Solution to UKCA Chemistry and Aerosol Tutorial 3 Task 3.1

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Task

You were asked to

Output the instantaneous UKCA ozone field to the pb/UPB stream every 6 hours.

and were given the hint

You will need to make the changes to the STASH table first, and remember to use Verify Diagnostics and correct any warnings generated for the pb/UPB stream (61).

Solution

Add the new diagnostic to the STASH table

Go to Model Selection → Atmosphere → STASH → STASH. Specification of Diagnostic requirements.

You will need to add the following to the STASH table

34   1 O3 MASS MIXING RATIO AFTER TIMESTEP T6H      DALLTH   UPB      Y +  Y  

i.e.

• STASH section = 34
• STASH item = 1
• Time Profile = T6H
• Domain Profile = DALLTH
• Usage Profile = UPB

Verify the Diagnostics

Verifing the diagnostics (either Control-v or Diagnostics → Verify Diagnostics) gives

PP-Field Count Estimates 


Warning!!! You may exceed the maximum number of PP fields per file
	      
Estimated number of PP files to be written:

30600 fields in stream 61.  Maximum allowed is 4096.
22835 fields in Climate mean Period_1
22835 fields in Climate mean Period_2
22835 fields in Climate mean Period_3
22835 fields in Climate mean Period_4

Maximum allowed is 4096 fields per Climate Mean Period.

You don't need to worry about the Climate Mean Period here, and in fact this job will run perfectly happily with this many fields. The line that is of more concern is

30600 fields in stream 61.  Maximum allowed is 4096.

The value of 30600 comes from the fact that you are requesting 4x85 level variables for 90 days: 4x90x85=30600.

Fix

There are two ways to fix this. They both need you to go to Model Selection → Post Processing → Initialization and processing of mean and standard PP files.

Method 1: Increase the Override size

Increasing the value in the Override size column from 0 to 16000 for the PP1/PB/61 stream will remove this error. However, the Help text explicitly states here

Override size.
Fieldsfiles usually can only contain 4096 fields. The recommended way to work around this restriction is to use periodic re-initialisation of the fieldsfiles. In the rare case that this is not a suitable option (e.g. for analysis time in a forecast) it is possible to extend the 4096 field restriction by overriding the default size. Be careful not to override the size by too much - large numbers of fieldsfile headers can be inefficient for both runtime and memory use and may cause problems with some small executables.

So the UMUI is explicitly suggesting that the frequency of output should be altered. This is Method 2.

Method 2: Change the output frequency

In this method we change the Period from 90 to 1, i.e. there will be a new file created every day.

We will use Method 2.

Output

Now save, process, and submit your job. When the job has run the output in your archive directory will now contain 4 output files (*.p*):

$ ls *.p*
xjllba.pa20051201  xjllba.pb20051201  

Open the pb file. The variable list should look like

0    : 192   145   85    4     Stash code = 34001

Select this field and click the t radio button, which will list the times of each point in the field. This should give

2005/12/01:06.00 / 0.250000
2005/12/01:12.00 / 0.500000
2005/12/01:18.00 / 0.750000
2005/12/02:00.00 / 1.000000

Sample output from this job can be found in

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task3.1/

on ARCHER, and in

/projects/ukca/Tutorial/vn8.4/sample_ouput/Task3.1/

on MONSooN.

Worked Solution

There is a worked solution to this problem in the UMUI Tutorial experiment. This is job b: Tutorial: solution to Task 3.1 - outputting a diagnostic.

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Written by Luke Abraham 2014