nml filetype = 5 output_filename = "${EXPNAME}_P1Y_3d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1Y" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. ml_varlist = 'to', 'so', 'u', 'v', 'w', 'tke', 'A_veloc_v', 'A_tracer_v_to', 'A_tracer_v_so', 'normal_velocity', 'rho', 'rhopot', 'mass_flux', 'heat_content_liquid_water', 'swrab', 'rsdoabsorb' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_2d" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" operation = "mean" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. m_levels = 1 ml_varlist = 'to', 'so', 'zos', 'hi', 'hs', 'conc', 'ice_u', 'ice_v', 'heat_content_seaice', 'heat_content_snow', 'heat_content_total', 'atmos_fluxes_stress_xw', 'atmos_fluxes_stress_yw', 'atmos_fluxes_stress_x', 'atmos_fluxes_stress_y', 'sea_level_pressure', 'Wind_Speed_10m', 'Qtop', 'Qbot', 'Qbot_slow', 'ice_vn', 'mld', 'condep', 'draftave', 'mlotst', 'zHeatOceI', 'heatOceI', 'heatOceW', 'zUnderIce', 'HeatFlux_Total', 'HeatFlux_ShortWave', 'HeatFlux_LongWave', 'HeatFlux_Sensible', 'HeatFlux_Latent', 'FrshFlux_Runoff', 'FrshFlux_Precipitation', 'FrshFlux_Evaporation', 'FrshFlux_TotalOcean', 'FrshFlux_VolumeIce', 'totalsnowfall', 'FrshFlux_VolumeTotal', 'swsum', 'heatabs' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_mon" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" filename_format = "_" file_interval = "${file_interval}" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:ocean_monitor' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1M_moc" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1M" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:ocean_moc' / &output_nml filetype = 5 output_filename = "${EXPNAME}_P1Y_tke" output_start = "${start_date}" output_end = "${end_date}" output_interval = "P1Y" file_interval = "${file_interval}" filename_format = "_" mode = 1 include_last = .FALSE. output_grid = .TRUE. operation = "mean" ml_varlist = 'group:oce_vmix_tke', 'group:oce_vmix_iwe' / EOF fi cat >> ${ocean_namelist} << EOF ! ¶llel_nml nproma = ${nproma} nblocks_c = ${nblocks_c} p_test_run = .FALSE. l_fast_sum = .TRUE. num_prefetch_proc = 0 pio_type = 1 ! io_process_stride = 8 ! io_proc_chunk_size = 16 num_io_procs = ${num_io_procs} num_restart_procs = ${no_of_nodes} / &grid_nml dynamics_grid_filename = "${ocean_grids}", use_dummy_cell_closure = .TRUE. use_duplicated_connectivity = .FALSE. / &dynamics_nml / &run_nml modelTimeStep = "${modelTimeStep}" ! model timestep in seconds output = 'nml' ! namelist controlled output scheme activate_sync_timers = .TRUE. profiling_output = 1 msg_timestamp = .FALSE. timers_level = 10 debug_check_level = 0 restart_filename = "${EXPNAME}_restart_oce_.nc" / EOF cat >> ${ocean_namelist} << EOF &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 = 5 ! 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 = 'all' ! define modules to print out in debug mode / &ocean_dynamics_nml vert_cor_type = ${vert_cor_type} minVerticalLevels = ${minVerticalLevels} n_zlev = ${n_zlev} dzlev_m(1:${n_zlev}) = ${dzlev_m} l_edge_based = .FALSE. ! edge- or cell-based mimetic discretization l_partial_cells = .FALSE. ! partial bottom cells=true: local varying bottom depth l_max_bottom = .TRUE. ! maximize bottom depth select_solver = 4 ! 1=gmres_oce_old; 2=ocean_restart_gmres, 3=mixed precisison restart ! 4=CG (default) 5=CGJ 6=BiCG 7=GMRES restart (legacy) 8=MINRES use_absolute_solver_tolerance = .TRUE. solver_tolerance = 1.0E-10 ! this may further be reduced select_lhs = ${select_lhs} ! 1=operator based (default) 2=matrix based l_lhs_direct = ${l_lhs_direct} ! .TRUE.= use lhs implementation directly .FALSE.= matrix scanner (default) solver_FirstGuess = 2 ! 