diff --git a/docs/css/access-nri.css b/docs/css/access-nri.css
index 725ccbcb8..b90f371ac 100644
--- a/docs/css/access-nri.css
+++ b/docs/css/access-nri.css
@@ -75,7 +75,7 @@
--terminal-animation-directory: var(--nri-green);
--terminal-animation-buttons: var(--nri-orange);
--terminal-animation-buttons-hover: var(--nri-dark-blue);
-
+ --note: var(--nri-orange);
}
[data-md-color-scheme="custom-light"] {
@@ -148,6 +148,7 @@
--terminal-animation-directory: var(--nri-blue);
--terminal-animation-buttons: var(--nri-dark-blue);
--terminal-animation-buttons-hover: var(--nri-orange);
+ --note: var(--nri-blue);
}
@@ -606,6 +607,12 @@ pre>code {
Miscellaneous
*/
+/* Highlight 'Note:' kwyqord before noted comment */
+.note {
+ font-weight: 500;
+ color: var(--note);
+}
+
/* Justified text */
.justified {
text-align: justify;
diff --git a/docs/models/run-a-model/run-access-cm.md b/docs/models/run-a-model/run-access-cm.md
index ad8cfb96d..3fd1fd8f3 100644
--- a/docs/models/run-a-model/run-access-cm.md
+++ b/docs/models/run-a-model/run-access-cm.md
@@ -147,6 +147,7 @@ To edit a suite configuration, on accessdev:
If, for example, we belong to the tm70 Project (ACCESS-NRI), we will insert tm70
in the Compute project field:
+ Note: You should be part of a project with allocated Service Units (SU) to be able to run {{ model }}. For more information please check (TO DO reference projects).
git
commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run module purge
first, before trying again.
+Note: Some modules might interfere with the git
commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run module purge
first, before trying again.
----------------------------------------------------------------------------------------
## Edit ACCESS-ESM configuration
git checkout -b example_run
tm70
project (TO DO add Getting started, join a NCI Project link), add the following line to this section:
project: tm70
+ Note: You should be part of a project with allocated Service Units (SU) to be able to run {{ model }}. For more information please check (TO DO reference projects).
runtime
) can be different from the total run length. Also, the runtime
value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check Run configuration for multiple years.
+ Note: The internal run length (controlled by runtime
) can be different from the total run length. Also, the runtime
value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check Run configuration for multiple years.
runspersub: 5
ACCESS-ESM configurations are often run in multiple steps (or cycles), with payu running a maximum of runspersub
internal runs for every PBS job submission.
runspersub
, we might need to increase the walltime in the PBS resources.
+ Note: If we increase runspersub
, we might need to increase the walltime in the PBS resources.
config.yaml
file, please check how to configure your experiment with payu.
@@ -262,7 +264,7 @@ This will prepare the model run, based on the experiment configuration.
payu run -f
This will submit a single job to the queue with a total run length of runtime
. It there is no previous run, it will start from the start
date indicated in the config.yaml
file, otherwise it will perform a warm restart from a precedently saved restart file.
-Note:The -f
option ensures that payu will run even if there is an existing non-empty work directory, which happens if a run crashes.
+Note:The -f
option ensures that payu will run even if there is an existing non-empty work directory, which happens if a run crashes.
payu run -f
Loading input manifest: manifests/input.yaml
diff --git a/docs/models/run-a-model/run-access-om.md b/docs/models/run-a-model/run-access-om.md
index 12f2ef974..ca3a30393 100644
--- a/docs/models/run-a-model/run-access-om.md
+++ b/docs/models/run-a-model/run-access-om.md
@@ -22,6 +22,9 @@ For the general requirements needed to run all ACCESS models, please refer to th
module load conda/analysis3
+
+ qv56, ik11 and hh5
+
----------------------------------------------------------------------------------------
@@ -46,13 +49,14 @@ In order to get it, on gadi, create a directory where to keep the model c
git
commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run module purge
first, before trying again.
+Note: Some modules might interfere with the git
commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run module purge
first, before trying again.
----------------------------------------------------------------------------------------
## Edit {{ model }} configuration
git checkout -b example_run
/scratch/$PROJECT/$USER/access-esm
.
+ The laboratory is the directory where all parts of the model are kept. For {{ model }}, it is typically /scratch/$PROJECT/$USER/access-om2
.
~/access-esm/esm-pre-industrial
).
+ The control directory, where the model configuration is kept and from where the model is run (in our case is the cloned directory ~/access-om/1deg_jra55_iaf
).
$HOME
directory (being the only filesystem on gadi that is actively backed up), without overloading it with too much data.
@@ -79,13 +83,13 @@ This will create the laboratory directory, along with other subdirectorie
work
→ temporary directory where the model is actually run. It gets cleaned after each run.archive
→ directory where the output is placed after each run.jobname: pre-industrial
- queue: normal
- walltime: 20:00:00
+ queue: normal
+ walltime: 3:00:00
+ jobname: 1deg_jra55_iaf
+ mem: 1000GB
These are settings for the PBS scheduler. Edit lines in this section to change any of the PBS resources.
