Create sites

Externals.cfg

@@ -29,8 +29,8 @@ required = True
 [cime]
 local_path = cime
 protocol = git
-repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.23_a01
+repo_url = https://github.com/NordicESMhub/cime.git
+tag = release-emerald2.0.0
 externals = ../Externals_cime.cfg
 required = True
 

README_fates_emerald_api

@@ -0,0 +1,148 @@
+$CTSMROOT/README_fates_emerald_api                                          22/04/2020
+
+Version 1.0, 22/04/2020 : 
+  Developed based on:
+    CLM5.0: release-clm5.0.32
+    FATES:  sci.1.34.0_api.9.0.0
+    CIME:   cime5.6.33
+  Basic setup for runing CLM-FATES on 12 SeedClim sites, using 
+    (1) GSWP3v1 (0.5 degree) atm forcing, 
+    (2) Default surface data file
+    (3) Default FATES parameterfile (12 pfts) 
+    (4) No initial file ("initial cold start from bare ground")
+    (5) Only simulation for present-day (2000) in equilibrium state are available and tested
+
+Version 1.1, ??/??/????:   
+  Improved setup for runing CLM-FATES on 12 SeedClim sites, using 
+    (1) COSMO-Rea 6km, ERALAND 9km, atm forcing ?
+    (2) Modify surface data file to better represent the sites ?
+    (3) Modify FATES parameterfile to better represent the sites ?
+    (4) Initial file available for all the sites to run FATES and CLM50BGC ?
+
+Version 1.2, ??/??/????:
+  Improved setup for runing CLM-FATES on 12 SeedClim sites
+    (1) Set up simulations with prescribed standing structure
+    (2) Set up and test transient simulations from pre-industrial (1850) to present (2020) 
+
+
+
+=============================================================================================
+    QUICKSTART on SAGA:
+=============================================================================================
+#### You need to have access to SAGA and the NorESM shared folder on SAGA: /cluster/shared/noresm/inputdata/
+
+#### Clone git repository
+git clone https://github.com/NordicESMhub/ctsm.git
+
+#### For developer, please checkout branch "fates_emerald_api"
+  cd ~/ctsm
+  git checkout fates_emerald_api  # The branch will have the same name as the branch name. 
+  or:
+  git checkout fates_emerald_api -b new_branch_name   # if you want to create a new branch name.
+#### For user, please checkout "release tag" of the platform, e.g., release-emerald-platform1.0.0.
+  cd ~/ctsm
+  git checkout release-emerald-platform1.0.0                      # The branch will have the same name as the tag name. 
+  or
+  git checkout release-emerald-platform1.0.0 -b new_branch_name   # if you want to create a new branch name.
+#### More details on the workflow for developing the platform are available at ??????
+
+
+#### Download other external codes
+./manage_externals/checkout_externals 
+
+#### Create a case: 
+#--case: which directory your case will be create
+#--compset: which model component will be used, only DATM%1PTGSWP3 is available at the moment 
+#--res: currently available resolution are as following. More details about each sites can be found in: ?????
+           SeedClim Sites: 1x1_ALP1,61.0243N,8.12343E
+                           1x1_ALP2,60.8231N,7.27596E
+                           1x1_ALP3,60.8328N,7.17561E
+                           1x1_ALP4,60.9335N,6.41504E
+                           1x1_SUB1,60.8203N,8.70466E
+                           1x1_SUB2,60.8760N,7.17666E
+                           1x1_SUB3,61.0866N,6.63028E
+                           1x1_SUB4,60.5445N,6.51468E
+                           1x1_BOR1,61.0355N,9.07876E
+                           1x1_BOR2,60.8803N,7.16982E
+                           1x1_BOR3,60.6652N,6.33738E
+                           1x1_BOR4,60.6901N,5.96487E
+           LandPress Sites:1x1_LYG,60.70084N,5.092566E  
+                           1x1_BUO,65.83677N,12.224506E
+                           1x1_HAV,64.779N,11.2193E
+                           1x1_SKO,65.79602N,12.219299E
+           Three-D Sites:  1x1_VIKE,60.88019N,7.16990E
+                           1x1_JOAS,60.86183N,7.16800E
+                           1x1_LIAH,60.85994N,7.19504E
