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Update 1deg_jra55_iaf_bgc configuration (#65)
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* update 1deg_jra55_iaf_bgc for ACCESS-NRI release
* don't use mppnccombine-fast because it ain't
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dougiesquire authored Apr 8, 2024
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22 changes: 0 additions & 22 deletions .travis.yml

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14 changes: 5 additions & 9 deletions README.md
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# 1deg_jra55_iaf with BGC
Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2) with JRA55-do interannual forcing (IAF) and coupled biogeochemistry in the ocean and sea ice.
Standard configuration for 1 degree [ACCESS-OM2](https://github.com/ACCESS-NRI/access-om2) experiment (ACCESS-OM2) with JRA55-do interannual forcing (IAF) and coupled biogeochemistry in the ocean and sea ice.

This is the BGC version, on the `master+bgc` branch. For the physics-only version (no BGC), use the `master` branch.
This is the BGC version. This BGC setup includes both ocean and sea ice BGC. To turn off the sea ice BGC and have BGC only in the ocean, set `skl_bgc = .false.` in `ice/cice_input.nml`.

This BGC setup includes both ocean and sea ice BGC. To turn off the sea ice BGC and have BGC only in the ocean, set `skl_bgc = .false.` in `ice/cice_input.nml`.

For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/access-om2/wiki).
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 5400 seconds, and the model is stable with this timestep right from the start. However if you alter the configuration you may need a shorter timestep during the first year or two of model equilibration.

**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:
COSIMA requests 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 they can add them to [their list](https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ).
95 changes: 66 additions & 29 deletions config.yaml
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# 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
# 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: 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/ik11/inputs/access-om2/input_20201102/common_1deg_jra55
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/ik11/inputs/access-om2/bin/yatm_d750b4b.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/ik11/inputs/access-om2/input_20201102/yatm_1deg
- /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
- /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/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_730f0bf_libaccessom2_d750b4b.x
exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/fms_ACCESS-OM-BGC.x
input:
- /g/data/ik11/inputs/access-om2/input_bgc_20220224/mom_1deg
- /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/bgc_param.nc
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/co2_iaf.nc
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/co2_ryf.nc
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/csiro_bgc.res.nc
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/csiro_bgc_sediment.res.nc
- /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/dust.nc
- /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/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_edcfa6f_libaccessom2_d750b4b.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_360x300_24x1_24p.exe
input:
- /g/data/ik11/inputs/access-om2/input_bgc_20220224/cice_1deg
- /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg
- /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.1deg/2022.02.24/i2o.nc
- /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.1deg/2022.02.24/o2i.nc
- /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/u_star.nc
- /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.1deg/2020.05.30/monthly_sstsss.nc
ncpus: 24

# Collation
Expand All @@ -58,23 +91,27 @@ collate:
mem: 30GB
ncpus: 4
queue: normal
exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine
exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/mppnccombine.spack

manifest:
reproduce:
exe: true

# Misc
runlog: true
stacksize: unlimited
restart_freq: 1 # use tidy_restarts.py instead
restart_freq: 5YS
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: resub.sh
error: tools/resub.sh
run: rm -f resubmit.count

# DANGER! Do not uncomment this without checking the script is syncing to the correct location!
# postscript: sync_data.sh
sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh
24 changes: 12 additions & 12 deletions manifests/exe.yaml
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format: yamanifest
version: 1.0
---
work/atmosphere/yatm_d750b4b.exe:
fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_d750b4b.exe
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-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe
hashes:
binhash: 52a975e3d202c0047a9ec9be1346c23c
md5: fcc373fb59917cada96c2776201b362d
work/ice/cice_auscom_360x300_24p_edcfa6f_libaccessom2_d750b4b.exe:
fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_edcfa6f_libaccessom2_d750b4b.exe
binhash: 4e8b4ef76e971c4af3b26cfac632e160
md5: 5baa1d417fe6708fc30cbeaa57d82f96
work/ice/cice_auscom_360x300_24x1_24p.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_360x300_24x1_24p.exe
hashes:
binhash: 7cca1a89ede5c5196f2c9c0bb1f4bfde
md5: 3bb0804115c5b37c7a4c66f2317c0f97
work/ocean/fms_ACCESS-OM-BGC_730f0bf_libaccessom2_d750b4b.x:
fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_730f0bf_libaccessom2_d750b4b.x
binhash: 3a65f67d21152e77034da28c22a94c66
md5: 37866455b057c85c3ea50c0ef0ea840b
work/ocean/fms_ACCESS-OM-BGC.x:
fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/fms_ACCESS-OM-BGC.x
hashes:
binhash: cb0aac284ca7bf8128f80f4f394b1f5a
md5: f9a8f286f3baef5f415fd5043b9d7419
binhash: 45352e33876da49ca042014a9f6686e5
md5: a909552e85690be692ad3ec94016181b
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