wiki:access/T-AMIP_GA6


GA6 N96L85(JULES) Transpose-AMIP II procedure


SUMMARY: Basic steps to run accessdev GA6 T-AMIP

This section shows the minimum number of steps needed to do a single GA6 T-AMIP. These steps are explained in more detail in the following sections, and are similar to those for the ACCESS 1.3 T-AMIP run.

  • setup initial files on raijin:
    • login to raijin eg (note we are using p66/glr548 as the example project/user login)
      ssh -X glr548@raijin.nci.org.au
      
    • create a directory where you will keep the initial condition and ancillary version files for your run
      mkdir /short/dp9/glr548/tamip_ic
      
    • decide which T-AMIP date you want to use (here I select 0600 UTC on 2009-01-16) and in this dir create soft links to the corresponding initial dump file and the appropriate SST and SICE ancillary files
      cd /short/dp9/glr548/tamip_ic [[BR]]
         ln -s /projects/access/AMEL/TransposeAMIPII/ga6/sstice/iceN96_20090101nd59ga6    tamipice
         ln -s /projects/access/AMEL/TransposeAMIPII/ga6/sstice/sstN96_20090101nd59ga6    tamipsst
         ln -s /projects/access/AMEL/TransposeAMIPII/ga6/ga6ic/ga6tamip2009-01-16-h06     GA6tamipic 
      
      Note: mon17nov14: GA6 T-AMIP data is in /g/data/p66/glr548/tamip_sam/ga6 and is also now in /projects/access/AMEL/TransposeAMIPII/ga6
    • get a copy of the ancillary version files - these point to which ancillary files we want to use for GA6, in particular the sst+sice files
      cd /short/dp9/glr548/tamip_ic [[BR]]
         cp /projects/access/AMEL/TransposeAMIPII/ga6/ga6ancdirnames .
         cp /projects/access/AMEL/TransposeAMIPII/ga6/ga6ancfilnames .
         edit ga6ancdirnames and change TAMIPga6 and TAMIPga6anc to point to your tamip_ic dir eg in my case /short/dp9/glr548/tamip_ic, and the anc files ie
           export TAMIPga6=/short/dp9/glr548/tamip_ic
           export TAMIPga6anc=/projects/access/AMEL/TransposeAMIPII/ga6/ga6anc
      
  • get a copy of the GA6 T-AMIP RUN job on accessdev:
    • login to accessdev and open umuix
      ssh -X glr548@accessdev.nci.org.au
      umuix
      
    • in umuix cp glr548 "RUN GA6 N96: cp vacea 03062014" vaceb to your own job eg to vacew
    • edit your new job (vacew) to point to the directory of the initial condition files you created via links on rajin above
         umuix -> vacew -> Input -> Time_convention:
           change TAMIP_DATA
             from /short/dp9/glr548/tamip_ic
             to   your new dir (in my case I leave it as /short/dp9/glr548/tamip_ic)
      
    • edit your new job (vacew) to point to the ancillary version files you copied above
         umuix -> vacew -> Atm -> Anc -> In file related options -> Ancillary version files:
           change Ancil filenames version
             from /g/data1/p66/glr548/tamip_sam/ga6/ga6ancfilnames
             to   /short/dp9/glr548/tamip_ic/ga6ancfilnames
           change Ancil versions file
             from /glr548/tamip_sam/ga6/ga6ancdirnames
             to   /short/dp9/glr548/tamip_ic/ga6ancdirnames
      
  • submit your new job:

umuix -> vacew -> Check/Save/Process/Submit
Check == you will get 1 error, related to the STASH but just ignore this - in fact you need not do this step
Save/Process == this saves and then processes the job and so creates the umui_jobs/vacew directory

