From 103806924a3de2a5f53cec518897ec3b624d88e4 Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Mon, 16 Jun 2025 15:14:31 +1000 Subject: [PATCH 1/7] Update run-access-om.md The much discussed workflow update for using ACCESS-NRI executables with COSIMA created restarts. Thanks to @ezhilsabareesh8 @minghangli-uni for their help and input. --- docs/models/run_a_model/run_access-om2.md | 37 +++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index 6a7023238..b729b9a2d 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -622,6 +622,43 @@ env: UCX_LOG_LEVEL: 'error' ``` +#### Workflow for using high-resolution COSIMA restarts for ACCESS-NRI ACCESS-OM2 JRA configurations +!!! warning + This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of a spun ocean and restart files from a sea-ice model that goes from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. + +As highlighted above: `Start the run from a specific restart file`, there are situations where it is preferable to use an existing restart file rather than start the model from rest (particularly true when the configuration is very expensive to run). New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. + +Here we provide a workflow for doing these manual adjustments for two key configurations, namely i) `release-01deg_jra55_ryf` and ii) `release-01deg_jra55_iaf`. The below gives instructions for `ryf` but it is basically the same for `iaf`. + +We need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to [consult this thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. + +We then need to make a template restart file that works, so we run the ACCESS-NRI configuration from rest. To start, one clones the relevant configuration and runs it: +```bash +cd ~ +mkdir access-om2 +cd access-om2 +payu clone -b expt -B release-01deg_jra55_ryf https://github.com/ACCESS-NRI/access-om2-configs release-01deg_jra55_ryf +cd release-01deg_jra55_ryf +payu run +``` + +Once the above run is complete. We use a mix of restart files. We use the restart file from a sea-ice model that goes from rest (the run you just did) and from the COSIMA restart file we take the ocean variables. This does the bulk of the spin up for us. We do this as follows: +```bash +mkdir -p /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf +cd ~/USERNAME/access-om2/release-01deg_jra55_ryf/archive/restart000 +cp -r accessom2_restart.nml ice /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf + +cd /g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795 +cp -r ocean /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf +``` + +We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/USERNAME/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier `Start the run from a specific restart file`): +```bash +restart: + /scratch/tm70/cyb561/access-om2/restart_hackom201ryf +``` +Then submit this new run with `payu run`. + ### Edit a single {{ model }} component configuration Each of [{{ model }} components][model components] contains additional configuration options that are read in when the model component is running.
From b2353de133fb0fd07a1f85d0f6665526ad8675ce Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Mon, 16 Jun 2025 15:45:53 +1000 Subject: [PATCH 2/7] Update run-access-om.md Fixing a bunch of typos and bits that were hard to read. --- docs/models/run_a_model/run_access-om2.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index b729b9a2d..2ed24268e 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -622,15 +622,15 @@ env: UCX_LOG_LEVEL: 'error' ``` -#### Workflow for using high-resolution COSIMA restarts for ACCESS-NRI ACCESS-OM2 JRA configurations +#### Using COSIMA restarts with an ACCESS-NRI ACCESS-OM2 JRA configuration !!! warning - This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of a spun ocean and restart files from a sea-ice model that goes from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. + This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of restart files: a spun ocean and a sea-ice model that has started almost from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. -As highlighted above: `Start the run from a specific restart file`, there are situations where it is preferable to use an existing restart file rather than start the model from rest (particularly true when the configuration is very expensive to run). New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. +As highlighted above ([Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)), there are situations where it is preferable to use an existing restart file rather than start the model from rest, e.g. when the configuration is very expensive to run. New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. -Here we provide a workflow for doing these manual adjustments for two key configurations, namely i) `release-01deg_jra55_ryf` and ii) `release-01deg_jra55_iaf`. The below gives instructions for `ryf` but it is basically the same for `iaf`. +Here we provide a workflow for doing these manual adjustments for two key configurations, namely i) `release-01deg_jra55_ryf` and ii) `release-01deg_jra55_iaf`. The below gives instructions for `ryf` but it is essentially the same for `iaf`. -We need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to [consult this thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. +We first need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to [consult this thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. We then need to make a template restart file that works, so we