# Ancillaries files for nudging the UKESM1-AMIP suite **URL:** \ **Category:** Uncategorized\ **Tags:** ARCHER2\ **Created:** [6 March 2023 16:59 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937 "2023-03-06T16:59:50Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![alokpandey](https://avatars.discourse-cdn.com/v4/letter/a/e47c2d/32.png) [@alokpandey](https://cms-helpdesk.ncas.ac.uk/u/alokpandey)\ **Post date:** [6 March 2023 16:59 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/1 "2023-03-06T16:59:50Z")
Dear CMS, I am trying to convert the UKESM1-AMIP Vn11.1 free-running suite to a nudged one. It is a copy of u-be303, further developed for adding organic + inorganic Iodine emissions along with wet and dry deposition fluxes. I am unable to find/locate the ancillaries files required to nudge the suite (u-cv133) on ARCHER2. Can you please point me to where I can get the ancillaries files (e.g. SO2, CH4\_biomass) for the Gregorian Calendar? I hope the current sea ice and sst is Okay for the nudged run, if not please point the seaice\_amip\_n96e.anc and sst\_amip\_n96e.anc. Regards, Alok ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [26 April 2023 09:29 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/2 "2023-04-26T09:29:37Z")
And I would also like to do this. Though, my related question, for CMS, is how do I convert a free-running model to be nudged? My model is also a copy of u-be303. Simon ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [26 April 2023 10:35 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/3 "2023-04-26T10:35:27Z")
Hi Alok, Simon, Reanalysis datasets used for nudging can be found here /work/y07/shared/umshared/ukca/nudging i.e. $UMDIR/ukca/nudging Note that to use ERA5 you will need to include a branch, originally created at vn11.5, for this in ticket [um:#5336](https://code.metoffice.gov.uk/trac/um/ticket/5336). I believe that this is the equivalent vn11.1 branch [fcm:um.x\_br/dev/mohitdalvi/vn11.1\_nudge\_era5](https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn11.1_nudge_era5) note that there are metadata changes needed for Rose. Instructions for turning a free-running UKESM1 suite to a nudged suite can be found on the [UKCA website](https://www.ukca.ac.uk/wiki/index.php/Nudged_UKESM1-AMIP). Best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [26 April 2023 10:44 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/4 "2023-04-26T10:44:40Z")
Hi Luke, thanks very much. Simon ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [26 April 2023 10:51 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/5 "2023-04-26T10:51:24Z")
Hi Alok, Simon, Further, some Gregorian SO2 emissions can be found here: $UMDIR/ukca/ancil/n96e/cmip6/AeroChemEms/clim\_2000/v1/aerocom/ It should be straight-forward to convert 360-day monthly mean emissions files to Gregorian ones using `ncatted`, e.g. take a copy of the file you want to use, and then run the command `ncatted -O -a calendar_flexible,time,o,l,1 CH4_biomass_low_2014_2020_time_series.nc` which will operate on the copy of the file in place to make use of the calendar\_flexible metadata to tell UKCA to use a 360-day file for a Gregorian run. More information on the metadata used in netcdf emissions files can be found on the [UKCA website](https://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_8#Emission_field_metadata). Best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [13 November 2023 11:06 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/6 "2023-11-13T11:06:37Z")
> [@Luke](#): > > /work/y07/shared/umshared/ukca/nudging Hi Luke – a long delayed response to this. I am now working with UKESM1.1 which is at UM version 12.1 – is there ERA-5 nudging code for that version? Though I note that the model has an option for ERA-5 so perhaps the code has been wrapped into the trunk. Simon ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [13 November 2023 11:26 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/7 "2023-11-13T11:26:31Z")
