2: mid-Holocene case

2: mid-Holocene case#

The Holocene Epoch started ~11,700 before present (11.7 ka BP) and is the current period of geologic time.

Although humans were already well established before the Holocene, this period of time is also referred to as the Anthropocene Epoch because its primary characteristic is the global changes caused by human activity.

The Holocene is an interglacial period, marked by receding ice sheets and rising greenhouse gases that were accompanied by changes in the Earth’s orbit around the Sun.

Today, we will use CESM to investigate influence of Holocene orbital forcing on climate.

Exercise: Run a mid-Holocene simulation with orbital forcing

Create, configure, build and run a fully coupled mid-Holocene (~6 ka BP) case called b.e21.B1850.f19_g17.midHolocene.001 following CESM naming conventions.

Run for 1 year.

Compare and visualize differences between preindustrial and mid-Holocene runs using NCO and Ncview.

Click here for hints

What is the compset for fully coupled mid-Holocene run?

Use B1850 and modify preindustrial orbital configuration (no mid-Holocene compset available)

What is the resolution for B1850?

Use resolution f19_g17 for fast throughput

What was the orbital configuration 6 ka BP?

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)

How to modify orbital configuration in CESM world?

Edit user_nl_cpl
orb_mode = 'fixed_parameters'
orb_eccen = 0.018682
orb_obliq = 24.105
orb_mvelp = 0.87

Click here for the solution

# Set environment variables

Set environment variables with the commands:

For tcsh users

set CASENAME=b.e21.B1850.f19_g17.midHolocene.001
set CASEDIR=/glade/u/home/$USER/cases/$CASENAME
set RUNDIR=/glade/derecho/scratch/$USER/$CASENAME/run
set COMPSET=B1850
set RESOLUTION=f19_g17
set PROJECT=UESM0013

You should use the project number given for this tutorial.

For bash users

export CASENAME=b.e21.B1850.f19_g17.midHolocene.001
export CASEDIR=/glade/u/home/$USER/cases/$CASENAME
export RUNDIR=/glade/derecho/scratch/$USER/$CASENAME/run
export COMPSET=B1850
export RESOLUTION=f19_g17
export PROJECT=UESM0013

You should use the project number given for this tutorial.

# Make a case directory

If needed create a directory cases into your home directory:

mkdir /glade/u/home/$USER/cases/

# Create a new case

Create a new case with the command create_newcase:

cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/
./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --project $PROJECT

# Change the job queue

If needed, change job queue.
For instance, to run in the queue main.

cd $CASEDIR
./xmlchange JOB_QUEUE=main

This step can be redone at anytime in the process.

# Setup

Invoke case.setup with the command:

cd $CASEDIR
./case.setup    

You build the namelists with the command:

./preview_namelists

This step is optional as the script preview_namelists is automatically called by case.build and case.submit. But it is nice to check that your changes made their way into:

$CASEDIR/CaseDocs/atm_in

# Set run length

./xmlchange STOP_N=1,STOP_OPTION=nyears

# Add the following to user_nl_cpl

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

# Build and submit

qcmd -A $PROJECT -- ./case.build
./case.submit

# Validate your simulation setup

(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).

Note: The less command in Linux is a terminal pager program used to view (but not change) the contents of a text file one screen at a time. It is particularly useful for large files, as it does not need to read the entire file before starting, hence it loads large files faster than editors like vi or emacs.

To skip to the bottom of the file, press <shift> + g To stop viewing the contents of the file with less, press q.

less /glade/derecho/scratch/$USER/$CASENAME/run/cpl.log.* 
less /glade/derecho/scratch/$USER/archive/$CASENAME/logs/cpl.log.*.gz 

Alternatively, use the real-time monitoring mode with less that you can activate with the +F (forward) option. Now, new lines will be continuously displayed as they are added to the file during the run. To exit forward mode and revert to the standard interactive mode of less, press <ctrl> + C.

less +F /glade/derecho/scratch/$USER/$CASENAME/run/cpl.log.*

(2) 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

# Check your solution

When the run is completed, look at the history files into the archive directory.

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

cd /glade/derecho/scratch/$USER/archive/$CASENAME/atm/hist
ls 

As your run is one-year, there should be 12 monthly files (h0) for each model component.

Click here to visualize results

# Use Ncview to visualize solar insolation

Earth’s orbital configuration influences incoming solar insolation. Take a look at the SOLIN CAM variable for August in the pre-industrial and mid-Holocene runs.

module load ncview
cd /glade/derecho/scratch/$USER/archive
ncview b.e21.B1850.f19_g17.piControl.001/atm/hist/b.e21.B1850.f19_g17.piControl.001.cam.h0.0001-08.nc b.e21.B1850.f19_g17.midHolocene.001/atm/hist/b.e21.B1850.f19_g17.midHolocene.001.cam.h0.0001-08.nc

Using the right arrow button in the Ncview window, you can toggle between pre-industrial and mid-Holocene August SOLIN and other variables.

A few side notes on comparing pre-industrial and mid-Holocene runs:

Changes in Earth’s orbit alter the length of months or seasons over time, this is referred to as the ‘paleo calendar effect’
This means that the modern fixed-length definition of months do not apply when the Earth traversed different portions of its orbit
Tools exist to adjust monthly CESM output to account for the ‘paleo calendar effect’
See PaleoCalAdjust tool from Bartlein & Shafer et al. (2019) for more information
For simplicity, we assume in this exercise that the definition of months is the same for the pre-industrial and mid-Holocene

Now, let’s take a look at the differences between the two cases more clearly using NCO.

module load nco
cd /glade/derecho/scratch/$USER/archive
ncdiff b.e21.B1850.f19_g17.piControl.001/atm/hist/b.e21.B1850.f19_g17.midHolocene.001.cam.h0.0001-08.nc b.e21.B1850.f19_g17.piControl.001/atm/hist/b.e21.B1850.f19_g17.piControl.001.cam.h0.0001-08.nc diff_MH-PI_0001-08.nc 
ncview diff_MH-PI_0001-08.nc 

Note: Running ncdiff this way will place diff_MH-PI_0001-08.nc in your archive directory. You may use mv to move diff_MH-PI_0001-08.nc to another directory.

# Questions for reflection:

Which orbital parameters are different at the middle Holocene (6 ka BP)?
How does the orbital parameter impact the top-of-atmosphere shortwave radiation (solar insolation) during summertime in the Northern Hemisphere?
Do the results look correct? You can compare your results with Figure 3b of Otto-Bliesner et al., (2017)
What other aspects of climate are different between the mid-Holocene and pre-industrial runs?