run the ACCESS-NRI configuration from rest. To start, one clones the relevant configuration and runs it: ```bash @@ -641,8 +641,9 @@ payu clone -b expt -B release-01deg_jra55_ryf https://github.com/ACCESS-NRI/acc cd release-01deg_jra55_ryf payu run ``` +Note: these instructions were tested using commit `83885a45017b3a34ea4fad15d155449c7217ad70`. -Once the above run is complete. We use a mix of restart files. We use the restart file from a sea-ice model that goes from rest (the run you just did) and from the COSIMA restart file we take the ocean variables. This does the bulk of the spin up for us. We do this as follows: +Once the above run is complete. We use a mix of restart files. We use the restart file from a sea-ice model that goes almost from rest (the run you just did) and from the COSIMA restart file we take the ocean variables. This does the bulk of the spin up for us. We do this as follows: ```bash mkdir -p /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf cd ~/USERNAME/access-om2/release-01deg_jra55_ryf/archive/restart000 @@ -652,10 +653,10 @@ cd /g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/resta cp -r ocean /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf ``` -We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/USERNAME/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier `Start the run from a specific restart file`): +We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/USERNAME/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): ```bash restart: - /scratch/tm70/cyb561/access-om2/restart_hackom201ryf + /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf ``` Then submit this new run with `payu run`. From 48a247079d15844b5830ab96b4a1cf7a17d2453a Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Mon, 16 Jun 2025 17:34:33 +1000 Subject: [PATCH 3/7] Update run-access-om.md Few more typo/updates. --- docs/models/run_a_model/run_access-om2.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index 2ed24268e..5c7672809 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -622,7 +622,7 @@ env: UCX_LOG_LEVEL: 'error' ``` -#### Using COSIMA restarts with an ACCESS-NRI ACCESS-OM2 JRA configuration +#### Using COSIMA restarts with an ACCESS-NRI configuration !!! warning This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of restart files: a spun ocean and a sea-ice model that has started almost from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. @@ -645,18 +645,18 @@ Note: these instructions were tested using commit `83885a45017b3a34ea4fad15d1554 Once the above run is complete. We use a mix of restart files. We use the restart file from a sea-ice model that goes almost from rest (the run you just did) and from the COSIMA restart file we take the ocean variables. This does the bulk of the spin up for us. We do this as follows: ```bash -mkdir -p /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf -cd ~/USERNAME/access-om2/release-01deg_jra55_ryf/archive/restart000 -cp -r accessom2_restart.nml ice /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf +mkdir -p /scratch/tm70/$USER/access-om2/restart_hackom201ryf +cd ~/access-om2/release-01deg_jra55_ryf/archive/restart000 +cp -r accessom2_restart.nml ice /scratch/tm70/$USER/access-om2/restart_hackom201ryf cd /g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795 -cp -r ocean /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf +cp -r ocean /scratch/tm70/$USER/access-om2/restart_hackom201ryf ``` -We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/USERNAME/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): +We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): ```bash restart: - /scratch/tm70/USERNAME/access-om2/restart_hackom201ryf + /scratch/tm70/$USER/access-om2/restart_hackom201ryf ``` Then submit this new run with `payu run`. From ac1172cdfca8250bc44692d601ceece60b0d99c7 Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Wed, 18 Jun 2025 09:54:54 +1000 Subject: [PATCH 4/7] Update run-access-om.md Updating the workflow to get around the cice restart date issue. --- docs/models/run_a_model/run_access-om2.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index 5c7672809..638e8fc90 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -647,18 +647,20 @@ Once the above run is complete. We use a mix of restart files. We use the restar ```bash mkdir -p /scratch/tm70/$USER/access-om2/restart_hackom201ryf cd ~/access-om2/release-01deg_jra55_ryf/archive/restart000 -cp -r accessom2_restart.nml ice /scratch/tm70/$USER/access-om2/restart_hackom201ryf +cp -r ice /scratch/tm70/$USER/access-om2/restart_hackom201ryf cd /g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795 -cp -r ocean /scratch/tm70/$USER/access-om2/restart_hackom201ryf +cp -r accessom2_restart.nml ocean /scratch/tm70/$USER/access-om2/restart_hackom201ryf ``` -We then need to modify the payu configuration to restart from this mix of restart files. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): +We then need to modify the payu configuration to restart from this mix of restart files, there are two steps: +1. We tell CICE that it should not check the date of the restart file, this is because the `accessom2_restart.nml` file in the example above (folder `restart795`) is looking to start at `EXP_CUR_DATE = 2100-01-01T00:00:00` which is not the start date the sea-ice model will have from the one we have just made above in `restart000`, it will have `1900-04-01T00:00:00`. For the first run you'll need to `set use_restart_time = .false.` in `ice/cice_in.nml`. After the first run, we suggest reverting `use_restart_time = .true.` in `ice/cice_in.nml` because having run the model once it will output correct dates on the new restart files. See `More complicated cases` [here](https://github.com/COSIMA/access-om2/wiki/Tutorials#updating-an-experiment) for further details. +1. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): ```bash restart: /scratch/tm70/$USER/access-om2/restart_hackom201ryf ``` -Then submit this new run with `payu run`. +Finally, submit this new run with `payu run`. Once complete, don't forget to swap back the `ice/cice_in.nml`! ### Edit a single {{ model }} component configuration From 445ab714a82c2abe237e2ea02d24c7ff7f477306 Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Wed, 18 Jun 2025 10:04:50 +1000 Subject: [PATCH 5/7] Update run-access-om.md Trying to fix the numbered list. --- docs/models/run_a_model/run_access-om2.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index 638e8fc90..1de31cd54 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -654,8 +654,11 @@ cp -r accessom2_restart.nml ocean /scratch/tm70/$USER/access-om2/restart_hackom2 ``` We then need to modify the payu configuration to restart from this mix of restart files, there are two steps: + 1. We tell CICE that it should not check the date of the restart file, this is because the `accessom2_restart.nml` file in the example above (folder `restart795`) is looking to start at `EXP_CUR_DATE = 2100-01-01T00:00:00` which is not the start date the sea-ice model will have from the one we have just made above in `restart000`, it will have `1900-04-01T00:00:00`. For the first run you'll need to `set use_restart_time = .false.` in `ice/cice_in.nml`. After the first run, we suggest reverting `use_restart_time = .true.` in `ice/cice_in.nml` because having run the model once it will output correct dates on the new restart files. See `More complicated cases` [here](https://github.com/COSIMA/access-om2/wiki/Tutorials#updating-an-experiment) for further details. -1. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): + +2. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): + ```bash restart: /scratch/tm70/$USER/access-om2/restart_hackom201ryf From dd0af1eb20be01ea71c1abcec291f41d4b11a9e3 Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Tue, 24 Jun 2025 14:05:18 +1000 Subject: [PATCH 6/7] Apply suggestions from code review Adding handy suggestions from @atteggiani. Co-authored-by: Davide Marchegiani --- docs/models/run_a_model/run_access-om2.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index 1de31cd54..ef0b9a854 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -626,11 +626,11 @@ env: !!! warning This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of restart files: a spun ocean and a sea-ice model that has started almost from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. -As highlighted above ([Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)), there are situations where it is preferable to use an existing restart file rather than start the model from rest, e.g. when the configuration is very expensive to run. New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. +As highlighted above in [Start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart), there are situations where it is preferable to use an existing restart file rather than start the model from rest, e.g. when the configuration is very expensive to run. New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. Here we provide a workflow for doing these manual adjustments for two key configurations, namely i) `release-01deg_jra55_ryf` and ii) `release-01deg_jra55_iaf`. The below gives instructions for `ryf` but it is essentially the same for `iaf`. -We first need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to [consult this thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. +We first need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to consult [this forum thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. We then need to make a template restart file that works, so we run the ACCESS-NRI configuration from rest. To start, one clones the relevant configuration and runs it: ```bash @@ -657,7 +657,7 @@ We then need to modify the payu configuration to restart from this mix of restar 1. We tell CICE that it should not check the date of the restart file, this is because the `accessom2_restart.nml` file in the example above (folder `restart795`) is looking to start at `EXP_CUR_DATE = 2100-01-01T00:00:00` which is not the start date the sea-ice model will have from the one we have just made above in `restart000`, it will have `1900-04-01T00:00:00`. For the first run you'll need to `set use_restart_time = .false.` in `ice/cice_in.nml`. After the first run, we suggest reverting `use_restart_time = .true.` in `ice/cice_in.nml` because having run the model once it will output correct dates on the new restart files. See `More complicated cases` [here](https://github.com/COSIMA/access-om2/wiki/Tutorials#updating-an-experiment) for further details. -2. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml` (this is the same effect as adding a `--restart FILE_NAME` command to Payu discussed earlier -- [Start the run from a specific restart file](https://docs.access-hive.org.au/models/run-a-model/run-access-om/#specific-restart)): +2. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml`: ```bash restart: @@ -665,6 +665,8 @@ restart: ``` Finally, submit this new run with `payu run`. Once complete, don't forget to swap back the `ice/cice_in.nml`! +!!! tip + This has the same effect as adding `--restart FILE_NAME` to the `payu clone` command, as discussed above in [Start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart) ### Edit a single {{ model }} component configuration Each of [{{ model }} components][model components] contains additional configuration options that are read in when the model component is running.
From af7621418261a053b00d8bac61166cc9c7620e79 Mon Sep 17 00:00:00 2001 From: Christopher Bull <5499680+chrisb13@users.noreply.github.com> Date: Tue, 24 Jun 2025 14:20:17 +1000 Subject: [PATCH 7/7] few tweaks, decided to not document iaf for now --- docs/models/run_a_model/run_access-om2.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/models/run_a_model/run_access-om2.md b/docs/models/run_a_model/run_access-om2.md index ef0b9a854..3e6f277d5 100644 --- a/docs/models/run_a_model/run_access-om2.md +++ b/docs/models/run_a_model/run_access-om2.md @@ -626,9 +626,9 @@ env: !!! warning This workflow is only for advanced users and provided to help users use COSIMA restart files with ACCESS-NRI executables for two key configurations. This workflow will use a mix of restart files: a spun ocean and a sea-ice model that has started almost from rest. This is physically inconsistent and so the model requires an extended spin up and re-evaluation to produce scientifically credible results. -As highlighted above in [Start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart), there are situations where it is preferable to use an existing restart file rather than start the model from rest, e.g. when the configuration is very expensive to run. New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. +As highlighted above in [start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart), there are situations where it is preferable to use an existing restart file rather than start the model from rest, e.g. when the configuration is very expensive to run. New ACCESS-NRI executables may be preferable to use because they contain bug fixes and a newer code base. However, in some cases, if the supplied restart file is not fully compatible with the model configuration, experiments using a custom restart file may require additional manual adjustments to run correctly. -Here we provide a workflow for doing these manual adjustments for two key configurations, namely i) `release-01deg_jra55_ryf` and ii) `release-01deg_jra55_iaf`. The below gives instructions for `ryf` but it is essentially the same for `iaf`. +Here we provide a workflow for doing these manual adjustments for a popular configuration, namely `release-01deg_jra55_ryf`. We first need to identify the restart file we wish to use. For this example we will use `/g/data/cj50/access-om2/raw-output/access-om2-01/01deg_jra55v13_ryf9091/restart795`. It may be useful to consult [this forum thread](https://forum.access-hive.org.au/t/access-om2-control-experiments/258) for making this choice. @@ -655,7 +655,7 @@ cp -r accessom2_restart.nml ocean /scratch/tm70/$USER/access-om2/restart_hackom2 We then need to modify the payu configuration to restart from this mix of restart files, there are two steps: -1. We tell CICE that it should not check the date of the restart file, this is because the `accessom2_restart.nml` file in the example above (folder `restart795`) is looking to start at `EXP_CUR_DATE = 2100-01-01T00:00:00` which is not the start date the sea-ice model will have from the one we have just made above in `restart000`, it will have `1900-04-01T00:00:00`. For the first run you'll need to `set use_restart_time = .false.` in `ice/cice_in.nml`. After the first run, we suggest reverting `use_restart_time = .true.` in `ice/cice_in.nml` because having run the model once it will output correct dates on the new restart files. See `More complicated cases` [here](https://github.com/COSIMA/access-om2/wiki/Tutorials#updating-an-experiment) for further details. +1. We tell CICE that it should not check the date of the restart file, this is because the `accessom2_restart.nml` file in the example above (folder `restart795`) is looking to start at `EXP_CUR_DATE = 2100-01-01T00:00:00` which is not the start date the sea-ice model will have from the one we have just made above in `restart000`, it will have `1900-04-01T00:00:00`. For the first run you'll need to `set use_restart_time = .false.` in `ice/cice_in.nml`. For additional information, see `More complicated cases` in the [COSIMA/access-om2/wiki](https://github.com/COSIMA/access-om2/wiki/Tutorials#updating-an-experiment). 2. Add the following two lines to `~/$USER/access-om2/release-01deg_jra55_ryf/config.yaml`: @@ -663,10 +663,10 @@ We then need to modify the payu configuration to restart from this mix of restar restart: /scratch/tm70/$USER/access-om2/restart_hackom201ryf ``` -Finally, submit this new run with `payu run`. Once complete, don't forget to swap back the `ice/cice_in.nml`! +Finally, submit this new run with `payu run`. !!! tip - This has the same effect as adding `--restart FILE_NAME` to the `payu clone` command, as discussed above in [Start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart) + This has the same effect as adding `--restart FILE_NAME` to the `payu clone` command, as discussed above in [start the run from a specific restart file](/models/run-a-model/run-access-om/#specific-restart) ### Edit a single {{ model }} component configuration Each of [{{ model }} components][model components] contains additional configuration options that are read in when the model component is running.