$CTSMROOT/README 04/19/2023 Community Terrestrial Systems Model (CTSM) science version 5.2 series -- source code, tools, offline-build and test scripts. This gives you everything you need to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRU NCEP or GSWP3 forcing data in place of a modeled atmosphere. CMEPS is the Community Mediator for Earth Prediction Systems. And CDEPS is the Community Data Models for Earth Prediction System. They are both NUOPC based models used to drive the CESM (Community Earth System Model) of which CTSM is a component of. NUOPC is the National Unified Operational Prediction Capability a standard way of building coupled model systems. The NUOPC layer is based on the Earth System Modeling Framework (ESMF). For lists of current bugs (issues) and current development see the CTSM GitHub page: https://github.com/ESCOMP/CTSM INFORMATION ON THE CMEPS DRIVER: https://escomp.github.io/CMEPS https://earthsystemmodeling.org/nuopc/ IMPORTANT NOTE ON CESM CHECKOUT VERSUS A CTSM CHECKOUT: If this is the top level directory from making a clone of CTSM the directory structure is a little bit different than if CTSM is from a clone of the entire CESM. If this is part of CESM this directory will be under components/clm alongside other CESM component models. For a CTSM checkout this will be the top level directory. Other documentation will refer to $CTSMROOT and it means the directory that this file is at. CIMEROOT is the directory where "cime" is for this checkout. For a CESM checkout $CIMEROOT will be the "cime" directory beneath the top level directory. For a CTSM checkout $CIMEROOT will be $CTSMROOT/cime. IMPORTANT NOTE ABOUT (deprecated) Anything marked with (deprecated) is something is going to be removed in a future update. Often this means it will be replaced with something else. General directory structure ($CTSMROOT): doc --------------- Documentation of CTSM. bld --------------- build-namelist scripts for CTSM. src --------------- CTSM Source code. lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model) test -------------- CTSM Testing scripts for CTSM offline tools (deprecated) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings manage_externals -- Script to manage the external source directories (deprecated) py_env_create ----- Script to setup the python environment for CTSM python tools using conda python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts Directory structure only for a CTSM checkout: components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models) libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO (deprecated) share ------------- CESM shared code ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM cime/scripts --------------- cesm/cime driver scripts components/cmeps -------------------- CESM top level driver (for NUOPC driver [which is the default]) source code. components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver). components/cism --------------------- CESM Community land Ice Sheet Model. components/mosart ------------------- Model for Scale Adaptive River Transport components/rtm ---------------------- CESM River Transport Model. components/cpl7 --------------------- CESM top level driver for MCT driver (deprecated will be removed) Top level documentation ($CTSMROOT): README ------------------- This file README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git README.rst --------------- File that displays under the project in github README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated) CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project Copyright ---------------- CESM Copyright file doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the ChangeLog/ChangeSum files doc/ChangeLog ------------ Documents different CTSM versions doc/ChangeSum ------------ Summary documentation of different CTSM versions doc/design --------------- Software Engineering and code design document files Checklists for standard Software Engineering tasks ./doc/README.CHECKLIST.master_tags ./bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md Documentation of Namelist Items: (view the following in a web browser) bld/namelist_files/namelist_definition_ctsm.xml --- Definition of all namelist items bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values ============================================================================================= Important files in main directories (under $CTSMROOT): ============================================================================================= Externals.cfg --------------- File for management of the main high level external (deprecated) Externals_CLM.cfg ----------- File for management of the CTSM specific externals (i.e. FATES) run_sys_tests --------------- Python script to send the standard CTSM testing off (submits the create_test test suite for several different compilers on the machines we do standard CTSM testing on). parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test (can be used along with run_sys_tests) doc/Quickstart.GUIDE -------- Quick guide to using NUOPC scripts. doc/IMPORTANT_NOTES --------- Some important notes about this version of CTSM, configuration modes and namelist items that are not validated or functional. doc/ChangeLog --------------- Detailed list of changes for each model version. doc/ChangeSum --------------- Summary one-line list of changes for each model version. doc/UsersGuide -------------- CTSM Users Guide doc/IMPORTANT_NOTES --------- Some important notes on caveats for some configurations/namelist items bld/README ------------------ Description of how to use the build-namelist scripts. bld/build-namelist ---------- Script to build CTSM namelists. cime_config/buildnml ------------- Build the CTSM namelist for CIME cime_config/buildlib ------------- Build the CTSM library cime_config/config_compsets.xml -- Define CTSM compsets cime_config/config_component.xml - Define CTSM XML settings cime_config/config_tests.xml ----- Define CTSM specific tests cime_config/config_pes.xml ------- Define Processor layouts for various CTSM grids and compsets cime_config/testdefs ------------- Directory for specification of CTSM testing cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs (These are directories that add specific user modifications to simulations created using "cime/scripts/create_newcase --user-mods-dir".) tools/mksurfdata_esmf --------- Directory to build program to create surface dataset at any resolution. tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded format. tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid (deprecated) tools/crop_calendars ---------- Tools to process and process and create crop calendar datasets for CTSM tools/modify_input_files ------ Script to modify existing CTSM input datasets in standard ways tools/site_and_regional ------- Scripts to create input datasets for single site and regional cases, primarily by modifying existing global datasets tools/contrib ----------------- Miscellansous useful scripts for pre and post processing as well as case management of CTSM. These scripts are contributed by users and may not be as well tested or supported as other tools. ============================================================================================= Source code directory structure: ============================================================================================= src/biogeochem ---- Biogeochemisty src/main ---------- Main control and high level code src/cpl ----------- Land model high level caps for NUOPC driver (and MCT and LILAC) src/biogeophys ---- Biogeophysics (Hydrology) src/dyn_subgrid --- Dynamic land unit change src/init_interp --- Online interpolation scr/fates --------- FATES model and sub-directories Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Experimental Ecosystem Demography model src/utils --------- Utility codes src/self_tests ---- Internal testing (unit tests run as a part of a CTSM simulation) src/unit_test_shr - Unit test shared modules for unit testing src/unit_test_stubs Unit test stubs that replicate CTSM code simpler ============================================================================================= QUICKSTART: using the NUOPC driver scripts ============================================================================================= cd $CIMEROOT/scripts ./create_newcase # get help on how to run create_newcase ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm60BgcCrop # create new "I" case for default machine at 1.9x2.5_gx1v7 # "I2000Clm60BgcCrop" case is clm6_0 physics, CDEPS, and inactive ice/ocn/glc # and MOSART for river-routing cd testI ./case.setup # create the $CASE.run file ./case.build # build model and create namelists ./case.submit # submit script # (NOTE: ./xmlchange RESUBMIT=10 to set RESUBMIT to number # # of times to automatically resubmit -- 10 in this example)