Run_tower: NEON

Run_tower: NEON#

Exercise: use the run_tower script to run a single point case at a NEON site

Create a case at the Abby Road site called ABBY.transient using the run_tower script in tools/site_and_regional that uses the NEON v4 input data.

Note: You will need to activate the ctsm_pylib conda environment to use the run_tower script. After creating you case you can check the status of the run after submitting.

Please ensure that you have completed all steps in the Download CTSM Tutorial before starting this exercise!

TODO, make sure we set up ctsm_pylib in the one_time_setup

Background#

NEON sites include the following:

 ABBY,BARR,BART,BLAN,BONA,CLBJ,CPER,DCFS,
 DEJU,DELA,DSNY,GRSM,GUAN,HARV,HEAL,JERC,
 JORN,KONA,KONZ,LAJA,LENO,MLBS,MOAB,NIWO,
 NOGP,OAES,ONAQ,ORNL,OSBS,PUUM,RMNP,SCBI,
 SERC,SJER,SOAP,SRER,STEI,STER,TALL,TEAK,
 TOOL,TREE,UKFS,UNDE,WOOD,WREF,YELL

You can find out more information about all of the terrestrial sites at the NEON science website

Assumptions#

Here are some assumptions we’ve built into NEON simulations that use the run_tower script:

  • Surface datasets: have a single plant functional type (PFT) that we consider ‘dominant’ for each NEON tower.

  • Surface datasets: have modified soil properties that are intended to match observations from the NEON MegaPit sampling.

  • DATM: are gap filled from NEON and mostly cover 2018-2024, although individual sites may have custom data ranges

  • Compset: You’ll be running a BGC case, but if you run an SP case the LAIs have not been adjusted with site conditions.

  • Parameter file: are default for the physics version of CLM being used. They have not been calibrated to site-level observations

  • Initial conditions: We provide initial conditions that were generated using an AD and postAD spinup for each site. Therefore, the default run-type is called ‘transient’, which means you’ll get time varrying CO2, nitrogen deposition, and aerosol deposition (from CMIP6 era forcings). Our aim is to generate new initial condition files that are consistent with major release version of CLM (e.g. CLM6). You may need to spinup the model if you’re using a different code base, parameter file, surface dataset.

Get started:#

Let’s use run_tower at a NEON site

Click here for hints

Is my workspace set up?

Did you already create a cases directory where you will put all new cases

cd /glade/u/home/$USER
mkdir cases

How do you use run_tower?

activate ctsm_pylib:

conda activate ctsm_pylib

move into the tools/site_and_regional directory and ask for help!

./run_tower --help

Look at all the options you have for running tower sites!

HINT: use the --neon-version flag to get the latest (v4) NEON data.

Use run_tower to create, setup, build and submit a case

Run_tower handles all four steps of the CESM workflow.

  1. First run_tower creates, sets up, and builds a base case.

  • This will take a few minutes; then

  1. Clones the base case

  2. Dowloads the DATM data and initial conditions from a NEON server

  • This prints a bunch of information to the screen.

  • It also can cause issues if the NEON server gets overloaded or goes down.

  1. Submits the {$SITE}.transient case

After you submit the run_tower script successfully you can check your job status.

How do I check my job status?

You can check job status using the command:

qstat -u $USER
Click here for the solution

Create a new case i1850_sp.basics with the command:

TODO, do we want to use the –output-root flag here?

cd /glade/u/home/$USER/code/my_clm_code/tools/site_and_regional
./run_tower --neon-sites ABBY \
            --output-root ~/cases/. \
            --neon-version v4 \
            --xmlchange PROJECT=tutorial

Case setup:

cd /glade/u/home/$USER/cases/ABBY.transient

Check the status:

qstat -u $USER

When the run is completed, look into the archive directory for: ABBY.transient.

Check that your archive directory on derecho (The path will be different on other machines):

cd ~/cases/archive/ABBY.transient
ls

Test your understanding#

  • Did your run complete successfully?

  • Where is your case directory?

  • Where is your run directory?

  • What sorts of files did you get as output?

  • What years did you run over?

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