Updates for 0.25 RYF config

README.md

@@ -1,16 +1,16 @@
 # 025deg_jra55_ryf
 Standard configuration for 0.25 degree [ACCESS-OM2](https://github.com/ACCESS-NRI/access-om2) experiment (ACCESS-OM2-025) with JRA55-do 1 May 1990 - 30 April 1991 repeat-year forcing (RYF9091).
 
-This is the physics-only version, on the `master` branch.
+This is the physics-only version.
 
-For usage instructions, see the [ACCESS-Hive Docs](https://access-hive.org.au/models/run-a-model/run-access-om/)
+For usage instructions, see the [ACCESS-Hive docs](https://access-hive.org.au/models/run-a-model/run-access-om/)
 
 Run length and timestep are set in `accessom2.nml`. The default timestep for this configuration is 1350 seconds, and the model is stable with this timestep right from the start. After the first year or two of model equilibration you may be able to run with a 1800s timestep for faster throughput.
 
 ## Conditions of use
 
-COSIMA requests that users of this or other ACCESS-OM2 model code:
+COSIMA request that users of this or other ACCESS-OM2 model code:
 1. consider citing Kiss et al. (2020) ([http://doi.org/10.5194/gmd-13-401-2020](http://doi.org/10.5194/gmd-13-401-2020))
 2. include an acknowledgement such as the following:
 *The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; [http://www.cosima.org.au](http://www.cosima.org.au)) for making the ACCESS-OM2 suite of models available at [https://github.com/COSIMA/access-om2](https://github.com/COSIMA/access-om2).*
-3. let us know of any publications which use these models or data so we can add them to [our list](https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ).
+3. let COSIMA know of any publications which use these models or data so we can add them to [their list](https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ).

config.yaml

@@ -1,17 +1,22 @@
 # 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
+# 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
-# (you may need to add the corresponding PBS -l storage flag in sync_data.sh)
-# shortpath: /scratch/v45
+# shortpath: /scratch/PROJECT_CODE
 
 queue: normal
 walltime: 5:00:00
 jobname: 025deg_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
@@ -22,15 +27,15 @@ input:
 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-ieiy3e7hidn4dzaqly3ly2yu45mecgq4/bin/yatm.exe
+      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.025deg/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-ewcdbrfukblyjxpkhd3mfkj4yxfolal4/bin/fms_ACCESS-OM.x
+      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.025deg/2020.05.30/grid_spec.nc
           - /g/data/vk83/experiments/inputs/access-om2/ocean/grids/mosaic/global.025deg/2020.05.30/ocean_hgrid.nc
@@ -49,10 +54,10 @@ submodels:
 
     - 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-rh3xfkrgajya3ghtliacuhlx3pgvrzqs/bin/cice_auscom_1440x1080_48x40_480p.exe
+      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_1440x1080_48x40_480p.exe
       input:
-        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2020.11.02/grid.nc
-        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2023.05.15/kmt.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2024.04.17/grid.nc
+        - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2024.04.17/kmt.nc
         - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.025deg/2020.05.30/i2o.nc
         - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.025deg/2020.10.22/o2i.nc
         - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.025deg/2020.05.30/u_star.nc
@@ -64,20 +69,24 @@ collate:
   restart: true
   mpi: true
   walltime: 1:00:00
-  mem: 16GB
+  mem: 30GB
   ncpus: 4
   queue: normal
-  exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine-fast
+  exe: /g/data/vk83/apps/mppnccombine-fast/0.2/bin/mppnccombine-fast
 
 # Misc
 runlog: true
 stacksize: unlimited
-restart_freq: '5Y'
+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
@@ -86,3 +95,4 @@ platform:
 userscripts:
     error: tools/resub.sh
     run: rm -f resubmit.count
+    sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh

manifests/exe.yaml

@@ -2,17 +2,17 @@ format: yamanifest
 version: 1.0
 ---
 work/atmosphere/yatm.exe:
-  fullpath: /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-ieiy3e7hidn4dzaqly3ly2yu45mecgq4/bin/yatm.exe
+  fullpath: /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
   hashes:
-    binhash: 61890159678b68a1699cb989d2c2864e
-    md5: 7bbd1014eb48b16406877d1b93ae1a47
+    binhash: 4e8b4ef76e971c4af3b26cfac632e160
+    md5: 5baa1d417fe6708fc30cbeaa57d82f96
 work/ice/cice_auscom_1440x1080_48x40_480p.exe:
-  fullpath: /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-rh3xfkrgajya3ghtliacuhlx3pgvrzqs/bin/cice_auscom_1440x1080_48x40_480p.exe
+  fullpath: /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_1440x1080_48x40_480p.exe
   hashes:
-    binhash: 338ca3c4f516525cbc348b23ce57a9b7
-    md5: 49b5440e84158b7c762d9c2d094ae184
+    binhash: 22813654d4a52914003c563fa083e245
+    md5: 38bbb933238af1adc63c6d7eb0b6f7d1
 work/ocean/fms_ACCESS-OM.x:
-  fullpath: /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-ewcdbrfukblyjxpkhd3mfkj4yxfolal4/bin/fms_ACCESS-OM.x
+  fullpath: /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
   hashes:
-    binhash: c5c24bc2ab515b08e47d6d3ab2b54cc6
-    md5: 2432c23048525b384fd57e8cd2ed7e3b
+    binhash: 92ce1ff1a38f44f92ceafd67e8e7142c
+    md5: a3f10baeadb88e813b4a8121f61a6226

