climate-cms wikis.unsw.edu.au - User contributions [en]

YOTC

2019-02-20T03:46:33Z

Admin:

==YOTC - Year of Tropical Convection==

The Year of Tropical Convection is a joint project of the WWRP-THORPEX and the WCRP that combines high resolution analysis and forecast data with satellite data and a 
[http://tropicalcyclone.jpl.nasa.gov/hurricane/index.jsp | Tropical Cyclone Satellite Information System].
YOTC is a Year of coordinated observing, modeling and forecasting of organized tropical convection and its influences on predictability as a contribution to the United Nations Year of Planet Earth to complement the International Polar Year (IPY). This effort is intended to exploit the vast amounts of existing and emerging observations, the expanding computational resources and the development of new, high-resolution modeling frameworks, with the objective of advancing the characterization, diagnosis, modeling, parameterization and prediction of multi-scale convective/dynamic interactions, including the two-way interaction between tropical and extra-tropical weather/climate*.

The CMS is managing a replica of the re-analysis data produced by ECMWF on the NCI RDSI disk storage which is mounted on raijin (raijin.nf.nci.org.au)
We copied across the pressure levels analysis data at the highest available resolution 0.125X0.125 degrees, the original format is grib and
the data is momentarily located on fast access disk in the following directories
/g/data/rq7/YOTC/grib/oper_an_pl/<variable>/<year>
The data has been converted to netcdf to facilitate its use, the netcdf files are stored under
/g/data/rq7/YOTC/netcdf/oper_an_pl/<variable>/<year>/
{|
| Variable || || File || || Converted to netcdf
|-
| Divergence || || D || || Y
|-
| Geopotential || || Z || || Y
|-
| Ozone mass mixing ratio || || O3 || || Y
|-
| Potential vorticity || || PV || || Y
|-
| Relative humidity || || R || || Y
|-
| Specific humidity || || Q || || Y
|-
| Temperature || || T || || Y
|-
| U component of wind || || U || || Y
|-
| V component of wind || || V || || Y
|-
| Vertical velocity || || W || || Y
|-
| Vorticity (relative) || || VO || || Y
|-
|}
To access the data you need to register with ECMWF to accept their [http://apps.ecmwf.int/datasets/data/yotc_od/licence/ | terms and conditions of use] and then request access to rq7 by using your NCI account to access [https://my.nci.org.au/ | My NCI portal] or e-mail [[mailto:climate_help@nf.nci.org.au | NCI climate_help]] if you need any help.
For more information on the original ECMWF collection: [http://www.ecmwf.int/en/forecasts/datasets/year-tropical-convection-yotc | YOTC page on ECMWF website]

For more information about this project and to access the satellite data visit the [http://www.ucar.edu/yotc/data.html | YOTC project webpage].

GES-DISC developed a web-based data analysis tool to support coordinated observing, modeling, and forecasting, focusing on organized tropical convection.
For more information on the YOTC-Giovanni tool go to 
[[http://disc.sci.gsfc.nasa.gov/gesNews/new-goddard-giovanni-tools-for-supporting-year-of-tropical-convection-yotc]].

====='''Conversion to netcdf'''=====

To facilitate the use of this dataset, we converted the grib files to netcdf, we have recently upgraded our conversion routine, to produce compressed netcdf4 files.
We use cdo for the conversion itself and nco to enhance the metadata. Details of the procedure are described below.
{{#iDisplay:https://docs.google.com/document/d/19NeYTF-nO8GKDffFHGlWhaRPWd12ZbMI1nvmPf4jRAM/pub?embedded=true|1200|1500}}

* extract from http://www.ucar.edu/yotc/about.html

MERRA2

2019-02-20T03:39:24Z

Admin:

The Modern Era Retrospective-Analysis for Research and Applications (MERRA) is a NASA reanalysis integrating satellite observations using a major new version of the Goddard Earth Observing System Data Assimilation System Version 5 (GEOS-5).
MERRA focuses on historical analyses of the hydrological cycle on a broad range of weather and climate time scales covering the modern satellite era from 1979 to present.
The state-of-the-art GEOS-5 data assimilation system includes many modern observing systems (such as EOS) in a climate framework Specifically, the GEOS-DAS Version 5 implements Incremental Analysis Updates (IAU) to slowly adjust the model states toward the observed state.