/home/548/glr548/umui_jobs/vaceb
and this holds the job parameter control files
CNTLALL FCM_BLD_COMMAND IOSCNTL SHARED USR_MACH_OVRDS
CNTLATM FCM_UMATMOS_CFG JOBSHEET SIZES USR_PATHS_OVRDS
CNTLGEN FCM_UMRECON_CFG MAIN_SCR STASHC
COMP_SWITCHES FCM_UMSCRIPTS_CFG PPCNTL SUBMIT
EXTR_SCR INITFILEENV PRESM_A UMSUBMIT
EXT_SCRIPT_LOG INITHIS SCRIPT USR_FILE_OVRDS

Submit == submits the job

  • check on run and its outputs on raijin:
    • login to raijin
      ssh -X glr548@raijin.nci.org.au
      
    • Check on the running job
      qstat -u $USER
      
    • using 256 processors the single 5day forecast should take ~4min
      Standard Error and Output will be in your home_dir/um_output eg in my case

cd /home/548/glr548/um_output
vacew000.vacew.d14322.t153807.leave

Data output files will be in

DATAM = DATAW = /short/$PROJECT/$USER/$RUNID eg /short/dp9/glr548/vacew in my case
cd /short/dp9/glr548/vacew
vahdb.astart = start dump
vacewa.p* = forecast output files which show 3hrly outputs for the 5day forecast

  • you can view the pp output, plot them or convert them to netcdf using xconv eg
    cd /short/dp9/glr548/vacew
    xconv vacewa.pc20090802
    
    We can create TOA (top of atmosphere) OLR (outgoing longwave radiation) and outgoing shortwave radiation plots at day 5.25 of the forecast run, and they are shown in the section "Example of GA6 T-AMIP outputs" below.
    Note: As of wed29oct14 the T-AMIP data which is in

/g/data/p66/glr548/tamip_sam/ga6

is also now also in

/projects/access/AMEL/TransposeAMIPII/ga6

so all projects should be able to access it


In the sections below we explain the procedure in more detail but the above steps are all you need to start running a GA6 T-AMIP job.

Preliminary steps

The following steps, covering those listed in the T-AMIP experimental design, were taken to setup the GA6 T-AMIP procedure. These do not need to be re-done by new users, but are here to explain how we setup the run.

  • (1) Model state variables are to be initialised from ECMWF YOTC analyses available from http://data-portal.ecmwf.int/data/d/yotc. Guidance on carrying out the interpolation can be found in the ECMWF IFS documentation.

To do this we follow the procedure of Roff et al. (2012) and download four 3D fields (U, V, T and Q) and four surface fields (Surface pressure, Skin Temperature, Geopotential and Land-sea mask with the latter two being invariant) and combine them into one grib file. This is then supplied as the start “dump”, or initial conditions, for the UM reconfiguration run job (raijin:vacee) to produce a N96L85 um-formatted initial condition file. They can also be produced by the automatic script based on vacee and seen in /short/p66/glr548/tamipGA6_run_recon/run_tamipGA6_recon. Note: as GA6 is UM 8.5 code it can directly convert the grib file; GA6 is run on the endgame grid, so is different from the ACCESS grid; GA6 uses the JULES LSM.

  • (2) Atmospheric composition, solar forcing and land use should be as the final year of the CMIP5 AMIP experiment (2008).

The atmospheric mixing ratios of CO2, CH4 (Methane), N2O, CFC11, CFC12, CFC113, HCFC22, HFC125 and HFC134A for the T-AMIP period have been set to the same values as used in the ACCESS 1.3 AR5 RCP4.5 experiment. Similarly, the solar forcing and the volcanic forcing are also set to the values from the AR5 RCP4.5 run.

  • (3) SSTs from ECMWF YOTC should be used in the hindcasts.

The 0.75o resolution SST and Seaice YOTC fields were downloaded for the relevant dates as grib files and were then processed via: converted to netcdf using cdo operators; split into separate SST and Seaice files using nco operators; the SST fields were then extrapolated over land using convsh scripts; converted to ancillary format using Xancil; then interpolated in space to N96L38 resolution using the UM Central Ancillary Program.

