diff --git a/docs/css/access-nri.css b/docs/css/access-nri.css index fa06846b7..51d2dc1f8 100644 --- a/docs/css/access-nri.css +++ b/docs/css/access-nri.css @@ -165,6 +165,15 @@ --note-bg: rgba(var(--nri-orange-color),.05); /* Note background */ } + +/* =============================================================== + Main body grid +*/ +.md-grid { + max-width: 70rem; +} + + /* =============================================================== Main headings */ @@ -680,7 +689,7 @@ pre:has(code) { } pre>code { - white-space: pre-line !important; + white-space: pre-wrap !important; padding: 0.5em 0.8em !important; word-break: break-all !important; } diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md index d5ad09107..eb0616186 100644 --- a/docs/getting_started/index.md +++ b/docs/getting_started/index.md @@ -196,14 +196,13 @@ To simplify the login and avoid being prompted every time to enter your NCI pass The following lines should be added to your ~/.ssh/config to describe the SSH configuration for Gadi (replace <your-NCI-username> with your NCI username, e.g., ab1234): 
Host gadi
-       Hostname gadi.nci.org.au
-       User <your-NCI-username>
-       ForwardX11 true
-       ForwardX11Trusted yes
-       IdentityFile ~/.ssh/id_gadi
-       AddKeysToAgent yes
-       UseKeychain yes
-
+ Hostname gadi.nci.org.au + User <your-NCI-username> + ForwardX11 true + ForwardX11Trusted yes + IdentityFile ~/.ssh/id_gadi + AddKeysToAgent yes + UseKeychain yes
If you already have an existing ~/.ssh/config file which contains configurations for every Host (e.g., by using Host *), make sure you delete any of the keywords present in that SSH configuration from the Gadi configuration above.
@@ -244,7 +243,7 @@ For example, if you want to change your default project to `tm70` on Gadi exit logout Connection to gadi.nci.org.au closed. - ssh gadi + ssh gadi ############################################################################### #           Welcome to the NCI National Facility!             # #    This service is for authorised clients only. It is a criminal      # diff --git a/docs/models/run-a-model/run-access-cm.md b/docs/models/run-a-model/run-access-cm.md index c7ca4b02e..a43e11c9d 100644 --- a/docs/models/run-a-model/run-access-cm.md +++ b/docs/models/run-a-model/run-access-cm.md @@ -228,13 +228,12 @@ After the initial tasks are executed, the Cylc GUI will open. You can now
After running the command rose suite-run, if you get an error similar to the following: 
[FAIL] Suite "<suite-ID>" appears to be running:
-            [FAIL] Contact info from: "/home/565/<$USER>/cylc-run/<suite-ID>/.service/contact"
-            [FAIL]   CYLC_SUITE_HOST=accessdev.nci.org.au
-            [FAIL]   CYLC_SUITE_OWNER=<$USER>
-            [FAIL]   CYLC_SUITE_PORT=<port>
-            [FAIL]   CYLC_SUITE_PROCESS=<PID> python2 /usr/local/cylc/cylc-7.8.3/bin/cylc-run <suite-ID>
-            [FAIL] Try "cylc stop '<suite-ID>'" first?
-
+[FAIL] Contact info from: "/home/565/<$USER>/cylc-run/<suite-ID>/.service/contact" +[FAIL] CYLC_SUITE_HOST=accessdev.nci.org.au +[FAIL] CYLC_SUITE_OWNER=<$USER> +[FAIL] CYLC_SUITE_PORT=<port> +[FAIL] CYLC_SUITE_PROCESS=<PID> python2 /usr/local/cylc/cylc-7.8.3/bin/cylc-run <suite-ID> +[FAIL] Try "cylc stop '<suite-ID>'" first? you should run: 
rm /home/565/<$USER>/cylc-run/<suite-ID>/.service/contact
before running the rose suite-run command again. diff --git a/docs/models/run-a-model/run-access-esm.md b/docs/models/run-a-model/run-access-esm.md index c5117eb4a..7e67880ce 100644 --- a/docs/models/run-a-model/run-access-esm.md +++ b/docs/models/run-a-model/run-access-esm.md @@ -20,8 +20,7 @@ Before running {{ model }}, you need to fulfil general requirements outlined in
After obtaining hh5 project membership, load the conda/analysis3 environment to automatically retrieve payu as follows: 
module use /g/data/hh5/public/modules
-            module load conda/analysis3
-
+module load conda/analysis3 To check that payu is available, run: 
payu --version
@@ -102,9 +101,8 @@ This file, which controls the general model configuration, contains several part PBS resources 
jobname: pre-industrial
-            queue: normal
-            walltime: 20:00:00
-
+queue: normal +walltime: 20:00:00 These lines can be edited to change the settings for the PBS scheduler.
For example, to run {{ model }} under the tm70 project (ACCESS-NRI), add the following line: @@ -117,8 +115,7 @@ This file, which controls the general model configuration, contains several part Link to the laboratory directory 
# note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER
-            laboratory: access-esm
-
+laboratory: access-esm These lines set the laboratory directory path, which is relative to /scratch/$PROJECT/$USER. Absolute paths can also be specified.
  • @@ -131,32 +128,31 @@ This file, which controls the general model configuration, contains several part Submodels 
    submodels:
-              - name: atmosphere
-                model: um
-                ncpus: 192
-                exe: /g/data/access/payu/access-esm/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
    
