UKCA Release Jobs

This page contains documentation on UKCA standard jobs that have been released or will soon be released.

You may also wish to look at the bugfixes page.

Getting Started

PUMA

The UK Met Office's Unified Model (UM) is provided for the NERC community from NCAS Computational Modelling Services via the PUMA (Providing UM Access) resource. To use UKCA you must have an account on PUMA. To obtain one, please go to the NCAS-CMS PUMA page.

FCM

The UM uses code management software, built around subversion, called FCM (Flexible Configuration Management).

If you have not used the UM with FCM, we ask that you first familiarise yourself with the system by doing the UM FCM Tutorial.

As well as being a good introduction to FCM and the UM User Interface (UMUI), it will also teach you how to set-up some configuration files that will be needed in the day-to-day running of the UM and UKCA.

Standard Release Jobs

UKCA can be configured through the UMUI, via it's own configuration panel. This mostly controls all the options required to run UKCA, although some extra changes have been made with hand-edits. To make it easy to get started with UKCA, several standard jobs have been created at various resolutions. To get started with UKCA, it should be a simple matter to take a copy of the UKCA job that you wish to run, changing a few user-specific options, and submitting the job.

Code Changes

To run a UKCA standard job, please take a copy of one of the jobs listed below. If you need to make code changes, you must make a new FCM branch, and merge in the UKCA branch which is used in the job that you are taking, then use your branch instead.

Please do not take a checkout of the UKCA branch used in the UMUI FCM panel (e.g. fcm:um_br/dev/luke/VN7.3_UKCA_CheM) and run from this as a working copy. If the fcm commit command is run from this directory it would commit any changes you have made to this branch. In this case, this would affect the branch for other UKCA users.

Job List

Available release jobs are:

UM Version	UMUI Job-ID	Climate Model	Horizontal Resolution	Vertical Levels	Model Top	Scheme Used	FCM Branch	Revision Number
7.3	HECToR:xfvfa,xfvfc MONSooN: xfvfb	QESM-A	N48 (2.5°×3.75°)	L60	~84km	Tropospheric Chemistry with Isoprene	fcm:um_br/dev/luke/VN7.3_UKCA_CheM	9278
7.3		HadGEM3-A r2.0	N96 (1.25°×1.875°)	L63	~40km	Tropospheric Chemistry with Isoprene	fcm:um_br/dev/luke/VN7.3_UKCA_CheM	9278
7.3	HECToR:xfvga,xfvgc MONSooN:xfvgb	QESM-A	N48	L60	~84km	Stratospheric Chemistry	fcm:um_br/dev/luke/VN7.3_UKCA_CheM	9278
7.3		HadGEM3-A r2.0	N96	L85	85km	Stratospheric Chemistry	fcm:um_br/dev/luke/VN7.3_UKCA_CheM	9278
7.3		QESM-A	N48	L60	~84km	Simple Tropospheric Chemistry with MODE Aerosol
7.3	HECToR: MONSooN:xfxlb		N96	L38	~40km	Simple Tropospheric Chemistry with MODE Aerosol	fcm:um_br/dev/mdalvi/VN7.3_MODEBLN_Rad_Indir	5953
7.3	HECToR: MONSooN:xfxld		N96	L38	~40km	Simple Tropospheric Chemistry with MODE Aerosol (Nudged)	fcm:um_br/dev/mdalvi/VN7.3_MODEBLN_Rad_Indir fcm:um_br/dev/mdalvi/VN7.3_nudged_new	5953 5586

Required UMUI Changes

Before submitting a UKCA job, you must first alter several options in the UMUI:

User-id, Mail-id (email address), and Tic-Code:
Model Selection -> User Information and Target Machine -> General Details
The user-id is your username on the target machine (i.e. HECToR).
The tic-code will be the HECToR charging code, e.g. n02-chem. This code can be found by logging into the HECToR SAFE pages, and viewing your account information.
Target machine root extract directory (UM_ROUTDIR):
Model Selection -> FCM Configuration -> FCM Extract and Build directories and Output levels
This needs to be the full path to one of your directories on the target machine (HECToR /home directory or MONSooN /projects directory).

