Auto update dev-1deg_jra55_ryf to use access-om2/pr133-4

config.yaml

@@ -1,112 +1,85 @@
-# PBS configuration
-
-# If submitting to a different project to your default, uncomment line below
-# and replace PROJECT_CODE with appropriate code. This may require setting shortpath
-# project: PROJECT_CODE
-
-# Force payu to always find, and save, files in this scratch project directory
-# shortpath: /scratch/PROJECT_CODE
-
-queue: normal
-walltime: 3:00:00
-jobname: 1deg_jra55_ryf
-mem: 1000GB
-
-# 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)
-
-# Modules for loading model executables
-modules:
-  use:
-      - /g/data/vk83/modules
-  load:
-      - access-om2/2025.12.000
-      - model-tools/fre-nctools/2024.05-1
-
-# Model configuration
-name: common
-model: access-om2
-input:
-  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_conserve2nd.nc
-  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_patch.nc
-  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_1st_conserve.nc
-  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_2nd_conserve.nc
-  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_patch.nc
-submodels:
-    - name: atmosphere
-      model: yatm
-      exe: yatm.exe
-      input:
-            - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc
-            - /g/data/vk83/configurations/inputs/JRA-55/RYF/v1-4/data
-      ncpus: 1
-
-    - name: ocean
-      model: mom
-      exe: mom5_access_om
-      input:
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/grid_spec.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_mosaic.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/topog.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/ocean_mask.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/vertical/global.1deg/2020.10.22/ocean_vgrid.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/processor_masks/global.1deg/216.16x15/2020.05.30/ocean_mask_table
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/chlorophyll/global.1deg/2020.05.30/chl.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/tideamp.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_amp.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_cdbot.nc
-          - /g/data/vk83/configurations/inputs/access-om2/ocean/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
-      ncpus: 216
-
-    - name: ice
-      model: cice5
-      exe: cice_auscom_360x300_24x1_24p.exe
-      input:
-        - /g/data/vk83/configurations/inputs/access-om2/ice/grids/global.1deg/2024.04.17/grid.nc
-        - /g/data/vk83/configurations/inputs/access-om2/ice/grids/global.1deg/2024.04.17/kmt.nc
-        - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/i2o.nc
-        - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/o2i.nc
-        - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/u_star.nc
-        - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/monthly_sstsss.nc
-      ncpus: 24
-
-# Collation
 collate:
-  restart: true
-  walltime: 1:00:00
+  exe: mppnccombine
   mem: 30GB
   ncpus: 4
   queue: normal
-  exe: mppnccombine
-
-# Misc
-runlog: true
-stacksize: unlimited
-restart_freq: 5YS
-mpi:
-  flags:
-    - --mca io ompio --mca io_ompio_num_aggregators 1
-qsub_flags: -W umask=027
+  restart: true
+  walltime: 3600
 env:
-    UCX_LOG_LEVEL: 'error'
-
+  UCX_LOG_LEVEL: error
+input:
+- /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_conserve2nd.nc
+- /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_patch.nc
+- /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_1st_conserve.nc
+- /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_2nd_conserve.nc
+- /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_patch.nc
+jobname: 1deg_jra55_ryf
 manifest:
   reproduce:
-    exe: True
-
-# set number of cores per node (28 for normalbw, 48 for normal on gadi)
+    exe: false
+mem: 1000GB
+model: access-om2
+modules:
+  load:
+  - access-om2/pr133-4
+  - model-tools/fre-nctools/2024.05-1
+  use:
+  - /g/data/vk83/modules
+  - /g/data/vk83/prerelease/modules
+mpi:
+  flags:
+  - --mca io ompio --mca io_ompio_num_aggregators 1
+name: common
+payu_minimum_version: 1.2.1
 platform:
-    nodesize: 48
-
-# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771
+  nodesize: 48
+qsub_flags: -W umask=027
+queue: normal
+restart_freq: 5YS
+runlog: true
+stacksize: unlimited
+submodels:
+- exe: yatm.exe
+  input:
+  - /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc
+  - /g/data/vk83/configurations/inputs/JRA-55/RYF/v1-4/data
+  model: yatm
+  name: atmosphere
+  ncpus: 1
+- exe: mom5_access_om
+  input:
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/grid_spec.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_mosaic.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/topog.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/ocean_mask.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/grids/vertical/global.1deg/2020.10.22/ocean_vgrid.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/processor_masks/global.1deg/216.16x15/2020.05.30/ocean_mask_table
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/chlorophyll/global.1deg/2020.05.30/chl.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/tideamp.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_amp.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_cdbot.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ocean/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
+  model: mom
+  name: ocean
+  ncpus: 216
+- exe: cice_auscom_360x300_24x1_24p.exe
+  input:
+  - /g/data/vk83/configurations/inputs/access-om2/ice/grids/global.1deg/2024.04.17/grid.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ice/grids/global.1deg/2024.04.17/kmt.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/i2o.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/o2i.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/u_star.nc
+  - /g/data/vk83/configurations/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/monthly_sstsss.nc
+  model: cice5
+  name: ice
+  ncpus: 24
+sync:
+  enable: false
+  path: null
 userscripts:
-    error: tools/resub.sh
-    run: rm -f resubmit.count
-    sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh
-
-payu_minimum_version: 1.2.1
+  error: tools/resub.sh
+  run: rm -f resubmit.count
+  sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh
+walltime: 10800