MERRA-2 is produced with the GMAO/GEOS-5 Data Assimilation System Version 5.12.4 and its native resolution is 0.5° x 0.625° x 72 hybrid sigma/pressure levels. Hourly data intervals are used for two-dimensional products, while 3-hourly intervals are used for three-dimensional products. These may be on the model’s native 72-layer vertical grid or at 42 pressure surfaces extending to 0.1 hPa.
MERRA-2 spans from 1979 to present (with about 5 months lag).

The 42 pressure levels are: 1000, 975, 950, 925, 900, 875, 850, 825, 800, 775, 750, 725, 700, 650, 600, 550, 500, 450, 400, 350, 300, 250, 200, 150,100, 70, 50, 40, 30, 20,10, 7, 5, 4, 3, 2, 1,0.7, 0.5, 0.4, 0.3, 0.1 hPa
The 72 native grid levels are:

Information retrieved from [https://climatedataguide.ucar.edu/climate-data/nasa-merra | NCAR climate re-analysis guide] and
[http://wiki.seas.harvard.edu/geos-chem/index.php/MERRA-2 | GEOS-CHEM MERRA-2 wiki]. The data was downloaded from the [https://disc.sci.gsfc.nasa.gov/information/glossary/581b59c65fa71421a68e64fa/merra-2?tags=mission | GES DISC data store] where
information on all the MERRA-2 products is available.

==='''License and Acknowledgements'''===
Access to GES DISC data requires all users to be registered with the Earthdata Login system, even if we downloaded the data for you you should register. It is important for the data providers to have an estimate of users to justify the work that goes with providing the data services.
Complete terms of use and information on how to sign up are available on the [https://wiki.earthdata.nasa.gov/display/EL/Earthdata+Login+Overview+and+Policy%2C+v1.2 | GEOS-DISC data policy webpage] .
Example of citation including the DOI, each product has its own (see below).
Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 inst6_3d_ana_Np: 3d,6-Hourly,Instantaneous,Pressure-Level,Analysis,Analyzed Meteorological Fields V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/A7S6XP56VZWS
==='''MERRA-2 on raijin'''===

We are hosting a copy of some of the MERRA-2 products on raijin in new "Global Observations and Re-analysis Datasets" group rr7, in collaboration with CAWCR.
The data is available in /g/data1/rr7/MERRA2/raw/<MERRA-product>/<year>/<files>
Filenames are <runid>.<collection>.<timestamp>.nc4

Last update on 24th of October 2016: updated to September 2016 included.

We started with the following products, that will be regularly updated:
* '''tavg1_2d_rad_Nx'''
** MERRA 2D,1-hourly,time-averaged,single-level,assimilation,radiation diagnostics
** /M2T1NXRAD.5.12.4/yyyy/mm/MERRA2_100.tavg1_2d_rad_Nx.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 1 hourly
** doi: 10.5067/Q9QMY5PBNV1T
** file size: 209 Mb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 tavg1_2d_rad_Nx: 2d,1-Hourly,Time-Averaged,Single-Level,Assimilation,Radiation Diagnostics V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/Q9QMY5PBNV1T
* '''tavg1_2d_flx_Nx'''
** MERRA2 2D 1-hourly,time-averaged,single-level,assimilation,surface flux diagnostics
** /M2T1NXFLX.5.12.4/yyyy/mm/MERRA2_100.tavg1_2d_flx_Nx.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 1 hourly
** doi: 10.5067/7MCPBJ41Y0K6
** file size: 380 Mb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 tavg1_2d_flx_Nx: 2d,1-Hourly,Time-Averaged,Single-Level,Assimilation,Surface Flux Diagnostics V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/7MCPBJ41Y0K6
* '''tavg1_2d_int_Nx'''
** MERRA 2D ,1-hourly,time-averaged,single-level,assimilation,vertically integrated diagnostics
** /M2T1NXINT.5.12.4/yyyy/mm/MERRA2_100.tavg1_2d_int_Nx.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 1 hourly
** doi: 10.5067/Q5GVUVUIVGO7
** file size: 1.3 Gb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 tavg1_2d_int_Nx: 2d,1-Hourly,Time-Averaged,Single-Level,Assimilation,Vertically Integrated Diagnostics V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/Q5GVUVUIVGO7
* '''inst6d_3d_ana_Np'''
** MERRA 3D,6-hourly,instantaneous,pressure-level,analysis,analyzed meteorological fields
** /M2I1NPANA.5.12.4/yyyy/mm/MERRA2_100.inst6_3d_ana_Np.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 6 hourly Levels: 42
** doi: 10.5067/A7S6XP56VZWS
** file size: 511 Mb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 inst6_3d_ana_Np: 3d,6-Hourly,Instantaneous,Pressure-Level,Analysis,Analyzed Meteorological Fields V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/A7S6XP56VZWS
* '''tavg1_2d_slv_Nx'''
** MERRA 2D,1-hourly,Time-Averaged,Single-Level,Assimilation,Single-Level Diagnostics
** /M2T1NXSLV.5.12.4/yyyy/mm/MERRA2_100.tavg1_2d_slv_Nx.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 1 hourly
** doi: 10.5067/VJAFPLI1CSIV
** file size: 400 Mb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 tavg1_2d_slv_Nx: 2d,1-Hourly,Time-Averaged,Single-Level,Assimilation,Single-Level Diagnostics V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/VJAFPLI1CSIV
* '''inst3d_3d_asm_Np'''
** MERRA 3D,3-hourly,Instantaneous,Pressure-Level,Assimilation,Assimilated Meteorological Fields
** /M2I3NPASM.5.12.4/yyyy/mm/MERRA2_100.inst3_3d_asm_Np.yyyymmdd.nc4
** resolution: lat/lon - 0.5 /0.625 degrees Timestep: 3 hourly Levels: 42
** doi: 10.5067/QBZ6MG944HW0
** file size: 1.2 Gb
** citation: Global Modeling and Assimilation Office (GMAO)(2015), MERRA-2 inst3_3d_asm_Np: 3d,3-Hourly,Instantaneous,Pressure-Level,Assimilation,Assimilated Meteorological Fields V5.12.4, Greenbelt, MD, USA, Goddard Earth Sciences Data and Information Services Center (GES DISC), Accessed [Data Access Date] 10.5067/QBZ6MG944HW0
>>
* '''List of variables available for each product'''
{{#iDisplay:https://docs.google.com/spreadsheets/d/1rkCZegrJoY5fJV50uxXlb3AsywcvzJKEk56ZVigpQ_U/pubhtml?widget=true&headers=false|1000|500}}

