This page should show you how to set up a simple atmosphere-only UM job
You should probably also read the NCAS pages on setting up a job on HPCX.
Using the UMUI and copying an existing Job
Start the UMUI using
umui
- Click on Search - Filter
- Type the name of another user in the Owner box. Click Filter
- Copy the experiment by selecting the an experiment (highlights in blue) and click Experiment-Copy . then Click OK .
- Enter a name for the Experiment in the requestor, and click OK .
- Return to your experiments by using filter, as above, with you username.
Altering parameters
The first parameters to change in your copied expt are the personal details.
- Click on the folder icon of your new expt to open the expt.
- Click on one of Jobs contained in the expt. then click File - Open Read/Write.
- Click on Model Selection - User Information … - General Details
- Change the Target Machine User-id and the Mail-id to your own. Click Close
Choosing output variables
You’ll probably want some output from your model run! This is done via the STASH Submenu. This can be somewhat confusing. Again - it’s helpful to look at an existing job, to work out what’s going on here.
You can find a full list of Possible output variables and their associated STASH codes here.
Processing and Submiting the Job
- Click on the PROCESS button at the bottom of the Job window. The files will then be saved in
~/umui_jobs/ in a directory with the relevant job name.
- To submit a job you first need to create a
~/.umrc file. Copy Jeff’s example file from ~jeff/.umrc.example to ~/.umrc
- Change the PASSWORD to your password on the relevant machines. Change jwc to your username on the relevant machine. Then protect the file by doing
chmod 600 ~/.umrc
- Now, to submit a given job you need to run eg:
~jeff/bin/umsubmit xbaqa
- alternatively you can specify a particular machine using
~jeff/bin/umsubmit -h newton xbaqa
where xbaqa is the jobname You should get a message like:
To start um job xbaqd, logon to machine newton.cfs.ac.uk and issue command:
ksh $HOME/umui_runs/xbaqd-175173936/SUBMIT
- ssh to the machine you plan to run the experiment on and issue the command above.
- If this doesn’t work - ensure that you have the lines
export UMSETUP=/hpcx/home/n02/n02/umx/setvars_4.5
. $UMSETUP # set up UM environment variables
in your .profile on eg. hpcx.
- monitor the progress of your jobs with
qstat -a (on Green/Wren use: bjobs -a)
Continuation Runs
When you (or at least when I) set a model running, it only runs for the first Year and then halts. This is to allow you to check everything is running OK. Once done you can now procede with a continuation run. TO do this:
- on your local machine do cd
~/umui_jobs/ jobname
- edit the SUBMIT file
- change the line TYPE=NRUN to TYPE=CRUN
- save and exit
- resubmit the job to turing with
~jeff/bin/umsubmit jobname as above
- log onto turing and start the job as above
The model should now start from the end of the first year and run to completion.
If you’re running for more than a year or so, you should probably read about Automatic Resubmission
Model Output
When the model finishes it writes a .leave file in ~/um/umui_out/
‘grep ATMOS filename.leave’ shows the number of timesteps completed. The atmos timestepis half an hour. Hence 4320 timesteps is 90 days.
- output files live in $DUMP2HOLD/um/
- restart files and pp output are directed to $DUMP2HOLD/um/
Channels A, B, C and D are used for the atmosphere, E for the slab ocean and F, G and H for the coupled ocean. The channels can be described as follows:
| A | Daily upper air fields |
| B | Daily surface and near surface fields |
| C | Monthly mean upper air fields |
| D | Monthly mean surface fields |
| E | Monthly mean slab ocean fields |
| F | Monthly mean ocean potential temperature |
| G & H | Seasonal Mean Ocean Fields |
Brief summary of actual fields is:
- pa - daily height and temperature on four pressure levels
- pb - daily PMSL and surface temperature
- pc - monthly mean u,v, omega, height, temperature, diabatic heating
on four pressure levels. Plus PV on four isentropic levels and
surface pressure
- pd - monthly mean surface fields: lots, including surface temperature
windstress and surface fluxes.
- pe - monthly mean slab ocean fields including temperature and ocean
heat flux convergence
Data volumes: One year of data requires approx:
pa - 81Mb; pb - 20Mb; pc - 10Mb; pd - 15Mb; pe - 3Mb
(from Rowan’s pages)
- Use ~lrum/bin/uminfo filename to examine file in $DUMP2HOLD/um/
- The output fields are labelled by their Stash Codes? - here a list of stash codes and their associated field descriptions.
- use xconv to view the data
CRACERU files list the outpur files. All files are UM files (not pp)? Some files are TAR’d others are not.
Did it work?
Did your run work? You probably want to read this first. And then look at the .leave file in ~/um/umui_out
Archiving Data
You may want to read The UGAMP documentation of Automatic Archiving
Data is archived to /hold/year/lrdlrh/um_archive/
Extracting fields from the archive
I? suggest using getf
Cancel a Job!!
do (on HPCX)
llq -u <username>
then use the JOB_ID_NUMBER from that to do:
llcancel JOB_ID_NUMBER
See the HPCX pages for more detail.
— Dan Hodson?- 08 Jul 2004
