Skip to content

Example CTSM (CLM5) run: US NR1 (Niwot Ridge, Colorado)

Jump to bottom
Shawn P. Serbin edited this page Sep 18, 2019 · 7 revisions

Option 1: Run the Jupyter notebook https://github.com/serbinsh/ctsm_containers/blob/master/notebooks/ctsm/run_ctsm_example_1.ipynb

Option 2: Run in the basic bash terminal

  1. Install the Docker engine: https://www.docker.com/get-started

  1. Pull down the latest version of the basic CTSM Docker container
    docker pull serbinsh/ctsm_containers:ctsm-release-clm5.0.18

  1. Setup and run the docker container to develop the CTSM (CLM5) example case at US-NR1 Options: output folder on the host and container: ~/scratch:/ctsm_output Start year: '1998-01-01' Number of run years: 2
docker run -t -i --hostname=docker --user clmuser -v ~/Data/cesm_input_data:/data -v ~/scratch:/ctsm_output serbinsh/ctsm_containers:ctsm-release-clm5.0.18 /ctsm_run_scripts/create_case_1pt_example_USNR1.sh '1998-01-01' 2

This will start building the case, example:

130-199-9-234:~ sserbin$ docker run -t -i --hostname=docker --user clmuser -v ~/Data/cesm_input_data:/data -v ~/scratch:/ctsm_output serbinsh/ctsm_containers:ctsm-release-clm5.0.18 /ctsm_run_scripts/create_case_1pt_example_USNR1.sh '1998-01-01' 2
/ctsm_run_scripts
Start year: 1998-01-01
Number of years: 2
*** start: 1552924779
*** Building CASE: /ctsm_output/CLM5_1552924779
Running with CTSM location: /ctsm
Compset longname is 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV
Compset specification file is /ctsm/cime/../cime_config/config_compsets.xml
Compset forcing is 1972-2004
ATM component is  Data driven ATM  GSWP3v1 data set
LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:
ICE component is Stub ice component
OCN component is Stub ocn component
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is Stub glacier (land ice) component
WAV component is Stub wave component
ESP component is
Pes     specification file is /ctsm/cime/../cime_config/config_pes.xml
Machine is docker
Pes setting: grid match    is l%0.9x1.25
Pes setting: grid          is a%0.9x1.25_l%0.9x1.25_oi%null_r%r05_g%null_w%null_m%gx1v6
Pes setting: compset       is 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV
Pes setting: tasks       is {'NTASKS_ATM': -4, 'NTASKS_ICE': -4, 'NTASKS_CPL': -4, 'NTASKS_LND': -4, 'NTASKS_WAV': -4, 'NTASKS_ROF': -4, 'NTASKS_OCN': -4, 'NTASKS_GLC': -4}
Pes setting: threads     is {'NTHRDS_ICE': 1, 'NTHRDS_ATM': 1, 'NTHRDS_ROF': 1, 'NTHRDS_LND': 1, 'NTHRDS_WAV': 1, 'NTHRDS_OCN': 1, 'NTHRDS_CPL': 1, 'NTHRDS_GLC': 1}
Pes setting: rootpe      is {'ROOTPE_OCN': 0, 'ROOTPE_LND': 0, 'ROOTPE_ATM': 0, 'ROOTPE_ICE': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0, 'ROOTPE_ROF': 0, 'ROOTPE_GLC': 0}
Pes setting: pstrid      is {}
Pes other settings: {}
Pes comments: none
 Compset is: 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV
 Grid is: a%0.9x1.25_l%0.9x1.25_oi%null_r%r05_g%null_w%null_m%gx1v6
 Components in compset are: ['datm', 'clm', 'sice', 'socn', 'mosart', 'sglc', 'swav', 'sesp', 'drv', 'dart']
No project info available
No charge_account info available, using value from PROJECT
No project info available
cesm model version found: release-clm5.0.18
Batch_system_type is none
 Creating Case directory /ctsm_output/CLM5_1552924779
*** Switching directory to CASE: /ctsm_output/CLM5_1552924779
...

Take note of the auto-generated output folder in ~/scratch CLM5_1552924779


  1. Once the build is finished, run the case:
docker run -t -i --hostname=docker --user clmuser -v ~/Data/cesm_input_data:/data -v ~/scratch:/ctsm_output serbinsh/ctsm_containers:ctsm-release-clm5.0.18 /bin/sh -c 'cd /ctsm_output/CLM5_1552924779/ && ./case.submit'

  1. Explore the outputs!

e.g. concatenate the outputs together and plot using ncview

130-199-9-234:run sserbin$ cd ~/scratch/CLM5_1552927029/run/

130-199-9-234:run sserbin$ ncrcat CLM5_1552927029.clm2.h0.* all_years.nc

130-199-9-234:run sserbin$ ncview all_years.nc
Clone this wiki locally