4a. Option 1: Run a pair of piControl and midHolocene simulations

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4a. Option 1: Run a pair of piControl and midHolocene simulations#

Tutorials at the 2025 paleoCAMP | June 16–June 30, 2025

Jiang Zhu
jiangzhu@ucar.edu
Climate & Global Dynamics Laboratory
NSF National Center for Atmospheric Research

Learning Objectives:

  • Run simple CESM simulations

  • Gain hands-on skills on customizing the run length and namelists

  • Know the importance of validating your numerical experiments

Time to learn: 60 minutes

How to get started?

Use terminal from your system directly

ssh -XY YOUR_SUERNAME@derecho.hpc.ucar.edu

Type in your CIT password (the one you set up with CISL) and approve the DUO push

Derecho SSH

REMINDER: CESM directories

  • Source Code Directory (“Headquarter”): /glade/work/jiangzhu/paleocamp/cesm2.1.5/

  • Case Directory (“Production Control Room”): e.g., ~/b.e21.B1850.f19_g17.piControl.001

  • Run directory (“Factory”): e.g., /glade/derecho/scratch/jiangzhu/b.e21.B1850.f19_g17.piControl.001/run

  • Archive directory (“Storage”): /glade/derecho/scratch/jiangzhu/archive/b.e21.B1850.f19_g17.piControl.001/

Task 1: run a fully coupled preindustrial simulation for one year#

Hints:#

  • What are the four steps?

  • What is the compset for fully coupled preindustrial?

  • Use resolution of f19_g17 for fast throughput

  • Following the CESM naming conventions, use b.e21.B1850.f19_g17.piControl.001 as the case name

  • Which XML variable should you change to tell the model to run for one year? (do this before ./case.submit)

  • It may take ~16 minutes to finish the one-year simulation.

Click here for the solution

1. create a new case: go into the scripts directory in the CESM Code and run the create_newcase command

cd /glade/work/jiangzhu/paleocamp/cesm2.1.5/cime/scripts
./create_newcase --case ~/b.e21.B1850.f19_g17.piControl.001 --compset B1850 --res f19_g17 --project UAZN0042

2. case setup: go into the Case Directory and run case.setup

cd ~/b.e21.B1850.f19_g17.piControl.001
./case.setup

3. case build: stay in the Case Directory and run case.build (change the run length using xmlchange)

./xmlchange STOP_OPTION=nyears,STOP_N=1
./case.build

4. Build and submit

./case.submit

Further information#

  • Building the executable may take more than 10 minutes.

  • While you wait, open a second terminal and practice your Unix commands (such as cd, ls, and grep) by visiting your directories of “Production Control Room”, “Factory”, and “Headquarter”, and see what are there.

  • After submitting the job, use qstat -u YOUR_USERNAME to check the status of your job.

  • Once the model is running, select one of your favorite components and read the log file (in the Run Directory, “Factory”) and see what the model is doing.

Task 2: run a fully coupled mid-Holocene simulation with the orbital forcing for one year#

Hints:#

  • Use compset B1850 and edit user_nl_cpl to set up the orbital configuration (no mid-Holocene compset available)

  • Following the CESM naming conventions, use b.e21.B1850.f19_g17.midHolocene.001 as the case name

  • According to Table 1 of Otto-Bliesner et al., (2017), Eccentricity = 0.018682, Obliquity (degrees) = 24.105, Perihelion = 0.87 (for simplicity, we don’t consider the other forcings here, i.e., CO2)

    • In the CESM world, this means

      • orb_mode = “fixed_parameters”

      • orb_eccen = 0.018682

      • orb_obliq = 24.105

      • orb_mvelp = 0.87

    • Search orb_ here to learn more

  • Use Unix editor vi/emacs/nano to open, edit, and save (Use nano if you are not familiar with the other two)

    • nano user_nl_cpl

  • These namelist changes can be done after case.build but before case.submit

Click here for the solution

1. create a new case: go into scripts directory in the CESM Code and run the create_newcase command

cd /glade/work/jiangzhu/paleocamp/cesm2.1.5/cime/scripts
./create_newcase --case ~/b.e21.B1850.f19_g17.midHolocene.001 --compset B1850 --res f19_g17  --project UAZN0042

2. case setup: go into the Case Directory and run case.setup

cd ~/b.e21.B1850.f19_g17.midHolocene.001
./case.setup

3. case build: stay in the Case Directory and run case.build

  • Add the following to user_nl_cpl

 orb_mode = "fixed_parameters"
 orb_eccen = 0.018682
 orb_obliq = 24.105
 orb_mvelp = 0.87

  • Change run length and build the case

./xmlchange STOP_OPTION=nyears,STOP_N=1
./case.build

4. Build and submit

./case.submit

Task 3: how to validate your simulation setup#

Hints:#

  • Going through the log files (in the RUN directory, aka “Factory”) is one way to see how the model is being run.

  • Examining *_in files (e.g., CasesDocs/drv_in in the Case Directory) is another way to check the setup.

Click here for the solution

  1. If you want to check the log file, cpl.log.xxx, in the Run Directory (when model is still running) or in your Storage Directory (when the simulation and archiving have finished).

e.g.,
vi /glade/derecho/scratch/jiangzhu/archive/b.e21.B1850.f19_g17.midHolocene.001/logs/cpl.log.3950708.desched1.240330-011322.gz

type /orb_params to search, you should see the following

 (shr_orb_params) Calculate characteristics of the orbit:
 (shr_orb_params) Calculate orbit for year:     -4050
 (shr_orb_params) ------ Computed Orbital Parameters ------
 (shr_orb_params) Eccentricity      =   1.868182E-02
 (shr_orb_params) Obliquity (deg)   =   2.410538E+01
 (shr_orb_params) Obliquity (rad)   =   4.207183E-01
 (shr_orb_params) Long of perh(deg) =   8.696128E-01
 (shr_orb_params) Long of perh(rad) =   3.156770E+00
 (shr_orb_params) Long at v.e.(rad) =  -5.751115E-04

Try also grep shr_orb_params YOUR_cpl.log

  1. If you want to check the drv_in file

vi /glade/u/home/jiangzhu/b.e21.B1850.f19_g17.midHolocene.001/CaseDocs/drv_in

type /orb_ to search, you should see the following

   orb_eccen = 0.018682
   orb_mode = "fixed_parameters"
   orb_mvelp = 0.87
   orb_obliq = 24.105

Try also grep orb_ CaseDocs/drv_in in the Case Directory

Tip: Quick visualization of CESM output on Derecho#

  • Option 1: Use ncvis (recommended)

cd /glade/derecho/scratch/jiangzhu/archive/b.e21.B1850.f19_g17.piControl.001/atm/hist
ncvis b.e21.B1850.f19_g17.piControl.001.cam.h0.0001-07.nc

If the system cannot find ncvis, you can use /glade/u/home/ullrich/ncvis/ncvis b.e21.B1850.f19_g17.piControl.001.cam.h0.0001-07.nc

  • Option 2: Use ncview (lightweight alternativ)

module load ncview
cd /glade/derecho/scratch/jiangzhu/archive/b.e21.B1850.f19_g17.piControl.001/atm/hist
ncview b.e21.B1850.f19_g17.piControl.001.cam.h0.0001-07.nc

Summary#

  • Set up and run a CESM simulation in four steps

  • Customize the simulation with xmlchange and namelist modifications

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