GA7 Performance

2019-02-20T03:33:08Z

Admin:

The following charts show the performance of the UM running GA7 at various processor decomposition, to help you decide the best tradeoff between walltime and SU cost

While increasing the number of CPUs in a run will speed it up, as you add more CPUs the model becomes more inefficient - more time gets spent by the CPUs communicating instead of computing.

This data was calculated from a number of 10 model day runs. Real run times will also be affected by writing output, and time spent in the queue can increase the walltime spent waiting for the model to complete considerably (changing the restart length / walltime to different values may improve this)

Changing the science settings can also improve the model performance - for example for longer runs you might consider using the `EasyAerosol` scheme instead of the default aerosols.

=Recommended settings=

We recommend for general GA 7 runs running on Raijin's Broadwell nodes the following settings:

{|
| Description || Config Setting || Value || Comment
|-
| Restart length || RESUB || P4Y || 4 model years
|-
| Walltime || CLOCK || '24:00:00' || 24 hours
|-
| X Decomposition || PE_ATM_NPROCX || 34
|-
| Y Decomposition || PE_ATM_NPROCY || 28
|-
| OpenMP Threads || OMPTHR_ATM || 1
|-
|}

This will run 4 model years in approximately 18 wall hours, and cost 21 kSU

To conserve SU, a decomposition of 18 x 28 will run 4 model years in 24 hours and cost 15 kSU

To speed up the model (at the expense of SU cost) it is important to enable OpenMP threads, by setting OMPTHR_ATM to 2, otherwise the model becomes very inefficient at CPU counts above 1000 (the total CPU count is NPROCX * NPROCY * OMPTHR)

=Performance by CPU count=

NCI recommend starting out choosing a decomposition setting by minimising the value (walltime x SU cost), which can be seen below for UM versions 10.6 and 11.0

{{#iDisplay:https://docs.google.com/spreadsheets/d/e/2PACX-1vRTqfedW7WxkTeam0WehVmNouUd5R9N6Ho0lHGPii_CdnD9joiL7vxZG3QQ_9m6TH8ks-ucS3XXxp5d/pubchart?oid=1569957188&format=interactive|861.1859838274931|532.5}}

{{#iDisplay:https://docs.google.com/spreadsheets/d/e/2PACX-1vRTqfedW7WxkTeam0WehVmNouUd5R9N6Ho0lHGPii_CdnD9joiL7vxZG3QQ_9m6TH8ks-ucS3XXxp5d/pubchart?oid=82600298&format=interactive|853.5|527.7475}}