0=start from zeros 1=last timestep smoothed 2=last timestep (default) solver_max_iter_per_restart = 14 solver_max_restart_iterations = 100 ! outer (restart solver) fast_performance_level = 200 ! performance level 12: for cell-based; 5: default use_continuity_correction = .TRUE. ! height adjustment according to vertical velocity in dynamics cfl_check = .FALSE. cfl_write = .FALSE. i_bc_veloc_top = 1 i_bc_veloc_bot = 1 ! 0: (def) bottom friction off, 1: on / &ocean_tracer_transport_nml no_tracer = 2 ! 2 normal setup; 3 with age tracer; 4 with age tracer squared FLUX_CALCULATION_HORZ = 5 ! 1=upwind, 2=central, 3=Lax-Friedrichs, 4=Miura, 5=FCT with Zalesak limiter (default) FLUX_CALCULATION_VERT = 7 ! 6=adpo; 7=upwind biased ppm (default); 8=FCT with zalesak limiter ! define low and high order methods to be used in horizontal flux corrected transport methods (flux_calculation_horz=4,5) fct_low_order_flux = 1 ! horizontal low order method: 1=upwind (def), no other implemented fct_high_order_flux = 5 ! horizontal high order method: 1=upwind, 2=central, 3=lax_friedrichs, 4=miura_order1 fct_limiter_horz = 100 ! zalesak threshold_min_T = -2.0 ! to avoid abort / &ocean_horizontal_diffusion_nml laplacian_form = 1 ! 1=curlcurl-graddiv VelocityDiffusion_order = 2 ! 21=biharmonic+laplacian (for the laplacian leith) BiharmonicViscosity_scaling = 1 BiharmonicViscosity_reference = 3.5E12 ! [m2/s] constant horizontal viscosity coefficient for velocity BiharmonicViscosity_background = 0.0 ! [m2/s] constant horizontal viscosity coefficient for velocity HarmonicViscosity_scaling = 1 HarmonicViscosity_reference = 0.0 ! [m2/s] constant horizontal viscosity coefficient for velocity HarmonicViscosity_background = 0.0 TracerHorizontalDiffusion_scaling = 1 Temperature_HorizontalDiffusion_Background = 0.0 Temperature_HorizontalDiffusion_Reference = 0 Salinity_HorizontalDiffusion_Background = 0.0 Salinity_HorizontalDiffusion_Reference = 0 / EOF if [ x${vert_mix} = xPP ] ; then cat >> ${ocean_namelist} << EOF &ocean_vertical_diffusion_nml vert_mix_type = 1 ! 1: PP; 2: TKE; 4 TKE+IDEMIX PPscheme_type = 0 velocity_VerticalDiffusion_background = 5.0E-5 ! [m2/s] vertical background viscosity coefficient for velocity Temperature_VerticalDiffusion_background = 1.0E-5 ! [m2/s] vertical background diffusion coefficient for temperature Salinity_VerticalDiffusion_background = 1.0E-5 ! [m2/s] vertical background diffusion coefficient for salinity tracer_convection_MixingCoefficient = 0.1 ! max vertical tracer diffusion for convection used in case of instability convection_InstabilityThreshold = -1.0E-6 ! used in update_ho_params - default=-5e-8 RichardsonDiffusion_threshold = 0.0 ! used in update_ho_params - default=+5e-8 tracer_RichardsonCoeff = 2.0E-3 ! factor for vertical diffusion coefficient in PP scheme velocity_RichardsonCoeff = 2.0E-3 ! factor for vertical viscosity coefficient in PP scheme bottom_drag_coeff = 3.0E-3 ! default=2.5E-3; active for i_bc_veloc_bot=1 use_wind_mixing = .TRUE. ! true: use wind mixing scheme in MPIOM-type pp-scheme lambda_wind = 0.03 tracer_TopWindMixing = 0.5E-3 ! [m2/s] windmixing diffusivity in MPIOM-type pp-scheme velocity_TopWindMixing = 0.5E-3 ! [m2/s] windmixing viscosity in MPIOM-type pp-scheme / EOF elif [ x${vert_mix} = xTKE ] ; then cat >> ${ocean_namelist} << EOF &ocean_vertical_diffusion_nml vert_mix_type = 2 ! 1: PP; 2: TKE; 4 TKE+IDEMIX only_tke = .TRUE. ! .TRUE. for TKE; .FALSE. for TKE+IDEMIX ! vmix/tke parameters c_k = 0.3 c_eps = 0.7 alpha_tke = 30.0 mxl_min = 1.d-8 kappaM_min = 0.0 kappaM_max = 100.0 cd = 3.75 tke_min = 1.d-6 tke_mxl_choice = 2 tke_surf_min = 1.d-4 l_lc = .FALSE. ! Use Langmuir parameterisation (Axell, 2002) clc = 0.15 ! Factor in the vertical velocity profile of the Langmuir circulation (default clc=0.1 in Axell (2002)) use_ubound_dirichlet = .FALSE. use_lbound_dirichlet = .FALSE. / EOF fi cat >> ${ocean_namelist} << EOF &ocean_GentMcWilliamsRedi_nml GMRedi_configuration = ${GMRedi_configuration} ! 