http://climate-cms.wikis.unsw.edu.au/api.php?action=feedcontributions&user=D.eisenberg&feedformat=atomclimate-cms wikis.unsw.edu.au - User contributions [en]2024-03-28T11:44:55ZUser contributionsMediaWiki 1.31.0http://climate-cms.wikis.unsw.edu.au/index.php?title=Configuring_MOM&diff=1867Configuring MOM2019-12-12T04:11:32Z<p>D.eisenberg: </p>
<hr />
<div><br />
[[Category:MOM]]<br />
<br />
This page outlines basic configuration of MOM4 experiments.<br />
<br />
= MOM4/5 Configuration Files =<br />
<br />
MOM4 configuration is managed primarily through four text files:<br />
<br />
*<span style="font-family:monospace">input.nml</span>: Principal configuration <br />
*<span style="font-family:monospace">diag_table</span>: Diagnostic output management <br />
*<span style="font-family:monospace">data_table</span>: Input and boundary condition data field management <br />
*<span style="font-family:monospace">field_table</span>: Initial condition and advection scheme configuration <br />
<br />
= Basic Configuration =<br />
<br />
== Setting the simulation time ==<br />
<br />
Simulation time (or integration time) is set in the <span style="font-family:monospace">input.nml}} namelist file, in either {{ocean_solo_nml}} (for ocean-only runs) or {{coupler_nml</span> (for coupled runs).<br />
<br />
===Ocean-only (solo) configuration=== <br />
<br />
An example <span style="font-family:monospace">ocean_solo_nml</span> namelist record is shown below:<br />
'"`UNIQ--syntaxhighlight-00000001-QINU`"'<br />
The major namelist fields are described below:<br />
<br />
* <span style="font-family:monospace">date_init}}: Simulation start time (if no {{ocean_solo.res</span> timestamp is present, such as from a previous simulation, then this field is ignored)<br />
* <span style="font-family:monospace">calendar</span>: Simulation calendar type. Four calendars are supported:<br />
** <span style="font-family:monospace">gregorian</span>: Modern calendar will full leap-year support<br />
** <span style="font-family:monospace">julian</span>: 365-day calendar with 4-year leap years<br />
** <span style="font-family:monospace">noleap</span>: 365-day calendar with no leap years<br />
** <span style="font-family:monospace">thirty_day</span>: 30-day months (or 360 days per year)<br />
<br />
* <span style="font-family:monospace">months}}, {{days</span>, etc.: Simulation (or integration) time<br />
* <span style="font-family:monospace">dt_cpld</span>: Timestep (in seconds) to external data fields (usually atmospheric)<br />
<br />
===Coupled configuration=== <br />
<br />
An example <span style="font-family:monospace">coupler_nml</span> record follows a similar structure:<br />
'"`UNIQ--syntaxhighlight-00000002-QINU`"'<br />
Many of the fields are identical to the <span style="font-family:monospace">ocean_solo_nml</span> fields. The new or modified fields are listed below:<br />
<br />
* <span style="font-family:monospace">current_date}}: Simulation start time, similar to {{date_init}} in {{ocean_solo_nml}} (in this case, the timestamp override file is named {{coupler.res</span>)<br />
* <span style="font-family:monospace">do_atmos}}, {{do_land</span>, etc.: Use to enable or disable submodel components<br />
* <span style="font-family:monospace">dt_atmos</span>: Atmospheric model timestep (in seconds), including its coupling to land and ice (or the "fast" coupling timestep)<br />
* <span style="font-family:monospace">dt_cpld}}: Ocean-atmosphere coupling (or the "slow" coupling timestep). This must be a multiple of {{dt_atmos}} and {{dt_ocean</span>.<br />
<br />
==Timestep configuration== <br />
<br />
The predominant numerical parameter in model configuration is timestep size. MOM4 timestepping is configured in the <span style="font-family:monospace">ocean_model_nml</span> namelist record. An example record is provided below:<br />
'"`UNIQ--syntaxhighlight-00000003-QINU`"'<br />
Some typical timestep settings are as follows:<br />
<br />
* <span style="font-family:monospace">dt_ocean</span>: Ocean model timestep size (in seconds)<br />
* <span style="font-family:monospace">vertical_coordinate</span>: Vertical coordinate type, the most common options are listed below:<br />
** <span style="font-family:monospace">geopotential</span>: Geopotential (equivalent to depth in many cases)<br />
** <span style="font-family:monospace">zstar</span>: Quasi-horizontal depth<br />
** <span style="font-family:monospace">pressure</span>: Pressure-based vertical coordiante<br />
** <span style="font-family:monospace">pstar</span>: Quasi-horizontal pressure<br />
<br />
* <span style="font-family:monospace">barotropic_split}}: Split timestepping between the ocean free surface (or barotropic) and internal (or baroclinic) flow. A barotropic timestep of 60 means that there are sixty free surface timesteps per model timesteps (set by {{dt_ocean</span>).<br />
<br />
=Advanced Configuration= <br />
<br />
A typical <span style="font-family:monospace">input.nml</span> file will usually contain a large number of namelist records, sometimes as many as 100 for fully coupled models. Much of the configuration settings are determined through experiment design, which is a nontrivial task and often a subject of ongoing research.<br />
<br />
==data_table== <br />
<br />
The <span style="font-family:monospace">data_table</span> file is used to supply a MOM experiment with external data forcing fields, such as surface winds or radiative heating.<br />
<br />
''Note that MOM usually expects external fields to be in netCDF format, and that the grid variables must be formatted in a particular manner.''<br />
<br />
Example <span style="font-family:monospace">data_table</span> record:<br />
'"`UNIQ--syntaxhighlight-00000004-QINU`"'<br />
* <span style="font-family:monospace">"OCN"}}: Identifies the class of the field. It contains one of the following values: {{ATM}}, {{OCN}}, {{LND}}, {{ICE</span><br />
* <span style="font-family:monospace">"u_flux"</span>: The field variable name as defined in MOM4.<br />
* <span style="font-family:monospace">"taux"</span>: The field variable name as defined in the netCDF provided by the user.<br />
* <span style="font-family:monospace">"INPUT/stress.nc"</span>: The path (including filename) for the netCDF file containing the forcing field. Local paths can be used.<br />
* <span style="font-family:monospace">.true.}}: Indicates whether or not the field is on the the ocean model grid. A value of {{.false.</span> indicates that it does not match the model grid and requires interpolation (as computed by MOM).<br />
* <span style="font-family:monospace">1.0}}: A rescaling factor applied to the field. A value of {{1.0}} indicates no rescaling, while a value of {{0.</span> will set all values to zero.<br />
<br />
[[Category:MOM]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CABLE&diff=1858CABLE2019-12-12T04:06:53Z<p>D.eisenberg: </p>
<hr />
<div><br />
= <span style="font-size: 1.4em;">CABLE</span> =<br />
<br />
<br />
== Overview ==<br />
<br />
The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model simulates the exchanges of radiation, moisture, heat and carbon at the land surface. It is provided with meteorological conditions (its inputs) and, based on these, predicts fluxes (its outputs, e.g. latent heat flux, upward long-wave radiation, net ecosystem exchange of CO2 or drainage through deep soil). The CABLE model is also the land surface component of the ACCESS coupled model. It can be used in both coupled (online) and uncoupled (offline) environment.<br />
<br />
If you have any corrections, comments or contributions, please feel free to email us on <span style="background-color: initial;">[[mailto:cable_help@nf.nci.org.au| cable_help@nf.nci.org.au]]</span> so that we can continue to update and upgrade the guides over time.<br />
<br />
<span style="font-size: 1.4em;">'''Guides:'''</span><br />
<br />
[[How_to_obtain_CABLE_code|How to obtain CABLE code]]<br />
<br />
[[CABLE_Build_with_FCM_Make|How to build CABLE with FCM Make]]<br />
<br />
<span style="font-size: 1.4em;">Related links:</span><br />
<br />
*[http://www.accessimulator.org.au/cable/index.html CAWCR - CABLE Home Page] <br />
*[https://trac.nci.org.au/trac/cable NCI CABLE Trac Site] <br />
*[[CABLE_Ancils|CABLE Ancils for ACCESS 1.3]] <br />
<br />
[[Category:CABLE]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CABLE&diff=1852CABLE2019-12-12T04:04:55Z<p>D.eisenberg: </p>
<hr />
<div><br />
= <span style="font-size: 1.4em;">CABLE</span> =<br />
<br />
== Overview ==<br />
<br />
The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model simulates the exchanges of radiation, moisture, heat and carbon at the land surface. It is provided with meteorological conditions (its inputs) and, based on these, predicts fluxes (its outputs, e.g. latent heat flux, upward long-wave radiation, net ecosystem exchange of CO2 or drainage through deep soil). The CABLE model is also the land surface component of the ACCESS coupled model. It can be used in both coupled (online) and uncoupled (offline) environment.<br />
<br />
If you have any corrections, comments or contributions, please feel free to email us on <span style="background-color: initial;">[[mailto:cable_help@nf.nci.org.au| cable_help@nf.nci.org.au]]</span> so that we can continue to update and upgrade the guides over time.<br />
<br />
<span style="font-size: 1.4em;">'''Guides:'''</span><br />
<br />
[[How_to_obtain_CABLE_code|How to obtain CABLE code]]<br />
<br />
[[CABLE_Build_with_FCM_Make|How to build CABLE with FCM Make]]<br />
<br />
<span style="font-size: 1.4em;">Related links:</span><br />
<br />
*[http://www.accessimulator.org.au/cable/index.html CAWCR - CABLE Home Page] <br />
*[https://trac.nci.org.au/trac/cable NCI CABLE Trac Site] <br />
*[[CABLE_Ancils|CABLE Ancils]] <br />
<br />
[[Category:CABLE]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CABLE&diff=1851CABLE2019-12-12T04:04:22Z<p>D.eisenberg: added CABLE ancils</p>
<hr />
<div><br />
= <span style="font-size: 1.4em;">CABLE</span> =<br />
<br />
== Overview ==<br />
<br />
The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model simulates the exchanges of radiation, moisture, heat and carbon at the land surface. It is provided with meteorological conditions (its inputs) and, based on these, predicts fluxes (its outputs, e.g. latent heat flux, upward long-wave radiation, net ecosystem exchange of CO2 or drainage through deep soil). The CABLE model is also the land surface component of the ACCESS coupled model. It can be used in both coupled (online) and uncoupled (offline) environment.<br />
<br />
If you have any corrections, comments or contributions, please feel free to email us on <span style="background-color: initial;">[[mailto:cable_help@nf.nci.org.au| cable_help@nf.nci.org.au]]</span> so that we can continue to update and upgrade the guides over time.<br />
<br />
<span style="font-size: 1.4em;">'''Guides:'''</span><br />
<br />
[[How_to_obtain_CABLE_code|How to obtain CABLE code]]<br />
<br />
[[CABLE_Build_with_FCM_Make|How to build CABLE with FCM Make]]<br />
<br />
<span style="font-size: 1.4em;">Related links:</span><br />
<br />
*[http://www.accessimulator.org.au/cable/index.html CAWCR - CABLE Home Page] <br />
*[https://trac.nci.org.au/trac/cable NCI CABLE Trac Site] <br />