The 0.75o resolution SST and Seaice YOTC fields were downloaded for the relevant dates as grib files and were then processed via: converted to netcdf using cdo operators; split into separate SST and Seaice files using nco operators; then the UM8.2 CAP scheme was run using run.sh and n96e.xml on raijin as listed in the README file.

  • (4) Land surface models should be initialised using one of the following methods:
    • Initialise from fields produced by a land surface assimilation system (e.g. ECMWF or GLDAS)
    • Initialise using a suitable climatology: e.g. from GSWP2 or derived from the model’s AMIP simulation.
    • Initialised with a nudging method as described by Boyle et al. (2005).

We initialize the LSM from the GA6 AMIP climatology and, as GA6 runs with the JULES LSM, we just need the monthly means of the 3 fields: SNOW AMOUNT, SOIL MOISTURE and DEEP SOIL TEMPERATURE (STASH codes [0,3], [8,223], and [8,223] taken from Martin’s GA6 N96L85 AMIP run (accessdev. vaamc) with outputs in /short/p66/mrd599/vaamc on raijin. These pp files are then processed via scripts as described in the README file.

  • (5) Aerosols concentrations should either be initialised using a climatology calculated from the model’s AMIP simulation, or initialised using the nudging method of Boyle et al. (2005).

As we do not have aerosol climatologies we have taken the aerosol concentrations from the ancillary files that were used for the CMIP5 experiment. As the T-AMIP period is in 2008-9 and CMIP5 runs cease in 2005, we have extended the aerosol concentrations to this period by using those ancillaries from the ACCESS 1.3 AR5 RCP4.5 experiment where needed. Details are in the README file.

  • (6) Non-state variable prognostics which spin-up quickly (such as cloud fraction for models with a prognostic scheme) can either be initialised from zero, or initialised using the nudging method of Boyle et al. (2005).

We initialize to zero all the cloud fields: QCF AFTER TIMESTEP, CONV CLOUD BASE LEVEL NO. AFTER TS, CONV CLOUD TOP LEVEL NO. AFTER TS, CONV CLOUD LIQUID WATER PATH, QCL AFTER TIMESTEP, AREA CLOUD FRACTION IN EACH LAYER., BULK CLOUD FRACTION IN EACH LAYER, LIQUID CLOUD FRACTION IN EACH LAYER, and FROZEN CLOUD FRACTION IN EACH LAYER (STASH codes: 12, 14, 15, 16, 254, 265, 266, 267, and 268)

  • (7) The AGCMs submitted should be the same (both in terms of physics and resolution) as those used for the CMIP5 AMIP experiment in order to compare model biases across timescales.

GA6 (Global Atmosphere 6.0) is the current U.K. Met Office global atmospheric model configuration and is the atmospheric component of the GC2 (Global Coupled configuration 2) climate model configuration. The configuration here is based on the vn8.5 code with Met Office GA6.0 patches for both the Unified Model (UM) and the Joint UK Land Environment Simulator (JULES). See the Library of standard ACCESS experiments and test cases, Climate experiment configurations, GA6 configurations https://trac.nci.org.au/trac/access/wiki/GA6.0_testcases for more information.

GA6 T-AMIP run procedure

On NCI accessdev the T-AMIP GA6 build/run/reconfig jobs are vacea/vaceb/vacee which are based on vaamc, the standard GA6 N96L85 job martin obtained from the Met Office. The executable we use comes from vacea while vacee is based on vaceb and is used to create reconfigured dump files from the ECMWF YOTC input grib files discussed above. We then changed the original run job vaceb by: applying the Atmospheric composition, solar forcing and land use changes in (2); point to the SST and SICE field ancillary files created in (3) and the aerosol ancillaries mentioned in (5); and point to the GA6 initial condition dump file discussed in (1).

This run job can then be run from the UMUI or we can use a raijin script (run_tamipGA6_recon or run_tamipGA6 for automatic reconfiguration or run job submission, respectively) described in the README file to submit several jobs in series. The run job uses 256 processors and takes ~4minutes to complete a 5 day hindcast for one date, so ~4 hours for a full T-AMIP run over all 64 dates.