+           Finnmark Site:  1x1_FINN,69.341088N,25.293524E
+
+           Other sites will be available:
+                  Finse (FNS) : 60.5938694N, 7.5272352E  (contact Yeliz, LATICE project) 
+                  Bayelva (BYV) : 78.92094N, 11.83334E   (contact Yeliz, LATICE project) 
+                  Iskoras (ISK) : 69.3405665N, 25.2956747E (contact Yeliz, LATICE project) 
+                  Hedmark/Trysil : the mire site with EC-flux measurements run by Norbert (Lena, Norbert)
+                  Svanhovd: has also an extensive record of environmental data (Stefanie, DoublePunch project)
+                  Adventdalen (ADVN) : 78.18333N, 15.91667E (Dev, Frans-Jan)
+                  Hurdal (HUR): ??? (Hanna)
+
+
+#--machine: where to run the model, saga is the only option at the moment
+#--project: your project number on saga
+
+cd ~/ctsm/cime/scripts
+./create_newcase --case ../../../ctsm_cases/YOUR_CASE_NAME --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --res 1x1_ALP1 --machine saga --run-unsupported --project nn2806k
+
+
+#### Copy inputdata for the site to your working directory, e.g.:
+
+cp /cluster/shared/noresm/inputdata_fates_platform/inputdata_version1.0.0_ALP1.tar /cluster/work/users/$USER/
+cd /cluster/work/users/$USER/
+tar xvf inputdata_version1.0.0_ALP1.tar
+
+#### Run a case
+
+cd ~/ctsm_cases/YOUR_CASE_NAME
+./case.setup      # create the $CASE.run file
+./case.build      # build model and create namelists
+./case.submit     # submit script
+                  # default setting only allow you to run 5 days test run.
+
+#### To run a longer simulation
+
+# Following parameters can be adapted for longer simulation
+
+./xmlchange --file env_run.xml --id RUN_STARTDATE --val 0001-01-01      # set up the starting date of your simulation 
+./xmlchange --file env_run.xml --id STOP_OPTION --val nyears            # set the simulation periods to "years"
+./xmlchange --file env_run.xml --id STOP_N --val 5                      # set the length of simulation, i.e, how many years
+./xmlchange --file env_run.xml --id CONTINUE_RUN --val TRUE             # if you want to continue your simulation from restart file, set it to TRUE
+./xmlchange --file env_run.xml --id RESUBMIT --val 10                   # set up how many times you want to resubmit your simulation.
+                                                                        # e.g, STOP_N=5, RESUBMIT=10, you will have simulation for 5+5*10=55 
+./xmlchange --file env_run.xml --id DATM_CLMNCEP_YR_START --val 1901    # set up the start year of the atmospheric forcing 
+./xmlchange --file env_run.xml --id DATM_CLMNCEP_YR_END --val 1950      # set up the end year of the atmospheric forcing
+./xmlchange --file env_workflow.xml --id JOB_WALLCLOCK_TIME --val 01:00:00   # set up longer time for runing the simulation 
+
+./case.submit 
+
+#### Checking the status of your simulation
+
+squeue -u YOUR_SAGA_ACCOUNT
+
+#### Checking the results of your simulation
+
+cd /cluster/work/users/YOUR_SAGA_ACCOUNT/ctsm/YOUR_CASE_NAME/run       # when model is running, model results and restart file are kept here
+cd /cluster/work/users/YOUR_SAGA_ACCOUNT/archive/YOUR_CASE_NAME        # when model is finished, model results and restart file are kept here
+
+=============================================================================================
+For more detail on the platform and its usage, please refere to "README_fates_emerald_api_expert_only"     
+=============================================================================================
+
+=============================================================================================
+    QUICKSTART on GALAXY:
+=============================================================================================
+Tutorials can be found at: https://github.com/NordicESMhub/galaxy-training-material/blob/fates/topics/climate/tutorials/fates/tutorial.md
+
+Available exerpiments and results using FATES_emerald_platform can be found: https://docs.google.com/spreadsheets/d/1yHFbRDTyYBv61klcgdJpIWNc5rN-FzBmMF50AgiPeWc/edit?usp=sharing
+
+
+
+
+