*[[CABLE_Ancils]] <br />
<br />
[[Category:CABLE]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Unified_Model&diff=1842Unified Model2019-12-12T04:00:26Z<p>D.eisenberg: </p>
<hr />
<div><br />
The Unified Model is the atmospheric component of [[ACCESS|ACCESS]], developed by the UK's Met Office. The Centre of Excellence sublicences the UM from CAWCR, our licence allows us to run the UM at NCI only. To run the UM you will first need an NCI account, then ask for connection to the ACCESS group through [https://my.nci.org.au/mancini/project/access/join NCI's account website].<br />
<br />
The ACCESS climate models are based on version 7.3 of the UM, most Australian university research uses this version. The Bureau makes use of the more recent version 7.8 for forecasting, and is evaluating moving to version 8.2. These are the primary versions supported at NCI, other versions are available but may not be quite as well tested. Different versions include changed science configurations, for details see the [https://code.metoffice.gov.uk/trac/um/wiki/ReleaseNotes release notes].<br />
<br />
= Getting Started =<br />
<br />
The UM is configured through a graphical interface, which is run from the server [[Accessdev|accessdev.nci.org.au]]. See [https://accessdev.nci.org.au/trac/wiki/GettingConnected Setting up the environment] for how to connect.<br />
<br />
*[https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_000.pdf Unified Model User's Guide] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM Documentation Papers] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
<br />
There are two ways to run the model. Older versions (pre UM 10) use a program called [[UMUI|UMUI]], newer versions (post UM 10) use [[Rose_&_Cylc|Rose & Cylc]]<br />
<br />
= UM 10 / Global Atmosphere / ACCESS 2.x =<br />
<br />
The current version of the Unified Model is available from the Met Office's repository site [https://code.metoffice.gov.uk https://code.metoffice.gov.uk].<br />
<br />
ARCCSS researchers need to email [mailto:climate_help@nci.org.au climate_help@nci.org.au] to request an account on the Met Office server.<br />
<br />
== Links & More Information ==<br />
<br />
*[https://accessdev.nci.org.au/trac/wiki/GettingConnected Connecting to Accessdev and running Rose] <br />
*[[Running_the_UM_with_Rose|Tips on using Rose with the UM]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2016 UM User Tutorial 2016] <br />
<br />
*[[GA7_Performance|GA7 Performance]] <br />
<br />
= UM 7.3 / ACCESS 1.x =<br />
<br />
The ACCESS climate model as used in CMIP5 uses model version 7.3. This version of the model uses the older `UMUI` user interface<br />
<br />
== Links & More Information ==<br />
<br />
*[[UM_Environment|Setting up the UMUI environment]] <br />
*[[Introduction_to_UMUI|Introduction to UMUI]] <br />
*[https://accessdev.nci.org.au/umdocs/7.3 UM 7.3 Documentation] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2013 UM User Tutorial 2013] <br />
<br />
= Experiments =<br />
<br />
A full list of experiments we support or have helped set up can be found at [[UM_Experiments|UM Experiments]]<br />
<br />
These configurations are currently our primary support targets:<br />
<br />
*[[ACCESS_2.0|ACCESS 2.0]] <br />
*[[ACCESS-ESM|ACCESS-ESM]] <br />
*[[GlobalAtmosphere|GA 7]] <br />
*[[Nesting_Suite|Nesting Suite]] <br />
<br />
= Guides =<br />
<br />
Assorted information on running the UM and available job configurations is listed in the sections below. Feel free to email [[mailto:climate_help@nci.org.au| climate_help@nci.org.au]] if you have any difficulties using the UM or suggestions for how we can make using the UM simpler.<br />
<br />
*[[Getting_Help_with_the_UM|Getting Help with the UM]] <br />
*[[Um-errors|Common Errors]] <br />
<br />
== Starting Up ==<br />
<br />
*[[New_UM_User_message|New UM User message]] <br />
*[[Building_the_UM|Building the UM]] <br />
*[[Standard_UM_Runs|Standard UM Runs]] <br />
*[[Restarting_UM_Runs|Running the UM using automatic resubmission]] <br />
*[[Recovering_from_an_interrupted_job|Recovering from an interrupted job]] <br />
*[[UM_Helper_Scripts|UM Helper Scripts]] <br />
*[[Moving_UM_jobs_to_Raijin|Moving UM jobs to Raijin]] <br />
*[[Running_the_UM_with_Rose|Running the UM with Rose]] <br />
<br />
== Run Types ==<br />
<br />
*[[AMIP|AMIP]] <br />
*[[ACCESS|CMIP]] <br />
*[https://trac.nci.org.au/trac/access/wiki/SCM_testcases Single Column] <br />
*[[KPP_Coupling|KPP Coupling]] <br />
*[https://trac.nci.org.au/trac/access/wiki/APS1_ACCESS_C ACCESS-C High-resolution NWP] <br />
*[[UM_Nested_Models|UM Nested Models]] <br />
*[[Limited_Area|Limited Area]] <br />
*[[UKCA|UKCA]] <br />
<br />
*[http://www.ukca.ac.uk/wiki/index.php/UKCA_&_UMUI_Tutorials UKCA Tutorials] <br />
*[https://trac.nci.org.au/trac/access/wiki/AccessModelExperimentLibrary CAWCR's ACCESS experiment library] (log in with your NCI account) <br />
<br />
= Common Errors =<br />
<br />
If a run fails, search for 'UM ERROR' in the .leave file to see what went wrong. Common issues are listed here<br />
<br />
*[[Um-errors#pp-headers|REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH]] <br />
*[https://code.metoffice.gov.uk/trac/um/wiki/KnownUMFailurePoints Known UM failures at UKMO] <br />
<br />
== Job Input ==<br />
<br />
*[[UM_Ancillary_files|UM Ancillary files]] <br />
*[[Concatenate_AMIP_Ancillaries|Concatenate AMIP Ancillaries]] <br />
*[[Copying_CO2_values|Copying CO2 values]] <br />
*[[Modifying_UM_Files|Modifying UM files with Mule]] <br />
<br />
== Job Output ==<br />
<br />
*[[Using_STASH|Using STASH]] <br />
*[[Copying_STASH_settings_between_jobs|Copying STASH settings between jobs]] <br />
*[[UM_Filenames|UM output filename convention]] <br />
*[[Analysing_UM_outputs|Analysing UM outputs & Converting to NetCDF]] <br />
*[[Archiving_Output|Archiving Output]] <br />
*[[Comparing_UM_Files|Comparing UM Files]] <br />
*[https://code.metoffice.gov.uk/trac/UKESM/wiki/CMIP6/DiagnosticMappings Mapping UM outputs to CMIP fields] <br />
<br />
== Modifying the UM ==<br />
<br />
*[[UM_Source_Control|UM Source Control]] <br />
*[[User_fields|User fields]] <br />
*[[Oasis_Coupling_with_the_UM|Oasis Coupling with the UM]] <br />
*[[Oasis_coupling_in_UM_8.5|Oasis coupling in UM 8.5]] <br />
*[[Profiling_with_IPM_and_Vampir|Profiling MPI]] <br />
*[[Hand_Edits|Hand Edits]] <br />
<br />
== Informative ==<br />
<br />
*[[UM_Version_Summaries|UM Version Summaries]] <br />
*[[UM_Run_Scripts|UM Run Scripts]] <br />
*[[UMUI_over_VNC|UMUI over VNC]] <br />
*[[Downloading_from_MASS|Downloading from MASS]] <br />
*[[Vertical_Coordinates|Vertical Coordinates]] <br />
<br />
<br />
== [[UM_and_ACCESS_FAQ|UM and ACCESS FAQs]] ==<br />
<br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#Who_can_gain_access_to_the_UM_and_the_ACCESS_models.3F Who can gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_gain_access_to_the_UM_and_the_ACCESS_models.3F What to do to gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_use_the_software_in_.2Fprojects.2Faccess.2Fbin.3F What to do to use the software in /projects/access/bin?]<br />
<br />
== Work in progress ==<br />
<br />
*[[SCM_with_ERA-Interim|SCM with ERA-Interim]] <br />
<br />
= Resources =<br />
<br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[https://nf.nci.org.au/facilities/software/UM/7.8/umdoc_system/UM_docs/papers/html/X0/X0.html Getting started with UM and UMUI] <br />
*[http://cms.ncas.ac.uk/ NCAS] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Main/WebHome Met Office Wiki] - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] or [mailto:climate_help@nf.nci.org.au climate_help] to register <br />
*Met Office mailing list (Read by scientists at the Met Office) - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] <br />
*ACCESS users mailing list (Notifications about ACCESS systems) - Contact [mailto:climate_help@nf.nci.org.au climate_help] <br />
<br />
*[[UM_Admin|UM Admin]] <br />
*[[UM_Partial_guides|UM Partial guides]] <br />
<br />
[[Category:Unified Model]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Unified_Model&diff=1839Unified Model2019-12-12T03:59:53Z<p>D.eisenberg: </p>
<hr />
<div><br />
The Unified Model is the atmospheric component of [[ACCESS|ACCESS]], developed by the UK's Met Office. The Centre of Excellence sublicences the UM from CAWCR, our licence allows us to run the UM at NCI only. To run the UM you will first need an NCI account, then ask for connection to the ACCESS group through [https://my.nci.org.au/mancini/project/access/join NCI's account website].<br />
<br />
The ACCESS climate models are based on version 7.3 of the UM, most Australian university research uses this version. The Bureau makes use of the more recent version 7.8 for forecasting, and is evaluating moving to version 8.2. These are the primary versions supported at NCI, other versions are available but may not be quite as well tested. Different versions include changed science configurations, for details see the [https://code.metoffice.gov.uk/trac/um/wiki/ReleaseNotes release notes].<br />
<br />
= Getting Started =<br />
<br />
The UM is configured through a graphical interface, which is run from the server [[Accessdev|accessdev.nci.org.au]]. See [https://accessdev.nci.org.au/trac/wiki/GettingConnected Setting up the environment] for how to connect.<br />
<br />
*[https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_000.pdf Unified Model User's Guide] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM Documentation Papers] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
<br />
There are two ways to run the model. Older versions (pre UM 10) use a program called [[UMUI|UMUI]], newer versions (post UM 10) use [[Rose_&_Cylc|Rose & Cylc]]<br />
<br />
= UM 10 / Global Atmosphere / ACCESS 2.x =<br />
<br />
The current version of the Unified Model is available from the Met Office's repository site [https://code.metoffice.gov.uk https://code.metoffice.gov.uk].<br />
<br />
ARCCSS researchers need to email [mailto:climate_help@nci.org.au climate_help@nci.org.au] to request an account on the Met Office server.<br />
<br />
== Links & More Information ==<br />
<br />
*[https://accessdev.nci.org.au/trac/wiki/GettingConnected Connecting to Accessdev and running Rose] <br />
*[[Running_the_UM_with_Rose|Tips on using Rose with the UM]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2016 UM User Tutorial 2016] <br />
<br />
*[[GA7_Performance|GA7 Performance]] <br />
<br />
= UM 7.3 / ACCESS 1.x =<br />
<br />
The ACCESS climate model as used in CMIP5 uses model version 7.3. This version of the model uses the older `UMUI` user interface<br />
<br />
== Links & More Information ==<br />
<br />
*[[UM_Environment|Setting up the UMUI environment]] <br />
*[[Introduction_to_UMUI|Introduction to UMUI]] <br />
*[https://accessdev.nci.org.au/umdocs/7.3 UM 7.3 Documentation] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2013 UM User Tutorial 2013] <br />
<br />
= Experiments =<br />
<br />
A full list of experiments we support or have helped set up can be found at [[UM_Experiments|UM Experiments]]<br />
<br />
These configurations are currently our primary support targets:<br />
<br />
*[[ACCESS_2.0|ACCESS 2.0]] <br />
