Run_tower: PLUMBER2

Run_tower: PLUMBER2#

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

Create a case called BR-Sa3.test0 using the run_tower script in tools/site_and_regional.

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!

Background#

PLUMBER2 sites include the following:

AR-SLu,ARSLu,AT-Neu,AU-ASM,AU-Cow,AU-Cpr,AU-Ctr,AU-Cum,AU-DaP,AU-DaS,AU-Dry,AU-Emr,AU-GWW,AU-Gin,AU-How,AU-Lit,AU-Otw,AU-Rig,AU-Rob,AU-Sam,AU-Stp,AU-TTE,AU-Tum,AU-Whr,AU-Wrr,AU-Ync,BE-Bra,BE-Lon,BE-Vie,BR-Sa3,BW-Ma1,CA-NS1,CA-NS2,CA-NS4,CA-NS5,CA-NS6,CA-NS7,CA-Qcu,CA-Qfo,CA-SF1,CA-SF2,CA-SF3,CH-Cha,CH-Dav,CH-Fru,CH-Oe1,CN-Cha,CN-Cng,CN-Dan,CN-Din,CN-Du2,CN-HaM,CN-Qia,CZ-wet,DE-Bay,DE-Geb,DE-Gri,DE-Hai,DE-Kli,DE-Meh,DE-Obe,DE-Seh,DE-SfN,DE-Tha,DE-Wet,DK-Fou,DK-Lva,DK-Ris,DK-Sor,DK-ZaH,ES-ES1,ES-ES2,ES-LMa,ES-LgS,ES-VDA,ESLgS,FI-Hyy,FI-Kaa,FI-Lom,FI-Sod,FR-Fon,FR-Gri,FR-Hes,FR-LBr,FR-Lq1,FR-Lq2,FR-Pue,GF-Guy,HU-Bug,ID-Pag,IE-Ca1,IE-Dri,IT-Amp,IT-BCi,IT-CA1,IT-CA2,IT-CA3,IT-Col,IT-Cpz,IT-Isp,IT-LMa,IT-Lav,IT-MBo,IT-Mal,IT-Noe,IT-Non,IT-PT1,IT-Ren,IT-Ro1,IT-Ro2,IT-SR2,IT-SRo,JP-SMF,NL-Ca1,NL-Hor,NL-Loo,PL-wet,PT-Esp,PT-Mi1,PT-Mi2,RU-Che,RU-Fyo,RU-Zot,SD-Dem,SE-Deg,UK-Gri,UK-Ham,UK-PL3,US-AR1,US-AR2,US-ARM,US-Aud,US-Bar,US-Bkg,US-Blo,US-Bo1,US-Cop,US-FPe,US-GLE,US-Goo,US-Ha1,US-Ho1,US-KS2,US-Los,US-MMS,US-MOz,US-Me2,US-Me4,US-Me6,US-Myb,US-NR1,US-Ne1,US-Ne2,US-Ne3,US-PFa,US-Prr,US-SP1,US-SP2,US-SP3,US-SRG,US-SRM,US-Syv,US-Ton,US-Tw4,US-Twt,US-UMB,US-Var,US-WCr,US-Whs,US-Wkg,ZA-Kru,ZM-Mon

You can find out more information about the PLUMBER2 dataset and project in Ukkola et al (2022) with data available from this site (last accessed Oct 2026)

Assumptions#

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

  • Surface datasets: may have a single plant functional type (PFT), or multiple PFTs, depending on the site, othewise surface datasets have not been modified.

  • Data Atmosphere (DATM): Are of various lengths and set individually for each site.

  • Compset: You’ll be running a BGC case, but if you run an SP case we have LAI streams for each site.

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

  • Initial conditions: Are not provided, you’ll need to do your own spinup for PLUMBER2 cases, therefore the default run-type is for accelerated decomposition (AD) model.

Get started:#

Let’s use run_tower at a PLUMBER2 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 --experiment flag to add test0 to your case name

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. Configures the case to use the correct surface dataset and DATM data

  • we have copies of this for PLUMBER2 sites.

  1. Submits the {\(SITE}.{\)EXPERIMENT}.ad 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 BR-Sa.test0 with the command:

cd /glade/u/home/$USER/code/my_clm_code/tools/site_and_regional
./run_tower --plumber-sites BR-Sa \
            --output-root /glade/u/home/$USER/cases \
            --experiment test0 \
            --xmlchange PROJECT=tutorial

Move to your case directory: BR-Sa3.test0.ad:

cd /glade/u/home/$USER/cases/BR-Sa3.test0.ad

Check the status:

qstat -u $USER

When the run is completed, look into the archive directory for: BR-Sa3.test0.ad.

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

cd ~/cases/archive/BR-Sa3.test0.ad
ls

Test your understanding#

  • Did your run complete successfully?

  • What sorts of files did you get as output?

  • How long is the simulation?

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