-              - name: ocean
-                model: mom
-                ncpus: 180
-                exe: /g/data/access/payu/access-esm/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
    
-              - name: ice
-                model: cice
-                ncpus: 12
-                exe: /g/data/access/payu/access-esm/bin/coe/cicexx
-                input:
-                  - /g/data/access/payu/access-esm/input/pre-industrial/ice
    
-              - name: coupler
-                model: oasis
-                ncpus: 0
-                input:
-                  - /g/data/access/payu/access-esm/input/pre-industrial/coupler
-
    + - name: atmosphere + model: um + ncpus: 192 + exe: /g/data/access/payu/access-esm/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
    + - name: ocean + model: mom + ncpus: 180 + exe: /g/data/access/payu/access-esm/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
    + - name: ice + model: cice + ncpus: 12 + exe: /g/data/access/payu/access-esm/bin/coe/cicexx + input: + - /g/data/access/payu/access-esm/input/pre-industrial/ice
    + - name: coupler + model: oasis + ncpus: 0 + input: + - /g/data/access/payu/access-esm/input/pre-industrial/coupler {{ model }} is a coupled model deploying multiple submodels (i.e. model components). This section specifies the submodels and configuration options required to execute the model correctly.
    @@ -166,10 +162,9 @@ This file, which controls the general model configuration, contains several part Collate 
    collate:
-              exe: /g/data/access/payu/access-esm/bin/mppnccombine
-              restart: true
-              mem: 4GB
-
    + exe: /g/data/access/payu/access-esm/bin/mppnccombine + restart: true + mem: 4GB The collate process combines a number of smaller files, which contain different parts of the model grid, into target output files. Restart files are typically tiled in the same way and will also be combined together if the restart option is set to true.
  • @@ -182,15 +177,14 @@ This file, which controls the general model configuration, contains several part Start date and internal run length 
    calendar:
-              start:
-                year: 101
-                month: 1
-                days: 1
    
-              runtime:
-                years: 1
-                months: 0
-                days: 0
-
    + start: + year: 101 + month: 1 + days: 1
    + runtime: + years: 1 + months: 0 + days: 0 This section specifies the start date and internal run length.
    The internal run length (controlled by runtime) can be different from the total run length. Also, while runtime can be reduced, it should not be increased to more than 1 year to avoid errors. For more information about the difference between internal run and total run lengths, or how to run the model for more than 1 year, refer to the section Run configuration for multiple years. @@ -302,9 +296,8 @@ Now some practical examples:
    To have a total run length of 3 months and 10 days in a single submission, set the runtime as follows: 
    years: 0
-            months: 3
-            days: 10
-
    +months: 3 +days: 10 Set runspersub to 1 (or any value > 1) and run the configuration without option -n (or with -n set to 1): 
    payu run -f
    • @@ -313,9 +306,8 @@ Now some practical examples:
    To have a total run length of 1 year and 4 months (16 months), you need to split it into multiple internal runs. For example, 4 internal runs of 4 months each. In this case, set the runtime as follows: 
    years: 0
-            months: 4
-            days: 0
-
    +months: 4 +days: 0 Since the internal run length is set to 4 months, set runspersub to 1 to resubmit your jobs every 4 months (i.e. every internal run). Then, run the configuration with -n set to 4: 
    payu run -f -n 4
    diff --git a/docs/models/run-a-model/run-access-om.md b/docs/models/run-a-model/run-access-om.md index 1cae26c1a..ddbd22acc 100644 --- a/docs/models/run-a-model/run-access-om.md +++ b/docs/models/run-a-model/run-access-om.md @@ -20,8 +20,7 @@ Before running {{ model }}, you need to fulfil general requirements outlined in
    After obtaining hh5 project membership, load the conda/analysis3 environment to automatically retrieve payu as follows: 
    module use /g/data/hh5/public/modules
-            module load conda/analysis3
-
    +module load conda/analysis3 To check that payu is available, run: 
    payu --version
    @@ -105,10 +104,9 @@ This file, which controls the general model configuration, contains several part PBS resources 
    queue: normal
-            walltime: 3:00:00
-            jobname: 1deg_jra55_iaf
-            mem: 1000GB
-
    +walltime: 3:00:00 +jobname: 1deg_jra55_iaf +mem: 1000GB These lines can be edited to change the settings for the PBS scheduler.
    For example, to run {{ model }} under the tm70 project (ACCESS-NRI), add the following line: @@ -121,9 +119,8 @@ This file, which controls the general model configuration, contains several part Model configuration 
    name: common
-            model: access-om2
-            input: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55
-
    +model: access-om2 +input: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55 These lines let payu know which driver to use for the main model configuration (access-om).
    The name field here is not actually used for the configuration run so you can safely ignore it. @@ -132,34 +129,33 @@ This file, which controls the general model configuration, contains several part Submodels 
    submodels:
-              - name: atmosphere
-                model: yatm
-                exe: /g/data/access/payu/access-om2/bin/coe/um7.3x
-                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
-                ncpus: 1
    
