UKCA Chemistry and Aerosol Tutorials: Things to know before you start
Back to UKCA Chemistry and Aerosol Tutorials
UKCA jobs at UM8.4 are currently being prepared and scientifically validated prior to release.
PUMA and ARCHER/MONsooN
Before you begin this tutorial you should first get a PUMA and an ARCHER or MONSooN account as the UKCA Tutorial is based around jobs which run on these supercomputers, using PUMA to submit them.
Further information about how to apply for these account can be found on the Getting Started with UKCA page.
This tutorial can be run on both ARCHER and MONSooN. In the UMUI Search → Filter... for:
- The ARCHER experiment is xjrn
The MONSooN experiment is xjrjMONSooN Tutorials do not currently work on the XCM
UM Training and the FCM Tutorial
There is some information about the UM here:
http://cms.ncas.ac.uk/wiki/UmTraining
You must also have completed the NCAS-CMS UM FCM Tutorial. This tutorial assumes that you have had some experience in using the UM, and know how to copy an existing job to your account and run it.
If you have never used the UM before you should also view the NCAS-CMS UM Training pages, which has a basic introduction to the UMUI.
You will also find the NCAS-CMS pages very useful: cms.ncas.ac.uk.
Location of output data files
By default the UKCA Tutorial jobs are not set to archive any data, and so the output data files can be found in the
/work/n02/n02/userid/jobid
directory on ARCHER, and in the
/projects/ukca/userid/jobid
directory on MONSooN (if you are not in the ukca project group you will need to set your project group here).
For consistency these will be known as your job directory throughout the rest of this tutorial.
Archiving (where data may be processed and moved to another disk or to tape) is controlled in the UMUI in the Model Selection → Post Processing → Main Switch + General Questions panel.
Knowledge of scripting and programming languages
UKCA (and the UM) is written in Fortran 90, and so you should have some knowledge of this language, as well as some knowledge of the Unix/Linux command-line. You will not be asked to do anything advanced, but you will need to add to arrays and other code blocks.
Structure
UKCA is not one particular chemistry scheme, but is in fact a framework for adding a chemistry scheme to the UM. Although in this tutorial you will adapt an exisiting scheme, you could extend this to replacing all tracers and reactions and add in a completely different scheme.
UKCA Chemistry Tutorials
These Tutorials are actually one large problem which someone who uses UKCA may be required to do: add some tracers, reactions, deposition, and diagnostics. To make this problem more manageable it has broken down into a series of small tasks which you will be asked to complete. Each Tutorial explains how to make the necessary changes (in general terms), and then you will be asked to make the required changes to your UKCA job.
To accompany each Task which requires UMUI or UKCA code changes, there are worked solutions (held in the same UMUI Experiment as the original Tutorial Base Job) along with sample output and a wiki page detailing the changes in full. If at any point you have difficulty completing one of the Tasks you can take a copy of the worked solution job and carry on from there. There is also sample output provided for each of the tasks.
Solutions
The solutions to these tasks can be found in the UMUI (as other jobs in the Tutorial experiments xirb and xirc) under the ukca user. The code-changes required can be viewed at the vn8.4_UKCA_Tutorial_Solns PUMA Trac page (password required).
Model Configuration
The UKCA Tutorial job is at UM version 8.4 job using a Global Atmosphere 4.0 atmosphere-only configuration. It has a resolution of N96L85 (1.875 degrees by 1.25 degrees, with 85 vertical levels up to 85km). The current UKCA Chemistry and Aerosol Tutorial job uses the CheST/StratTrop+GLOMAP-mode chemistry and aerosol schemes.
While you may be interested in using UKCA at a different UM version, many aspects of this tutorial will be directly transferable. For instance, many of the UMUI panels and much of the UKCA source code are the same at UM7.3 and UM8.2 as at UM8.4.
Data Manipulation and Plotting
In these Tutorials you will only be asked to use Xconv for basic data manipulation and plotting. Xconv can be found on ARCHER at
/work/n02/n02/hum/bin/xconv
and on the MONSooN ibm02 at
/projects/um1/bin/xconv
and the MONSooN postproc at
/usr/local/bin/xconv
and which can also be used to extract UM fields as netCDF. Xconv should already be in your $PATH.
Both IDL (using the Met Office library) and Python (using either cf-python or Iris) are able read the UM PP/FieldsFile format directly, although use of these tools will not be covered by these Tutorials.
Command-line tools
There are command-line tools available that can manipulate fieldsfiles/pp-files and netCDF files in various ways.
convsh
Convsh is the command-line backend of Xconv, and can be found in the same directories as Xconv on the supercomputer, i.e.
/work/n02/n02/hum/bin/convsh
on ARCHER,
/projects/um1/bin/convsh
on the MONSooN ibm02, and
/usr/local/bin/convsh
on the MONSooN postproc.
A handy list of convsh commands is available.
nco
The netCDF operators (nco) are a set of generic netCDF manipulation tools. On ARCHER, you can load nco by
module swap PrgEnv-cray PrgEnv-gnu module load nco
You need to swap out the PrgEnv-cray environment (used with the UM) to the PrgEnv-gnu environment, as nco has been compiled with the gnu compiler.
This will now point your $PATH to see the location of ncdump in
/opt/cray/netCDF/4.3.0/bin
and the netCDF operators in
/work/y07/y07/cse/nco/4.4.2/install/bin
for nco version 4.4.2.
On the MONSooN postproc ncdump can be found at
/usr/bin/ncdump
and the netCDF operators can be found in
/project/ukmo/rhel6/nco/bin
cdo
The climate data operators (cdo) are an expanded set of command line tools that are designed to work with netCDF files that contain climate data. They can be loaded on ARCHER by
module swap PrgEnv-cray PrgEnv-gnu module load cdo
You need to swap out the PrgEnv-cray environment (used with the UM) to the PrgEnv-gnu environment, as cdo has been compiled with the gnu compiler.
This will now point your $PATH to see the location of cdo at
/work/y07/y07/cse/cdo/1.6.3-build1/bin/cdo
for cdo version 1.6.3.
On the MONSooN postproc cdo version 1.5.4 can be found at
/opt/ukmo/utils/bin/cdo
Further Information
More information on UKCA can be found by browsing this wiki. More detailed information on UKCA can also be found in the 
The UKCA documentation paper for vn8.4 of the MetUM 
.
Written by Luke Abraham 2014