{{#iDisplay:https://docs.google.com/spreadsheets/d/e/2PACX-1vRTqfedW7WxkTeam0WehVmNouUd5R9N6Ho0lHGPii_CdnD9joiL7vxZG3QQ_9m6TH8ks-ucS3XXxp5d/pubchart?oid=819705058&format=interactive|847.5|524.0375}}

[[include component="page" wikiName="climate-cms" page="Index UM" editable="1"]]
[[Category:UM]]

ERA Interim current status

2019-02-20T03:25:01Z

Admin:

==='''Current status of ERA-Interim grib download and conversion to netcdf on dcc'''===

Last updated on 06/01/2014

Data available on ECMWF data server: from 01/1979 to 10/2013

{{#iDisplay:https://docs.google.com/spreadsheet/pub?key=0AlKncyYETiZqdGxnVFZBMkJuNllYY1pfYmN0X0RsU3c&single=true&gid=0&output=html&widget=true|1200|450}}

**Lists of variables available for each dataset'''
{{#iDisplay:https://docs.google.com/spreadsheet/pub?key=0AlKncyYETiZqdGIyOVdUOGlZbklxM3d2Q2I3T0xjYkE&single=true&gid=0&output=html&widget=true|1200|350}}

{|
|||!! '''oper_an_sfc --> Operational Analysis at Surface'''
|-
|~ original grib !! !! variable name !! !! netcdf !! !! original grib !! !! variable name !! !! netcdf
|-
| || || Temperature of snow layer [K] || ||= || || || || Sea-ice cover [(0 - 1)] || ||
|-
| || || Soil temperature level 4 [K] || ||= || || || || Total cloud cover [(0 - 1)] || ||
|-
| || || Skin temperature [K] || ||= x || || || || Mean sea level pressure [Pa] || || x
|-
| || || Logarithm of surface roughness length for heat [] || ||= || || || || Charnock [] || ||
|-
| || || Total column ozone [kg m'''-2]''' || ||= || || || || Snow depth [m of water equivalent] || ||
|-
| || || Skin reservoir content [m of water] || ||= || || || || Soil temperature level 1 [K] || ||
|-
| || || High cloud cover [(0 - 1)] || ||= || || || || Total column water vapour [kg m-2] || || x
|-
| || || Medium cloud cover [(0 - 1)] || ||= || || || || Total column water [kg m'''-2]''' || || x
|-
| || || Low cloud cover [(0 - 1)] || ||= || || || || Surface pressure [Pa] || || x
|-
| || || Soil temperature level 3 [K] || ||= || || || || Volumetric soil water layer 4 100-255 cm [m3 m'''-3]''' || ||
|-
| || || Albedo [(0 - 1)] || ||= || || || || Volumetric soil water layer 3 28-100 cm [m3 m'''-3]''' || ||
|-
| || || Surface roughness [m] || || || || || || Volumetric soil water layer 2 7-28 cm [m3 m'''-3]''' || ||
|-
| || || Soil temperature level 2 [K] || || || || || || Volumetric soil water layer 1 0-7 cm [m3 m'''-3]''' || ||
|-
| || || 2 metre dewpoint temperature [K] || || x || || || || Ice surface temperature layer 4100-255 cm [K] || ||
|-
| || || 2 metre temperature [K] || || x || || || || Ice surface temperature layer 328-100 cm [K] || ||
|-
| || || 10 metre V wind component [m s-1] || || x || || || || Ice surface temperature layer 17-28 cm [K] || ||
|-
| || || 10 metre U wind component [m s'''-1]''' || || x || || || || Ice surface temperature layer 10-7 cm [K] || ||
|-
| || || Snow density [kg m-3] || || || || || || Sea surface temperature [K] || || x
|-
| || || Snow albedo [(0 - 1)] || || || || || || || ||
|-
|}

ERA Interim current status

2019-02-20T03:23:07Z

Admin:

==='''Current status of ERA-Interim grib download and conversion to netcdf on dcc'''===

Last updated on 06/01/2014

Data available on ECMWF data server: from 01/1979 to 10/2013

{{#iDisplay:1200|450|https://docs.google.com/spreadsheet/pub?key=0AlKncyYETiZqdGxnVFZBMkJuNllYY1pfYmN0X0RsU3c&single=true&gid=0&output=html&widget=true}}