0=cartesian diffusion 1=GM-Redi: bolus advection + isopycnal diffusion tapering_scheme = 1 GMRedi_usesRelativeMaxSlopes = .FALSE. S_max = 1.0e-3 S_d = 0.0001 ! 1e-3 to 1e-4 k_tracer_GM_kappa_parameter = ${k_tracer_GM_kappa_parameter} k_tracer_isoneutral_parameter = ${k_tracer_isoneutral_parameter} ! value for cell-based cartesian diffusion - mpiom: 1000/400km = 400/160km k_tracer_dianeutral_parameter = 0.0 ! 1.0E-5 SWITCH_OFF_DIAGONAL_VERT_EXPL = .TRUE. GMREDI_COMBINED_DIAGNOSTIC = .FALSE. SWITCH_ON_REDI_BALANCE_DIAGONSTIC = .FALSE. REVERT_VERTICAL_RECON_AND_TRANSPOSED = .TRUE. SLOPE_CALC_VIA_TEMPERTURE_SALINITY = .TRUE. INCLUDE_SLOPE_SQUARED_IMPLICIT = .TRUE. !think of l_with_vert_tracer_diffusion SWITCH_ON_TAPERING_HORIZONTAL_DIFFUSION = .TRUE. / &ocean_physics_nml i_sea_ice = 1 ! 0 = no sea ice; 1 = sea ice model on; default=1 / &sea_ice_nml i_ice_therm = 1 ! 1=zero-layer (default), 2=Winton, 0/2: not allowed i_ice_dyn = ${DYN} ! 1/0=switch on/off AWI ice dynamics ! i_Qio_type = 3 ! 3 (default): energy of whole grid-area used for melting (MPIOM-type) ! use_constant_tfreez = .TRUE. ! default: true ! use_no_flux_gradients = .FALSE. ! default: true leadclose_1 = 0.25 ! default: 0.5 - value of MPIOM: 0.25 leadclose_2n = 0.666 ! default: 0.0 - value of MPIOM: 2/3 albedoW_sim = 0.10 ! albedo of the ocean used in sea ice model albs = 0.80 ! Albedo of snow (not melting) albsm = 0.65 ! Albedo of snow (melting) albi = 0.70 ! Albedo of ice (not melting) albim = 0.65 ! Albedo of ice (melting) initialize_seaice_fromfile = .true. !evp ! alpha_evp = 800 ! beta_evp = 800 ! n_ice_iter = 120 delta_min = 2.0e-09 cd_io = 5.5e-3 ! luse_replacement_pressure = .true. / &ocean_forcing_nml iforc_oce = ${iforc} ! ocean forcing forcing_timescale = ${forcing_timescale} ! length of ocean forcing data set, see above forcing_frequency = 86400.0 init_oce_relax = ${init_relax} ! read ocean surface relaxation file, see above type_surfRelax_Temp = 0 ! 0: no relaxation used ! 1: relaxation switched on for reading (init_oce_relax=1) or some testcases only para_surfRelax_Temp = 1.0 ! strength of 2-dim relaxation for temperature (months) ! this value is divided by number of seconds per month (=30*24*3600) type_surfRelax_Salt = 1 ! 2-dim relaxation of salinity - see temperature relaxation for type values para_surfRelax_Salt = 3.0 ! strength of 2-dim relaxation for salinity (months) forcing_windstress_u_type = 1 ! read from file forcing_windstress_v_type = 1 ! read from file forcing_fluxes_type = 1 ! read from file ! forcing_enable_freshwater = .TRUE. ! apply freshwater forcing boundary condition (OMIP only) ! forcing_set_runoff_to_zero = .FALSE. ! set runoff to zero for comparison to MPIOM; default: false ! zero_freshwater_flux = .FALSE. ! set external freshwater flux to zero; default: false ! salt-change due to internal fluxes only limit_seaice = .TRUE. ! default: true seaice_limit = ${LIMIT} ! hard limit set to 80% of upper layer for sea ice limit_elevation = .TRUE. atm_pressure_included_in_ocedyn = .FALSE. ! use atm. pressure in the ocean dynamics atm_pressure_included_in_icedyn = .FALSE. ! use atm. pressure in the ice dynamics use_tides = .FALSE. tides_mod = 1 ! 