*[[ACCESS-ESM|ACCESS-ESM]] <br />
*[[GlobalAtmosphere|GA 7]] <br />
*[[Nesting_Suite|Nesting Suite]] <br />
<br />
= Guides =<br />
<br />
Assorted information on running the UM and available job configurations is listed in the sections below. Feel free to email [[mailto:climate_help@nci.org.au| climate_help@nci.org.au]] if you have any difficulties using the UM or suggestions for how we can make using the UM simpler.<br />
<br />
*[[Getting_Help_with_the_UM|Getting Help with the UM]] <br />
*[[Um-errors|Common Errors]] <br />
<br />
== Starting Up ==<br />
<br />
*[[New_UM_User_message|New UM User message]] <br />
*[[Building_the_UM|Building the UM]] <br />
*[[Standard_UM_Runs|Standard UM Runs]] <br />
*[[Restarting_UM_Runs|Running the UM using automatic resubmission]] <br />
*[[Recovering_from_an_interrupted_job|Recovering from an interrupted job]] <br />
*[[UM_Helper_Scripts|UM Helper Scripts]] <br />
*[[Moving_UM_jobs_to_Raijin|Moving UM jobs to Raijin]] <br />
*[[Running_the_UM_with_Rose|Running the UM with Rose]] <br />
<br />
== Run Types ==<br />
<br />
*[[AMIP|AMIP]] <br />
*[[ACCESS|CMIP]] <br />
*[https://trac.nci.org.au/trac/access/wiki/SCM_testcases Single Column] <br />
*[[KPP_Coupling|KPP Coupling]] <br />
*[https://trac.nci.org.au/trac/access/wiki/APS1_ACCESS_C ACCESS-C High-resolution NWP] <br />
*[[UM_Nested_Models|UM Nested Models]] <br />
*[[Limited_Area|Limited Area]] <br />
*[[UKCA|UKCA]] <br />
<br />
*[http://www.ukca.ac.uk/wiki/index.php/UKCA_&_UMUI_Tutorials UKCA Tutorials] <br />
*[https://trac.nci.org.au/trac/access/wiki/AccessModelExperimentLibrary CAWCR's ACCESS experiment library] (log in with your NCI account) <br />
<br />
= Common Errors =<br />
<br />
If a run fails, search for 'UM ERROR' in the .leave file to see what went wrong. Common issues are listed here<br />
<br />
*[[Um-errors#pp-headers|REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH]] <br />
*[https://code.metoffice.gov.uk/trac/um/wiki/KnownUMFailurePoints Known UM failures at UKMO] <br />
<br />
== Job Input ==<br />
<br />
*[[UM_Ancillary_files|UM Ancillary files]] <br />
*[[Concatenate_AMIP_Ancillaries|Concatenate AMIP Ancillaries]] <br />
*[[Copying_CO2_values|Copying CO2 values]] <br />
*[[Modifying_UM_Files|Modifying UM files with Mule]] <br />
<br />
== Job Output ==<br />
<br />
*[[Using_STASH|Using STASH]] <br />
*[[Copying_STASH_settings_between_jobs|Copying STASH settings between jobs]] <br />
*[[UM_Filenames|UM output filename convention]] <br />
*[[Analysing_UM_outputs|Analysing UM outputs & Converting to NetCDF]] <br />
*[[Archiving_Output|Archiving Output]] <br />
*[[Comparing_UM_Files|Comparing UM Files]] <br />
*[https://code.metoffice.gov.uk/trac/UKESM/wiki/CMIP6/DiagnosticMappings Mapping UM outputs to CMIP fields] <br />
<br />
== Modifying the UM ==<br />
<br />
*[[UM_Source_Control|UM Source Control]] <br />
*[[User_fields|User fields]] <br />
*[[Oasis_Coupling_with_the_UM|Oasis Coupling with the UM]] <br />
*[[Oasis_coupling_in_UM_8.5|Oasis coupling in UM 8.5]] <br />
*[[Profiling_with_IPM_and_Vampir|Profiling MPI]] <br />
*[[Hand_Edits|Hand Edits]] <br />
<br />
== Informative ==<br />
<br />
*[[UM_Version_Summaries|UM Version Summaries]] <br />
*[[UM_Run_Scripts|UM Run Scripts]] <br />
*[[UMUI_over_VNC|UMUI over VNC]] <br />
*[[Downloading_from_MASS|Downloading from MASS]] <br />
*[[Vertical_Coordinates|Vertical Coordinates]] <br />
<br />
== [[UM_and_ACCESS_FAQ|UM_and_ACCESS_FAQ]] ==<br />
<br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#Who_can_gain_access_to_the_UM_and_the_ACCESS_models.3F Who can gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_gain_access_to_the_UM_and_the_ACCESS_models.3F What to do to gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_use_the_software_in_.2Fprojects.2Faccess.2Fbin.3F What to do to use the software in /projects/access/bin?] <br />
<br />
== Work in progress ==<br />
<br />
*[[SCM_with_ERA-Interim|SCM with ERA-Interim]] <br />
<br />
= Resources =<br />
<br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[https://nf.nci.org.au/facilities/software/UM/7.8/umdoc_system/UM_docs/papers/html/X0/X0.html Getting started with UM and UMUI] <br />
*[http://cms.ncas.ac.uk/ NCAS] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Main/WebHome Met Office Wiki] - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] or [mailto:climate_help@nf.nci.org.au climate_help] to register <br />
*Met Office mailing list (Read by scientists at the Met Office) - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] <br />
*ACCESS users mailing list (Notifications about ACCESS systems) - Contact [mailto:climate_help@nf.nci.org.au climate_help] <br />
<br />
*[[UM_Admin|UM Admin]] <br />
*[[UM_Partial_guides|UM Partial guides]] <br />
<br />
[[Category:Unified Model]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Unified_Model&diff=1835Unified Model2019-12-12T03:59:12Z<p>D.eisenberg: </p>
<hr />
<div><br />
The Unified Model is the atmospheric component of [[ACCESS|ACCESS]], developed by the UK's Met Office. The Centre of Excellence sublicences the UM from CAWCR, our licence allows us to run the UM at NCI only. To run the UM you will first need an NCI account, then ask for connection to the ACCESS group through [https://my.nci.org.au/mancini/project/access/join NCI's account website].<br />
<br />
The ACCESS climate models are based on version 7.3 of the UM, most Australian university research uses this version. The Bureau makes use of the more recent version 7.8 for forecasting, and is evaluating moving to version 8.2. These are the primary versions supported at NCI, other versions are available but may not be quite as well tested. Different versions include changed science configurations, for details see the [https://code.metoffice.gov.uk/trac/um/wiki/ReleaseNotes release notes].<br />
<br />
= Getting Started =<br />
<br />
The UM is configured through a graphical interface, which is run from the server [[Accessdev|accessdev.nci.org.au]]. See [https://accessdev.nci.org.au/trac/wiki/GettingConnected Setting up the environment] for how to connect.<br />
<br />
*[https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_000.pdf Unified Model User's Guide] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM Documentation Papers] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
<br />
There are two ways to run the model. Older versions (pre UM 10) use a program called [[UMUI|UMUI]], newer versions (post UM 10) use [[Rose_&_Cylc|Rose & Cylc]]<br />
<br />
= UM 10 / Global Atmosphere / ACCESS 2.x =<br />
<br />
The current version of the Unified Model is available from the Met Office's repository site [https://code.metoffice.gov.uk https://code.metoffice.gov.uk].<br />
<br />
ARCCSS researchers need to email [mailto:climate_help@nci.org.au climate_help@nci.org.au] to request an account on the Met Office server.<br />
<br />
== Links & More Information ==<br />
<br />
*[https://accessdev.nci.org.au/trac/wiki/GettingConnected Connecting to Accessdev and running Rose] <br />
*[[Running_the_UM_with_Rose|Tips on using Rose with the UM]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2016 UM User Tutorial 2016] <br />
<br />
*[[GA7_Performance|GA7 Performance]] <br />
<br />
= UM 7.3 / ACCESS 1.x =<br />
<br />
The ACCESS climate model as used in CMIP5 uses model version 7.3. This version of the model uses the older `UMUI` user interface<br />
<br />
== Links & More Information ==<br />
<br />
*[[UM_Environment|Setting up the UMUI environment]] <br />
*[[Introduction_to_UMUI|Introduction to UMUI]] <br />
*[https://accessdev.nci.org.au/umdocs/7.3 UM 7.3 Documentation] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2013 UM User Tutorial 2013] <br />
<br />
= Experiments =<br />
<br />
A full list of experiments we support or have helped set up can be found at [[UM_Experiments|UM Experiments]]<br />
<br />
These configurations are currently our primary support targets:<br />
<br />
*[[ACCESS_2.0|ACCESS 2.0]] <br />
*[[ACCESS-ESM|ACCESS-ESM]] <br />
*[[GlobalAtmosphere|GA 7]] <br />
*[[Nesting_Suite|Nesting Suite]] <br />
<br />
= Guides =<br />
<br />
Assorted information on running the UM and available job configurations is listed in the sections below. Feel free to email [[mailto:climate_help@nci.org.au| climate_help@nci.org.au]] if you have any difficulties using the UM or suggestions for how we can make using the UM simpler.<br />
<br />
*[[Getting_Help_with_the_UM|Getting Help with the UM]] <br />
*[[Um-errors|Common Errors]] <br />
<br />
== Starting Up ==<br />
<br />
*[[New_UM_User_message|New UM User message]] <br />
*[[Building_the_UM|Building the UM]] <br />
*[[Standard_UM_Runs|Standard UM Runs]] <br />
*[[Restarting_UM_Runs|Running the UM using automatic resubmission]] <br />
*[[Recovering_from_an_interrupted_job|Recovering from an interrupted job]] <br />
*[[UM_Helper_Scripts|UM Helper Scripts]] <br />
*[[Moving_UM_jobs_to_Raijin|Moving UM jobs to Raijin]] <br />
*[[Running_the_UM_with_Rose|Running the UM with Rose]] <br />
<br />
== Run Types ==<br />
<br />
*[[AMIP|AMIP]] <br />
*[[ACCESS|CMIP]] <br />
*[https://trac.nci.org.au/trac/access/wiki/SCM_testcases Single Column] <br />
*[[KPP_Coupling|KPP Coupling]] <br />
*[https://trac.nci.org.au/trac/access/wiki/APS1_ACCESS_C ACCESS-C High-resolution NWP] <br />
*[[UM_Nested_Models|UM Nested Models]] <br />
*[[Limited_Area|Limited Area]] <br />
*[[UKCA|UKCA]] <br />
<br />
*[http://www.ukca.ac.uk/wiki/index.php/UKCA_&_UMUI_Tutorials UKCA Tutorials] <br />
*[https://trac.nci.org.au/trac/access/wiki/AccessModelExperimentLibrary CAWCR's ACCESS experiment library] (log in with your NCI account) <br />
<br />
= Common Errors =<br />
<br />
If a run fails, search for 'UM ERROR' in the .leave file to see what went wrong. Common issues are listed here<br />
<br />
*[[Um-errors#pp-headers|REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH]] <br />
*[https://code.metoffice.gov.uk/trac/um/wiki/KnownUMFailurePoints Known UM failures at UKMO] <br />
<br />
== Job Input ==<br />
<br />
*[[UM_Ancillary_files|UM Ancillary files]] <br />
*[[Concatenate_AMIP_Ancillaries|Concatenate AMIP Ancillaries]] <br />
*[[Copying_CO2_values|Copying CO2 values]] <br />
*[[Modifying_UM_Files|Modifying UM files with Mule]] <br />
<br />
== Job Output ==<br />
<br />
*[[Using_STASH|Using STASH]] <br />
*[[Copying_STASH_settings_between_jobs|Copying STASH settings between jobs]] <br />
*[[UM_Filenames|UM output filename convention]] <br />
*[[Analysing_UM_outputs|Analysing UM outputs & Converting to NetCDF]] <br />
*[[Archiving_Output|Archiving Output]] <br />
*[[Comparing_UM_Files|Comparing UM Files]] <br />
*[https://code.metoffice.gov.uk/trac/UKESM/wiki/CMIP6/DiagnosticMappings Mapping UM outputs to CMIP fields] <br />
<br />
== Modifying the UM ==<br />
<br />
*[[UM_Source_Control|UM Source Control]] <br />
*[[User_fields|User fields]] <br />
*[[Oasis_Coupling_with_the_UM|Oasis Coupling with the UM]] <br />
*[[Oasis_coupling_in_UM_8.5|Oasis coupling in UM 8.5]] <br />
*[[Profiling_with_IPM_and_Vampir|Profiling MPI]] <br />
*[[Hand_Edits|Hand Edits]] <br />
<br />
== Informative ==<br />
<br />
*[[UM_Version_Summaries|UM Version Summaries]] <br />
*[[UM_Run_Scripts|UM Run Scripts]] <br />
*[[UMUI_over_VNC|UMUI over VNC]] <br />