Optional UMUI Changes

As well as the required changes above, you may also want to change the following, depending on your experiments:

Model start date and run length:
Model Selection -> Input/Output Control and Resources -> Start Date and Run Length Options
NOTE: For Stratospheric Chemistry, the CFC and other long-lived trace gas concentrations will be highly dependent on the date - you will need to think about your chemical tracer initial conditions if you change the start date of a Stratospheric Chemistry run.
Reference date for meaning:
Model Selection -> Atmosphere -> Control -> Post processing, Dumping & Meaning -> Dumping and meaning
If you have changed the start date (above), you may need to change the reference date. If you do not do this, climate meaning may not work. Climate means will only be produced for a date after the reference date.
Archiving:
Model Selection -> Post Processing -> Main Switch + General Questions
Currently archiving is switched ON for most jobs.
On HECToR all model output will placed in a directory called archive which is a sub-directory of your run directory.
ON MONSooN, all data is copied to /nerc/PROJECT/USERID/JOBID.
Superseded model restart dumps will be deleted.
You will also need to ensure that your Monsoon project group name is correct.
UKCA Surface Emissions (as user single-level ancillary file):
Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies and potential climatologies -> User single-level ancillary files and fields
The emissions data-sets are taken from those used for AR5 integrations, and represent the year 2000. You may wish to change these emissions - to do this we recommend the use of Xancil, provided by NCAS-CMS.
UKCA 3D Emissions (as user multi-level ancillary file):
Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies and potential climatologies -> User multi-level ancillary files and fields
The standard aircraft emissions data-set comes from the Aero2K project, and represents the year 2000. You may wish to change these emissions - to do this we recommend the use of Xancil, provided by NCAS-CMS.
Tracer Initial Conditions:
Model Selection -> Atmosphere -> STASH -> Initialisation of User Prognostics
The table in this UMUI panel gives a listing of all the initial conditions of the STASH items defined by the user. They are given a STASH code, which the UM uses to identify the field. The UKCA tracers have a 5 digit code beginning at 34001 and ending at 34150, although 34149 and 34150 need to be initialised to zero. Several (or all) tracers will be initialised to some initial conditions, contained in the file listed by each tracer.

Continuation Run

After the job has run the first step, you will probably wish to turn on a continuation run.

Turn off compilation:
Model Selection -> Compilations and Modifications -> Compile options for the UM model
Model Selection -> Compilations and Modifications -> Compile options for the UM reconfiguration
Set to Run from existing executable, as named below in both panels
Set to CRUN:
Model Selection -> Input/Output Control and Resources -> User hand edit files
Find the hand-edit crun.ed and set this to Y

Running a Perpetual Year

For some experiments, you may wish to run a perpetual year (i.e. a simulation of multiple years in length, each one representing the same year). There are two ways to two this:

Manually re-run the same year
- In this case you would run up until you have the 1st January start dump, then manually restart the simulation from this dump, run for 1 year and then send a new job off, running from the new 1st January start dump. You would need to ensure that the date used for each of these steps is for the year that you are interested in. To do this you will need to change how reconfiguration is performed.
- Reconfiguration:
  Model Selection -> Atmosphere -> Ancillary and input data files -> Start Dump
  You will need to alter the directory path and name of file to point to the start-dump you are interested in. You must then turn off the radio button Using the reconfiguation and make sure that the start-date (listed at the top of this panel) matches that in the dump file.
Create a multi-year simulation where all the input files are for a single year
- This method is particularly useful when you want to run a perpetual year for more than a few years, as might be the case for Stratospheric Chemistry when 15-20 year spin-ups are needed. There are a few changes that need to be made to several ancillary files and the UMUI:
1. Change Ancillary files:
  - The following acillary files will need to be changed, since these are not climatologies by default, but time-series. You may find that the directory that these files are placed in is set by an environment variable (e.g. $ANCIL_ATMOS etc.). This environment variable points to a directory on the target machine (HECToR or MONSooN). To find out what these variables are set to, go to:
    Model Selection -> Input/Output Control and Resources -> Time Convention and SCRIPT Environment Variables.
    - The single-level and multi-level (see above) user ancillary files may need to be changed to the year you are interested in.
    - Sea-Surface Temperature:
      Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies & potential climatologies -> Sea surface temperatures
    - Sea-Ice:
      Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies & potential climatologies -> Sea ice fields
    - 2D Sulphur Emissions:
      Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies & potential climatologies -> Sulphur cycle emissions (2D)
      NOTE: you should not need to change the DMS emissions
    - Soot Emissions:
      Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies & potential climatologies -> Soot Emissions
    - Biomass Emissions:
      Model Selection -> Atmosphere -> Ancillary and input data files -> Climatologies & potential climatologies -> Biomass Emissions
  - To create perpetual-year ancillary files:
    1. For each of the the ancillary files specified in these UMUI panels above, open in Xconv and select only the year that you are interested in and export this as a NetCDF file.
    2. Use Xancil to create replacement ancillary files for each of the above files. You will need to make sure that these are made as periodic in time.
    3. In the UMUI, replace the time-series ancillary files with your climatologies.
2. UKCA changes:
  These changes are describing code and UMUI changes specific to the branch fcm:um_br/dev/luke/VN7.3_UKCA_Chem.
  - The changes to UKCA are controlled by two hand-edits:
    Model Selection -> Input/Output Control and Resources -> User hand edit files
    1. CheM_aerosol_background_on.ed/CheM_aerosol_background_off.ed
      - This hand-edit either specifies using a background aerosol climatology for all years (_on), or using a time-series of atmospheric aerosols (_off). The default used is CheM_aerosol_background_off.ed.
    2. CheM_trgas_presentday_full.ed (a pre-industrial version is also supplied, CheM_trgas_preI_full.ed)
      - This hand-edit gives values of certain trace-gases to UKCA. Some are taken from the UMUI:
        Model Selection -> Atmosphere -> Scientific Parameters and Sections -> Spec of Trace Gases
        These are:
        $CO_{2}$
        
        $CH_{4}$
        
        $N_{2}O$
        
        $CFC11$ ( $CFCl_{3}$ )
        
        $CFC12$ ( $CF_{2}Cl_{2}$ )
        
        $CFC113$ ( $CF_{2}ClCFCl_{2}$ )
        
        $HCFC22$ ( $CHF_{2}Cl$ )
      - Some gases are used by UKCA to specify constant values for the chemical solver.
        These are:
        $CH_{4}$ (TropIsop chemistry only)
        
        $CO_{2}$
        
        $H_{2}$
        
        $N_{2}$
        
        $O_{2}$
      - Some trace-gases are used in Stratospheric Chemistry, to specify the surface concentration of certain UKCA species ( $N_{2}O$ , $CF_{2}Cl_{2}$ , $CFCl_{3}$ , $CH_{3}Br$ , $H_{2}$ , and $CH_{4}$ ). Some species are lumped together, so the surface concentrations of the following species can be set by the hand-edit:
        $CH_{3}Br$ (as MeBr)
        
        $CH_{3}Cl$ (as MeCl)
        
        $CH_{2}Br_{2}$
        
        $H_{2}$
        
        $N_{2}$
        
        $CFC114$
        
        $CFC115$
        
        $CCl_{4}$
        
        $CH_{3}CCl_{3}$ (as MeCCl3)
        
        $HCFC141b$
        
        $HCFC142b$
        
        $H1211$
        
        $H1202$
        
        $H1301$
        
        $H2402$
      - A program to determine the mass mixing ratios of these species routine can be found at /home/ukca/bin/scenario on PUMA. It is run by typing
        scenario YYYY/MM/DD <which scenario>
        on the command line, where
        <which scenario> can either be WMOA1, RCP2.6, RCP4.5, RCP6.0 or RCP8.5
        