1 Default 2 MPIOM lswr_jerlov = .TRUE. ! use jerlov water types for sw absorption jerlov_atten = 0.08 ! jerlov water type IB jerlov_bluefrac = 0.36 ! jerlov water type IB / &ocean_initialConditions_nml initial_salinity_type = 1 ! read from file initial_temperature_type = 1 ! read from file sea_surface_height_type = 0 initial_velocity_type = 0 / &ocean_diagnostics_nml diagnose_age = .FALSE. diagnose_green = .FALSE. diagnostics_level = 1 diagnose_for_horizontalvelocity = .FALSE. diagnose_for_heat_content = .TRUE. eddydiag = .FALSE. diagnose_for_tendencies = .TRUE. / &io_nml restart_file_type = 5 write_last_restart = .TRUE. lkeep_in_sync = .TRUE. ! sync after each timestep restart_write_mode = "joint procs multifile" / EOF #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- # add standard atmo_non-hydrostatic_files #. ${thisdir}/add_required_ocean_files add_link_file ${ocean_data_InputFolder}/${GRID}${LEV}_oras5-2010-01-01.nc initial_state.nc add_link_file ${ocean_data_InputFolder}/${GRID}_ocean-flux.nc ocean-flux.nc add_link_file ${ocean_data_InputFolder}/${GRID}_ocean-relax.nc ocean-relax.nc # IDEMIX forcing fields #add_link_file /home/mpim/m300602/work/proj_vmix/icon/idemix_forcing/fourier_smooth_2005_cfsr_inert_OceanOnly_Global_IcosSymmetric_0039km_rotatedZ37d_BlackSea_Greenland_modified_srtm30_1min.nc idemix_surface_forcing.nc #add_link_file /home/mpim/m300602/work/proj_vmix/icon/idemix_forcing/tidal_energy_gx1v6_20090205_OceanOnly_Global_IcosSymmetric_0039km_rotatedZ37d_BlackSea_Greenland_modified_srtm30_1min.nc idemix_bottom_forcing.nc #----------------------------------------------------------------------------- # ICON # # --------------------------------------------------------------- # Copyright (C) 2004-2025, DWD, MPI-M, DKRZ, KIT, ETH, MeteoSwiss # Contact information: icon-model.org # See AUTHORS.TXT for a list of authors # See LICENSES/ for license information # SPDX-License-Identifier: BSD-3-Clause # --------------------------------------------------------------- #============================================================================= # # This section of the run script prepares and starts the model integration. # # MODEL and START must be defined as environment variables or # they must be substituted with appropriate values. # # Marco Giorgetta, MPI-M, 2010-04-21 # #----------------------------------------------------------------------------- final_status_file=${basedir}/run/${job_name}.final_status rm -f ${final_status_file} #----------------------------------------------------------------------------- # # directories definition # RUNSCRIPTDIR=${basedir}/run if [ x$grids_folder = x ] ; then HGRIDDIR=${basedir}/grids else HGRIDDIR=$grids_folder fi make_and_change_to_experiment_dir for dir in ${ADDITIONAL_SUBDIRS[@]}; do mkdir -p $dir done #----------------------------------------------------------------------------- final_status_file=${RUNSCRIPTDIR}/${job_name}.final_status rm -f ${final_status_file} #----------------------------------------------------------------------------- # set up the model lists if they do not exist # this works for single model runs # for coupled runs the lists should be declared explicilty if [ x$namelist_list = x ]; then # minrank_list=( 0 ) # maxrank_list=( 65535 ) # incrank_list=( 1 ) minrank_list[0]=0 maxrank_list[0]=65535 incrank_list[0]=1 if [ x$atmo_namelist != x ]; then # this is the atmo model namelist_list[0]="$atmo_namelist" modelname_list[0]="atm" modeltype_list[0]=1 run_atmo="true" elif [ x$ocean_namelist != x ]; then # this is the ocean model namelist_list[0]="$ocean_namelist" modelname_list[0]="oce" modeltype_list[0]=2 elif [ x$psrad_namelist != x ]; then # this is the psrad model namelist_list[0]="$psrad_namelist" modelname_list[0]="psrad" modeltype_list[0]=3 elif [ x$hamocc_namelist != x ]; then # this is the hamocc model namelist_list[0]="$hamocc_namelist" modelname_list[0]="hamocc" modeltype_list[0]=4 elif [ x$jsbach_namelist != x ]; then # this is the jsbach standalone model namelist_list[0]="$jsbach_namelist" modelname_list[0]="jsbach" modeltype_list[0]=5 run_jsbach_standalone="true" elif [ x$wave_namelist != x ]; then # this is the wave model