Training - Video Tutorial

A series of videos for helping you to get started running JULES with rose/cylc

Tutorial 1 – Check Out and Go

Objective – [Duplicate and] check out an existing suite and modify for your computer system

  1. Cache met office repository password
  2. Checkout JULES at version 5.2 release to an appropriate location
    • fcm checkout fcm:jules.x_tr@vn5.2 $HOME/JULES/vn5.2
    • [If you don't have the fcm keywords set up use: fcm checkout https://code.metoffice.gov.uk/svn/jules/main/trunk@12251 $HOME/JULES/vn5.2]
  3. Start rosie using: “rosie go”
  4. Search for and copy suite number: u-bb219
    • Right click on the suite and select copy. This will create your own suite, with aunique ID, that you are free to edit and commit to the repository to save any changes you make.
  5. Open your newly created suite, this will trigger a couple of warning messages regarding your meta data, hence the first task:
  6. Update the fcm-make and jules metadata paths to your JULES version 5.2 release location
    1. Click on the fcm-make tab in the left hand column, and replace the dummy path with ~/JULES/vn5.2/rose-meta/jules-fcm-make/HEAD
    2. Click on the jules tab in the left hand column, and replace the dummy path with ~/JULES/vn5.2/rose-meta/jules-standalone/HEAD
    • Your suite now knows how to treat all the options you want to provide
  7. Configure the fcm-make options:
    1. Click on the fcm make -> Build Configuration tab.
    2. If you are using a platform known by jules, select the appropriate platform from the drop down box.
    3. If not you need to know your fortran compiler and the location of your netCDF libraries. You do not need to include the OMP or MPI parallesation options for this suite.
  8. Configure the JULES configuration:
    • Choose an appropriate output location (I recommend '$HOME/JULES_Tutorial/output' for compatibility with my plotting script)
    • ensure you create this output directory: mkdir -p '$HOME/JULES_Tutorial/output'
  9. Check and Save the suite (the "ABC" button), then Run the suite (the play button)
    • This will open a gui control window which informs you of the status of your "job".
    • There are 2 stages for this job, fcm_make and jules.
  10. When the job has succeeded open up the suite location from the "Tools" drop down menu.
  11. You can plot the output using JT_plot_output.py from this terminal:
    • ./JT_plot_output.py [-data_dir /your/output/directory]
  12. If all this has worked you can commit your changes to your repository using the "fcm commit" command
    • This opens your terminal defaul text editor, usually vi. Enter here a message you want to accompany your suite revision, e.g. "my first successful jules run".
      • To start typing in vi press the "i" jey, when  you have finished typing press "Esc", to save and close type ":wq" then hit return.
    • After you close you the text editor confirm that you want to commit the changes.

 

Tutorial 2 – Spin Me Round

Objective – Familiarise yourself with run options in the rose/cylc environment by Investigating the effect of model spin up.

  1. Continue from Tutorial 1
  2. Go to the spin up tab in the rose suite
  3. Set up and run a simulation with no spin up and output the data with an appropriate run_id (e.g. spinup_0).
  4. Set up and run simulations with 1, 5 and 10 year spin up durations and output with appropriate run-ids (e.g. spinup_1, spinup_5 and spinup_10)
  5. When all are complete plot the output using JT_plot_output_multi.py from your rose suite directory (~/roses/u-bb219/), i.e. if the recommend run_ids were used:
    • ./JT_plot_output_multi.py -run_ids spinup_0,spinup_1,spinup_5,spinup_10

 

TUTORIAL 3 – Go Green

Objective - Familiarise yourself with science options in the rose/cylc environment by investigating various vegetation options.

  1. Continue from Tutorial 2
  2. Head to the science settings -> vegetation tab. Nothing is set to true, in particular the l_phenol and l_triffid options. This means we are using static vegetation (constant lai and canopy height), which will be our first simulation.
  3. Whilst we are here, lets activate the various _fix options, set l_trait_phys=True, can_model=4 and can_rad_mod=6 which will make our simulation a little more up-to-date. To see the documentation regarding these options please refer to the JULES user guide.
  4. Head back to the output tab and change the run_id to something relevant, e.g. Static_Vegetation.
  5. Head to the output -> profiles -> (1) tab and add gpp_gb to the output variables (for a  full list of output variables refer to the JULES user guide)
  6. Save and Run the simulation.
  7. For our next run we are going to activate leaf phenology, head to the science options -> vegetation tab and set l_phenol to True…. Various warning messages have popped up, address all these issues:
    1. phenol_period = 1
    2. add lai to the initial conditions with a constant value of 3
  8. Head back to the output tab and change the run_id to something relevant, e.g. Phenol_Vegetation.
  9. Save and Run the simulation.
  10. For our next run we are going to activate leaf phenology, head to the science options -> vegetation tab and set l_triffid to True…. Various warning messages have popped up, address all these issues:
    1. triffid_period = 1
    2. soil biogeochemistry model = RothC
    3. add canht to the initial conditions with a constant value of 3
  11. Head back to the output tab and change the run_id to something relevant, e.g. TRIFFID_Vegetation.
  12. Save and run the simulation
  13. When all are complete plot the output using JT_plot_output_multi.py from your rose suite directory (~/roses/u-bb219/), i.e. if the recommend run_ids were used:
    • ./JT_plot_output_multi.py -run_ids Static_Vegetation,Phenol_Vegetation,TRIFFID_Vegetation