Hi Simon, The ERA-5 code should already be in the trunk at that version, so you all you should do is point to the reanalysis files. While there isn’t a vn12.1 job listed here [https://www.ukca.ac.uk/wiki/index.php/GA7.1\_StratTrop\_suites#TS2000\_nudged\_suites](https://www.ukca.ac.uk/wiki/index.php/GA7.1_StratTrop_suites#TS2000_nudged_suites) the vn12.0 or vn13.0 jobs will be similar enough for you to take the settings needed from them. Note that there are changes that might be needed to how the fieldsfiles are output as well as settings for the Gregorian calendar. Are you working on Monsoon2 or ARCHER2? I’ve got UKESM1.1 nudged suites at UM13.0 on Monsoon2 which I’m trying to get working on ARCHER2 at the moment. Best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [13 November 2023 11:53 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/8 "2023-11-13T11:53:29Z")
@Luke I think from the nudged UKESM1 page ([Nudged UKESM1-AMIP - UKCA](https://www.ukca.ac.uk/wiki/index.php/Nudged_UKESM1-AMIP)) that the only files that need something done to work for 365 day calendar is UKCA emissions for SO2\_nat.nc I see there is /work/y07/shared/umshared/ancil/atmos/n96e/ukca\_emiss/aerocom/v2/ukca\_emiss\_SO2\_nat.nc which can use the 365 day calendar. But differs from the vn1. Any reason to use vn2 rather than vn1? Simon ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [13 November 2023 11:57 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/9 "2023-11-13T11:57:51Z")
Hi Luke, thanks. I have a UKESM1.1 version working on archer2 – a few changes needed from the default. Config is u-da865. I am working on u-db167 which has a much reduced entirely netcdf output setup. I am first going to make that work with 365 day then nudged. Simon ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [21 November 2023 12:21 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/10 "2023-11-21T12:21:27Z")
@Luke Looks like I can’t have netcdf output and gregorian calendar as outputs (from your guidance) as outputs need to go through the climate meaning. I can not see any way of having climate meaning make netcdf ☹ However, I have a more significant issue. UKESM1.1 uses easyaerosol for the volcanic files – with files at $CMIP6\_ANCILS/n96e/timeseries\_1850-2014/VolcanicAod/v3. Those files need the calendar\_flexible attribute added. But when I try to do this, I get hdf5 errors. I’ve also tried with the v1 & v2 versions but get the same error. Have you got versions of these with calendar\_flexible attributes (or which ncatted works)? Alternatively, have you got a version 13.0 of UKESM1.1 working on Archer2? If you do, I think it might be a lot easier to move to that and just change the diagnostics I want! Simon ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [21 November 2023 12:33 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/11 "2023-11-21T12:33:40Z")
Answer is not to use in place attribute editing… So ncatted -a calendar\_flexible,time,o,l,1 in.nc out.nc To convert all the existing easyaersol files do, in the directory where you want the modified files, the following: for f in /work/y07/shared/umshared/CMIP6\_ANCIL/data/ancils/n96e/timeseries\_1850-2014/VolcanicAod/v3/\*.nc ; do g=$(basename $f ) ; echo “$f -\>$g” ; ncatted -O -a calendar\_flexible,time,o,l,1 $f $g ; done ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [21 November 2023 16:27 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/12 "2023-11-21T16:27:51Z")
Hi Simon, I do have a nudged vn13.0 job on ARCHER2, although I have realised that I’ve made some mistakes in setting up the nudging that I need to address. I know what needs fixing though, so these should be straight-forward. It is also straight-forward to upgrade this to vn13.1 as needed. I’ll let you know when I have a working suite-id. Best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [22 November 2023 16:55 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/13 "2023-11-22T16:55:32Z")
And the files I needed to add calendar\_flexible to are all below /work/n02/n02/tetts/ and are: ancil/365\_day/n96e/timeseries\_1850-2014/AerosolChemistryEmissions/v3/CH4\_biomass\_low\_1849\_2015\_time\_series.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_asymmetry\_lw.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_extinction\_lw.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_absorption\_sw.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_asymmetry\_sw.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_absorption\_lw.nc ancil/365\_day/n96e/timeseries\_1850-2014/VolcanicAod/v3/volc\_aer\_extinction\_sw.nc ancil/365\_day/atmos/n96e/ukca\_emiss/aerocom/v1/ukca\_emiss\_SO2\_nat.nc ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [22 November 2023 17:47 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/14 "2023-11-22T17:47:49Z")