*[[Downloading_from_MASS|Downloading from MASS]] <br />
*[[Vertical_Coordinates|Vertical Coordinates]] <br />
<br />
<br />
== [[UM_and_ACCESS_FAQ|UM_and_ACCESS_FAQ]] ==<br />
<br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#Who_can_gain_access_to_the_UM_and_the_ACCESS_models.3F Who can gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_gain_access_to_the_UM_and_the_ACCESS_models.3F What to do to gain access to the UM and the ACCESS models?] <br />
*[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_use_the_software_in_.2Fprojects.2Faccess.2Fbin.3F What to do to use the software in /projects/access/bin?]<br />
<br />
== Work in progress ==<br />
<br />
*[[SCM_with_ERA-Interim|SCM with ERA-Interim]] <br />
<br />
= Resources =<br />
<br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[https://nf.nci.org.au/facilities/software/UM/7.8/umdoc_system/UM_docs/papers/html/X0/X0.html Getting started with UM and UMUI] <br />
*[http://cms.ncas.ac.uk/ NCAS] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Main/WebHome Met Office Wiki] - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] or [mailto:climate_help@nf.nci.org.au climate_help] to register <br />
*Met Office mailing list (Read by scientists at the Met Office) - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] <br />
*ACCESS users mailing list (Notifications about ACCESS systems) - Contact [mailto:climate_help@nf.nci.org.au climate_help] <br />
<br />
*[[UM_Admin|UM Admin]] <br />
*[[UM_Partial_guides|UM Partial guides]] <br />
<br />
[[Category:Unified Model]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Unified_Model&diff=1833Unified Model2019-12-12T03:58:42Z<p>D.eisenberg: Added FAQs</p>
<hr />
<div><br />
The Unified Model is the atmospheric component of [[ACCESS|ACCESS]], developed by the UK's Met Office. The Centre of Excellence sublicences the UM from CAWCR, our licence allows us to run the UM at NCI only. To run the UM you will first need an NCI account, then ask for connection to the ACCESS group through [https://my.nci.org.au/mancini/project/access/join NCI's account website].<br />
<br />
The ACCESS climate models are based on version 7.3 of the UM, most Australian university research uses this version. The Bureau makes use of the more recent version 7.8 for forecasting, and is evaluating moving to version 8.2. These are the primary versions supported at NCI, other versions are available but may not be quite as well tested. Different versions include changed science configurations, for details see the [https://code.metoffice.gov.uk/trac/um/wiki/ReleaseNotes release notes].<br />
<br />
= Getting Started =<br />
<br />
The UM is configured through a graphical interface, which is run from the server [[Accessdev|accessdev.nci.org.au]]. See [https://accessdev.nci.org.au/trac/wiki/GettingConnected Setting up the environment] for how to connect.<br />
<br />
*[https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_000.pdf Unified Model User's Guide] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM Documentation Papers] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
<br />
There are two ways to run the model. Older versions (pre UM 10) use a program called [[UMUI|UMUI]], newer versions (post UM 10) use [[Rose_&_Cylc|Rose & Cylc]]<br />
<br />
= UM 10 / Global Atmosphere / ACCESS 2.x =<br />
<br />
The current version of the Unified Model is available from the Met Office's repository site [https://code.metoffice.gov.uk https://code.metoffice.gov.uk].<br />
<br />
ARCCSS researchers need to email [mailto:climate_help@nci.org.au climate_help@nci.org.au] to request an account on the Met Office server.<br />
<br />
== Links & More Information ==<br />
<br />
*[https://accessdev.nci.org.au/trac/wiki/GettingConnected Connecting to Accessdev and running Rose] <br />
*[[Running_the_UM_with_Rose|Tips on using Rose with the UM]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2016 UM User Tutorial 2016] <br />
<br />
*[[GA7_Performance|GA7 Performance]] <br />
<br />
= UM 7.3 / ACCESS 1.x =<br />
<br />
The ACCESS climate model as used in CMIP5 uses model version 7.3. This version of the model uses the older `UMUI` user interface<br />
<br />
== Links & More Information ==<br />
<br />
*[[UM_Environment|Setting up the UMUI environment]] <br />
*[[Introduction_to_UMUI|Introduction to UMUI]] <br />
*[https://accessdev.nci.org.au/umdocs/7.3 UM 7.3 Documentation] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2013 UM User Tutorial 2013] <br />
<br />
= Experiments =<br />
<br />
A full list of experiments we support or have helped set up can be found at [[UM_Experiments|UM Experiments]]<br />
<br />
These configurations are currently our primary support targets:<br />
<br />
*[[ACCESS_2.0|ACCESS 2.0]] <br />
*[[ACCESS-ESM|ACCESS-ESM]] <br />
*[[GlobalAtmosphere|GA 7]] <br />
*[[Nesting_Suite|Nesting Suite]] <br />
<br />
= Guides =<br />
<br />
Assorted information on running the UM and available job configurations is listed in the sections below. Feel free to email [[mailto:climate_help@nci.org.au| climate_help@nci.org.au]] if you have any difficulties using the UM or suggestions for how we can make using the UM simpler.<br />
<br />
*[[Getting_Help_with_the_UM|Getting Help with the UM]] <br />
*[[Um-errors|Common Errors]] <br />
<br />
== Starting Up ==<br />
<br />
*[[New_UM_User_message|New UM User message]] <br />
*[[Building_the_UM|Building the UM]] <br />
*[[Standard_UM_Runs|Standard UM Runs]] <br />
*[[Restarting_UM_Runs|Running the UM using automatic resubmission]] <br />
*[[Recovering_from_an_interrupted_job|Recovering from an interrupted job]] <br />
*[[UM_Helper_Scripts|UM Helper Scripts]] <br />
*[[Moving_UM_jobs_to_Raijin|Moving UM jobs to Raijin]] <br />
*[[Running_the_UM_with_Rose|Running the UM with Rose]] <br />
<br />
== Run Types ==<br />
<br />
*[[AMIP|AMIP]] <br />
*[[ACCESS|CMIP]] <br />
*[https://trac.nci.org.au/trac/access/wiki/SCM_testcases Single Column] <br />
*[[KPP_Coupling|KPP Coupling]] <br />
*[https://trac.nci.org.au/trac/access/wiki/APS1_ACCESS_C ACCESS-C High-resolution NWP] <br />
*[[UM_Nested_Models|UM Nested Models]] <br />
*[[Limited_Area|Limited Area]] <br />
*[[UKCA|UKCA]] <br />
<br />
*[http://www.ukca.ac.uk/wiki/index.php/UKCA_&_UMUI_Tutorials UKCA Tutorials] <br />
*[https://trac.nci.org.au/trac/access/wiki/AccessModelExperimentLibrary CAWCR's ACCESS experiment library] (log in with your NCI account) <br />
<br />
= Common Errors =<br />
<br />
If a run fails, search for 'UM ERROR' in the .leave file to see what went wrong. Common issues are listed here<br />
<br />
*[[Um-errors#pp-headers|REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH]] <br />
*[https://code.metoffice.gov.uk/trac/um/wiki/KnownUMFailurePoints Known UM failures at UKMO] <br />
<br />
== Job Input ==<br />
<br />
*[[UM_Ancillary_files|UM Ancillary files]] <br />
*[[Concatenate_AMIP_Ancillaries|Concatenate AMIP Ancillaries]] <br />
*[[Copying_CO2_values|Copying CO2 values]] <br />
*[[Modifying_UM_Files|Modifying UM files with Mule]] <br />
<br />
== Job Output ==<br />
<br />
*[[Using_STASH|Using STASH]] <br />
*[[Copying_STASH_settings_between_jobs|Copying STASH settings between jobs]] <br />
*[[UM_Filenames|UM output filename convention]] <br />
*[[Analysing_UM_outputs|Analysing UM outputs & Converting to NetCDF]] <br />
*[[Archiving_Output|Archiving Output]] <br />
*[[Comparing_UM_Files|Comparing UM Files]] <br />
*[https://code.metoffice.gov.uk/trac/UKESM/wiki/CMIP6/DiagnosticMappings Mapping UM outputs to CMIP fields] <br />
<br />
== Modifying the UM ==<br />
<br />
*[[UM_Source_Control|UM Source Control]] <br />
*[[User_fields|User fields]] <br />
*[[Oasis_Coupling_with_the_UM|Oasis Coupling with the UM]] <br />
*[[Oasis_coupling_in_UM_8.5|Oasis coupling in UM 8.5]] <br />
*[[Profiling_with_IPM_and_Vampir|Profiling MPI]] <br />
*[[Hand_Edits|Hand Edits]] <br />
<br />
== Informative ==<br />
<br />
*[[UM_Version_Summaries|UM Version Summaries]] <br />
*[[UM_Run_Scripts|UM Run Scripts]] <br />
*[[UMUI_over_VNC|UMUI over VNC]] <br />
*[[Downloading_from_MASS|Downloading from MASS]] <br />
*[[Vertical_Coordinates|Vertical Coordinates]] <br />
<br />
== [[UM_and_ACCESS_FAQ]] ==<br />
<br />
*<br />
[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#Who_can_gain_access_to_the_UM_and_the_ACCESS_models.3F Who can gain access to the UM and the ACCESS models?]<br />
<br />
*<br />
[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_gain_access_to_the_UM_and_the_ACCESS_models.3F What to do to gain access to the UM and the ACCESS models?]<br />
<br />
*<br />
[http://climate-cms.wikis.unsw.edu.au/UM_and_ACCESS_FAQ#What_to_do_to_use_the_software_in_.2Fprojects.2Faccess.2Fbin.3F What to do to use the software in /projects/access/bin?]<br />
<br />
<br />
== Work in progress ==<br />
<br />
*[[SCM_with_ERA-Interim|SCM with ERA-Interim]] <br />
<br />
= Resources =<br />
<br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[https://nf.nci.org.au/facilities/software/UM/7.8/umdoc_system/UM_docs/papers/html/X0/X0.html Getting started with UM and UMUI] <br />
*[http://cms.ncas.ac.uk/ NCAS] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Main/WebHome Met Office Wiki] - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] or [mailto:climate_help@nf.nci.org.au climate_help] to register <br />
*Met Office mailing list (Read by scientists at the Met Office) - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] <br />
*ACCESS users mailing list (Notifications about ACCESS systems) - Contact [mailto:climate_help@nf.nci.org.au climate_help] <br />
<br />
*[[UM_Admin|UM Admin]] <br />
*[[UM_Partial_guides|UM Partial guides]] <br />
<br />
[[Category:Unified Model]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Unified_Model&diff=1783Unified Model2019-12-12T03:28:57Z<p>D.eisenberg: add link to FAQ</p>
<hr />
<div><br />
The Unified Model is the atmospheric component of [[ACCESS|ACCESS]], developed by the UK's Met Office. The Centre of Excellence sublicences the UM from CAWCR, our licence allows us to run the UM at NCI only. To run the UM you will first need an NCI account, then ask for connection to the ACCESS group through [https://my.nci.org.au/mancini/project/access/join NCI's account website].<br />
<br />
The ACCESS climate models are based on version 7.3 of the UM, most Australian university research uses this version. The Bureau makes use of the more recent version 7.8 for forecasting, and is evaluating moving to version 8.2. These are the primary versions supported at NCI, other versions are available but may not be quite as well tested. Different versions include changed science configurations, for details see the [https://code.metoffice.gov.uk/trac/um/wiki/ReleaseNotes release notes].<br />
<br />
= Getting Started =<br />
<br />
The UM is configured through a graphical interface, which is run from the server [[Accessdev|accessdev.nci.org.au]]. See [https://accessdev.nci.org.au/trac/wiki/GettingConnected Setting up the environment] for how to connect.<br />
<br />
*[https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_000.pdf Unified Model User's Guide] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM Documentation Papers] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
<br />
