NCAS Computational Modelling Services

Unified Model

Ozone redistribution

Instructions for adding ozone redistribution to a GC3.1 suite

About ozone redistribution

The ozone redistribution (OR) scheme for GC3.1 (CMIP6) is described here

The code lives in the moci repository. It was ported to ARCHER2 by CMS, and works slightly differently than in the Met Office, due to the difference in infrastructure.

These instructions are for adding OR to a GC3.1 suite. The run must start from 1st January, and the cycle length can not be longer than 1 year.

How it works in a suite

This is just a technical outline of what the suite is doing. The science is descibed in the paper above.

A new task retrieve_ozone runs before the UM and checks the input data required for the OR code is available.
It then sets up symlinks to the orography and ozone ancillary in a directory: share/data/ozone_redistribution. It also sets up a symlink to the ozone file the model will use for the first year of the simulation in share/data/etc/ozone. This just points to the original ozone ancil.

The UM uses an optional configuration (app/um/opt/rose-app-ozone.conf) which tells it to use the ozone file defined above. It also specifies some additonal STASH needed for the OR:

(0, 253)  DENSITY*R*R AFTER TIMESTEP
(30, 453) Height at Tropopause Level

These are output as monthly means to a stream po with one file for the full year.

At the end of the year, postproc converts these to pp format, and keeps two years worth of files on disk for processing.

Then retrieve_ozone runs again. This time it adds in symlinks for the po file(s) in share/data/ozone_redistribution.

Next the redistribute_ozone runs the actual OR code, which generates a new ozone ancillary file for the next model year in share/data/etc/ozone.

So the OR is not run until the end of the first year of the simulation, and then it just uses data from this first year. For subsequent years, it uses the previous two years worth of data. This is a bit different to the system at the Met Office, where data is extracted from MASS from a previous run so that the redistribution can be done before the start of the simulation.

Adding ozone redistribution to a suite.

1. Upgrade postproc

Make sure postproc is using version 2.4. If necessary set up JASMIN transfer. Test that postproc works correctly, then proceed to the next step.

2. Checkout the refrence suite.

The reference suite is u-cr335, which is an Eocene suite with the OR code working in it. We will copy the new app files in from here.

rosie co u-cr335

3. Copy in the OR configuration files

Navigate to the suite you want to edit, and copy in the following files:

cd <your-suite>
cp -r ../u-cr335/app/redistribute_ozone ./app
cp -r ../u-cr335/app/retrieve_ozone ./app
cp ../u-cr335/app/install_ancil/opt/rose-app-ozone.conf ./app/install_ancil/opt
cp ../u-cr335/app/um/opt/rose-app-ozone.conf ./app/um/opt
cp ../u-cr335/bin/copy_ozone.sh ./bin
cp ../u-cr335/bin/python_env ./bin
cp -r ../u-cr335/meta/ozone ./meta
cp ../u-cr335/ozone-redistribution.rc .
cp ../u-cr335/site/archer2_ozone.rc ./site
cp ../u-cr335/site/archer2_python_env ./site

4. Add in the include files and suite variables.

  • Open meta/rose-meta.conf and add the following line to the top of the file:
    import=meta/ozone
    
  • In rose-suite.conf add the following lines to the top of the file:
[file:bin/redistribute_ozone.py]
source=fcm:ancil_contrib.xm_br/dev/simonwilson/r9929_ozone_pp_header/OzoneConc/bin/redistribute_ozone.py

[file:bin/redistribute_ozone.sh]
source=fcm:ancil_contrib.xm_br/dev/simonwilson/r9929_ozone_pp_header/OzoneConc/bin/redistribute_ozone.sh

[file:bin/retrieve_ozone_data.py]
source=fcm:moci.xm_tr/Utilities/ozone_redistribution/retrieve_ozone_data.py@postproc_2.4
  • Then add the following lines to the list of variables (we will configure these settings in the next step):
OZONE_HOST='archer2'
OZONE_INITIAL='/work/n02/n02/ssteinig/ancils/PI/n96e/ozone/timeslice_1850/mmro3_monthly_CMIP6_1850_N96_edited-ancil_2anc'
OZONE_INPUT_SPLIT_ANCIL=false
!!OZONE_INPUT_SPLIT_NAME='/work/n02/n02/simon/canari/ozone/ancil/mmro3_monthly_CMIP6_\${THISYEAR}_N216_edited-ancil_2anc'
OZONE_PRIMARY_ARCHIVE='\${OZONE_STREAM_DIR}/\${OZONE_STREAM_PREFIX}'
OZONE_REDISTRIBUTE=true
OZONE_SECONDARY_ARCHIVE=''
OZONE_USE_UPDATED_ANCIL=false
  • In site/archer2.rc add the following lines to the bottom of the file:
      {% include 'site/' + SITE + '_ozone.rc' %}
    
  • In suite.rc, add the following line to the bottomr of the file, or above the [visualization] line if there is one:
      {% include 'ozone-redistribution.rc' %}
    

5. Configure the suite

  • Make sure the run starts from 1 Jan of the year, and the cycle length is a year or less.

  • The standard code requires you to use a 3D ozone ancillary file. If this is not already set up, then set the following variables in app/um/rose-app.conf or in the um section of the rose edit GUI:
    zon_av_ozone=.false.
    i_ozone_int=1
    
  • In the rose edit GUI, under “suite conf -> Ozone redistribution”, set “Initial ozone ancillary” to be your 3D ozone ancillary file. If the file is large because it contains a long time-series this can slow down the code, so we recommend you can split it into individual years (contact the CMS helpdesk for advice on this). In this case you should select “Use split input ozone ancillaries”, then edit “Name of split input ancillaries” as in the example below:
    /work/n02/n02/simon/canari/ozone/ancil/mmro3_monthly_CMIP6_\${THISYEAR}_N216_edited-ancil_2anc
    
  • Check the name and location of the orography file used in the suite. If the top-level location is anything other than $UMDIR/ancil, then edit the variable UM_MODEL_ANCILS_LINK in site/archer2_ozone.rc. Next check the path set in app/retrieve_ozone/rose-app.conf as below. (Note that this may also be specified using an optional configuration.)
    [file:$OZONE_SHARE/qrparm.orog]
    mode=symlink+
    source=${UM_MODEL_ANCILS_LINK}/orography/globe30/qrparm.orog
    
  • Check the UM output streams. By default the new po stream goes to a file id pp145 and usage profile UPO. If these clash with existing settings in your suite, you will need to rename them in app/um/opt/rose-app-ozone.conf.

  • Set up postproc to convert the po stream to pp, and make sure it is saved for the OR. In “postproc -> Atmosphere”, either set process_all_stream=true, or make sure po is in the list under process_streams. Under “Atmosphere -> File transformation” make sure the po stream is being converted to pp, usually with convert_pp=true and convpp_all_streams=true. Next set preserve_ozone=true and ozone_source_stream=po.

The OR scheme is quite complicated, and your suite may require some additional changes to get it working properly. Contact the CMS helpdesk if you need advice.

Checking the output

Follow the technical description above (link) and check that the correct links are being set up at each stage.

When you think that you have the scheme working, take a look the output dump from a cycle when OR is active to ensure that the correct ozone ancil is being read in by the model. The ozone at heights ~10000 should look like the image below. There should be some horizontal banding added in by the OR; if there’s no banding, then something’s gone wrong somewhere.

Ozone at ~ 10,000 after redistribution