Merge pull request #2 from codegat-test-org/dev-config-update

Add config stuff
codegat-test-org · Jun 13, 2024 · ccbb1c7 · ccbb1c7
2 parents 29238ae + 8934a40
commit ccbb1c7
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
   pr-comment:
     name: Comment
     if: github.event_name == 'issue_comment'
-    uses: codegat-test-org/meta-model-configs/.github/workflows/config-pr-2-comment.yml@main
+    uses: codegat-test-org/meta-model-configs/.github/workflows/config-pr-2-confirm.yml@main
     secrets: inherit
     permissions:
       contents: write  # For updating metadata.yaml version and committing checksums

diff --git a/accessom2.nml b/accessom2.nml
@@ -0,0 +1,20 @@
+&accessom2_nml
+    log_level = 'DEBUG'
+
+    ! ice_ocean_timestep defines the MOM baroclinic timestep, CICE thermodynamic timestep
+    ! and MOM-CICE coupling interval, in seconds.
+    ! ice_ocean_timestep is normally a factor of the JRA55-do forcing period of 3hr = 10800s,
+    ! e.g. one of 100, 108, 120, 135, 144, 150, 180, 200, 216, 225, 240, 270, 300, 360, 400, 432,
+    ! 450, 540, 600, 675, 720, 900, 1080, 1200, 1350, 1800, 2160, 2700, 3600 or 5400 seconds.
+    ! The model is usually stable with a 5400s timestep, including in the initial spinup from rest.
+    ice_ocean_timestep = 5400
+&end
+
+&date_manager_nml
+    forcing_start_date = '1958-01-01T00:00:00'
+    forcing_end_date = '2019-01-01T00:00:00'
+
+    ! Runtime for a single segment/job/submit, format is years, months, seconds,
+    ! two of which must be zero.
+    restart_period = 5, 0, 0
+&end
diff --git a/atmosphere/atm.nml b/atmosphere/atm.nml
@@ -0,0 +1,6 @@
+&atm_nml
+/
+
+&runoff_nml
+    remap_weights_file = 'INPUT/rmp_jrar_to_cict_CONSERV.nc'
+/
diff --git a/atmosphere/forcing.json b/atmosphere/forcing.json
@@ -0,0 +1,62 @@
+{
+  "description": "JRA55-do v1.4.0 IAF forcing",
+  "inputs": [
+    {
+      "filename": "INPUT/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010130-{{year}}12312230.nc",
+      "fieldname": "rsds",
+      "cname": "swfld_ai"
+    },
+    {
+      "filename": "INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010130-{{year}}12312230.nc",
+      "fieldname": "rlds",
+      "cname": "lwfld_ai"
+    },
+    {
+      "filename": "INPUT/prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010130-{{year}}12312230.nc",
+      "fieldname": "prra",
+      "cname": "rain_ai"
+    },
+    {
+      "filename": "INPUT/prsn_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010130-{{year}}12312230.nc",
+      "fieldname": "prsn",
+      "cname": "snow_ai"
+    },
+    {
+      "filename": "INPUT/psl_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010000-{{year}}12312100.nc",
+      "fieldname": "psl",
+      "cname": "press_ai"
+    },
+    {
+      "filename": "INPUT/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}0101-{{year}}1231.nc",
+      "fieldname": "friver",
+      "cname": "runof_ai",
+      "domain": "land"
+    },
+    {
+      "filename": "INPUT/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010000-{{year}}12312100.nc",
+      "fieldname": "tas",
+      "cname": "tair_ai"
+    },
+    {
+      "filename": "INPUT/huss_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010000-{{year}}12312100.nc",
+      "fieldname": "huss",
+      "cname": "qair_ai"
+    },
+    {
+      "filename": "INPUT/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010000-{{year}}12312100.nc",
+      "fieldname": "uas",
+      "cname": "uwnd_ai"
+    },
+    {
+      "filename": "INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}01010000-{{year}}12312100.nc",
+      "fieldname": "vas",
+      "cname": "vwnd_ai"
+    },
+    {
+      "filename": "INPUT/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{{year}}0101-{{year}}1231.nc",
+      "fieldname": "licalvf",
+      "cname": "licalvf_ai",
+      "domain": "land"
+    }
+  ]
+}
diff --git a/config.yaml b/config.yaml
@@ -0,0 +1,110 @@
+# 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_iaf
+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)
+
+# Model configuration
+name: common
+model: access-om2
+input:
+  - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_conserve2nd.nc
+  - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_patch.nc
+  - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_1st_conserve.nc
+  - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jra55_cice_2nd_conserve.nc
+  - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/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.1deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prsn/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/psl/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/land/day/friver/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/tas/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/huss/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/uas/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/vas/gr/v20190429
+            - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/landIce/day/licalvf/gr/v20190429
+      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.1deg/2020.05.30/grid_spec.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.1deg/2020.05.30/ocean_mosaic.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/topog.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/bathymetry/global.1deg/2020.10.22/ocean_mask.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/vertical/global.1deg/2020.10.22/ocean_vgrid.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/processor_masks/global.1deg/216.16x15/2020.05.30/ocean_mask_table
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/chlorophyll/global.1deg/2020.05.30/chl.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/tideamp.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_amp.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/tides/global.1deg/2020.05.30/roughness_cdbot.nc
+          - /g/data/vk83/experiments/inputs/access-om2/ocean/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
+      ncpus: 216
+
+    - 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_360x300_24x1_24p.exe
+      input:
+        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.1deg/2020.05.30/grid.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.1deg/2020.10.22/kmt.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/i2o.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/o2i.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/u_star.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/monthly_sstsss.nc
+      ncpus: 24
+
+# Collation
+collate:
+  restart: true
+  walltime: 1:00:00
+  mem: 30GB
+  ncpus: 4
+  queue: normal
+  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/mppnccombine.spack
+
+# Misc
+runlog: true
+stacksize: unlimited
+restart_freq: 5YS
+mpirun: --mca io ompio --mca io_ompio_num_aggregators 1
+qsub_flags: -W umask=027
+env:
+    UCX_LOG_LEVEL: 'error'
+
+manifest:
+  reproduce:
+    exe: True
+
+# 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
diff --git a/doc/Fabio2018_Namelist_meeting_final.pdf b/doc/Fabio2018_Namelist_meeting_final.pdf