There are two ways to run the model. Older versions (pre UM 10) use a program called [[UMUI|UMUI]], newer versions (post UM 10) use [[Rose_&_Cylc|Rose & Cylc]]<br />
<br />
= UM 10 / Global Atmosphere / ACCESS 2.x =<br />
<br />
The current version of the Unified Model is available from the Met Office's repository site [https://code.metoffice.gov.uk https://code.metoffice.gov.uk].<br />
<br />
ARCCSS researchers need to email [mailto:climate_help@nci.org.au climate_help@nci.org.au] to request an account on the Met Office server.<br />
<br />
== Links & More Information ==<br />
<br />
*[https://accessdev.nci.org.au/trac/wiki/GettingConnected Connecting to Accessdev and running Rose] <br />
*[[Running_the_UM_with_Rose|Tips on using Rose with the UM]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2017 UM User Tutorial 2017] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2016 UM User Tutorial 2016] <br />
<br />
*[[GA7_Performance|GA7 Performance]] <br />
<br />
= UM 7.3 / ACCESS 1.x =<br />
<br />
The ACCESS climate model as used in CMIP5 uses model version 7.3. This version of the model uses the older `UMUI` user interface<br />
<br />
== Links & More Information ==<br />
<br />
*[[UM_Environment|Setting up the UMUI environment]] <br />
*[[Introduction_to_UMUI|Introduction to UMUI]] <br />
*[https://accessdev.nci.org.au/umdocs/7.3 UM 7.3 Documentation] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Support/UMUserTutorial2013 UM User Tutorial 2013] <br />
<br />
= Experiments =<br />
<br />
A full list of experiments we support or have helped set up can be found at [[UM_Experiments|UM Experiments]]<br />
<br />
These configurations are currently our primary support targets:<br />
<br />
*[[ACCESS_2.0|ACCESS 2.0]] <br />
*[[ACCESS-ESM|ACCESS-ESM]] <br />
*[[GlobalAtmosphere|GA 7]] <br />
*[[Nesting_Suite|Nesting Suite]] <br />
<br />
= Guides =<br />
<br />
Assorted information on running the UM and available job configurations is listed in the sections below. Feel free to email [[mailto:climate_help@nci.org.au| climate_help@nci.org.au]] if you have any difficulties using the UM or suggestions for how we can make using the UM simpler.<br />
<br />
*[[Getting_Help_with_the_UM|Getting Help with the UM]] <br />
*[[Um-errors|Common Errors]] <br />
<br />
== Starting Up ==<br />
<br />
*[[New_UM_User_message|New UM User message]] <br />
*[[Building_the_UM|Building the UM]] <br />
*[[Standard_UM_Runs|Standard UM Runs]] <br />
*[[Restarting_UM_Runs|Running the UM using automatic resubmission]] <br />
*[[Recovering_from_an_interrupted_job|Recovering from an interrupted job]] <br />
*[[UM_Helper_Scripts|UM Helper Scripts]] <br />
*[[Moving_UM_jobs_to_Raijin|Moving UM jobs to Raijin]] <br />
*[[Running_the_UM_with_Rose|Running the UM with Rose]] <br />
<br />
== Run Types ==<br />
<br />
*[[AMIP|AMIP]] <br />
*[[ACCESS|CMIP]] <br />
*[https://trac.nci.org.au/trac/access/wiki/SCM_testcases Single Column] <br />
*[[KPP_Coupling|KPP Coupling]] <br />
*[https://trac.nci.org.au/trac/access/wiki/APS1_ACCESS_C ACCESS-C High-resolution NWP] <br />
*[[UM_Nested_Models|UM Nested Models]] <br />
*[[Limited_Area|Limited Area]] <br />
*[[UKCA|UKCA]] <br />
<br />
*[http://www.ukca.ac.uk/wiki/index.php/UKCA_&_UMUI_Tutorials UKCA Tutorials] <br />
*[https://trac.nci.org.au/trac/access/wiki/AccessModelExperimentLibrary CAWCR's ACCESS experiment library] (log in with your NCI account) <br />
<br />
= Common Errors =<br />
<br />
If a run fails, search for 'UM ERROR' in the .leave file to see what went wrong. Common issues are listed here<br />
<br />
*[[Um-errors#pp-headers|REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH]] <br />
*[https://code.metoffice.gov.uk/trac/um/wiki/KnownUMFailurePoints Known UM failures at UKMO] <br />
<br />
== Job Input ==<br />
<br />
*[[UM_Ancillary_files|UM Ancillary files]] <br />
*[[Concatenate_AMIP_Ancillaries|Concatenate AMIP Ancillaries]] <br />
*[[Copying_CO2_values|Copying CO2 values]] <br />
*[[Modifying_UM_Files|Modifying UM files with Mule]] <br />
<br />
== Job Output ==<br />
<br />
*[[Using_STASH|Using STASH]] <br />
*[[Copying_STASH_settings_between_jobs|Copying STASH settings between jobs]] <br />
*[[UM_Filenames|UM output filename convention]] <br />
*[[Analysing_UM_outputs|Analysing UM outputs & Converting to NetCDF]] <br />
*[[Archiving_Output|Archiving Output]] <br />
*[[Comparing_UM_Files|Comparing UM Files]] <br />
*[https://code.metoffice.gov.uk/trac/UKESM/wiki/CMIP6/DiagnosticMappings Mapping UM outputs to CMIP fields] <br />
<br />
== Modifying the UM ==<br />
<br />
*[[UM_Source_Control|UM Source Control]] <br />
*[[User_fields|User fields]] <br />
*[[Oasis_Coupling_with_the_UM|Oasis Coupling with the UM]] <br />
*[[Oasis_coupling_in_UM_8.5|Oasis coupling in UM 8.5]] <br />
*[[Profiling_with_IPM_and_Vampir|Profiling MPI]] <br />
*[[Hand_Edits|Hand Edits]] <br />
<br />
== Informative ==<br />
<br />
*[[UM_Version_Summaries|UM Version Summaries]] <br />
*[[UM_Run_Scripts|UM Run Scripts]] <br />
*[[UMUI_over_VNC|UMUI over VNC]] <br />
*[[Downloading_from_MASS|Downloading from MASS]] <br />
*[[Vertical_Coordinates|Vertical Coordinates]] <br />
<br />
== Work in progress ==<br />
<br />
*[[SCM_with_ERA-Interim|SCM with ERA-Interim]] <br />
<br />
= Resources =<br />
<br />
*[[UM_and_ACCESS_FAQ|UM and ACCESS FAQ]] <br />
*[https://code.metoffice.gov.uk/trac/um UM code & issue tracker] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/umdp.html UM 10.X Documentation] <br />
*[https://code.metoffice.gov.uk/doc/um/latest/um-training/index.html Rose Interface Tutorial] <br />
*[https://nf.nci.org.au/facilities/software/UM/7.8/umdoc_system/UM_docs/papers/html/X0/X0.html Getting started with UM and UMUI] <br />
*[http://cms.ncas.ac.uk/ NCAS] <br />
*[http://collab.metoffice.gov.uk/twiki/bin/view/Main/WebHome Met Office Wiki] - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] or [mailto:climate_help@nf.nci.org.au climate_help] to register <br />
*Met Office mailing list (Read by scientists at the Met Office) - Contact [mailto:UM_collaboration@metoffice.gov.uk UM_collaboration@metoffice.gov.uk] <br />
*ACCESS users mailing list (Notifications about ACCESS systems) - Contact [mailto:climate_help@nf.nci.org.au climate_help] <br />
<br />
*[[UM_Admin|UM Admin]] <br />
*[[UM_Partial_guides|UM Partial guides]] <br />
<br />
[[Category:Unified Model]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1558CLEx induction2019-11-28T04:26:36Z<p>D.eisenberg: </p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
&nbsp;<br />
<br />
&nbsp;<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both gadi.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
<br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight><br />
Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown"><br />
Host gadi<br />
HostName gadi.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
<br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
<br />
#'''Distribute the key pair.''' On most systems, there is a useful script to distribute the key pairs called '''ssh-copy-id''': <syntaxhighlight lang="bash"><br />
$ ssh-copy-id gadi<br />
$ ssh-copy-id access<br />
</syntaxhighlight><br />
If that script fails, you have to distribute the keys manually with these commands: <syntaxhighlight lang="bash"><br />
$ cat ~/.ssh/id_rsa.pub | ssh gadi "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight><br />
<br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
&nbsp;<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming].<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
&nbsp;<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
{{NeedsUpdate|Refers to old supercomputer raijin}}<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained in '''Using restricted commands for transferring files '''[[Using_restricted_commands_for_transferring_files|here]]. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: gadi, accessdev and VDI. Gadi is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on gadi. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler<br />
| Load the default version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler/2019.3.199<br />
| Load a specific version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-compiler/2019.3.199<br />
| Switch to a different version of the intel compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-compiler/2019.3.199<br />
| Unload the specified version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on gadi is the scheduler PBS. This is the system for running software on dedicated nodes inside gadi. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/How+to+submit+a+job here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Gadi is comprised of nodes with 48 CPUs each. If you request less than 48 CPUs, you will get the number of CPUs that you request. If you request more, you will need to use a multiple of 48 CPUs.</span> <br />
*Nodes come with 192GB of memory to share within the 48 CPUs. So if your job requires 48 or more CPUs, you might as well request all the memory, for example 384GB for a 96-cpu job. <br />
<br />
Running a job on the queue costs so-called '''SU'''. On the old raijin, one SU was equivalent to one core for one hour. On the much faster new gadi, one core for one hour costs 2 SU. Note that on gadi, the SU cost is calculated using the higher of the number of cores and the memory usage. So if you request 5 cores but only 2GB memory, its SU cost is based on the 5 cores. If you request 1 core but 96GB of memory (half of the whole node), the cost will be based on 24 cores (half the whole node).<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
{{NeedsUpdate|refers to raijin}}<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice. <br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1528CLEx induction2019-11-28T04:06:15Z<p>D.eisenberg: Fixed link</p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
<br />
<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both gadi.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight> Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown"><br />
Host gadi<br />
HostName gadi.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
#'''Distribute the key pair.''' On most systems, there is a useful script to distribute the key pairs called '''ssh-copy-id''': <syntaxhighlight lang="bash"><br />
$ ssh-copy-id gadi<br />
$ ssh-copy-id access<br />
</syntaxhighlight> If that script fails, you have to distribute the keys manually with these commands: <syntaxhighlight lang="bash"><br />
$ cat ~/.ssh/id_rsa.pub | ssh gadi "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight><br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming].<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
This section refers to how to transfer data to the raijin supercomputer. It has not been updated for the new gadi supercomputer. {{NeedsUpdate}}<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained in '''Using restricted commands for transferring files '''[[Using_restricted_commands_for_transferring_files|here]]. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: raijin, accessdev and VDI. Raijin is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on gadi. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler<br />
