View source for Restarting an Atmos-Ocean Integration

== Restarting an Atmosphere Ocean Integration ==

UKCA is running in the QESM-AO configuration, which includes the NEMO ocean and CICE sea-ice models, using the ORCA2 grid. While restarting an atmospheric-only model has been described [[UKCA_Release_Jobs#Running_a_Perpetual_Year | elsewhere on this site]], restarting both NEMO and CICE add extra complications. 

=== 1. Pick your restart date ===

You will need to check the date in your UM dump, and select the NEMO and CICE dumps accordingly, e.g.:

* UM dump is <code>xfxfha.dac5610</code>, model date is 2285/06/01:00 / 44820.000000 - i.e. midnight on the first day of the month.
* The corresponding NEMO restart files are in fact <code>xfxfho_22850530_restart_0000.nc, xfxfho_22850530_restart_0001.nc, </code>and <code>xfxfho_22850530_restart_0002.nc</code>, when running the ocean over 3 processors - i.e. NEMO dumps are midnight on the 30th (last day) of the month.
* The corresponding CICE restart file is <code>xfxfhi.restart.2285-06-01-00000</code> - i.e. midnight on the first day of the month, the same as the UM.

=== 2. UM restart ===

* Copy your selected UM dump (e.g. <code>xfxfha.dac5510</code>) above to another directory. You may already have a <code>STARTDUMPS</code> directory defined in the UMUI, and may wish to copy it there.
* Go to '''Start dump''': <br/> Model Selection -> Atmosphere -> Ancillary and input data files -> Start Dump <br/> ''If you '''do not''' wish to reconfigure (e.g. to add in tracers etc.) 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.''

=== 3. NEMO restart ===

* To create the NEMO restart file, you will need to use the <code>rebuild_nemo</code>, which on MONSooN can be found in <code>/home/msmizi/scripts/rebuild/</code> and in <code>/home/n02/n02/annette/bin/</code> on HECToR.
* To run this, type: <br/> <code>rebuild_nemo JOBIDo_YYYYMMDD_restart NUMPROCS</code> <br/> e.g. <code>rebuild_nemo xfxfho_22850530_restart 3</code>
* This will (in this case) create the file <code>xfxfho_22850530_restart.nc</code>. You can then copy this file to another directory, e.g. <code>STARTDUMPS</code>.

=== 4. CICE restart ===

Making a CICE restart file is more involved!

* You will need to modify the CICE header, otherwise errors will occur in the naming of CICE monthly mean files. To do this, use the <code>modify_CICE_header</code> script, which can be found in <code>/home/aospre/bin/</code> on MONSooN or <code>/home/n02/n02/annette/bin/</code> on HECToR.
* This script will read-in an existing CICE restart file, and output a new file (which should not exist before the script is run). To run this, type: <br/> <code>modify_CICE_header</code>
*# Enter the input file name, e.g. <code>xfxfhi.restart.2285-06-01-00000</code>
*# Enter the output file name, e.g. <code>xfxfhi.restart.2285-06-01-00000_reset</code>
*# Enter the grid used - for QESM this will be ORCA2
*# Change the value of '''<code>istep0</code>''' to '''0'''
*# Change the value of '''<code>time</code>''' to the number in seconds since the start of the year. For a 1st June start this will be 5 months, 30 days per month, 24 hours per day, 60 minutes per hour, and 60 seconds per minute, so <code>5*30*24*60*60=12960000</code>, so enter, '''e.g. 12960000'''
*# Set the value of '''<code>time_forc</code>''' to '''0''' 
* The new file should now be written to e.g. <code>xfxfhi.restart.2285-06-01-00000_reset</code>. You can then copy this file to another directory, e.g. <code>STARTDUMPS</code>.

==== Big-Endian or Little-Endian? ====

While HECToR is little-endian, MONSooN is big-endian. While the UM and NEMO files work on both platforms, the CICE re-start files need to be byte-swaped. To do this, use the script '''<code>bindump_swap</code>''' which is available on HECToR in <code>/home/n02/n02/annette/bin/</code>.

==== Output to netCDF ====

It is also possible to output the CICE restart as a netCDF file so that it can be viewed or plotted. To do this, use the script '''<code>bindump_to_nc</code>''' which is available on HECToR in <code>/home/n02/n02/annette/bin/</code> and on MONSooN in <code>/home/aospre/bin/</code>. The value of '''<code>oceanmixed_ice</code>''' should be set to that in the CICE namelist used for the job.

=== 5. Namelist changes ===

* You should not need to change the NEMO namelist (e.g. <code>namelist_xfxfh_1m</code>), although you may need to change the CICE namelist if you are restarting in a different month to the original job.
* The variable that needs to be changed is '''<code>istep0</code>'''. This is set to the number of '''timesteps''' since the start of the year (as opposed to the number of ''seconds'' above).
* You may wish to copy the existing CICE namelist (e.g. ice_in_xfxfh_1m_CheM_sep) to a new file prior to editing.
* There are 15 timesteps per day (<code>dt=5760.0</code> seconds), and in this example, we want <code>5*30*15=2250</code>. So here the value of <code>istep0</code> is set to '''e.g. 2250'''.

== Useful Links ==

* [http://puma.nerc.ac.uk/trac/NEMOCICE PUMA NEMO/CICE page (login required)]