**Lists of variables available for each dataset'''
{{#iDisplay:1200|350|https://docs.google.com/spreadsheet/pub?key=0AlKncyYETiZqdGIyOVdUOGlZbklxM3d2Q2I3T0xjYkE&single=true&gid=0&output=html&widget=true}}
{|
|||!! '''oper_an_sfc --> Operational Analysis at Surface'''
|-
|~ original grib !! !! variable name !! !! netcdf !! !! original grib !! !! variable name !! !! netcdf
|-
| || || Temperature of snow layer [K] || ||= || || || || Sea-ice cover [(0 - 1)] || ||
|-
| || || Soil temperature level 4 [K] || ||= || || || || Total cloud cover [(0 - 1)] || ||
|-
| || || Skin temperature [K] || ||= x || || || || Mean sea level pressure [Pa] || || x
|-
| || || Logarithm of surface roughness length for heat [] || ||= || || || || Charnock [] || ||
|-
| || || Total column ozone [kg m'''-2]''' || ||= || || || || Snow depth [m of water equivalent] || ||
|-
| || || Skin reservoir content [m of water] || ||= || || || || Soil temperature level 1 [K] || ||
|-
| || || High cloud cover [(0 - 1)] || ||= || || || || Total column water vapour [kg m-2] || || x
|-
| || || Medium cloud cover [(0 - 1)] || ||= || || || || Total column water [kg m'''-2]''' || || x
|-
| || || Low cloud cover [(0 - 1)] || ||= || || || || Surface pressure [Pa] || || x
|-
| || || Soil temperature level 3 [K] || ||= || || || || Volumetric soil water layer 4 100-255 cm [m3 m'''-3]''' || ||
|-
| || || Albedo [(0 - 1)] || ||= || || || || Volumetric soil water layer 3 28-100 cm [m3 m'''-3]''' || ||
|-
| || || Surface roughness [m] || || || || || || Volumetric soil water layer 2 7-28 cm [m3 m'''-3]''' || ||
|-
| || || Soil temperature level 2 [K] || || || || || || Volumetric soil water layer 1 0-7 cm [m3 m'''-3]''' || ||
|-
| || || 2 metre dewpoint temperature [K] || || x || || || || Ice surface temperature layer 4100-255 cm [K] || ||
|-
| || || 2 metre temperature [K] || || x || || || || Ice surface temperature layer 328-100 cm [K] || ||
|-
| || || 10 metre V wind component [m s-1] || || x || || || || Ice surface temperature layer 17-28 cm [K] || ||
|-
| || || 10 metre U wind component [m s'''-1]''' || || x || || || || Ice surface temperature layer 10-7 cm [K] || ||
|-
| || || Snow density [kg m-3] || || || || || || Sea surface temperature [K] || || x
|-
| || || Snow albedo [(0 - 1)] || || || || || || || ||
|-
|}

Data Management Plan

2019-02-20T03:18:58Z

Admin:

{{#iDisplay:https://docs.google.com/document/d/1dyWlyvGeWRnO6MXqN2OdwVO4V4lXnxDxwsI_kAK5V7A/pub?embedded=true|1200|1500}}

Some tips about research papers that can be applied to DMP too:

...Pitfalls include using complicated jargon, including unnecessary details, and writing for your highly specialized colleagues instead of a wider audience. ...

Only abbreviations firmly established in the field are eligible, … avoiding those which are not broadly used ...

… when looking for keywords, avoid words with a broad meaning and words already included in the title.

… you need to include detailed information so a knowledgeable reader can reproduce the experiment. However, do not repeat the details of established methods; use References and Supporting Materials to indicate the previously published procedures.

… indicate uses and extensions if appropriate. Moreover, you can suggest future experiments and point out those that are underway ...

Effective research articles are interesting and useful to a broad audience, including scientists in other fields.

use standard systems … conventions

CMIP5 current state

2019-02-14T13:04:52Z

Admin:

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MediaWiki:Sidebar

2019-02-04T04:45:37Z

Admin:

MediaWiki:Sidebar

2019-02-04T04:45:10Z

Admin:

Um-errors

2019-02-03T06:18:52Z

Admin: Reverted edits by Admin (talk) to last revision by Hwolff

=Typical UM Errors=

''Note: This page is still a stub. Please add to this page.''

==Errors during Extract==

When compiling the UM, the first step is for the UMUI(x) to extract the source code. If an error occurs, check for these things:

Step 1: Did the error occur during the base, model, or reconfiguration extraction?
Step 2: Check for the extraction log, it is either in
<syntaxhighlight>
~/UM_OUTPUT/<JOBID>/<umbase or ummodel or umrecon>/ext.out
</syntaxhighlight>
or
<syntaxhighlight>
/scratch/users/$USER/<JOBID>/<umbase or ummodel or umrecon>/ext.out
</syntaxhighlight>

The final lines typically show at which command the error occurred.