namelist_list[0]="$wave_namelist" modelname_list[0]="wave" modeltype_list[0]=98 elif [ x$testbed_namelist != x ]; then # this is the testbed model namelist_list[0]="$testbed_namelist" modelname_list[0]="testbed" modeltype_list[0]=99 else check_error 1 "No namelist is defined" fi fi #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- # 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 ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then sleep 10; fi fi # fill some checks run_coupled=${run_coupled="false"} run_atmo=${run_atmo="false"} if [ x$atmo_namelist != x ]; then run_atmo="true" run_jsbach_standalone="false" fi run_jsbach=${run_jsbach="false"} if [ x$jsbach_namelist != x ]; then run_jsbach="true" fi run_ocean=${run_ocean="false"} if [ x$ocean_namelist != x ]; then run_ocean="true" if [ "${run_atmo}" = 'true' ]; then run_coupled="true" fi fi run_psrad=${run_psrad="false"} if [ x$psrad_namelist != x ]; then run_psrad="true" fi run_hamocc=${run_hamocc="false"} if [ x$hamocc_namelist != x ]; then run_hamocc="true" fi run_wave=${run_wave="false"} if [ x$wave_namelist != x ]; then run_wave="true" if [ "${run_atmo}" = 'true' ]; then run_coupled="true" fi fi #----------------------------------------------------------------------------- # add grids to required files all_grids="${atmo_dyn_grids} ${atmo_rad_grids} ${ocean_grids} ${wave_grids}" for gridfile in ${all_grids}; do # gridfile=${gridfile//\'/} # strip all ' in case ' is used to delimit the grid names gridfile=${gridfile//\"/} # strip all " in case " is used to delimit the grid names gridfile=${gridfile//\,/} # strip all , in case , is used to separate the grid names # grfinfofile=${gridfile%.nc}-grfinfo.nc # ls -l ${HGRIDDIR}/$gridfile check_error $? "${HGRIDDIR}/$gridfile does not exist." add_link_file ${HGRIDDIR}/${gridfile} ./ if [ -f ${HGRIDDIR}/${grfinfofile} ]; then add_link_file ${HGRIDDIR}/${grfinfofile} ./ fi done #----------------------------------------------------------------------------- # print_required_files copy_required_files link_required_files #----------------------------------------------------------------------------- # get restart files if [ x$restart_atmo_from != "x" ] ; then rm -f restart_atm_DOM01.nc # ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc ln -s cp_restart_atm.nc restart_atm_DOM01.nc restart=".true." fi if [ x$restart_ocean_from != "x" ] ; then rm -f restart_oce.nc # ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc restart=".true." fi #----------------------------------------------------------------------------- read_restart_namelists=${read_restart_namelists:=".true."} #----------------------------------------------------------------------------- # # create ICON master namelist # ------------------------ # For a complete list see Namelist_overview and Namelist_overview.pdf #----------------------------------------------------------------------------- # create master_namelist if [ -z "$dont_create_icon_master_namelist" ]; then master_namelist=icon_master.namelist calendar=${calendar:="proleptic gregorian"} calendar_type=${calendar_type:=1} { echo "&master_nml" echo " lrestart = $restart" echo " read_restart_namelists = $read_restart_namelists" echo "/" if [ -z "$nsteps" ]; then echo "&master_time_control_nml" echo " calendar = '$calendar'" echo " experimentStartDate = '$start_date'" echo " restartTimeIntval = '$restart_interval'" echo " checkpointTimeIntval = '$checkpoint_interval'" if [ -n "$end_date" ]; then echo " experimentStopDate = '$end_date'" fi echo "/" echo "&time_nml" echo " is_relative_time = .false." echo "/" else # $nsteps is set -> use time_nml:ini_datetime_string echo "&time_nml" echo " calendar = $calendar_type" echo " ini_datetime_string = '$start_date'" echo " dt_restart = $dt_restart" echo "/" fi } > $master_namelist fi #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- # add model component to master_namelist add_component_to_master_namelist() { model_namelist_filename=$1 if [ x${dont_create_icon_master_namelist+set} != xset ]; then model_name=$2 model_type=$3 model_min_rank=$4 model_max_rank=$5 model_inc_rank=$6 model_rank_group_size=$7 model_do_restart=$8 cat >> $master_namelist << EOF &master_model_nml model_name="$model_name" model_namelist_filename="$model_namelist_filename" model_type=$model_type model_min_rank=$model_min_rank model_max_rank=$model_max_rank model_inc_rank=$model_inc_rank model_rank_group_size=$model_rank_group_size ${model_do_restart:+model_do_restart='$model_do_restart'} / EOF fi #----------- #get namelist if [ -f ${RUNSCRIPTDIR}/$model_namelist_filename ] ; then mv -f ${RUNSCRIPTDIR}/$model_namelist_filename ${EXPDIR} check_error $? "mv -f ${RUNSCRIPTDIR}/$model_namelist_filename ${EXPDIR}" else check_error 1 "${RUNSCRIPTDIR}/$model_namelist_filename does not exist" fi } #----------------------------------------------------------------------------- no_of_models=${#namelist_list[*]} echo "no_of_models=$no_of_models" rank_group_size=1 j=0 while [ $j -lt ${no_of_models} ] do add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]} ${rank_group_size} "${model_do_restart_list[$j]}" j=`expr ${j} + 1` done #----------------------------------------------------------------------------- # Add JSBACH part to master_namelist # For several domains, $jsbach_namelist is only the basename for each domain's jsbach namelist; # the actual namelist files are appended by suffixes '_d1', '_d2', etc. if [ "${run_jsbach}" = 'yes' -o "${run_jsbach}" = 'true' ]; then cat >> $master_namelist << EOF &jsb_control_nml is_standalone = .${run_jsbach_standalone:=false}. restart_jsbach = ${restart} debug_level = 0 timer_level = 0 / EOF # if [[ -n ${atmo_dyn_grids} ]]; then no_of_domains=$(echo ${atmo_dyn_grids} | wc -w) else no_of_domains=1 fi echo "no_of_domains=$no_of_domains" domain="" domain_suffix="" j=1 while [ $j -le ${no_of_domains} ] do if [[ $no_of_domains -gt 1 ]]; then # no_of_domains < 10 ! domain=" DOM0${j}" domain_suffix="_d${j}" fi cat >> $master_namelist << EOF &jsb_model_nml model_id = $j model_name = "JSBACH${domain}" model_shortname = "jsb${domain_suffix}" model_description = 'JSBACH land surface model' model_namelist_filename = "${jsbach_namelist}${domain_suffix}" / EOF if [[ ${run_jsbach_standalone} != true ]]; then if [[ -f ${RUNSCRIPTDIR}/${jsbach_namelist}${domain_suffix} ]] ; then mv ${RUNSCRIPTDIR}/${jsbach_namelist}${domain_suffix} ${EXPDIR} check_error $? "mv ${RUNSCRIPTDIR}/${jsbach_namelist}${domain_suffix}" else check_error 1 "${RUNSCRIPTDIR}/${jsbach_namelist}${domain_suffix} does not exist" fi fi j=`expr ${j} + 1` done fi # # get model # ls -l ${MODEL} check_error $? "${MODEL} does not exist?" # ldd ${MODEL} # #----------------------------------------------------------------------------- # # configure START_MODEL_function # # TODO: be less atmospheric centric, i.e. do not assume that atmosphere is always component 1 ICON_COMPONENT1_VH_procs=$(( ${num_restart_procs:-0} + ${num_io_procs:-0} + ${num_prefetch_proc:-0} + ${num_io_procs_radar:-0})) # # start experiment # # Combine START and MODEL if START_MODEL is not already set. # START_MODEL is used to ease the execution of a machine that uses a complex # mpirun command with multiple binaries START_MODEL="${START_MODEL:=$START $MODEL}" if [ "${run_coupled}" = 'true' ]; then if [ "${run_atmo}" = 'true' ]; then rm -f finish_atmo.status fi if [ "${run_ocean}" = 'true' ]; then rm -f finish_ocean.status fi if [ "${run_waves}" = 'true' ]; then rm -f finish_waves.status fi else rm -f finish.status fi # date set -x ${START_MODEL} || exit 1 set +x date # if [ "${run_coupled}" == 'true' ]; then if [ \( "${run_atmo}" != 'true' -o -r finish_atmo.status \) -a \( "${run_ocean}" != 'true' -o -r finish_ocean.status \) -a \( "${run_waves}" != 'true' -o -r finish_waves.status \) ]; then check_final_status 0 "${START} ${MODEL}" else # handle errors check_final_status -1 "${START} ${MODEL}" fi if [ "${run_atmo}" = 'true' ]; then echo "Atmosphere ran successfully: $(< finish_atmo.status)" finish_status_atm=`cat finish_atmo.status` fi if [ "${run_ocean}" = 'true' ]; then echo "Ocean ran successfully: $(< finish_ocean.status)" finish_status_oce=`cat finish_ocean.status` fi if [ "${run_waves}" = 'true' ]; then echo "Waves ran successfully: $(< finish_waves.status)" finish_status_w=`cat finish_waves.status` fi else if [ -r finish.status ] ; then check_final_status 0 "${START} ${MODEL}" else check_final_status -1 "${START} ${MODEL}" fi #----------------------------------------------------------------------------- # finish_status=$(cat finish.status | tr -d ' ') echo "${finish_status}" echo "============================" echo "Script run successfully: $finish_status" echo "============================" fi #----------------------------------------------------------------------------- # rm output_schedule_steps* #----------------------------------------------------------------------------- if [[ "x$use_hamocc" = "xyes" ]]; then # store HAMOCC log file strg="$(ls -rt ${EXPNAME}_hamocc_EU*.nc* | tail -1 )" prefx="${EXPNAME}_hamocc_EU_tendencies" foo=${strg##${prefx}} foo=${foo%%.*} bgcout_file="bgcout_${foo}" mv bgcout $bgcout_file fi #----------------------------------------------------------------------------- namelist_list="" #----------------------------------------------------------------------------- # check if we have to restart, ie resubmit # Note: this is a different mechanism from checking the restart if [ "${run_coupled}" = 'true' ]; then if [ "${run_atmo}" = 'true' -a "${run_ocean}" = 'true' ]; then if [ \( $finish_status_atm = "RESTART" \) -o \( $finish_status_oce = "RESTART" \) ]; then echo "restart next experiment..." this_script="${RUNSCRIPTDIR}/${job_name}" echo 'this_script: ' "$this_script" touch ${restartSemaphoreFilename} cd ${RUNSCRIPTDIR} ${submit} $this_script $run_param_0 else [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename} fi elif [ "${run_atmo}" = 'true' -a "${run_waves}" = 'true' ]; then if [ \( "${finish_status_atm}" = "RESTART" \) -o \( "${finish_status_w}" = "RESTART" \) ]; then echo "restart next experiment..." this_script="${RUNSCRIPTDIR}/${job_name}" echo 'this_script: ' "$this_script" touch ${restartSemaphoreFilename} cd ${RUNSCRIPTDIR} ${submit} $this_script $run_param_0 else [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename} fi fi else if [ "${finish_status}" = "RESTART" ] ; then echo "restart next experiment..." this_script="${RUNSCRIPTDIR}/${job_name}" echo 'this_script: ' "$this_script" touch ${restartSemaphoreFilename} cd ${RUNSCRIPTDIR} ${submit} $this_script $run_param_0 else [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename} fi fi #----------------------------------------------------------------------------- # automatic call/submission of post processing if available if [ "x${autoPostProcessing}" = "xtrue" ]; then # check if there is a postprocessing is available cd ${RUNSCRIPTDIR} targetPostProcessingScript="./post.${EXPNAME}.run" [[ -x $targetPostProcessingScript ]] && ${submit} ${targetPostProcessingScript} cd - fi #----------------------------------------------------------------------------- cd $RUNSCRIPTDIR #----------------------------------------------------------------------------- # exit 0 # # vim:ft=sh #-----------------------------------------------------------------------------