ELM Example Case I. Point Mode

ELM Examples of Setting-up, Configuring, Building, and Running I

Updated: 04-29-2024

NOTE:

• In these examples, there are 4 user-defined ENVs variables of directories: $E3SM_INPUTDATA, $E3SM_ROOT, $PROJECT_E3SM, for inputdata, e3sm model source codes, and root directory for cases and runs, respectively. USERS must have created these, and cloned both data and e3sm codes.

• $E3SM_INPUTDATA is cloned repository of a few site-level full datasets to run offline ELM, from pt-e3sm-inputdata

• Upon user's machine, $MACH_NAME is needed for E3SM. In these examples, 'mymac' for MacOS/linux, 'WSL2' for Windows Subsystem for Linux, OR, 'cades' for a cluster in ORNL, may be directly used. Additionally the example assumes using mpich for MPI, and if not, change '-mpilib mpich' STEP 1 to what in your system, e.g. ' -mpilib openmpi' for OPENMPI.

- CASE I. Single-Point User-Defined datm-elm.

An extra note (04-04-29): If you're using python 3.12 or above, 'distutils' IS totally removed but which are required by CIME. The alternative is 'setuptools', and if install it like: pip3 install setuptools, it will work seamlessly.

• STEP 1. Create a PTELM case

  cd $E3SM_ROOT/cime/scripts

  ./create_newcase -case $PROJECT_E3SM/cases/Test_elm-I1850CNPRDCTCBC -mach $MACH_NAME -compiler gnu -mpilib mpich -res ELM_USRDAT -compset I1850CNPRDCTCBC

NOTE: $MACH_NAME is one of machines supported in E3SM, which names could be found in $PROJECT_E3SM/cime_config/machines/config_machine.xml.

• STEP 2. Build the case created in STEP 1 (user-defined 1 point dataset, namely '1x1pt_US-Brw' from 1985-2015)

cd $PROJECT_E3SM/cases/Test_elm-I1850CNPRDCTCBC

./xmlchange: (or, vi env_run.xml)
             DATM_MODE=CLM1PT
             DATM_CLMNCEP_YR_START=1985
             DATM_CLMNCEP_YR_END=2015
             ELM_USRDAT_NAME=1x1pt_US-Brw_GRID
             ELM_FORCE_COLDSTART=on
             
./xmlchange --append --id ELM_BLDNML_OPTS --val "-bgc_spinup on"
(if ad spinup stage)
  
./case.setup 
(./case.setup --clean FOR cleaning-up)

If it's the first time, the ./case.setup will generate a long sentence of error message something like:

failed with error 'ERROR : CLM build-namelist::ELMBuildNamelist::add_default() : No default value found for fsurdat.
            Are defaults provided for this resolution and land mask?' from dir '/Users/f9y/project_e3sm/cases/Test_elm-I1850CNPRDCTCBC/Buildconf/elmconf'

It indicates 'fsurdat' NOT correctly set up, and mostly it's due to 'pt-e3sm-inputdata' 's file name issue. So do a softlink to the correct file, such as:

./case.build
(./case.build --clean FOR cleaning-up ALL components, and you may want to clean-up one or two)

The above steps will create a 'bld/' and '/run' directories, for model building and running, under:

$PROJECT_E3SM/Test_elm-I1850CNPRDCTCBC/

• STEP 3. Run the case

  ./case.submit

NOTE: THIS Case example would be simulating AmeriFlux US-Brw tower site more reasonably, if using a phenologically-modified ELM, in which upper 3 soil-layer averaged temperature is used to drive leaf-out for stressed PFTs, SEE modified ELM phenology