Example of GA6 T-AMIP outputs

Plots of TOA (top of atmosphere) OLR (outgoing longwave radiation) and outgoing shortwave radiation plots at day 5.25 of the forecast run by GA6 T-AMIP for starting date 0600 UTC on 2009-01-16 (as described above) are:

As in the ACCESS 1.3 Transpose-AMIP II procedure" module https://trac.nci.org.au/trac/access/wiki/T-AMIP_ACCESS_1.3 we can calculate the surface air temperature (SAT) bias, relative to ERA-Interim reanalysis 1979-2008 data for GA6 (a) AMIP and (b) T-AMIP runs and these are displayed in the plot below.

The GA6 T-AMIP and AMIP land mass biases are very similar.

The SAT biases indicate that the GA6 T-AMIP experimental procedure is able to simulate the climate biases seen in the GA6 AMIP run. This, as well as the ACCESS 1.3 T-AMIP corresponding plot, suggests that the Transpose-AMIP II protocal could be a valuable tool in examining the development of systematic biases in the GA6 and ACCESS models.

GA6 T-AMIP scripts, datasets, sample outputs and documentation

All the GA6 T-AMIP scripts, datasets and example outputs discussed above - and covered in more detail in the README file - can be found on raijin at:

 raijin at /g/data/p66/glr548/tamip_sam/ga6 and /projects/access/AMEL/TransposeAMIPII/ga6

This directory holds sub-directories:

  • ../grib: holds the original ECMWF YOTC grib files used to create the GA6 N96L85 ic dump files
  • ../docs: holds a pdf copy of the paper "ACCESS Transpose-AMIP: Experimental Procedure and Preliminary Results", Greg Roff (accepted CAWCR Res.Let., Oct 2014) which describes in more detail the Transpose-AMIP II experimental design and its application to the ACCESS 1.3 model as well as a companion README file; also a pdf copy of the paper "GA6 Transpose-AMIP: Procedure and preliminary comparison with ACCESS 1.3", Greg Roff (accepted CAWCR Res.Let., Feb 2015) and its corresponding README file which descibe the GA6 T-AMIP setup in more detail - held in files tamip_access1.3_CAWCRresLet.pdf, tamip_access1.3_README.pdf, tamip_GA6N96L85_CAWCRresLet.pdf and tamip_GA6N96L85_README.pdf, respectively
  • ic: holds GA6 N96L85 T-AMIP ic dump files reconfigured from YOTC grib data
  • lsm: holds the Snow and Soil Moisture and Soil Temperature T-AMIP ancillaries and the scripts and files needed to create them from the GA6 AMIP climatology
  • sstsice: holds the GA6 N97L85 T-AMIP sst+ice ancillary files, listed below, as well as the scripts used to create to create them sstN96_20081001nd61ga6 sstN96_20090101nd59ga6 sstN96_20090401nd61ga6 sstN96_20090701nd62ga6 iceN96_20081001nd61ga6 iceN96_20090101nd59ga6 iceN96_20090401nd61ga6 iceN96_20090701nd62ga6
  • tamipGA6_run: which holds the GA6 T-AMIP automatic run script (run_tamipGA6), the corresponding control files directory (standard) and sample postprocessing scripts: postproc00_tamip_cloud_ga6, conv2ncREGRID_tamip02_uvtem_ga6 and conv2ncREGRID_tamip02_cloud_ga6.
  • tamipGA6_run_recon: which holds the GA6 T-AMIP reconfiguration automatic run script (run_tamipGA6_recon), the corresponding control files directory (standard).
  • example_output/tamipGA6_run_recon: example output files for GA6 T-AMIP reconfiguration for date 2008101500
  • example output/tamipGA6_run: example output files for GA6 T-AMIP for date 2008101500



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[19/11/2014] Review and updates by greg Roff

For further support on this suite, please contact g.roff@…

Last modified 3 years ago Last modified on Oct 20, 2016 2:22:42 PM

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