Hi Simon, I’ve made up a vn13.1 nudged UKESM1.1 suite that uses ERA-5 nudging and Reynolds SSTs/sea-ice. However, it still seems to have issues issues with file handling for the monthly means. I’ll ask Mohit at the Met Office for further advice. Many thanks and best wishes, Luke ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [23 November 2023 17:13 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/15 "2023-11-23T17:13:46Z")
Hi Simon, Please try taking my `u-db533` suite and see how you get on. Note that the Gregorian calendar means that you need to run in single month chunks. The pptransfer to JASMIN in the first job-step will have an issue as there are no files to archive, so right-click and set this to “succeeded”. You’ll need to change where it goes to on JASMIN as it’s going to the UKCA GWS. You’ll need to follow the instructions here > **[Configuring PPTransfer](https://cms.ncas.ac.uk/unified-model/pptransfer/)** > > The now-recommended method for transferring data between ARCHER2 and JASMIN is using GridFTP using certificate authentication. This allows data transfers to run on the ARCHER2 serial nodes using certificate-based authentication rather than SSH.... to get the pptransfer working. You can also archive straight to elastic tape > **[Migration of UM Data to JASMIN Elastic Tape](https://cms.ncas.ac.uk/unified-model/jdma)** > > Instructions on how to add the JDMA app to a UM Suite to enable migration of model data to JASMIN Elastic Tape as part of the UM Workflow. This is a bit more fiddly to set up, but I have suites that do this so let me know if you have any issues. Many thanks and best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [5 December 2023 09:46 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/16 "2023-12-05T09:46:46Z")
Hi Luke, many thanks! My take is 365 day calendar is not well supported even in the most recent UM configurations. Which is a shame. I will go and copy your suite and then massively reduce the diagnostics! Simon ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [5 December 2023 09:58 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/17 "2023-12-05T09:58:44Z")
Hi Simon, I believe for GC5/UKESM2 the aim is to use a Gregorian calendar as standard, which should hopefully make things easier! Hopefully everything works OK - let me know how you get on. Best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [6 December 2023 11:58 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/18 "2023-12-06T11:58:52Z")
So, I copied your case, modifed userid, target time (1m1d) and group but got a failure at the end of the month. Got the following warnings: ??? ??? WARNING ??? ? Warning code: -100 ? Warning from routine: REPLANCA ? Warning message: Ancillary time mean lookup items 1-12 are not compliant with UMDP F03. Field no: 4 ? Warning from processor: 0 ? Warning number: 68 ??? Then 2x repeats with different warning number’s and then a final fatal error… Atm\_Step: Timestep 2232 Model time: 1982-02-01 00:00:00 FLUSH\_UNIT\_BUFFER: Error Flushing Buffered Data FLUSH\_UNIT\_BUFFER: Status is 1 FLUSH\_UNIT\_BUFFER: Length Requested was 4194304 FLUSH\_UNIT\_BUFFER: Length written was 8192 ??? ???!!!???!!!???!!!???!!!???!!! ERROR ???!!!???!!!???!!!???!!!???!!! ? Error code: 1 ? Error from routine: portio2a:flush\_unit\_buffer ? Error message: Failed in output\_buffer() ? Error from processor: 0 ? Error number: 74 ??? Simon ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [6 December 2023 14:09 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/19 "2023-12-06T14:09:52Z")
Hi Simon, Looking at other people with the same error on this helpdesk, this seems to be a disk space issue. You may need to clear some space, if you can, or ask @Grenville to increase your quota. Many thanks and best wishes, Luke ---
**Author:** ![SimonTett](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@SimonTett](https://cms-helpdesk.ncas.ac.uk/u/SimonTett)\ **Post date:** [6 December 2023 19:38 UTC](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937/20 "2023-12-06T19:38:21Z")
Thanks. I will do that. Simon [Next page](https://cms-helpdesk.ncas.ac.uk/t/ancillaries-files-for-nudging-the-ukesm1-amip-suite/937.md?page=2)