Generic Single Point

Generic Single Point#

Exercise: Subset a global dataset to run a generic single point case

  1. Subset our global datasets to run for a single point

  2. Create and run a case called Boulder_bgc.generic using the:

  • compset I1PtClm60BgcRsGs, the

  • resolution CLM_USRDAT, and that

  • applies USERMODS to use the subset data

In this tutorial we’ll use the subset_data script to create a surface dataset and data atmosphere (datm) for a particular point. Then we’ll create a case using the CTSM workflow with the usermods created by subset_data.

Background#

Subset_data#

Exercise

  • Activate ctsm_pylib and

  • Move into the tools/site_and_regional directory:

conda activate ctsm_pylib
cd /glade/u/home/$USER/code/my_clm_code/tools/site_and_regional

  • Look at the arguments subset_data requires for single point applications:

./subset_data point --help

You should see lots of arguments, starting with:

  --lat PLAT            Single point latitude. [default: 42.5]
  --lon PLON            Single point longitude. [default: 287.8]
  --lon-type {180,360}  Whether longitudes are in the [-180, 180] format (centered around the
                        Prime/0th Meridian) or the [0, 360] format (centered around the 180th
                        Meridian). Choose by specifying the upper limit.
  --site SITE_NAME      Site name or tag. [default: ]
  --uniform-snowpack    Modify surface data to have a uniform snow fraction.
  --include-nonveg      Do not zero non-vegetation land units in the surface data.
  --cap-saturation      Modify surface data to not allow saturation excess.
  --evenly_split_cropland
                        Introduce equal areas of all crops
  --dompft [DOM_PFT ...]
                        Dominant PFT(s): if we set the grid to 100% one or multiple PFTs
                        [default: None]
  ....

The subset_data script provides lots of ways to customize your surface dataset! First let’s create a place to store your data and usermods

mkdir ~/boulder_point_data

The example that follows highlights some of the common ways you can do this. Specifically in this example we’ll create a:

  • surface dataset for a single point case centered around Boulder, Colorado that assumes 100% temperate needleleaf evergreen trees and uniform snow coverage across the gridcell.

  • Data atmosphere subset from CRUJRA for the year 2020

  • usermods that can point to the data we created.

./subset_data point --lat 40.015 --lon -105.27 \
                    --lon-type 180 --site Boulder \
                    --uniform-snowpack --dompft 1 \
                    --create-surface  \
                    --create-datm  \
                    --datm-syr 2020 --datm-eyr 2020 \
                    --create-user-mods \
                    --outdir ~/boulder_point_data \
                    --user-mods-dir ~/boulder_point_data/usermods

Look at the files created:

ls -1 ~/boulder_point_data

expected output includes:

datmdata
surfdata_Boulder_hist_2000_16pfts_c261014.nc
usermods

Check Your Understanding

What does your datm data look like?

What does your surface data look like?

Hint: use ncdump -h

Usermods#

A usermod directory (“user modifications” directory) is a bundle of case-specific settings that CLM/CIME can apply when you create or clone a case. It’s a convenient way to start from a known configuration rather than manually setting every option afterward. The usermods may include files such as CLM namelist settings (user_nl_clm), settings for other model components, and XML configuration changes.

You pass the bundle to CIME when creating a case. For example:

./create_newcase ... --user-mods-dir ~/boulder_point_data/usermods
Exercise

You can look to see what usermods settings your Boulder cases will inherit.

ls -1 ~/boulder_point_data/usermods

expected output includes:

shell_commands
user_nl_clm
user_nl_datm_streams

Check Your Understanding

How are Boulder site-level details passed to CLM?

Hint: look at files in the usermod directory

Get Started#

Let’s create a BGC case for a generic site in Boulder.

Exercise

  • Move into the NEON usermods directory:

cd /glade/u/home/$USER/code/my_clm_code/cime_config/usermods_dirs/clm/NEON

  • List its contents:

ls -1

You should see several directories, including:

ABBY
BARR
BART
BLAN
BONA
CLBJ
CPER
DCFS
defaults
DEJU
DELA
DSNY
FATES
GRSM
...

  • You’ll notice that FATES has its own directory. Have a look inside.

ls FATES

  • The default directory in NEON/FATES contains shell commands and user_nl_* settings that are shared across all sites. Look and see.

ls -1 FATES/defaults

expected output includes:

shell_commands
user_nl_clm
user_nl_cpl
user_nl_datm
user_nl_datm_streams

You can look to see what default settings your NEON cases will inherit.