| Load the default version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler/2019.3.199<br />
| Load a specific version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-compiler/2019.3.199<br />
| Switch to a different version of the intel compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-compiler/2019.3.199<br />
| Unload the specified version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on raijin is the scheduler PBS. This is the system for running software on dedicated nodes inside raijin. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/Job+Submission+and+Scheduling here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Raijin is comprised of nodes with 16 CPUs each. If you request less than 16 CPUs, you will get the number of CPUs that you request. If you request more, you will get as many nodes as you need. So it is usually a good idea for jobs with more than 16 CPUs to use a multiple of 16 CPUs.</span> <br />
*Nodes come with between 32GB and 126GB of memory to share within the 16 CPUs. So if your job requires 16 or more CPUs, you might as well request just under 32GB per node, for example 95GB for a 48-cpu job. <br />
*If you request more than 32GB per 16 CPUs, your job will possibly have to wait longer for enough high-memory nodes to become available.<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice.<br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1525CLEx induction2019-11-28T04:02:02Z<p>D.eisenberg: Indented paragraphs</p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
<br />
<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both gadi.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight> Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown"><br />
Host gadi<br />
HostName gadi.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
#'''Distribute the key pair.''' On most systems, there is a useful script to distribute the key pairs called '''ssh-copy-id''': <syntaxhighlight lang="bash"><br />
$ ssh-copy-id gadi<br />
$ ssh-copy-id access<br />
</syntaxhighlight> If that script fails, you have to distribute the keys manually with these commands: <syntaxhighlight lang="bash"><br />
$ cat ~/.ssh/id_rsa.pub | ssh gadi "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight><br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming].<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
This section refers to how to transfer data to the raijin supercomputer. It has not been updated for the new gadi supercomputer. {{NeedsUpdate}}<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained on this [http://nf.nci.org.au/facilities/software/SSH/ssh-without-passwds.php NCI page]. This page has not been updated since the Vayu machine. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: raijin, accessdev and VDI. Raijin is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on gadi. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler<br />
| Load the default version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler/2019.3.199<br />
| Load a specific version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-compiler/2019.3.199<br />
| Switch to a different version of the intel compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-compiler/2019.3.199<br />
| Unload the specified version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on raijin is the scheduler PBS. This is the system for running software on dedicated nodes inside raijin. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/Job+Submission+and+Scheduling here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Raijin is comprised of nodes with 16 CPUs each. If you request less than 16 CPUs, you will get the number of CPUs that you request. If you request more, you will get as many nodes as you need. So it is usually a good idea for jobs with more than 16 CPUs to use a multiple of 16 CPUs.</span> <br />
*Nodes come with between 32GB and 126GB of memory to share within the 16 CPUs. So if your job requires 16 or more CPUs, you might as well request just under 32GB per node, for example 95GB for a 48-cpu job. <br />
*If you request more than 32GB per 16 CPUs, your job will possibly have to wait longer for enough high-memory nodes to become available.<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice.<br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1524CLEx induction2019-11-28T04:01:18Z<p>D.eisenberg: Changed comments about Xming</p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both gadi.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight> Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown"><br />
Host gadi<br />
HostName gadi.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
#'''Distribute the key pair.''' On most systems, there is a useful script to distribute the key pairs called '''ssh-copy-id''': <syntaxhighlight lang="bash"><br />
$ ssh-copy-id gadi<br />
$ ssh-copy-id access<br />
</syntaxhighlight> If that script fails, you have to distribute the keys manually with these commands: <syntaxhighlight lang="bash"><br />
$ cat ~/.ssh/id_rsa.pub | ssh gadi "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight><br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming].<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
This section refers to how to transfer data to the raijin supercomputer. It has not been updated for the new gadi supercomputer. {{NeedsUpdate}}<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained on this [http://nf.nci.org.au/facilities/software/SSH/ssh-without-passwds.php NCI page]. This page has not been updated since the Vayu machine. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: raijin, accessdev and VDI. Raijin is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on gadi. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler<br />
| Load the default version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-compiler/2019.3.199<br />
| Load a specific version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-compiler/2019.3.199<br />
| Switch to a different version of the intel compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-compiler/2019.3.199<br />
| Unload the specified version of the intel compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on raijin is the scheduler PBS. This is the system for running software on dedicated nodes inside raijin. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/Job+Submission+and+Scheduling here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Raijin is comprised of nodes with 16 CPUs each. If you request less than 16 CPUs, you will get the number of CPUs that you request. If you request more, you will get as many nodes as you need. So it is usually a good idea for jobs with more than 16 CPUs to use a multiple of 16 CPUs.</span> <br />
*Nodes come with between 32GB and 126GB of memory to share within the 16 CPUs. So if your job requires 16 or more CPUs, you might as well request just under 32GB per node, for example 95GB for a 48-cpu job. <br />
*If you request more than 32GB per 16 CPUs, your job will possibly have to wait longer for enough high-memory nodes to become available.<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice.<br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1492CLEx induction2019-11-28T03:27:05Z<p>D.eisenberg: </p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both raijin.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight> Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown">Host raijin<br />
HostName raijin.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
#'''Distribute the key pair.''' The two commands below will each need your NCI password once. <br />
##for raijin: <syntaxhighlight lang="bash">$ cat ~/.ssh/id_rsa.pub | ssh raijin "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"</syntaxhighlight><br />
##for accessdev: <syntaxhighlight lang="bash">$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight> On Linux/Unix systems, there is sometimes a short-hand for these lines, called <span style="font-family:monospace">ssh-copy-id</span>, and used just like this: <span style="font-family:monospace">ssh-copy-id raijin</span>. But this program is not available on all systems, particularly not on MacOS.<br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming]. The last free version of Xming came out in 2007, this version should be sufficient. If you really want to, you can 'donate' GBP10 (ca. $20) to get an up-to-date version of Xming.<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained on this [http://nf.nci.org.au/facilities/software/SSH/ssh-without-passwds.php NCI page]. This page has not been updated since the Vayu machine. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: raijin, accessdev and VDI. Raijin is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on Raijin. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-fc<br />
| Load the default version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-fc/14.1.106<br />
| Load a specific version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-fc/13.4.183<br />
| Switch to a different version of the intel fortran compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-fc/13.4.183<br />
| Unload the specified version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on raijin is the scheduler PBS. This is the system for running software on dedicated nodes inside raijin. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/Job+Submission+and+Scheduling here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Raijin is comprised of nodes with 16 CPUs each. If you request less than 16 CPUs, you will get the number of CPUs that you request. If you request more, you will get as many nodes as you need. So it is usually a good idea for jobs with more than 16 CPUs to use a multiple of 16 CPUs.</span> <br />
*Nodes come with between 32GB and 126GB of memory to share within the 16 CPUs. So if your job requires 16 or more CPUs, you might as well request just under 32GB per node, for example 95GB for a 48-cpu job. <br />
*If you request more than 32GB per 16 CPUs, your job will possibly have to wait longer for enough high-memory nodes to become available.<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice.<br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEx_induction&diff=1491CLEx induction2019-11-28T03:26:12Z<p>D.eisenberg: </p>
<hr />
<div><br />
The CMS team is here to help you with the technical aspects of your work. A lot of you (probably all) will have to work with computer code and software, usually in a Linux/Unix environment. You might also need to access and/or share large amounts of data, work on different servers, etc.<br />
<br />
Some of you will be somewhat familiar with these tasks whereas they will be new to others. We are here to help whatever your technical knowledge is. We are happy to answer any question, we can't necessarily do everything but feel free to ask as we might have ideas or we might know who you should contact and what to exactly ask.<br />
<br />
The members of the [[CMS|CMS]] team are:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Name<br />
! Home-based Institution<br />
! Email<br />
|-<br />
| Claire Carouge<br />
| ANU<br />
| c.carouge@unsw.edu.au<br />
