From acde56b5109133c1824cab9becb33384c6d166ab Mon Sep 17 00:00:00 2001 From: atteggiani Date: Thu, 13 Jul 2023 13:09:55 +1000 Subject: [PATCH] Fixing --- docs/css/access-nri.css | 9 +- docs/models/run-a-model/run-access-cm.md | 1 + docs/models/run-a-model/run-access-esm.md | 14 +-- docs/models/run-a-model/run-access-om.md | 116 ++++++++++++---------- 4 files changed, 82 insertions(+), 58 deletions(-) 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:
Rose change Project + 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).
  • Total Run length / Cycling frequency diff --git a/docs/models/run-a-model/run-access-esm.md b/docs/models/run-a-model/run-access-esm.md index a0dd8463d..5f4707165 100644 --- a/docs/models/run-a-model/run-access-esm.md +++ b/docs/models/run-a-model/run-access-esm.md @@ -76,13 +76,14 @@ In order to get it, on Gadi, create a directory where to keep the model configur Receiving objects: 100% (767/767), 461.57 KiB | 5.24 MiB/s, done. Resolving deltas: 100% (450/450), done. -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. +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
    -In order to modify an ACCESS-ESM configuration, it is worth understanding a bit more how its job scheduler payu works. +First, is good practice to create another git branch where to keep all modifications we put in place for our run, and to keep the reference configuration unmodified. If we call the local branch "example_run", we can run: +
    git checkout -b example_run
    ### Payu @@ -137,6 +138,7 @@ This file controls the general model configuration and if we open it in a text e
    For example, to run ACCESS-ESM under the 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).
  • Link to the laboratory directory @@ -216,7 +218,7 @@ This file controls the general model configuration and if we open it in a text e This section specifies the start date and internal run length.
    - 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. + 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.
  • Number of runs per PBS submission @@ -224,7 +226,7 @@ This file controls the general model configuration and if we open it in a text e 
    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.
    - Note: If we increase 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.
    • To know more about other configuration settings for the 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. Writing manifests/restart.yaml Writing manifests/exe.yaml -Note: You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible. +Note: You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible. ### Run configuration @@ -271,7 +273,7 @@ To run ACCESS-ESM configuration for one internal run length (controlled by 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 Receiving objects: 100% (14715/14715), 35.68 MiB | 18.11 MiB/s, done. Resolving deltas: 100% (10707/10707), done. -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. +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
    -In order to modify an {{ model }} configuration, it is worth understanding a bit more how its job scheduler payu works. +First, is good practice to create another git branch where to keep all modifications we put in place for our run, and to keep the reference configuration unmodified. If we call the local branch "example_run", we can run: +
    git checkout -b example_run
    ### Payu @@ -62,10 +66,10 @@ In order to modify an {{ model }} configuration, it is worth understanding a bit The general layout of a payu-supported model run consists of two main directories: This distinction of directories keeps the small-size configuration files separated from the larger binary outputs and inputs. In this way, we can place the configuration files in the $HOME directory (being the only filesystem on gadi that is actively backed up), without overloading it with too much data. @@ -79,13 +83,13 @@ This will create the laboratory directory, along with other subdirectorie
  • work → temporary directory where the model is actually run. It gets cleaned after each run.
  • archive → directory where the output is placed after each run.
    • - cd ~/access-esm/esm-pre-industrial - payu init - laboratory path: /scratch/$PROJECT/$USER/access-esm - binary path: /scratch/$PROJECT/$USER/access-esm/bin - input path: /scratch/$PROJECT/$USER/access-esm/input - work path: /scratch/$PROJECT/$USER/access-esm/work - archive path: /scratch/$PROJECT/$USER/access-esm/archive + cd ~/access-om/1deg_jra55_iaf + payu init + laboratory path: /scratch/$PROJECT/$USER/access-om2 + binary path: /scratch/$PROJECT/$USER/access-om2/bin + input path: /scratch/$PROJECT/$USER/access-om2/input + work path: /scratch/$PROJECT/$USER/access-om2/work + archive path: /scratch/$PROJECT/$USER/access-om2/archive @@ -99,67 +103,77 @@ This file controls the general model configuration and if we open it in a text e
  • PBS resources
    - 
    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).