  • Each NEON site also includes custom XML changes. Look and see:

ls -1 FATES/BONA

expected output includes:

include_user_mods
shell_commands

Check Your Understanding

How are NEON site-level details passed to CLM?

Hint: look at the shell_commands in the CLM usermods_dirs for NEON

Get Started#

Let’s create a FATES sp case at a NEON 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

Did you create a new case?

You can create a new case with the command:

./create_newcase --case /glade/u/home/$USER/cases/CASE --res RES --compset COMPSET --user-mods-dir USERMODS --run-unsupported

Make sure you use the correct information for the CASE, RES, COMPSET, and USERMODS inputs.

How do you customize your case to run a FATES SP experiment?

Specifically you’ll want to make namelist changes that:

  • set up a FATES-SP case.

  • modify history file output for an SP case. NOTE These should be done with a compset in CLM6, but we don’t have a single point FATESsp compset at this time.

And XML changes to run:

  • From a ‘cold start’ (as we don’t have initial conditions);

  • A quick spinup to initialize the soil moisture state (~4 years should be enough?);

  • For the full observational record.

Did you set up the case?

You can invoke case set up as follows:

./case.setup

How do I check my case

You can check your CaseDocs (especially lnd_in) after you run:

./preview_namelists

How do I compile?

You can compile with the command:

qcmd -- ./case.build

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 BONA.FATESsp :#

cd /glade/u/home/$USER/code/my_clm_code/cime/scripts

Change the 4-character NEON site below.

export neon_site="BONA"

Then create a new case.

./create_newcase --case /glade/u/home/$USER/cases/${neon_site}.FATESsp \
    --res CLM_USRDAT \
    --compset I1PtClm60FatesRsGs \
    --run-unsupported \
    --user-mods-dir clm/NEON/FATES/${neon_site} \
    --handle-preexisting-dirs r

Case setup:#

cd /glade/u/home/$USER/cases/BONA.FATESsp
./case.setup

Case customization:#

user_nl_clm changes. We currently don’t have a FATES sp compset in CLM. We’re working on it, but in the meantime you can request this by adding the following into user_nl_clm.

echo "use_fates_sp = .true." >> user_nl_clm
echo "hist_fincl2 = 'FCEV','FCTR','FGEV','FIRA','FSA','FSH','FATES_GPP','FATES_GPP_PF','H2OSOI','SNOW_DEPTH','TBOT','TSOI'" >> user_nl_clm

XML changes First look and see what default settings are for:

  • Running from a cold start (without initial conditions)

  • What years of DATM data do we have?

  • How long are we running the case?

./xmlquery CLM_FORCE_COLDSTART
./xmlquery DATM_YR_START DATM_YR_ALIGN DATM_YR_END
./xmlquery STOP_OPTION STOP_N

Expected results are:

	CLM_FORCE_COLDSTART: off

	DATM_YR_START: 2018
	DATM_YR_ALIGN: 2018
	DATM_YR_END: 2021

	STOP_OPTION: ndays
	STOP_N: 5

For most NEON sites we have at least 4 complete years of data to work with (2018-2021). Now we’ll change this to:

  • Force a cold start

  • Cycle over the full 4 years of DATM data available two times

  • Start the simulation in 2014, then we’ll have 4 years of spinup and 4 years to compare with the observed data.

./xmlchange CLM_FORCE_COLDSTART=on
./xmlchange STOP_OPTION=nyears
./xmlchange STOP_N=8  
./xmlchange RUN_STARTDATE=2014-01-01

Case build:#

qcmd -- ./case.build

Preview namelist:#

./preview_namelists

Check that your lnd_in file looks OK, e.g.:

  • use_fates_sp = .true.,

  • fsurdat = 16pfts,

  • finidat = ‘ ‘

  • etc…

cat CaseDocs/lnd_in | head -50

Case submit:#

./case.submit

Check the status:

qstat -u $USER

When the run is completed, look into the archive directory for: BONA.FATESsp.

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

cd /glade/derecho/scratch/$USER/archive/BONA.FATESsp
ls

Test your understanding#

  • Did your run complete successfully?

  • Where is your case directory?

  • Where is your run directory?

  • What sorts of files did you get as output?

  • What years did you run over?

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