README_fates_emerald_api_expert_only

@@ -0,0 +1,74 @@
+$CTSMROOT/README_fates_emerald_api_expert_only                                          03/06/2020
+
+#################################################################################
+# This document explains how to update the model codes and 
+# how to create atmospheric forcing and inputdata for new sites
+# (No technical support will be promised, use at your own risk!)
+# See also Yeliz's notes: https://ctsm-docs.readthedocs.io/en/latest/ for additional details
+#################################################################################
+
+######## Two important things to watch out first!!!
+######## Two important things to watch out first!!!
+######## Two important things to watch out first!!!
+(1) Module environment on your supercomputer: DON'T load any module beforehand, except "StdEvn"!
+(2) Git version control: 
+    CLM-FATES have very complex and sperate repository system:
+      -> ctsm: always create your own branch, do not touch master!
+      -> cime: remember to create your own branch in cime folder also, to record all the changes you make.
+      -> fates: remember to create your own branch in fates folder also, to record all the changes you make.       
+      If you do not create your own branch for "cime" and "fates", when you run "./manage_externals/checkout_externals", your previous "cime" and "fates" will be overwritten.
+
+
+######## Download ctsm and update ctsm-fates (Only important steps are illustrated here!!!)
+**** If you are already using fates_emerald_api, skip this! ****
+e.g.:
+     git remote add ctsm_ncar https://github.com/ESCOMP/CTSM.git   # set a remote name for NCAR CTSM git repository
+     git fetch ctsm_ncar                    # get the most recent updates of CTSM
+     git merge ctsm_ncar/master             # update your current branch with the newest CTSM version
+     git merge ctsm_ncar/fates_next_api     # update your current branch with the newest CLM-FATES interface
+
+##To update fates, you need to go to fates folder
+e.g.:
+     git remote add NGEET_fates https://github.com/NGEET/fates.git
+     git fetch NGEET_fates    # get the most recent updates of FATES
+     git merge NGEET_fates.git/master # update your current branch with the newest FATES
+
+######## Adapt ctsm/cime to specific machine (e.g., SAGA and FRAM)
+**** If you are already using fates_emerald_api, skip this! ****
+Following file need to be modified
+..../cime/config/cesm/machines/config_batch.xml
+..../cime/config/cesm/machines/config_compilers.xml
+..../cime/config/cesm/machines/config_machines.xml
+
+See example here, you need look for the setup 
+https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_compilers.xml
+https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_machines.xml
+https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_batch.xml
+
+
+**** If you want to set up new sites, please follow the following steps ****
+######## Make script grids (see "prepare_inputdata.sh" in ~/ctsm/tools/emerald_sites_tools)
+######## Make domain file  (see "prepare_inputdata.sh" in ~/ctsm/tools/emerald_sites_tools)
+######## Make mapping file (see "prepare_inputdata.sh" in ~/ctsm/tools/emerald_sites_tools)
+######## Make surface data file (see "prepare_inputdata.sh" in ~/ctsm/tools/emerald_sites_tools)
+######## Make and modify FATES parameter file:
+         ## Use existing tools:
+           ./src/fates/tools/FatesPFTIndexSwapper.py        # Select PFTs interested. 
+           ./src/fates/tools/modify_fates_paramfile.py      # Modify PFT parameters  
+         ## To use these tools, netcdf and python modules need to be loaded.
+           module load netCDF-Fortran/4.4.4-intel-2018b 
+           module load Python/3.6.6-intel-2018b 
+          ./FatesPFTIndexSwapper.py --pft-indices=2,6,9,10 --fin=****.nc --fout=****.nc
+         ## The default FATES parameter file is in ./src/fates/parameter_files    
+         ## To create a netcdf parameter file: ncgen -o ****.nc fates_params_default.cdl
+######## Make atmospheric forcing for new sites (see "prepare_atm_forcing_****.ncl" in ./tools)
+
+######## Set each sites as a unique grid type. The following file need to be modified:
+~/ctsm/cime/config/cesm/config_grids.xml
+~/ctsm/cime/src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
+~/ctsm/bld/namelist_files/namelist_defaults_clm4_5.xml
+
+######## Set new atmospheric forcing for the sites
+~/ctsm/cime/src/components/data_comps/datm/cime_config/config_component.xml (for different climate forcing)
+~/ctsm/cime_config/config_component.xml (for different climate forcing)
+

bld/CLMBuildNamelist.pm

@@ -2341,9 +2341,9 @@ sub setup_logic_initial_conditions {
                 }
              }
           } else {
-             if ( $nl_flags->{'clm_start_type'} =~ /startup/  ) {
-                $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true");
-             }
+ #            if ( $nl_flags->{'clm_start_type'} =~ /startup/  ) {
+ #               $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true");
+#             }
              $try = $done;
           }
        } else {
@@ -3237,7 +3237,7 @@ sub setup_logic_popd_streams {
                     'sim_year_range'=>$nl_flags->{'sim_year_range'}, 'cnfireson'=>$nl_flags->{'cnfireson'});
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'},
-                 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+                 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
   } else {
      # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set
      if ( defined($nl->get_value('stream_year_first_popdens')) ||
@@ -3273,8 +3273,8 @@ sub setup_logic_urbantv_streams {
                  'sim_year_range'=>$nl_flags->{'sim_year_range'});
   }
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'},
-              'hgrid'=>"0.9x1.25" );
-}
+                  'hgrid'=>$nl_flags->{'res'} );
+  }
 
 #-------------------------------------------------------------------------------
 
@@ -3299,7 +3299,7 @@ sub setup_logic_lightning_streams {
                     'sim_year_range'=>$nl_flags->{'sim_year_range'});
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'use_cn'=>$nl_flags->{'use_cn'},
-                 'hgrid'=>$nl_flags->{'light_res'} );
+                 'hgrid'=>$nl_flags->{'res'} );
   } else {
      # If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set
      if ( defined($nl->get_value('stream_year_first_lightng')) ||