For example, to run {{ model }} under the tm70
project (ACCESS-NRI), add the following line to this section:
project: tm70
+ Note: You should be part of a project with allocated Service Units (SU) to be able to run {{ model }}. For more information please check (TO DO reference projects).
# note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER
- laboratory: access-esm
+ Model configuration
+ name: common
+ model: access-om2
+ input: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55
- This will set the laboratory directory. Relative paths are relative to /scratch/$PROJECT/$USER
. Absolute paths can be specified as well.
-
model: access
- The main model. This tells payu which driver to use (access stands for {{ model }}).
+ The main model configuration. This tells payu which driver to use (access-om).
+ name
field here is not actually used for the configuration run and you can safely disregard it.
submodels:
- name: atmosphere
- model: um
- ncpus: 192
- exe: /g/data/access/payu/access-esm/bin/coe/um7.3x
+ model: yatm
+ exe: /g/data/access/payu/access-om2/bin/coe/um7.3x
input:
- - /g/data/access/payu/access-esm/input/pre-industrial/atmosphere
- - /g/data/access/payu/access-esm/input/pre-industrial/start_dump
+ - /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
+
+ ncpus: 1
- name: ocean
model: mom
ncpus: 180
- exe: /g/data/access/payu/access-esm/bin/coe/mom5xx
+ exe: /g/data/access/payu/access-om2/bin/coe/mom5xx
input:
- - /g/data/access/payu/access-esm/input/pre-industrial/ocean/common
- - /g/data/access/payu/access-esm/input/pre-industrial/ocean/pre-industrial
+ - /g/data/access/payu/access-om2/input/pre-industrial/ocean/common
+ - /g/data/access/payu/access-om2/input/pre-industrial/ocean/pre-industrial
+ ncpus: 1
- name: ice
model: cice
ncpus: 12
- exe: /g/data/access/payu/access-esm/bin/coe/cicexx
+ exe: /g/data/access/payu/access-om2/bin/coe/cicexx
input:
- - /g/data/access/payu/access-esm/input/pre-industrial/ice
+ - /g/data/access/payu/access-om2/input/pre-industrial/ice
- name: coupler
model: oasis
ncpus: 0
input:
- - /g/data/access/payu/access-esm/input/pre-industrial/coupler
+ - /g/data/access/payu/access-om2/input/pre-industrial/coupler
{{ model }} is a coupled model, which means it has multiple submodels (i.e. model components).
~/access-esm/esm-pre-industrial/atmosphere
).
+ This section specifies the submodels and contains configuration options (for example the directories of input files) that are required to ensure the model can execute correctly. Each submodel also has additional configuration options that are read in when the submodel is running. These specific configuration options are found in the subdirectory of the control directory having the name of the submodel (e.g. in our case the configuration for the atmosphere submodel, i.e. the UM, will be in the directory ~/access-om2/esm-pre-industrial/atmosphere
).
collate:
- exe: /g/data/access/payu/access-esm/bin/mppnccombine
+ exe: /g/data/access/payu/access-om2/bin/mppnccombine
restart: true
mem: 4GB
@@ -168,7 +182,7 @@ This file controls the general model configuration and if we open it in a text e
restart: /g/data/access/payu/access-esm/restart/pre-industrial
+ restart: /g/data/access/payu/access-om2/restart/pre-industrial
The location of the files used for a warm restart.
runtime
) can be different from the total run length. Also, the runtime
value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check Run configuration for multiple years.
+ Note: The internal run length (controlled by runtime
) can be different from the total run length. Also, the runtime
value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check Run configuration for multiple years.
runspersub: 5
{{ model }} configurations are often run in multiple steps (or cycles), with payu running a maximum of runspersub
internal runs for every PBS job submission.
runspersub
, we might need to increase the walltime in the PBS resources.
+ Note: If we increase runspersub
, we might need to increase the walltime in the PBS resources.
config.yaml
file, please check how to configure your experiment with payu.
@@ -213,11 +227,11 @@ As a first step, from the control directory, is good practice to run:
This will prepare the model run, based on the experiment configuration.
payu run -f
This will submit a single job to the queue with a total run length of runtime
. It there is no previous run, it will start from the start
date indicated in the config.yaml
file, otherwise it will perform a warm restart from a precedently saved restart file.
-f
option ensures that payu will run even if there is an existing non-empty work directory, which happens if a run crashes.
+Note:The -f
option ensures that payu will run even if there is an existing non-empty work directory, which happens if a run crashes.
work
directory to the archive
directory, under /scratch/$PROJECT/$USER/access-esm/archive
(also symlinked in the control directory under ~/access-esm/esm-pre-industrial/archive
).
+While the configuration is running, output files (as well as restart files) are moved from the work
directory to the archive
directory, under /scratch/$PROJECT/$USER/access-om2/archive
(also symlinked in the control directory under ~/access-om2/esm-pre-industrial/archive
).
esm-pre-industrial
in our case), and inside the configuration folder, they are subdivided for each internal run.
<UM-suite-identifier>a.p<output-stream-identifier><time-identifier>
.