===SVN errors===

If you get a permission denied error from an SVN, it might be because svn needed your password, and didn't get it. The solution is to run

<syntaxhighlight>
$ svn ls https://access-svn.nci.org.au/svn/um/branches/
</syntaxhighlight>

If you get asked for a password, you need to supply your NCI password. And then it will ask you whether it should store it in plain text.
As much as I hate to say it: you need to answer 'yes'.

And immediately afterwards, you have to run the command:

<syntaxhighlight>
$ chmod -R go-rwx $HOME/.subversion
</syntaxhighlight>

===SCP and RSYNC errors===

If you get an error like this:

<syntaxhighlight>
mkdir: cannot create directory `/abc123': Permission denied
</syntaxhighlight>

(where abc123 is your username), the most likely explanation is that you haven't set the DATAOUTPUT environment variable on accessdev.
If you are using bash, add this line to your $HOME/.bashrc file:

<syntaxhighlight>
export DATAOUTPUT=/short/${PROJECT}/${USER}/UM_ROUTDIR
</syntaxhighlight>

If you are using tcsh or csh, add this line to your $HOME/.login

<syntaxhighlight>
setenv DATAOUTPUT /short/${PROJECT}/${USER}/UM_ROUTDIR
</syntaxhighlight>

Then log out of accessdev and log back in, open up umuix again, and check whether the error went away.

==Errors during Submit==

==Errors during Compile==

==Errors during Run==

===REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH===

The model is trying to update an ancillary field, but it is looking for a date that is past the end of the ancillary file. For instance, say an ancillary file is valid for dates between 1850-01-01 and 2001-01-01 and the model is trying to update fields for the date 2001-02-01. The model can't find this data in the file, so it crashes.

Near the end of the .leave file there will be a block that looks like

<syntaxhighlight>
STASH code in dataset 122 STASH code requested
58
'Start' position of lookup tables for dataset in overall lookup array
481
122 58 39
UP_ANCIL : Error in REPLANCA.

''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: UP_ANCIL
Error code: 239
Error message:
REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

The important bit here is ''''STASH code requested'''', which is in this case was 58. Internally the UM refers to each model field (U, V, temperature, etc.) by a numeric STASH code. You can check field is represented by a code by going to [[https://accessdev.nci.org.au/umdocs/7.3/stash_browse]]. The STASH codes are divided into different sections, for errors like this you'll find the variable in section '''0) Prognostic Variables'''. Scroll down the item list to find the name for the error code - the code 58 corresponds to SULPHUR DIOXIDE EMISSIONS.

To find out which file this corresponds to you'll need to go back to the UMUI, and check the screen 'Atmosphere -> Ancillary and Input data files -> Climatologies'. It should be fairly simple to work out the entry to use (in our example you'd look at 'Sulphur-Cycle Emissions') but if you have trouble check with the helpdesk. You'll need to replace the file here with one that covers the next part of your model run.

Its common for this error to occur when running an AMIP-type simulation and going past 2001, where the data changes from Historical to the RCP scenarios. If this is the case you'll need to change Ozone (files starting with SPARCO3), 2d Sulphur Cycle (sulp) Soot (BC_hi), Biomass (Bio), and OCFF (OCFF). You can find ancillary files for the different scenarios under /projects/access/data/ancil/CMIP5, or ask the CMS team at [[mailto:climate_help@nf.nci.org.au | climate_help@nf.nci.org.au]] and we'll help you locate the right ancillary file.

===INANCILA: Insufficient space for LOOKUP headers===

This section is currently tested. Ask Holger if you still see this message after 1/6/2018.

Error message is something along these lines:

<syntaxhighlight>
Field: 128 OCFFEMIS
Opening Anc File: /projects/access/data/ancil/CMIP5/OCFF_RCP85_1850_2100.N96
No room in LOOKUP table for Ancillary File 47
INANCCTL: Error return from INANCILA 14
INANCILA: Insufficient space for LOOKUP headers

Failure in call to INANCCTL
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: INITIAL
Error code: 14
Error message:
INANCILA: Insufficient space for LOOKUP headers
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

The UM needs an initial guess on how big the ancillary files are. It needs to reserve a little bit of memory for every level at every time step of every field. This number can be set at

Model Selection -> Atmosphere -> Ancillary and input data files -> In file related options >> Header record sizes.