manifests/input.yaml

@@ -83,10 +83,10 @@ work/atmosphere/INPUT/rmp_jrar_to_cict_CONSERV.nc:
     md5: 2e8cf1844fe7a1156ef47170a6eb5ef1
 work/ice/RESTART/grid.nc:
   copy: true
-  fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2020.11.02/grid.nc
+  fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2024.04.17/grid.nc
   hashes:
-    binhash: ef32f5ea0beca45e4aaf2f4833b339d0
-    md5: 24920ffb6c0fea5f6ec1e590a5f46280
+    binhash: e7d9cc022ad7c7b47a4f3cd2e2e62c94
+    md5: 0b96128ea22f20f952459339119193e2
 work/ice/RESTART/i2o.nc:
   copy: true
   fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.025deg/2020.05.30/i2o.nc
@@ -95,10 +95,10 @@ work/ice/RESTART/i2o.nc:
     md5: ca16c9eef58814b9ff13fd5e8bd88a25
 work/ice/RESTART/kmt.nc:
   copy: true
-  fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2023.05.15/kmt.nc
+  fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.025deg/2024.04.17/kmt.nc
   hashes:
-    binhash: 614d68eb75a67af836cb00e9d4307f8c
-    md5: 2e9743de8f4cb868d9802db8c8e6e9ca
+    binhash: d5d5ae9d65aa7f760688b9454c86e3b9
+    md5: f2fcc29da4712aa63449992f14c69352
 work/ice/RESTART/monthly_sstsss.nc:
   copy: true
   fullpath: /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.025deg/2020.05.30/monthly_sstsss.nc

metadata.yaml

@@ -2,31 +2,34 @@ contact: Add your name here
 email: Add your email address here
 created: Add the date you started the experiment here (YYYY-MM-DD)
 description: |-
-  0.25 degree ACCESS-OM2 global model configuration under the RYF9091 Repeat
-  Year Forcing strategy outlined by Stewart et al. (2020), 
-  https://doi.org/10.1016/j.ocemod.2019.101557.
+  0.25 degree ACCESS-OM2 global model configuration under interannual forcing.
   The configuration is based on that described in Kiss et al. (2020),
   https://doi.org/10.5194/gmd-13-401-2020, but with many improvements.
   Initial conditions are WOA13v2 potential temperature and practical salinity.
-  Run with JRA55-do v1.4.0 RYF9091 (1 May 1990 - 30 April 1991) repeated forcing
-  with all solid runoff converted to liquid runoff with no heat transfer.
+  Run with JRA55-do v1.4.0 interannually-varying forcing with all solid runoff
+  converted to liquid runoff with no heat transfer.
   Spin up starts from a nominal year of 1 Jan 1900.
 notes: |-
-  Source code: https://github.com/COSIMA/access-om2
-  License: Attribution-NonCommercial-NoDerivatives 4.0 International (http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode)
-  Conditions of use:
-  We request that users of this or other ACCESS-OM2 model code or output data:
+  COSIMA request that users of this or other ACCESS-OM2 model code or output data:
   (a) consider citing Kiss et al. (2020) [http://doi.org/10.5194/gmd-13-401-2020]
   (b) include an acknowledgement such as the following:
   "The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; http://www.cosima.org.au)
   for making the ACCESS-OM2 suite of models available at https://github.com/COSIMA/access-om2.
   Model runs were undertaken with the assistance of resources from the National Computational Infrastructure (NCI),
   which is supported by the Australian Government."
-  (c) let us know of any publications which use these models or data so we can add them to our list:
+  (c) let COSIMA know of any publications which use these models or data so they can add them to their list:
   https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ
 keywords:
-  - quarter
-  - cosima
-  - access-om2-025
-  - jra55-do-v1.4.0
-  - ryf
+- JRA55
+- access-om2-025
+- repeat-year
+- global
+realm:
+- ocean
+- seaIce
+nominal_resolution: 25 km
+reference: https://doi.org/10.5194/gmd-13-401-2020
+license: CC-BY-4.0
+model: ACCESS-OM2
+version: '2.0'
+url: https://github.com/ACCESS-NRI/access-om2-configs.git