Added serial dockerfile and OLMT ensemble examples

docker/elm/elm_v2-for-ngee/Dockerfile_serial_multiarch

@@ -5,7 +5,7 @@
 # AMD64/ARM64 version
 # ----------------------------------------------------------------------
 
-FROM fasstsimulation/baseos:gcc850ompi316-serial_multiarch
+FROM serbinsh/ngeearctic_elm_containers:baseos_gcc850ompi316-serial_multiarch
 LABEL maintainer.name="Shawn P. Serbin" \
       maintainer.email="[email protected]" \
       author.name="Shawn P. Serbin" \
@@ -15,9 +15,8 @@ LABEL maintainer.name="Shawn P. Serbin" \
       version.baseos="gcc8.5"
 
 # where to get the ELM source code
-ENV REPOSITORY_URL=https://github.com/FASSt-simulation/simulation_containers
-ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/simulation_containers
-ENV TOOLS_REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/fasst_simulation_tools
+ENV REPOSITORY_URL=https://github.com/TESTgroup-BNL/ngeearctic_elm_containers
+ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/TESTgroup-BNL/ngeearctic_elm_containers
 ENV USER=modeluser
 
 # Add new group, user, and user directory with user permissions
@@ -103,16 +102,16 @@ USER ${USER}
 RUN cd /tools \
     && git -c http.sslVerify=false clone -b Arctic-userpft --single-branch https://github.com/dmricciuto/OLMT.git \
     && cd OLMT/ \
-    # add specific git commit as src - to try and stabilize changes and avoid new potential bugs
-    && git reset --hard 'c208528360d59f46630ef94fe4a3a42cbfd3acab' \
+    # add specific git commit to version used in the October 2022 NGEE Arctic Modeling Workshop
+    && git reset --hard '1b2a02c34deda8a2a796bb68325a87ddb3764c32' \
     && chown $USER:dockerusers -R /tools/OLMT \
     && chmod -R 777 /tools/OLMT
 
 # Copy scripts into /scripts to make availible to users
 RUN cd /scripts \
-    && wget $TOOLS_REPOSITORY_RAW_URL/main/met_scripts/ngeearctic/download_elm_singlesite_forcing_data.sh \
-    && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/ngeearctic_elm_scripts/olmt_scripts/ngeearctic_site_fullrun_userdata_docker.sh \
-    && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/ngeearctic_elm_scripts/olmt_scripts/ngeearctic_ensemble_example_docker.sh \
+    && wget $REPOSITORY_RAW_URL/main/scripts/met_scripts/ngeearctic/download_elm_singlesite_forcing_data.sh \
+    && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/olmt_scripts/ngeearctic_site_fullrun_userdata_docker.sh \
+    && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/olmt_scripts/ngeearctic_ensemble_example_docker.sh \
     && mv ngeearctic_site_fullrun_userdata_docker.sh OLMT_docker_example.sh \
     && mv ngeearctic_ensemble_example_docker.sh OLMT_ens_docker_example.sh \
     && chown $USER:dockerusers download_elm_singlesite_forcing_data.sh \
@@ -121,9 +120,9 @@ RUN cd /scripts \
     && chown $USER:dockerusers OLMT_ens_docker_example.sh \
     && chmod +x OLMT_docker_example.sh \
     && chmod +x OLMT_ens_docker_example.sh \
-    && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/ngeearctic_elm_scripts/olmt_scripts/param_list_example_kougarok \
+    && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/olmt_scripts/param_list_example_kougarok \
     && chown $USER:dockerusers param_list_example_kougarok \
-    && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/ngeearctic_elm_scripts/olmt_scripts/param_list_example_beo \
+    && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/olmt_scripts/param_list_example_beo \
     && chown $USER:dockerusers param_list_example_beo \
     && cd /
 

scripts/elm_scripts/olmt_scripts/ngeearctic_ensemble_example_docker.sh

@@ -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
+# =======================================================================================

scripts/elm_scripts/olmt_scripts/param_list_example_beo

@@ -0,0 +1,12 @@
+flnr 11 0.02 0.20
+flnr 12 0.02 0.20
+vcmaxha 11 68000 77000
+vcmaxha 12 68000 77000
+jmaxha 11 48000 58000
+jmaxha 12 48000 58000
+roota_par 11 4 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

scripts/elm_scripts/olmt_scripts/param_list_example_kougarok

@@ -0,0 +1,12 @@
+flnr 11 0.07 0.145
+flnr 12 0.07 0.145
+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