AK K64G Demo Quick Start Guide 2: one year simulation of transient run - FASSt-simulation/fasst_simulation_tools GitHub Wiki

NGEE-Arctic: AK-K64G simulation example 2

This example 2 runs a single-point, extracted from half-degree Global data, ELM v2 simulation, within which NGEE Kougarok Mile 64 study site located.

(1) It will start from an initial restart file from after-final-spinup in regular run of a site, but with option --site_name=kougarok

(2) It will copy 4 default ELM point input files, namely domain.nc, surfdata.nc, surfdata.pftdyn.nc, and clm_parameters.nc, to a temporary work directory for purpose of user modification.

(3) The model run will output an EXTRA user-specified variables and for individual PFT if variable(s) are for plants. An example user namelist, user_nl_elm, for such a purpose is in the temporary work directory as well.

(4) Once again, the simulation is setup and executed using the Offline Land Model Testbed developed and maintained by Dan Ricciuto ([email protected]).

(5) Keep in mind that this demo is configured with ELM default input data of one half-degree grid which NGEE KM64 Site located within. AND you may notice that simulations would not be good if comparing to site-level observations.

FIELD/LAB Researchers can contribute a lot to make model reasonably well.

I. Quick Start Example 2

NOTE IF NOT YET but you'd like to try a NGEE-Arctic site other than Kougarok (code name: AK-64G), please do a full run of example using --site_name=beo, or --site_name=teller, or --site_name=council, as in regular full run of a site

Step 1. Create docker volume named "elmwork" 

docker volume create elmwork

OR, If you started Docker Desktop APP, it may be done like shown in following, by clicking upper-right corner button create+:

Step 2. Run the model of 1 year transient simulation using OLMT

  • This example uses an OLMT built-in example script /tools/OLMT/examples/site_fullrun_docker_transient_nyears.sh to setup the simulation for the AK-64G (Kougarok ELM grid) and set the options including:

  • Prior to run OLMT, a few ELM input data for a site including parameter files are copied into a work directory for purpose of modification.

  • the number of transient simulation years, one year;

  • using an initial restart file from final spinup stage.

docker run -t -i --hostname=docker --user=modeluser -v elmdata:/inputdata/ -v elmoutput:/output/ -v elmwork:/tmp/ fasstsimulation/elm-builds:elm_v2-for-ngee_multiarch /bin/bash /tools/OLMT/examples/site_fullrun_docker_transient_nyears.sh --transient_years=1

NOTE: /bin/bash /tools/OLMT/examples/site_fullrun_docker_transient_nyears.sh can have 4 options:

(1) --transient_years=* or -trsy=* : for user-provided transient run years from 1850, by default 10 (i.e. 1850-1859). Full transient run is 165 (i.e. from 1850 - 2014).

(2) --init_ncfile=* or -finit=* : for user-provided restart initial file, including full path. By default is /tools/OLMT/examples/site_fullrun_docker_tr_demo_ini.nc, which is provided for AK-K64G transient run as an example.

If you've already done regular run of a site, but with option --site_name=kougarok, you can set this option, like -finit=/output/cime_run_dirs/OLMT_AK-K64G_ICB1850CNPRDCTCBC/run/OLMT_AK-64G_ICB1850CNPRDCTCBC.elm.h0.0601-01-01-00000.nc

(3) --site_name=* or -sn=* : for user-provided NGEE Arctic site name, one of kougarok (default), council, teller, or beo. Other than default (kougarok), it must be used together with option (2), for an example, like -finit=/output/cime_run_dirs/OLMT_AK-BEOG_ICB1850CNPRDCTCBC/run/OLMT_AK-BEOG_ICB1850CNPRDCTCBC.elm.h0.0601-01-01-00000.nc, with --site_name=beo for NGEE-Arctic site Utqiagvik (beo stands for Barrow Ecological Observatory, a long-term ecological study sites outside Utqiagvik, AK).

(4) --case_prefix=* or -prefix=*: for user-defined simulation name prefix, default is My. For users to save and later compare ELM outputs of a different setups of a same site, this option is very useful. Otherwise, each time a total new simulation will run.

II. Visualizing elm outputs in jupyter notebook

NOTE:

(1) assuming you've already installed Docker and its Desktop App.

(2) assuming you've already had 'fasstsimulations/fasst_simulation_tools' docker pulled as shown here.

And better (but not necessary) to have practiced with example here.

STEP 1. Launch/run docker 'fasst_simuation_tools'.

In a NEW Terminal, type the following command (OR, when you moving mouse pointer over the following, a 'copy' ibutton will show up and click it to copy, and then Paste it into Terminal):

docker run -t -i  -v elmdata:/home/jovyan/inputdata -v elmoutput:/home/jovyan/output/ -v elmwork:/home/jovyan/work/ -p 8888:8888 fasstsimulation/fasst_simulation_tools:elmlab_3.3.2

if successful, the following message will show in your terminal window,

AS hinted, do one of 3 methods to lanuch jupyter notebook, e.g. copy the last line with http:// into YOUR internet browser. The following will be showing, maybe slightly different in yours. AND thereforward you're going to do visiualization in this browser windows.

OR, FROM Docker Desktop APP,

  • navigate to LEFT 'Containers', right-click the right column of 'ACTIONS' 3 vertical dots, of IMAGE 'fasstsimulation/fasst_simulation_tools' with STATUS 'Running'. It will show a few actions, like
  • Click View details, will show like:

The bottom line with http:// is clickable. By Clicking it will open in your internet brower.

STEP 3. Visualizing specified ELM output variable of customized starting/ending years.

  • Click-open LEFT pannel's scripts folder.

NOTE that: That blue-highlighted file, plot_ELM_variable_v2.ipynb, which is going to run in this example with a few editing.

  • Click-open the script file, plot_ELM_variable_v2.ipynb, it shall be showing:

NOTE: pay attention to the upper bar with a few useful buttons, like image

AND, Click that fast-forward button, it will run script for current simulations in elmoutput, and pick the first one and plot default variable, GPP. Scrolling down to bottom, you will see:

  • Choose or EDIT a few options, e.g. Case, Output file, Variable, starting year, ending year, ...

TIPS that elm run above only for 1 year, with output path of /output/cime_run_dirs/My_AK-K64G_ICB20TRCNPRDCTC/run/, file ELM_output.nc is default ELM output including a few hundred variables, and ELM_output_pft.nc is user-defined output with individual PFT specific varialbes (if any).

(1) ELM case.

Scrolling up to Cell [3], you will see:

The CASE name is My_AK-K64G_ICB20TRCNPRDCTC. If you have multiple runs done, will be shown if you click the drop-down arrow.

(2) ELM output file, Combined PFTs or Individual PFTs

Further Scrolling down to Cell [5], you will see file choosing for visualizing (by default Combined PFTs):

(3) ELM output variable, starting year, and/or ending year

Scrolling down to [8], it will show drop-down box for variable to pick up (By default, GPP, 1850, 1851 or 2015),

FOR AN EXAMPLE, Let's choose: Individual PFTs, TLAI (total leaf area index), 1850 - 1851, (AND moving mouse cursor or cell by clicking one-step advance button, image in the upper bar):

Until end of script, it will plot like following,

NOTE that there are 3 lines of data, each of which is for a PFT in the simulation. Here in this example, site vegetation is composed of 3 PFTs, even-green boreal trees (index 3), deciduous shrubs (index 11) and arctic grasses (index 12).

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