        The year (YYYY) is between 1950 and 2100 for the WMOA1 scenario and 1765-2500 for any of the RCP scenarios
        
        The code uses a 360 day calendar (12 months, 30 days per month).
      - To allow the specification of these gases in this way to be uses by UKCA, you will also need to turn on this option in the UMUI: UMUI values for CFCs etc
        Model Selection -> Atmosphere -> Model Configuration -> UKCA Chemistry and Aerosols -> STRAT

UMUI UKCA Panel

The UKCA configuration panel can be found at:

Model Selection -> Atmosphere -> Model Configuration -> UKCA Chemistry and Aerosols

The settings in the UMUI UKCA panel have been chosen for that specific chemistry/aerosol scheme, and choosing other options may not work. If you require extra functionality, please contact Luke Abraham to check on the current code status.

Tropospheric Chemistry with Isoprene - TropIsop

See also Tropospheric Chemistry with Isoprene description page.

Comparison of Tropospheric Chemistry with Isoprene in a number of model resolutions and UM versions.

This scheme using the FCM branch fcm:um_br/dev/luke/VN7.3_UKCA_CheM at revision 9278 (updated). It has 56 species (49 of which are tracers), 115 bimolecular reactions, 35 photolysis reactions (using rates determined using a 2D look-up table) and 15 termolecular reactions. 23 species are wet-deposited and 32 are dry-deposited (using a 2D dry-deposition scheme). Tropospheric $O_{x}$ and $CO$ budgets are outputted as standard, as are other diagnostics of interest, such as the $CH_{4}$ lifetime and Stratosphere-Troposphere Exchange of $O_{3}$ .

The chemistry is integrated using the ASAD chemical package, using a sparse-matrix Newton-Raphson solver. While the UM dynamical timestep is every 20 model minutes, chemistry is called every model hour, although emissions are still performed every dynamical timestep. Top boundary conditions are used for $O_{3}$ and $NO_{y}$ and $CH_{4}$ is treated as a constant. The tracers are initialised to spun-up fields from a previous TropIsop run, however, we recommend that a 15 month-spin-up should be performed.

The chemistry scheme used in these simulations is the same as in Telford et al, Atmos. Chem. Phys., 10, 7117-7125, doi:10.5194/acp-10-7117-2010 (2010). A model description paper is also in preparation (O'Connor et al, 2011).

The tropospheric ozone concentrations in UKCA-TropIsop are biased slightly high. This is improved with using an interactive photolysis scheme, which will be released for general use soon.

Timings

It should be noted that due to "jitter" on the HPC platform, all timings are approximate. As a simulation progresses the time per model month may increase as the fields spin-up from their initial state.

Machine	No. of Cores	No. of Nodes	Resolution	Time for 1 Model Month
HECToR Phase2b	96	4	N48L60	~50 minutes
MONSooN	64	2	N48L60	~59 minutes

Stratospheric Chemistry - StratChem

See also Stratospheric Chemistry description page.

Ozone column in Dobson Units (DU) calculated from a UM7.3 N48L60 UKCA-StratChem run using interactive UKCA ozone in the UM radiation scheme. This is the mean of 21 model years representing 1990.

This scheme using the FCM branch fcm:um_br/dev/luke/VN7.3_UKCA_CheM at revision 9278 (updated). It has 41 species (36 of which are tracers), 113 bimolecular reactions, 34 photolysis reactions (using rates determined using a 3D look-up table), 17 termolecular reactions and 5 heterogeneous reactions. 15 species are wet-deposited and 15 are dry-deposited (using a 2D dry-deposition scheme). A stratospheric $O_{3}$ is standard (based on the budget of Lee et al, JGR 107 DOI:10.1029/2001JD000538 (2002)), as are other diagnostics of interest, such as the $CH_{4}$ lifetime and Stratosphere-Troposphere Exchange of $O_{3}$ .

