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GA6 N216L85(JULES) Transpose-AMIP II procedure

SUMMARY: Basic steps to run accessdev GA6 N216L85 T-AMIP

The procedure is the same as described already for GA6 N96L85 so only a brief outline will be given here.

This section shows the minimum number of steps needed to do a single GA6 N216L85 T-AMIP case.

  • setup initial files on raijin:
  • login to raijin eg (note we are using p66/glr548 as the example project/user login)
ssh -X [email protected]
  • 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 1800 UTC on 2009-08-02) 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 

   ln -s /projects/access/AMEL/TransposeAMIPII/ga6/sstice/iceN216_20090701nd62ga6       GA6N216tamipice
   ln -s /projects/access/AMEL/TransposeAMIPII/ga6/sstice/sstN216_20090701nd62ga6       GA6N216tamipsst
   ln -s /g/data1/rr4/transpose-amip/n216l85eg/ic/ga6N216L85tamip2009-08-02-h18         GA6N216tamipic

Note: feb2015: GA6 N216L85 T-AMIP ic data is in /g/data1/rr4/transpose-amip/n216l85eg/ic

  • 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 

   cp /projects/access/AMEL/TransposeAMIPII/ga6/ga6N216ancdirnames .
   cp /projects/access/AMEL/TransposeAMIPII/ga6/ga6N216ancfilnames .
   edit ga6N216ancdirnames 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 TAMIPga6ancN216=/g/data1/rr4/transpose-amip/n216l85eg/anc
  • get a copy of the GA6 N216L85 T-AMIP RUN job on accessdev:
  • login to accessdev and open umuix
ssh -X [email protected]
umuix
  • in umuix cp glr548 "tamip RUN GA6 N216L85 cp vacep tue3feb15" vaceq to your own job eg to vacev
  • edit your new job (vacev) to point to the directory of the initial condition files you created via links on rajin above
   umuix -> vacev -> 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 (vacev) to point to the ancillary version files you copied above
   umuix -> vacev -> Atm -> Anc -> In file related options -> Ancillary version files:
     change Ancil filenames version
       from /g/data1/p66/glr548/tamip_sam/ga6/ga6N216ancfilnames
       to   /short/dp9/glr548/tamip_ic/ga6N216ancfilnames
     change Ancil versions file
       from /g/data1/p66/glr548/tamip_sam/ga6/ga6N216ancdirnames
       to   /short/dp9/glr548/tamip_ic/ga6N216ancdirnames
  • edit your run time from 12000s to 1200s (you will only need <20min for one 5day forecast)
   umuix -> vacev -> User -> Job submission -> PBSpro
     change Job time limit from 12000 to 1200

  • submit your new job:

    umuix -> vacev -> 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/vacev directory

    /home/548/glr548/umui_jobs/vacev

    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 [email protected]
  • Check on the running job
qstat -u $USER

  • using 512 processors the single 5day forecast should take <20min

    Standard Error and Output will be in your home_dir/um_output eg in my case

    cd /home/548/glr548/um_output

    vacev000.vacev.d15092.t100335.leave

    Data output files will be in

    DATAM # DATAW /short/$PROJECT/$USER/$RUNID eg /short/dp9/glr548/vacev in my case

    cd /short/dp9/glr548/vacev

    vacev.astart = start dump

    vaceva.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/vacev
xconv vaceva.pg20090806

We can create U and V zonal mean logP plots at day 5.6875 5.25 of the forecast run, and they are shown in the section "Example of GA6N216L85 T-AMIP outputs" below.

GA6 N216L85 T-AMIP run procedure

On NCI accessdev the T-AMIP GA6 build/run/reconfig jobs are vacea/vaceq/vacep which are based on vaamd, the standard GA6 N216L85 job martin obtained from the Met Office. The executable we use comes from vacea while vacep is based on vaceq and is used to create reconfigured dump files from the ECMWF YOTC input grib files discussed above. We then changed the original run job to vaceq 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_tamipGA6N216_recon or run_tamipGA6N216 for automatic reconfiguration or run job submission, respectively) which are similar to those described in the README file for GA6 N96L85 to submit several jobs in series. The run job uses 512 processors and takes ~20minutes to complete a 5 day hindcast for one date, so ~22 hours for a full T-AMIP run over all 64 dates.

Example of GA6 N216L85 T-AMIP outputs

Plots of U and V zonal mean logP at day 5.6875 5.25 of the forecast run by GA6 T-AMIP for starting date 0600 UTC on 2009-01-16 (as described above) are:

zmlogP_u_5.6875.png zmlogP_v_5.6875.png

GA6 N216L85 T-AMIP scripts, datasets, sample outputs and documentation

All the GA6 N216L85 T-AMIP scripts, datasets and example outputs discussed above - or required and corresponding to the equivalent outputs discussed in the GA6 N96L85 section - can be found on raijin in the following directories (large datasets are in rr4). Note that several files (eg ERA grib) are used for T-AMIP ACCESS1.3, GA6 N96L85 and N216L85 and so are also included here.

 raijin: /g/data1/rr4/transpose-amip/n216l85eg

This directory holds sub-directories:

  • anc: holds the GA6N216L85 anc files for BC, Bio, OCFF, sulp, slt(SoilTemp) and smow(SoilMoistureAndSnow) ie ga6ancBC_hi_RCP45_2000_2100.N216 , ga6ancOCFF_RCP45_2000_2100.N216 , ga6ancN216L85amip_slt

    ga6ancBio_RCP45_2000_2100.N216 , ga6ancsulp_RCP45_2000_2100f.N216 , ga6ancN216L85amip_smow

    and the Xancil jobs that created them as job_(anc_file_name).job

  • ic: holds GA6 N216L85 T-AMIP ic dump files reconfigured from the YOTC grib data

 raijin: /projects/access/AMEL/TransposeAMIPII/ga6

This directory holds the ga6N216ancdirnames and ga6N216ancfilnames files as well as the sub-directories:

  • ../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 N96L85 T-AMIP setup in more detail. These are the files: tamip_GA6N96L85_CAWCRresLet.pdf , tamip_GA6N96L85_README.pdf , tamip_access1.3_CAWCRresLet.pdf , tamip_access1.3_README.pdf
  • ../grib: holds the YOTC grib files used to create all the T-AMIP ic for ACCESS1.3, GA6 N96L85 and GA6N216L85
  • lsm: holds netcdf LSM climatology ts_clim_GA6N216L85amip.nc taken from the GA6 N216L85 AMIP run and used to create the slt and smow anc files above
  • sstice: holds the sst and ice anc files for the T-AMIP period ie sstN216_20081001nd61ga6 , sstN216_20090401nd61ga6 , sstN216_20090101nd59ga6 , sstN216_20090701nd62ga6 iceN216_20081001nd61ga6 , iceN216_20090401nd61ga6 , iceN216_20090101nd59ga6 , iceN216_20090701nd62ga6
  • sstice/method_files/N216: hold the CAP scripts/files needed to create the sst and ice anc files above
  • tamipGA6N216_run_recon: holds the GA6 N216L85 T-AMIP reconfiguration automatic run script (run_tamipGA6N216_recon) and the corresponding control files directory (standard)
  • tamipGA6N216_run: holds the GA6 N216L85 T-AMIP automatic run script (run_tamipGA6N216) and the corresponding control files directory (standard)

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[19] Review and updates by greg Roff

For further support on this suite, please contact [email protected]

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