-              - name: ocean
-                model: mom
-                exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_730f0bf_libaccessom2_d750b4b.x
-                input: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg
-                ncpus: 216
    
-              - name: ice
-                model: cice
-                exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_edcfa6f_libaccessom2_d750b4b.exe
-                input: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg
-                ncpus: 24
-
    + - name: atmosphere + model: yatm + exe: /g/data/access/payu/access-om2/bin/coe/um7.3x + 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 + ncpus: 1
    + - name: ocean + model: mom + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_730f0bf_libaccessom2_d750b4b.x + input: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg + ncpus: 216
    + - name: ice + model: cice + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_edcfa6f_libaccessom2_d750b4b.exe + input: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg + ncpus: 24 {{ model }} is a coupled model deploying multiple submodels (i.e. model components). This section specifies the submodels and configuration options required to execute the model correctly.
    @@ -169,13 +165,12 @@ This file, which controls the general model configuration, contains several part Collate 
    collate:
-              restart: true
-              walltime: 1:00:00
-              mem: 30GB
-              ncpus: 4
-              queue: normal
-              exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine
-
    + restart: true + walltime: 1:00:00 + mem: 30GB + ncpus: 4 + queue: normal + exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine The collate process combines a number of smaller files, which contain different parts of the model grid, into target output files. Restart files are typically tiled in the same way and will also be combined together if the restart option is set to true.
  • @@ -219,16 +214,14 @@ This file, which controls the general model configuration, contains several part Environment variables 
    env:
-              UCX_LOG_LEVEL: 'error'
-
    + UCX_LOG_LEVEL: 'error' Line to add the specified variables to the run environment.
  • Platform-specific defaults 
    platform: 
-              nodesize: 48
-
    + nodesize: 48 Lines to control the platform-specific default parameters.
    nodesize: 48 sets the default number of cpus per node to 48, to fully utilise nodes regardless of the requested number of cpus. @@ -237,9 +230,8 @@ This file, which controls the general model configuration, contains several part User scripts 
    userscripts:
-              error: resub.sh
-              run: rm -f resubmit.count
-
    + error: resub.sh + run: rm -f resubmit.count A namelist to include separate user scripts or subcommands at various stages of a payu submission.
    error gets called if the model does not run correctly and returns an error code; @@ -253,12 +245,12 @@ To find out more about other configuration settings for the config.yamlrestart_period field in the &date_manager_nml section of the ~/access-om/1deg_jra55_iaf/accessom2.nml file: 
    &date_manager_nml
-      forcing_start_date = '1958-01-01T00:00:00'
-      forcing_end_date = '2019-01-01T00:00:00'
    
-      ! Runtime for a single segment/job/submit, format is years, months, seconds,
-      ! two of which must be zero.
-      restart_period = 5, 0, 0
-
    + forcing_start_date = '1958-01-01T00:00:00' + forcing_end_date = '2019-01-01T00:00:00'
    + ! Runtime for a single segment/job/submit, format is years, months, seconds, + ! two of which must be zero. + restart_period = 5, 0, 0 +&end
    The internal run length (controlled by restart_period) can be different from the total run length. Also, while restart_period can be reduced, it should not be increased to more than 5 years to avoid errors. For more information about the difference between internal run and total run lengths, or how to run the model for more than 5 years, refer to the section Run configuration for multiple years.