The chemistry is integrated using the ASAD chemical package, using a sparse-matrix Newton-Raphson solver. While the UM dynamical timestep is every 20 model minutes, chemistry is called every model hour, although emissions are still performed every dynamical timestep. By default, lower boundary conditions set for the tracer concentrations of $N_{2}O$ , $CH_{4}$ , $H_{2}$ , $CF_{2}Cl_{2}$ , $CFCl_{3}$ , $CH_{3}Br$ , and $CH_{2}Br_{2}$ are specified for the years 1950-2100. These values are also used in the UM radiation scheme, along with $CO_{2}$ concentrations. The tracers are initialised to spun-up fields from a previous StratChem run, however it can take time for a Stratospheric run to equilibrate and spin-up times as long as 20 model years may be required if significant changes are made.

The chemistry scheme used in these simulations is the similar to that described in Morgenstern et al, Geosci. Model Dev., 2, 43-57, (2009).

Please also see the bugfixes page for further information on the initial conditions used in the release job.

Timings

It should be noted that due to "jitter" on the HPC platform, all timings are approximate. As a simulation progresses the time per model month may increase as the fields spin-up from their initial state.

Machine	No. of Cores	No. of Nodes	Resolution	Time for 1 Model Month
HECToR Phase2b	96	4	N48L60	~46 minutes
MONSooN	64	2	N48L60	~51 minutes

Simple Tropospheric Chemistry with GLOMAP-mode aerosol - UKCA-MODE

See also MODE Aerosol description page.

The UKCA aerosol scheme 'GLOMAP-mode' (sometimes called UKCA-MODE when in the UM) is described in detail in Mann et al (2010) and simulates aerosol microphysics (nucleation, condensation,coagulation and cloud processing), dry deposition, sedimentation and in-cloud/below-cloud scavenging. The scheme simulates atmospheric aerosol in a size-resolved manner with the chemical and aerosol microphysical processes determining the evolution of the size and composition of several size modes. The scheme transports the mass of sulphate, sea-salt, black carbon, organic matter and dust, along with the particle number concentration in each size mode. The aerosol scheme is coded flexibly to allow the same code to run with several alternative aerosol configurations via FORTRAN-90 modules.

UKCA-MODE can be coupled to all of the various UKCA chemistry schemes, but in this standard job uses the simple tropospheric chemistry scheme, extended to treat the degradation of the aerosol precursor species: sulphur dioxide (SO2);dimethylsulphide (DMS); and a lumped monoterpene tracer.

An interface between UKCA-MODE and the Edwards-Slingo radiation scheme allows the aerosol concentrations to interact with the radiation both directly (through scattering and absorption of incoming solar and outgoing long-wave radiation) and indirectly via modified cloud albedo. In the standard jobs, both these effects are computed in a passive/ diagnostic mode via use of a double-call to the radiation scheme.

One of the standard jobs also includes Nudging, wherein the model dynamics variables are nudged or relaxed towards ECMWF Reanalysis data. This configuration is particularly useful for evaluating the MODE scheme against measurements.

Timings

When run with all the 31 aerosol tracers switched on, the UKCA-MODE code adds 12% to the cost of the Atmosphere model (see O'Connor et al, 2011 ICP report to DECC/DEFRA).

Machine	No. of Cores	No. of Nodes	Resolution	Time for 1 Model Month
MONSooN (non-nudged)	64	2	N96L38	~2 hours
MONSooN (nudged)	64	2	N96L38	~2.5 hours

UKCA Release Jobs

Contents

Getting Started

PUMA

FCM

Standard Release Jobs

Code Changes

Job List

Required UMUI Changes

Optional UMUI Changes

Continuation Run

Running a Perpetual Year

UMUI UKCA Panel

Tropospheric Chemistry with Isoprene - TropIsop

Timings

Stratospheric Chemistry - StratChem

Timings

Simple Tropospheric Chemistry with GLOMAP-mode aerosol - UKCA-MODE

Timings

Useful Links