|-<br />
| Aidan Heerdegen<br />
| ANU<br />
| aidan.heerdegen@anu.edu.au<br />
|-<br />
| Paola Petrelli<br />
| U Tasmania<br />
| paola.petrelli@utas.edu.au<br />
|-<br />
| Scott Wales<br />
| U Melbourne<br />
| scott.wales@unimelb.edu.au<br />
|-<br />
| Holger Wolff<br />
| Monash<br />
| holger.wolff@monash.edu<br />
|-<br />
| Danny Eisenberg<br />
| UNSW<br />
| d.eisenberg@unsw.edu.au<br />
|}<br />
<br />
(Note: there is no typo, Claire is sitting at ANU but has a UNSW email address). Although we won't ignore emails sent to our individual addresses, our preferred way of contact is through our help desk email address: [mailto:cws_help@nf.nci.org.au cws_help@nf.nci.org.au]. Contacting the help desk will make sure your email is seen by one of us in case the person at your institution is away for example. Don't worry about the help desk email being an NCI account, you can still ask any question there.<br />
<br />
<br />
= Step 1: Get an account with NCI =<br />
<br />
NCI operates the computers that you will be doing most of your work on. NCI provides services to the Centre, they are not part of the Centre of Excellence.<br />
<br />
To get access to NCI servers, you need to do three things:<br />
<br />
1. You need to find out which project(s) you need to be connected to.<br />
<br />
Your project decides who gets billed for what you do on the NCI Servers. Your supervisor should be able to tell you which project(s) you should get connected to. Be mindful that there are two types of projects: projects for computation and projects for datasets. The mapping of the computational projects for CLEX can be found [[CLEX_projects_at_NCI|here]]. We recommend to join all the projects relevant to your research project but to choose 1 default project to work from. The same page with the list of computational projects explains how to set your default project. The projects for datasets do not have any computational time added to them so you need to make sure you ask for at least one computation project. Your supervisor should know. Note if you will run the ACCESS model or the UM model, you need to ask a connection to the "access" project in addition to at least one computation project.<br />
<br />
2. You need to register with NCI.<br />
<br />
This can be done on [https://my.nci.org.au/mancini/signup/0 NCI registration page] You will need to supply some information, and read and accept their policies. In order to be added to the system, you need to request connection to at least one project and be accepted on the project. Note that this can take a bit of time until&nbsp;the Lead chief investigator of the project has received and confirmed your request via email. Note that this is an automatic email process, you don't need to send an email to the lead chief investigator. Although, you might want to do so if you think you need to introduce yourself to him/her. Note that you should be able to request connection to several projects while getting signed up.<br />
<br />
3. You might want to ask your supervisor whether you also should be connected to any of the following data projects.<br />
<br />
These don’t provide any computing allowances, but they give access to certain datasets or models that you might need.<br />
<br />
{| class="wikitable"<br />
|-<br />
! Project<br />
! Purpose<br />
! Administrator<br />
|-<br />
| '''ua8'''<br />
| access to ARCCSS/CLEx published data, GSWP3, NCEP Polar sst, [[OSTIA-SST|ostia sst]], CMIP5 ocean processing<br />
| CMS<br />
|-<br />
| '''rq7'''<br />
| [[YOTC|ECMWF Year of Tropical Convection re-analysis]]<br />
| CMS<br />
|-<br />
| '''rq5'''<br />
| OFES - OGCM for the Earth Simulator ocean re-analysis<br />
| CMS<br />
|-<br />
| '''ub4'''<br />
| [[ERA_INTERIM|ECMWF ERA Interim re-analysis 6 hrs data]]<br />
| CMS<br />
|-<br />
| '''cb20'''<br />
| [[CMIP|CMIP3]] replica data<br />
| NCI<br />
|-<br />
| '''al33'''<br />
| [[CMIP|CMIP5]] replica data<br />
| NCI<br />
|-<br />
| '''rr3'''<br />
| [[CMIP|CMIP5]] published data<br />
| NCI<br />
|-<br />
| '''oi10'''<br />
| [[CMIP|CMIP6]] replica data<br />
| NCI<br />
|-<br />
| '''rr7'''<br />
| BoM re-analysis collection including ERA-Interim monthly data and JRA55, MERRA2<br />
| BoM<br />
|-<br />
| '''cable'''<br />
| Give access to the [https://trac.nci.org.au/trac/cable/wiki CABLE model] and [[CABLE_Data|CABLE benchmarking dataset]]. Please read the [https://trac.nci.org.au/trac/cable/wiki/CableRegistration CABLE registration] information.<br />
| CSIRO<br />
|-<br />
| '''access'''<br />
| Give access to the [[Unified_Model|Unified Model]] and ACCESS tools<br />
| CMS - BoM - CSIRO<br />
|}<br />
<br />
&nbsp;<br />
<br />
= Step 2: Set up your Connection =<br />
<br />
The standard method of connecting to the NCI systems is SSH. We want you to use a passphrase protected private key authorisation method with an ssh-agent and agent forwarding for convenience. If you understood every part of that sentence, go ahead and set it up. If not, the next part describes what to do.<br />
<br />
The instructions describe how to set up your connection to both raijin.nci.org.au and accessdev.nci.org.au. You '''can not''' set up a connection to accessdev if you are not going to use the ACCESS or UM models. So please only follow the instructions you need!<br />
<br />
&nbsp;<br />
<br />
== Linux and MacOS: ==<br />
<br />
#'''Create the ssh directory''' on your computer <syntaxhighlight lang="bash">$ mkdir -p ~/.ssh</syntaxhighlight><br />
#'''Create a config file''' <syntaxhighlight lang="bash">$ nano ~/.ssh/config </syntaxhighlight> Enter the following contents, replacing <span style="font-family:monospace">xx0000</span> with your NCI user name. <syntaxhighlight lang="unknown">Host raijin<br />
HostName raijin.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
Host access<br />
HostName accessdev.nci.org.au<br />
User xx0000<br />
ForwardX11 yes<br />
ForwardX11Trusted yes<br />
ForwardAgent yes<br />
</syntaxhighlight><br />
#'''Create a key pair.''' It is imperative that you select a strong passphrase when asked for it. <syntaxhighlight lang="bash">$ ssh-keygen -t rsa</syntaxhighlight><br />
#'''Distribute the key pair.''' The two commands below will each need your NCI password once. <br />
##for raijin: <syntaxhighlight lang="bash">$ cat ~/.ssh/id_rsa.pub | ssh raijin "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"</syntaxhighlight><br />
##for accessdev: <syntaxhighlight lang="bash">$ cat ~/.ssh/id_rsa.pub | ssh access "mkdir -p ~/.ssh/; cat >> ~/.ssh/authorized_keys"<br />
</syntaxhighlight> On Linux/Unix systems, there is sometimes a short-hand for these lines, called <span style="font-family:monospace">ssh-copy-id</span>, and used just like this: <span style="font-family:monospace">ssh-copy-id raijin</span>. But this program is not available on all systems, particularly not on MacOS.<br />
#'''Test whether you have an agent.''' If you have an agent already running, this command will ask for the passphrase for the just-created key pair: <syntaxhighlight lang="bash">$ ssh-add</syntaxhighlight><br />
<br />
If the last command told you that it couldn’t open a connection, then you don’t have an agent. Come talk to someone of the CMS team, we will help you set it up.<br />
<br />
== Windows ==<br />
<br />
Windows is not Unix based, so it doesn’t come with standard SSH programs. The most popular SSH program for Windows is PuTTY, available [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html here]. You will need at least PuTTY, Pageant (which is the agent), and PuTTYgen, the key generator. A nice video on how to set it up is on [https://youtu.be/2nkAQ9M6ZF8 YouTube]. Windows also doesn't come with an X11 Server, which is needed to display graphical user interfaces. At this point in time, we suggest something like [http://www.straightrunning.com/XmingNotes/ Xming]. The last free version of Xming came out in 2007, this version should be sufficient. If you really want to, you can 'donate' GBP10 (ca. $20) to get an up-to-date version of Xming.<br />
<br />
Another option is to install [https://cygwin.com/ Cygwin], which is a large collection of Linux utilities that run on Windows. Cygwin includes a shell, SSH, and an X11 server, as well as many other useful tools.<br />
<br />
== SSH-keys for file transfers ==<br />
<br />
Additionally, some groups transfer data from NCI to outside NCI, for example for storage on University maintained servers. For these transfers, the best way to proceed is to create a restricted ssh key pair used only for file transfer. The setup is explained on this [http://nf.nci.org.au/facilities/software/SSH/ssh-without-passwds.php NCI page]. This page has not been updated since the Vayu machine. Most of the instructions are still valid, except for step 3. The restricted command prefix should now be:<br />
<syntaxhighlight lang="unknown"><br />
from="chipmunk*.nci.org.au,r-dm*.nci.org.au,gopher*.nci.org.au,raijin*.nci.org.au",command="~/bin/rrsync /data/archive",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty,no-user-rc ssh-rsa<br />
</syntaxhighlight><br />
<br />
= Step 3: Basics of the NCI system =<br />
<br />
<span style="line-height: 1.5;">We are mainly using 3 systems of the NCI: raijin, accessdev and VDI. Raijin is the supercomputer that we run our models on. Accessdev is a virtual server that we have software installed that are required to allow the running the models. VDI is a virtual desktop designed for interactive analysis of your results. All these servers run Linux as operating system.</span><br />
<br />
== Read the manual! ==<br />
<br />
Considering you will be using systems that are provided by the NCI, you should take the time to read the documentation provided by them about their systems. That is everything on their [https://opus.nci.org.au/display/Help/NCI+Help help knowledge base].<br />
<br />
== Additional notes ==<br />
<br />
=== Modules: ===<br />
<br />
The servers have a lot of software installed, some of which they have multiple versions of. If you need to use a software, you usually will need to load a certain module. A full help of the module command is accessible through the man pages on Raijin. Here are the most important commands regarding the modules:<br />
<br />
{|<br />
|-<br />
| $ module <span style="color: #8000ff;">help</span><br />
| Show help about the module system<br />
|-<br />
| $ module <span style="color: #8000ff;">avail</span><br />
| List all available modules (a lot!)<br />
|-<br />
| $ module <span style="color: #8000ff;">list</span><br />
| List the currently loaded modules<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-fc<br />
| Load the default version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">load</span> intel-fc/14.1.106<br />
| Load a specific version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">switch</span> intel-fc/13.4.183<br />
| Switch to a different version of the intel fortran compiler (unload and load)<br />
|-<br />
| $ module <span style="color: #8000ff;">unload</span> intel-fc/13.4.183<br />
| Unload the specified version of the intel fortran compiler<br />
|-<br />
| $ module <span style="color: #8000ff;">use</span> /g/data/hh5/public/modules<br />
| Add our Centre's curated modules to the list of available modules<br />
