merge ak-dev branch

.gitignore

@@ -1,9 +1,8 @@
 archive
 work
+__pycache__
 access-om2.err
 access-om2.out
-*deg_jra55_*.[eo][0-9]+
-output_to_gdata.[eo][0-9]+
-restarts_to_gdata.[eo][0-9]+
+*.[eo][0-9]*
 .DS_Store
-._.DS_Store
+._*

README.md

@@ -3,6 +3,14 @@ Standard configuration for 0.25 degree [ACCESS-OM2](https://github.com/COSIMA/ac
 
 For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/access-om2/wiki).
 
-Run length and timestep are set in `accessom2.nml`. The timestep is normally set to a factor of the JRA55-do forcing period of 3hr = 10800s, for example 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 5400s. 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.
+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.
 
 **NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2), all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), and [payu](https://github.com/payu-org/payu) to be kept informed of updates, problems and bug fixes as they arise.
+
+## Conditions of use
+
+We 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).

accessom2.nml

@@ -1,5 +1,13 @@
 &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 default timestep is 1350s, which should be stable for an initial spinup from rest.
+    ! After the first year or two of equilibration you could try 1800s.
     ice_ocean_timestep = 1350
 &end
 

atmosphere/atm.nml

@@ -1,6 +1,6 @@
 &atm_nml
-&end
+/
 
 &runoff_nml
     remap_weights_file = 'INPUT/rmp_jrar_to_cict_CONSERV.nc'
-&end
+/

config.yaml

@@ -1,57 +1,65 @@
 # PBS configuration
-# If submitting to a different project to your default uncomment line below 
-# and change project code as appropriate
-# project: w35
+
+# 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: 025deg_jra55_ryf
-ncpus: 1824
-
-# Force payu to always find, and save, files in this scratch project directory
-# shortpath: /scratch/w35
 
 # Model configuration
 name: common
 model: access-om2
-input: /g/data/ik11/inputs/access-om2/input_236a3011/common_025deg_jra55
+input: /g/data/ik11/inputs/access-om2/input_20201102/common_025deg_jra55
 submodels:
     - name: atmosphere
       model: yatm
-      exe: /g/data/ik11/inputs/access-om2/bin/yatm_4198e150.exe
+      exe: /g/data/ik11/inputs/access-om2/bin/yatm_2617f7c.exe
       input:
-            - /g/data/ik11/inputs/access-om2/input_236a3011/yatm_025deg
+            - /g/data/ik11/inputs/access-om2/input_20201102/yatm_025deg
             - /g/data/ik11/inputs/JRA-55/RYF/v1-4
       ncpus: 1
 
     - name: ocean
       model: mom
-      exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_e837d05d_libaccessom2_4198e150.x
-      input: /g/data/ik11/inputs/access-om2/input_236a3011/mom_025deg
+      exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_2617f7c.x
+      input: /g/data/ik11/inputs/access-om2/input_20201102/mom_025deg
       ncpus: 1455
 
     - name: ice
       model: cice5
-      exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_1440x1080_480p_597e4561_libaccessom2_4198e150.exe
-      input: /g/data/ik11/inputs/access-om2/input_20200422/cice_025deg
+      exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_1440x1080_480p_015877c_libaccessom2_2617f7c.exe
+      input: /g/data/ik11/inputs/access-om2/input_20201102/cice_025deg
       ncpus: 361
 
 # Collation
 collate:
+  restart: true
+  mpi: true
   walltime: 1:00:00
-  mem: 30GB
+  mem: 16GB
   ncpus: 4
-  queue: express
-  exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine
+  queue: normal
+  exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine-fast
 
 # Misc
 runlog: true
 stacksize: unlimited
-mpirun: --mca orte_base_help_aggregate 0
+restart_freq: 1  # use tidy_restarts.py instead
+mpirun: --mca io ompio --mca io_ompio_num_aggregators 1
 qsub_flags: -W umask=027
 # 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: resub.sh
+    run: rm -f resubmit.count
 
-# DANGER! Do not uncomment this without checking the script is synching 
-# to the correct location!
-# postscript: sync_output_to_gdata.sh
+# DANGER! Do not uncomment this without checking the script is syncing to the correct location!
+# postscript: sync_data.sh