  • - Link to the laboratory directory -
    - 
    # 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 - 
    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). +
    + The name field here is not actually used for the configuration run and you can safely disregard it.
  • Submodels 
    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).
    - 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-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 
    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
    - 
    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.
  • @@ -186,7 +200,7 @@ This file controls the general model configuration and if we open it in a text e This section specifies the start date and internal run length.
    - 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. + 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.
  • Number of runs per PBS submission @@ -194,7 +208,7 @@ This file controls the general model configuration and if we open it in a text e 
    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.
    - Note: If we increase 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.
    • To know more about other configuration settings for the 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 setup - laboratory path: /scratch/$PROJECT/$USER/access-esm - binary path: /scratch/$PROJECT/$USER/access-esm/bin - input path: /scratch/$PROJECT/$USER/access-esm/input - work path: /scratch/$PROJECT/$USER/access-esm/work - archive path: /scratch/$PROJECT/$USER/access-esm/archive + laboratory path: /scratch/$PROJECT/$USER/access-om2 + binary path: /scratch/$PROJECT/$USER/access-om2/bin + input path: /scratch/$PROJECT/$USER/access-om2/input + work path: /scratch/$PROJECT/$USER/access-om2/work + archive path: /scratch/$PROJECT/$USER/access-om2/archive Loading input manifest: manifests/input.yaml Loading restart manifest: manifests/restart.yaml Loading exe manifest: manifests/exe.yaml @@ -232,7 +246,7 @@ This will prepare the model run, based on the experiment configuration. Writing manifests/restart.yaml Writing manifests/exe.yaml -Note: You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible. +Note: You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible. ### Run configuration @@ -241,7 +255,7 @@ To run {{ model }} configuration for one internal run length (controlled by 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 @@ -353,7 +367,7 @@ After the model has completed its run, or if it crashed, the output and error lo ## {{ model }} outputs
    -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-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).
    Both outputs and restarts are stored into subfolders for each different configuration (esm-pre-industrial in our case), and inside the configuration folder, they are subdivided for each internal run.
    @@ -363,10 +377,10 @@ In the respective folders, outputs and restarts are separated for each model com
    For the atmospheric output data, each file it is usually a UM fieldsfile, formatted as <UM-suite-identifier>a.p<output-stream-identifier><time-identifier>. - cd /scratch/$PROJECT/$USER/access-esm/archive/esm-pre-industrial - ls + cd /scratch/$PROJECT/$USER/access-om2/archive/esm-pre-industrial + ls output000 pbs_logs restart000 - ls output000/atmosphere + ls output000/atmosphere aiihca.daa1210 aiihca.daa1810 aiihca.paa1apr aiihca.paa1jun aiihca.pea1apr aiihca.pea1jun aiihca.pga1apr aiihca.pga1jun atm.fort6.pe0 exstat ihist prefix.CNTLGEN UAFLDS_A aiihca.daa1310 aiihca.daa1910 aiihca.paa1aug aiihca.paa1mar aiihca.pea1aug aiihca.pea1mar aiihca.pga1aug aiihca.pga1mar cable.nml fort.57 INITHIS prefix.PRESM_A um_env.py aiihca.daa1410 aiihca.daa1a10 aiihca.paa1dec aiihca.paa1may aiihca.pea1dec aiihca.pea1may aiihca.pga1dec aiihca.pga1may CNTLALL ftxx input_atm.nml SIZES xhist aiihca.daa1510 aiihca.daa1b10 aiihca.paa1feb aiihca.paa1nov aiihca.pea1feb aiihca.pea1nov aiihca.pga1feb aiihca.pga1nov CONTCNTL ftxx.new namelists STASHC aiihca.daa1610 aiihca.daa1c10 aiihca.paa1jan aiihca.paa1oct aiihca.pea1jan aiihca.pea1oct aiihca.pga1jan aiihca.pga1oct debug.root.01 ftxx.vars nout.000000 thist aiihca.daa1710 aiihca.daa2110 aiihca.paa1jul aiihca.paa1sep aiihca.pea1jul aiihca.pea1sep aiihca.pga1jul aiihca.pga1sep errflag hnlist prefix.CNTLATM UAFILES_A