|}<br />
<br />
Some modules conflict with one another, for example different versions of the same software. You might have to unload one module first to load a different one.<br />
<br />
=== PBS: ===<br />
<br />
The other important system you need to understand in order to work on raijin is the scheduler PBS. This is the system for running software on dedicated nodes inside raijin. Basically, a user tells PBS that they want to run this job on this many CPUs with these resources for at least so long, and PBS places it in a queue, and when the required resources are available, it will assign this job to them.<br />
<br />
Again, NCI has a very good documentation about how to run this [https://opus.nci.org.au/display/Help/Job+Submission+and+Scheduling here]<br />
<br />
The most important commands are:<br />
<br />
{|<br />
|-<br />
| qsub<br />
| Submit a job to the queue<br />
|-<br />
| qstat<br/> nqstat<br />
| Display the status of the queued jobs<br />
|-<br />
| qdel<br />
| Remove a job from the queue<br />
|}<br />
<br />
Of these, qsub is the most important, and there are so many parameters that we won’t tell them all here.<br />
<br />
In general, the fewer resources you request, the earlier your job will run. But if your program exceeds the requested resources at any time, PBS will kill the job, and you have to start over.<br />
<br />
More specifically:<br />
<br />
*<span style="line-height: 1.5;">Raijin is comprised of nodes with 16 CPUs each. If you request less than 16 CPUs, you will get the number of CPUs that you request. If you request more, you will get as many nodes as you need. So it is usually a good idea for jobs with more than 16 CPUs to use a multiple of 16 CPUs.</span> <br />
*Nodes come with between 32GB and 126GB of memory to share within the 16 CPUs. So if your job requires 16 or more CPUs, you might as well request just under 32GB per node, for example 95GB for a 48-cpu job. <br />
*If you request more than 32GB per 16 CPUs, your job will possibly have to wait longer for enough high-memory nodes to become available.<br />
<br />
= Step 4: How to run models =<br />
<br />
A lot of information to gain access to models or run the models can be found on the ARCCSS CMS wiki (see link at the end).<br />
<br />
A very important message from the CMS team: <span style="background-color: #fdf988; display: block; text-align: center;">Often you will work with source code. Please ensure that your version of the source code is under version control! We use SVN and git (usually hosted on github) for the model codes and smaller utilities.</span><span style="background-color: #fdf988; display: block; text-align: center;">'''DO NOT JUST COPY SOURCE CODE! CHECK IT OUT, OR CHECK IT IN!'''</span><br />
<br />
== UM ==<br />
<br />
The Unified model is currently transitioning from the old user environment umui to the new rose/cylc user interface. Either way, you need to log into accessdev.nci.org.au.<br />
<br />
=== umui(x) ===<br />
<br />
The old user interface has to be used for versions up to 7.x, and can be used for 8.x. umui was developed by the UM, umuix is very similar, but more convenient developed by CSIRO. An introduction into its use is on our wiki: [http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI http://climate-cms.unsw.wikispaces.net/Introduction+to+UMUI]<br />
<br />
=== rose/cylc ===<br />
<br />
The new user interface can be used from version 8.x, and has to be used for versions 9.0 and later.<br />
<br />
== WRF ==<br />
<br />
The CMS team ports the WRF model on Raijin. The latest versions can be found under /projects/WRF on Raijin. From WRF v3.6.0 onwards, the WRF codes under /projects are managed under Git. Information on using the model is on the CMS wiki. Users should also be aware that we do not reproduce the information from the [http://www2.mmm.ucar.edu/wrf/users/ WRF model users website] which stays a very important resource for all users. In particular, every new user is strongly encouraged to run through the official tutorials (found under User Support on the WRF model users site).<br />
<br />
== CABLE ==<br />
<br />
CABLE is under licence so you need to request access to the code. All the information you need to get access and use CABLE is on the [https://trac.nci.org.au/trac/cable CABLE trac site]<br />
<br />
= Data management =<br />
<br />
Most of the information on how the data is managed is stored in this wiki in the [[Data|Data Services]] page. Here you can find information on the datasets managed by the Center as well the relevant policies in regard to data. Take some time to get familiar with it, here are some suggestions:<br />
<br />
#Read the Center data policy and how to prepare a [[Data_Management_Plan|data management plan]]. You can use the [https://clex.dmponline.cloud.edu.au/ ARCCSS DMPonline tool] to do this. Because this tool stores your plan into a database, you can save it and access it as many times as you want, which means you can build your data management plan as you progress with your research. It is good though to start as soon as you can, DMPonline is structured as to teach about data practices and the resources available to you, it also informs the CMS team on which data, software and/or infrastructure you are planning to use, so we can better tailor our efforts to your needs. <br />
#Get familiar with [[Data_publishing_guidelines|publishing requirements]], while this might seem faraway, it is a good idea to keep track from now of what you are doing in regard to data and metadata, as it is often much more difficult to retrieve this information at the end of your project. There are also some technical times involved in getting data properly published. <br />
#Consider creating a [[Researcher-ID|researcher-ID]] to uniquely identify your work. <br />
#Make sure you browse through all the available data sources before you download data, probably even better send us an e-mail to the climate_help to make sure you are not wasting time downloading something which might be already available, or that we could download and manage for you <br />
#Become familiar with the different filesystems available on any server you are using, make sure you know which are meant to be working spaces, where you can archive your data, how to share data with collaborators and best practices to transfer data within and out of the system. If you are using raijin on NCI you can find this information on their [http://nci.org.au/nci-systems/national-facility/data-storage/filesystems/ user support ]and training sections. <br />
#You can explore a lot of data related information in the [http://ands.org.au Australian National Data Services] website <br />
#Don't hesitate in contacting climate_help for any question you might have, or also e-mail directly paola.petrelli@utas.edu.au, if you have a more general question or you are confused about data management. We are always available to discuss with you the details of your project and give you advice.<br />
<br />
= How to learn more =<br />
<br />
== General setup: ==<br />
<br />
a blog post by a UNSW's PhD student on a few things to know and learn: [http://web.maths.unsw.edu.au/~oangelil/blog/blog2/page_blog2.html Oliver Angélil's post]<br />
<br />
== CMS: ==<br />
<br />
this [[Home|wiki]]<br />
<br />
== NCI: ==<br />
<br />
[https://opus.nci.org.au/display/Help/NCI+Help Guides and reference pages]<br />
<br />
[http://nci.org.au/services-support/training/ Training material] and [https://training.nci.org.au/ this]<br />
<br />
== Version Control with git: ==<br />
<br />
(Note: git might also be very useful for your thesis!) [https://www.youtube.com/playlist?list=PLg7s6cbtAD165JTRsXh8ofwRw0PqUnkVH Git video tutorial by GitHub]<br />
<br />
== Data management: ==<br />
<br />
[[Data_induction|Data induction]]<br />
<br />
= Getting help =<br />
<br />
Your first port of call for help should be the CMS team via the help-desk: [mailto:cws_help@nci.org.au cws_help@nci.org.au]. This help desk is followed by all the members of the CMS team and by some staff from NCI.</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEX_projects_at_NCI&diff=1476CLEX projects at NCI2019-11-28T03:15:58Z<p>D.eisenberg: </p>
<hr />
<div>The projects are:<br />
{| <br />
! Project code !! Research Program (RP) !! Lead CI <br />
|-<br />
| v45 || Extra-tropical variability || Andy Hogg <br />
|-<br />
| w35 || Drought || Claire Carouge <br />
|-<br />
| w40 || Extreme Rainfall || Todd Lane <br />
|-<br />
| w42 || Extreme Rainfall || Steven Sherwood <br />
|-<br />
| w48 || Tropical Variability || Dietmar Dommenget <br />
|-<br />
| w97 || Heatwaves || Jason Evans <br />
|-<br />
|}<br />
===Which project to join if part of several RPs=== <br />
We recommend people join all relevant projects but choose one project to work from. This will help people to collaborate with researchers from all the RPs they are part of.<br />
<br />
<br />
<br />
=== Setup default project on Gadi ===<br />
<br />
*Check your default project. Connect to Gadi. Then type: <br />
<br />
&nbsp;<br />
<syntaxhighlight lang="unknown"><br />
echo $PROJECT<br />
</syntaxhighlight><br />
<br />
*Change your default project. If the output from the previous step is not what you want, you need to open the ~/.config&nbsp;file in a text editor. Change the project ID in this file then save and close the file. EXIT your login session (and all others you may have currently open) and log in back. Your default project should have changed (check as in step 1). <br />
<br />
[[Category:Admin]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=CLEX_projects_at_NCI&diff=1475CLEX projects at NCI2019-11-28T03:15:37Z<p>D.eisenberg: Changed Raijin to Gadi.</p>
<hr />
<div>The projects are:<br />
{| <br />
! Project code !! Research Program (RP) !! Lead CI <br />
|-<br />
| v45 || Extra-tropical variability || Andy Hogg <br />
|-<br />
| w35 || Drought || Claire Carouge <br />
|-<br />
| w40 || Extreme Rainfall || Todd Lane <br />
|-<br />
| w42 || Extreme Rainfall || Steven Sherwood <br />
|-<br />
| w48 || Tropical Variability || Dietmar Dommenget <br />
|-<br />
| w97 || Heatwaves || Jason Evans <br />
|-<br />
|}<br />
===Which project to join if part of several RPs=== <br />
We recommend people join all relevant projects but choose one project to work from. This will help people to collaborate with researchers from all the RPs they are part of.<br />
<br />
<br />
=== Setup default project on Gadi ===<br />
<br />
*Check your default project. Connect to raijin. Then type: <br />
<br />
&nbsp;<br />
<syntaxhighlight lang="unknown"><br />
echo $PROJECT<br />
</syntaxhighlight><br />
<br />
*Change your default project. If the output from the previous step is not what you want, you need to open the ~/.config&nbsp;file in a text editor. Change the project ID in this file then save and close the file. EXIT your login session (and all others you may have currently open) and log in back. Your default project should have changed (check as in step 1). <br />
<br />
[[Category:Admin]]</div>D.eisenberghttp://climate-cms.wikis.unsw.edu.au/index.php?title=Category:Rose&diff=989Category:Rose2019-04-01T21:24:53Z<p>D.eisenberg: Created page with "&nbsp;"</p>
<hr />
<div>&nbsp;</div>D.eisenberg