config.yaml

# PBS configuration

# If submitting to a different project to your default, uncomment line below 
# and change project code as appropriate; also set shortpath below
# project: v45

# Force payu to always find, and save, files in this scratch project directory
# (you may need to add the corresponding PBS -l storage flag in sync_data.sh)
# shortpath: /scratch/v45

queue: normal
walltime: 5:00:00
jobname: 01deg_jra55_ryf

# Sync options for automatically copying data from ephemeral scratch space to 
# longer term storage
sync:
    enable: False # set path below and change to true
    path: null # Set to location on /g/data or a remote server and path (rsync syntax)

# Model configuration
name: common
model: access-om2
input:
    - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.01deg/2020.05.30/rmp_jra55_cice_1st_conserve.nc
    - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.01deg/2020.05.30/rmp_jra55_cice_2nd_conserve.nc
    - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.01deg/2020.05.30/rmp_jra55_cice_patch.nc
submodels:
    - name: atmosphere
      model: yatm
      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe
      input:
            - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.01deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc
            - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data
      ncpus: 1

    - name: ocean
      model: mom
      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-qji4nlmr6utrribaiyhewe4je6mifguz/bin/fms_ACCESS-OM.x
      input: 
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.01deg/2020.05.30/grid_spec.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.01deg/2020.05.30/ocean_hgrid.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.01deg/2020.05.30/ocean_mosaic.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/bathymetry/global.01deg/2020.05.30/ocean_mask.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/bathymetry/global.01deg/2020.05.30/topog.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/vertical/global.01deg/2020.05.30/ocean_vgrid.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/processor_masks/global.01deg/4358.80x75/2020.05.30/ocean_mask_table
          - /g/data/vk83/experiments/inputs/access-om2/ocean/chlorophyll/global.01deg/2020.05.30/chl.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/initial_conditions/global.01deg/2020.10.22/ocean_temp_salt.res.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.01deg/2020.05.30/tideamp.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.01deg/2020.05.30/roughness_amp.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.01deg/2020.05.30/roughness_cdbot.nc
          - /g/data/vk83/experiments/inputs/access-om2/ocean/surface_salt_restoring/global.01deg/2020.05.30/salt_sfc_restore.nc
      ncpus: 4358

    - name: ice
      model: cice5
      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19=2023.10.19-v3zncpqjj2gyseudbwiudolcjq3k3leo/bin/cice_auscom_3600x2700_90x90_722p.exe
      input:
        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.01deg/2020.05.30/grid.nc
        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.01deg/2020.05.30/kmt.nc
        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/i2o.nc
        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/o2i.nc
        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/monthly_sstsss.nc
        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/u_star.nc
      ncpus: 722

# Collation
collate:
  restart: true
  mpi: true
  walltime: 1:00:00
  mem: 16GB
  ncpus: 4
  queue: normal
  exe: /g/data/vk83/apps/mppnccombine-fast/0.2/bin/mppnccombine-fast
# Misc
runlog: true
stacksize: unlimited
restart_freq: '1YS'  # use tidy_restarts.py instead
mpirun: --mca io ompio --mca io_ompio_num_aggregators 1
qsub_flags: -W umask=027
env:
    UCX_LOG_LEVEL: 'error'
# set number of cores per node (28 for normalbw, 48 for normal on gadi)
platform:
    nodesize: 48
# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771
userscripts:
    error: tools/resub.sh
    run: rm -f resubmit.count
    sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh
manifest:
  reproduce:
    exe: true