===DRLANDF1 : Error in FILE_OPEN===

Symptom: The UM aborts with the error message:
<syntaxhighlight>
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: UM_SHELL
Error code: 1
Error message:
DRLANDF1 : Error in FILE_OPEN.
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

This indicates that the start dump (NRUN) or restart dump (CRUN) could not be opened. Search the leave file for the string "Unit 21". You should find a line like this:

<syntaxhighlight>
OPEN: File <somefile> to be Opened on Unit 21 does not Exist
</syntaxhighlight>

<somefile>}} might be empty, in which case there will be 2 spaces between "{{File}}" and "{{to be Opened".
Otherwise, check that the file exists and that you have read permissions.

If this happens during an NRUN, check the settings in
**Model Selection''' -> '''Atmosphere''' -> '''Ancillary and input data files''' --> '''Start dump'''
Check the settings under "Specify initial dump"

If the file name is an empty string, and you are running a CRUN, open
**Model Selection''' -> '''Atmosphere''' -> '''Control''' -> '''Post processing, Dumping & Meaning''' --> '''Dumping and meaning'''
and ensure that the restart dump frequency is consistent with your per-submission run length.
(That is, if your run length is 1 year, you may have monthly or yearly restart dumps, but not 5-yearly restart dumps.)

===Unable to WGDOS pack to this accuracy===

Symptom: The UM aborts with the error message:
<syntaxhighlight>
????????????????????????????????????????????????????????????????????????????????
???!!!???!!!???!!!???!!!???!!! ERROR ???!!!???!!!???!!!???!!!???!!!
? Error code: 2
? Error from routine: COEX (cmps_all)
? Error message: Unable to WGDOS pack to this accuracy
? Error from processor: 0
? Error number: 85
????????????????????????????????????????????????????????????????????????????????
</syntaxhighlight>

There has been an error compressing one of the output files. Check the model output streams and 'Dumping and Meaning' sections, setting the 'packing profile' to 0 to turn off compression.

Um-errors

2019-02-03T06:17:33Z

Admin:

=Typical UM Errors=

''Note: This page is still a stub. Please add to this page.''

==Errors during Extract==

When compiling the UM, the first step is for the UMUI(x) to extract the source code. If an error occurs, check for these things:

Step 1: Did the error occur during the base, model, or reconfiguration extraction?
Step 2: Check for the extraction log, it is either in
<syntaxhighlight>
~/UM_OUTPUT/<JOBID>/<umbase or ummodel or umrecon>/ext.out
</syntaxhighlight>
or
<syntaxhighlight>
/scratch/users/$USER/<JOBID>/<umbase or ummodel or umrecon>/ext.out
</syntaxhighlight>

The final lines typically show at which command the error occurred.

===SVN errors===

If you get a permission denied error from an SVN, it might be because svn needed your password, and didn't get it. The solution is to run

<syntaxhighlight>
$ svn ls https://access-svn.nci.org.au/svn/um/branches/
</syntaxhighlight>

If you get asked for a password, you need to supply your NCI password. And then it will ask you whether it should store it in plain text.
As much as I hate to say it: you need to answer 'yes'.

And immediately afterwards, you have to run the command:

<syntaxhighlight>
$ chmod -R go-rwx $HOME/.subversion
</syntaxhighlight>

===SCP and RSYNC errors===

If you get an error like this:

<syntaxhighlight>
mkdir: cannot create directory `/abc123': Permission denied
</syntaxhighlight>

(where abc123 is your username), the most likely explanation is that you haven't set the DATAOUTPUT environment variable on accessdev.
If you are using bash, add this line to your $HOME/.bashrc file:

<syntaxhighlight>
export DATAOUTPUT=/short/${PROJECT}/${USER}/UM_ROUTDIR
</syntaxhighlight>

If you are using tcsh or csh, add this line to your $HOME/.login

<syntaxhighlight>
setenv DATAOUTPUT /short/${PROJECT}/${USER}/UM_ROUTDIR
</syntaxhighlight>

Then log out of accessdev and log back in, open up umuix again, and check whether the error went away.

==Errors during Submit==

==Errors during Compile==

==Errors during Run==

===REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH===

The model is trying to update an ancillary field, but it is looking for a date that is past the end of the ancillary file. For instance, say an ancillary file is valid for dates between 1850-01-01 and 2001-01-01 and the model is trying to update fields for the date 2001-02-01. The model can't find this data in the file, so it crashes.

Near the end of the .leave file there will be a block that looks like

<syntaxhighlight>
STASH code in dataset 122 STASH code requested
58
'Start' position of lookup tables for dataset in overall lookup array
481
122 58 39
UP_ANCIL : Error in REPLANCA.

