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Added serial dockerfile and OLMT ensemble examples
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Shawn P. Serbin
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Jun 13, 2023
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scripts/elm_scripts/olmt_scripts/ngeearctic_ensemble_example_docker.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,218 @@ | ||
| #!/bin/sh | ||
| # ======================================================================================= | ||
| # Setup and run an ELM OLMT simulation for an NGEE Arctic site | ||
| # | ||
| # | ||
| # availible site names: kougarok, teller, council, beo | ||
| # ======================================================================================= | ||
|
|
||
| cwd=$(pwd) | ||
| cd /tools/OLMT | ||
|
|
||
| # ======================================================================================= | ||
| ### Setup and run an example ELM OLMT ensemble simulation for a NGEE-Arctic research site | ||
| for i in "$@" | ||
| do | ||
| case $i in | ||
| -sn=*|--site_name=*) | ||
| site_name="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -sg=*|--site_group=*) | ||
| site_group="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -cp=*|--case_prefix=*) | ||
| case_prefix="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -adsy=*|--ad_spinup_years=*) | ||
| ad_spinup_years="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -fsy=*|--final_spinup_years=*) | ||
| final_spinup_years="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -trsy=*|--transient_years=*) | ||
| transient_years="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -tsp=*|--timestep=*) | ||
| timestep="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -pl=*|--param_list=*) | ||
| param_list="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -ne=*|--num_ens=*) | ||
| num_ens="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| -ng=*|--num_groups=*) | ||
| num_groups="${i#*=}" | ||
| shift # past argument=value | ||
| ;; | ||
| *) | ||
| # unknown option | ||
| ;; | ||
| esac | ||
| done | ||
| # ======================================================================================= | ||
|
|
||
| # ======================================================================================= | ||
| # Set defaults and print the selected options back to the screen before running | ||
| site_name="${site_name:-kougarok}" | ||
| site_group="${site_group:-NGEEArctic}" | ||
| case_prefix="${case_prefix:-OLMT_ens}" | ||
| ad_spinup_years="${ad_spinup_years:-200}" | ||
| final_spinup_years="${final_spinup_years:-600}" | ||
| transient_years="${transient_years:--1}" | ||
| timestep="${timestep:-1}" | ||
| param_list="${param_list:-/scripts/param_list_example_kougarok}" | ||
| num_ens="${num_ens:-6}" | ||
| num_groups="${num_groups:-3}" | ||
|
|
||
| # print back selected or set options to the user | ||
| echo " " | ||
| echo " " | ||
| echo "*************************** OLMT run options ***************************" | ||
| echo "Site Name = ${site_name}" | ||
| echo "Site Group = ${site_group}" | ||
| echo "Case Prefix = ${case_prefix}" | ||
| echo "Number of AD Spinup Simulation Years = ${ad_spinup_years}" | ||
| echo "Number of Final Spinup Simulation Years = ${final_spinup_years}" | ||
| echo "Number of Transient Simulation Years = ${transient_years}" | ||
| echo "Model Timestep = ${timestep}" | ||
| echo "Input parameter list = ${param_list}" | ||
| echo "Number of MCMC Ensembles = ${num_ens}" | ||
| echo "Number of MPI groups = ${num_groups}" | ||
| if [ ${transient_years} != -1 ]; then | ||
| sim_years="--nyears_ad_spinup ${ad_spinup_years} --nyears_final_spinup ${final_spinup_years} \ | ||
| --nyears_transient ${transient_years}" | ||
| else | ||
| sim_years="--nyears_ad_spinup ${ad_spinup_years} --nyears_final_spinup ${final_spinup_years}" | ||
| fi | ||
| echo " " | ||
| # ======================================================================================= | ||
|
|
||
| # ======================================================================================= | ||
| # Set site codes for OLMT | ||
| if [ ${site_name} = beo ]; then | ||
| site_code="AK-BEOG" | ||
| elif [ ${site_name} = council ]; then | ||
| site_code="AK-CLG" | ||
| elif [ ${site_name} = kougarok ]; then | ||
| site_code="AK-K64G" | ||
| elif [ ${site_name} = teller ]; then | ||
| site_code="AK-TLG" | ||
| else | ||
| echo " " | ||
| echo "**** EXECUTION HALTED ****" | ||
| echo "Please select a Site Name from beo, council, kougarok, teller" | ||
| exit 0 | ||
| echo " " | ||
| fi | ||
| echo "OLMT Site Code: ${site_code}" | ||
| # ======================================================================================= | ||
|
|
||
| # ======================================================================================= | ||
| # pause to show options before continuing | ||
| sleep 3 | ||
| echo " " | ||
| echo " " | ||
| # ======================================================================================= | ||
|
|
||
| # ======================================================================================= | ||
| echo "Building ensemble simulations with OLMT source: "$(pwd) | ||
| echo "*****************************************************************" | ||
| echo " " | ||
| echo " " | ||
| echo "**** User OLMT run command: " | ||
| runcmd="python3 ./site_fullrun.py \ | ||
| --site ${site_code} --sitegroup ${site_group} --caseidprefix ${case_prefix} \ | ||
| ${sim_years} --tstep ${timestep} --machine docker \ | ||
| --compiler gnu --mpilib mpi-serial \ | ||
| --cpl_bypass --gswp3 \ | ||
| --model_root /E3SM \ | ||
| --caseroot /output \ | ||
| --ccsm_input /inputdata \ | ||
| --runroot /output \ | ||
| --spinup_vars \ | ||
| --parm_list ${param_list} \ | ||
| --mc_ensemble ${num_ens} \ | ||
| --nopointdata \ | ||
| --metdir /inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v2.c180716_NGEE-Grid/cpl_bypass_${site_name}-Grid \ | ||
| --domainfile /inputdata/share/domains/domain.clm/domain.lnd.1x1pt_${site_name}-GRID_navy.nc \ | ||
| --surffile /inputdata/lnd/clm2/surfdata_map/surfdata_1x1pt_${site_name}-GRID_simyr1850_c360x720_c171002.nc \ | ||
| --landusefile /inputdata/lnd/clm2/surfdata_map/landuse.timeseries_1x1pt_${site_name}-GRID_simyr1850-2015_c180423.nc \ | ||
| & sleep 10" | ||
| echo ${runcmd} | ||
| echo " " | ||
| echo " " | ||
|
|
||
| # create the OLMT run command | ||
| if python3 ./site_fullrun.py \ | ||
| --site ${site_code} --sitegroup ${site_group} --caseidprefix ${case_prefix} \ | ||
| ${sim_years} --tstep ${timestep} --machine docker \ | ||
| --compiler gnu --mpilib mpi-serial \ | ||
| --cpl_bypass --gswp3 \ | ||
| --model_root /E3SM \ | ||
| --caseroot /output \ | ||
| --ccsm_input /inputdata \ | ||
| --runroot /output \ | ||
| --spinup_vars \ | ||
| --parm_list ${param_list} \ | ||
| --mc_ensemble ${num_ens} \ | ||
| --ng ${num_groups} \ | ||
| --nopointdata \ | ||
| --metdir /inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v2.c180716_NGEE-Grid/cpl_bypass_${site_name}-Grid \ | ||
| --domainfile /inputdata/share/domains/domain.clm/domain.lnd.1x1pt_${site_name}-GRID_navy.nc \ | ||
| --surffile /inputdata/lnd/clm2/surfdata_map/surfdata_1x1pt_${site_name}-GRID_simyr1850_c360x720_c171002.nc \ | ||
| --landusefile /inputdata/lnd/clm2/surfdata_map/landuse.timeseries_1x1pt_${site_name}-GRID_simyr1850-2015_c180423.nc \ | ||
| & sleep 10 | ||
|
|
||
| then | ||
| wait | ||
|
|
||
| echo "DONE docker ELM runs !" | ||
|
|
||
| else | ||
| exit &? | ||
| fi | ||
|
|
||
| cd ${cwd} | ||
| sleep 2 | ||
|
|
||
| #### Postprocess | ||
| # Copy the example parameter file to the OLMT ensemble output folder | ||
| cp ${param_list} /output/cime_run_dirs/UQ/${case_prefix}_${site_code}_ICB20TRCNPRDCTCBC/. | ||
| ### Collapse transient simulation output into a single netCDF file | ||
| echo " " | ||
| echo " " | ||
| echo " " | ||
| echo "**** Postprocessing ELM output in:" | ||
| echo "/output/cime_run_dirs/UQ/${case_prefix}_${site_code}_ICB20TRCNPRDCTCBC/" | ||
| echo " " | ||
| echo " " | ||
| cd /output/cime_run_dirs/UQ/${case_prefix}_${site_code}_ICB20TRCNPRDCTCBC/ | ||
| echo " " | ||
| echo "**** Concatenating netCDF output - Hang tight this will take awhile ****" | ||
| echo ${PWD} | ||
| for d in */ ; do | ||
| echo "Post-processing: $d" | ||
| cd /output/cime_run_dirs/UQ/${case_prefix}_${site_code}_ICB20TRCNPRDCTCBC/${d} | ||
| ncrcat --ovr *.h0.*.nc ELM_output.nc | ||
| chmod 777 ELM_output.nc | ||
| echo " " | ||
| done | ||
| echo " " | ||
| echo " " | ||
| echo "**** Concatenating netCDF output: DONE ****" | ||
| echo "**** OLMT Ensemble Simulation at ${site_name}: DONE ****" | ||
| echo " " | ||
| echo " " | ||
| echo " " | ||
| sleep 2 | ||
| # ======================================================================================= |
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| flnr 11 0.02 0.20 | ||
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| vcmaxha 11 68000 77000 | ||
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| jmaxha 11 48000 58000 | ||
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| roota_par 11 4 10 | ||
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scripts/elm_scripts/olmt_scripts/param_list_example_kougarok
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| @@ -0,0 +1,12 @@ | ||
| flnr 11 0.07 0.145 | ||
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| vcmaxha 11 68000 79000 | ||
| vcmaxha 12 68000 79000 | ||
| jmaxha 11 48000 58000 | ||
| jmaxha 12 48000 58000 | ||
| roota_par 11 4.0 10 | ||
| roota_par 12 6 15 | ||
| mbbopt 11 1 13 | ||
| mbbopt 12 1 13 | ||
| slatop 11 0.009 0.045 | ||
| slatop 12 0.009 0.045 |