''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: UP_ANCIL
Error code: 239
Error message:
REPLANCA: PP HEADERS ON ANCILLARY FILE DO NOT MATCH
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

The important bit here is ''''STASH code requested'''', which is in this case was 58. Internally the UM refers to each model field (U, V, temperature, etc.) by a numeric STASH code. You can check field is represented by a code by going to [[https://accessdev.nci.org.au/umdocs/7.3/stash_browse]]. The STASH codes are divided into different sections, for errors like this you'll find the variable in section '''0) Prognostic Variables'''. Scroll down the item list to find the name for the error code - the code 58 corresponds to SULPHUR DIOXIDE EMISSIONS.

To find out which file this corresponds to you'll need to go back to the UMUI, and check the screen 'Atmosphere -> Ancillary and Input data files -> Climatologies'. It should be fairly simple to work out the entry to use (in our example you'd look at 'Sulphur-Cycle Emissions') but if you have trouble check with the helpdesk. You'll need to replace the file here with one that covers the next part of your model run.

Its common for this error to occur when running an AMIP-type simulation and going past 2001, where the data changes from Historical to the RCP scenarios. If this is the case you'll need to change Ozone (files starting with SPARCO3), 2d Sulphur Cycle (sulp) Soot (BC_hi), Biomass (Bio), and OCFF (OCFF). You can find ancillary files for the different scenarios under /projects/access/data/ancil/CMIP5, or ask the CMS team at [[mailto:climate_help@nf.nci.org.au | climate_help@nf.nci.org.au]] and we'll help you locate the right ancillary file.

===INANCILA: Insufficient space for LOOKUP headers===

This section is currently tested. Ask Holger if you still see this message after 1/6/2018.

Error message is something along these lines:

<syntaxhighlight>
Field: 128 OCFFEMIS
Opening Anc File: /projects/access/data/ancil/CMIP5/OCFF_RCP85_1850_2100.N96
No room in LOOKUP table for Ancillary File 47
INANCCTL: Error return from INANCILA 14
INANCILA: Insufficient space for LOOKUP headers

Failure in call to INANCCTL
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: INITIAL
Error code: 14
Error message:
INANCILA: Insufficient space for LOOKUP headers
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

The UM needs an initial guess on how big the ancillary files are. It needs to reserve a little bit of memory for every level at every time step of every field. This number can be set at

Model Selection -> Atmosphere -> Ancillary and input data files -> In file related options >> Header record sizes.

===DRLANDF1 : Error in FILE_OPEN===

Symptom: The UM aborts with the error message:
<syntaxhighlight>
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
UM ERROR (Model aborting) :
Routine generating error: UM_SHELL
Error code: 1
Error message:
DRLANDF1 : Error in FILE_OPEN.
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''*
</syntaxhighlight>

This indicates that the start dump (NRUN) or restart dump (CRUN) could not be opened. Search the leave file for the string "Unit 21". You should find a line like this:

<syntaxhighlight>
OPEN: File <somefile> to be Opened on Unit 21 does not Exist
</syntaxhighlight>

<somefile>}} might be empty, in which case there will be 2 spaces between "{{File}}" and "{{to be Opened".
Otherwise, check that the file exists and that you have read permissions.

If this happens during an NRUN, check the settings in
**Model Selection''' -> '''Atmosphere''' -> '''Ancillary and input data files''' --> '''Start dump'''
Check the settings under "Specify initial dump"

If the file name is an empty string, and you are running a CRUN, open
**Model Selection''' -> '''Atmosphere''' -> '''Control''' -> '''Post processing, Dumping & Meaning''' --> '''Dumping and meaning'''
and ensure that the restart dump frequency is consistent with your per-submission run length.
(That is, if your run length is 1 year, you may have monthly or yearly restart dumps, but not 5-yearly restart dumps.)

===Unable to WGDOS pack to this accuracy===

Symptom: The UM aborts with the error message:
[code]
????????????????????????????????????????????????????????????????????????????????
???!!!???!!!???!!!???!!!???!!! ERROR ???!!!???!!!???!!!???!!!???!!!
? Error code: 2
? Error from routine: COEX (cmps_all)
? Error message: Unable to WGDOS pack to this accuracy
? Error from processor: 0
? Error number: 85
????????????????????????????????????????????????????????????????????????????????
[/code]

There has been an error compressing one of the output files. Check the model output streams and 'Dumping and Meaning' sections, setting the 'packing profile' to 0 to turn off compression.

MediaWiki:Sidebar

2019-02-03T06:06:22Z

Admin:

MediaWiki:Sidebar

2019-01-31T12:02:48Z

Admin: