Difference between pages "Restarting an Atmos-Ocean Integration" and "Bugfixes"

From UKCA
(Difference between pages)
 
(→‎RADAER update: add new cat)
 
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This page covers bug and bugfixes found in various UKCA branches or jobs. This page will be updated whenever a new bug/bugfix is found.
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== Restarting an Atmosphere Ocean Integration ==
  
   
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If you have any concerns, please contact [[User:Nla27 | Luke Abraham]]. If you think that you have found a bug, please report it to him, or alternatively you can add it to the [[Talk:Bugfixes | bugfix talk page]] (or click on the ''discussion'' link above).
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UKCA is running in the QESM-AO configuration, which includes the NEMO ocean and CICE sea-ice models, using the ORCA2 grid. While restarting an atmospheric-only model has been described [[UKCA_Release_Jobs#Running_a_Perpetual_Year | elsewhere on this site]], restarting both NEMO and CICE add extra complications. The following description is for MONSooN, although the equivalent steps would need to be done on HECToR also.
  
   
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=Compiler Bugs and Bugfixes=
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'''NOTE:''' These instructions are designed to describe how to restart an already running QESM-AO job (as a new job).
  
   
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=== 1. Pick your restart date ===
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===Cray compiler on HECToR XE6===
   
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Please also see advice from [http://cms.ncas.ac.uk/index.php/component/content/1583?task=view NCAS-CMS].
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You will need to check the date in your UM dump, and select the NEMO and CICE dumps accordingly, e.g.:
  
   
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To allow the VN7.3_UKCA_CheM branch to compile, please include the following compiler file over-ride:
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* UM dump is <code>xfxfha.dac5510</code>, model date is 2285/05/01:00 / 44790.000000 - i.e. midnight on the first day of the month.
  
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* The corresponding NEMO restart files are in fact <code>xfxfho_22850430_restart_0000.nc, xfxfho_22850430_restart_0001.nc, </code>and <code>xfxfho_22850430_restart_0002.nc</code>, when running the ocean over 3 processors - i.e. NEMO dumps are midnight on the 30th (last day) of the month.
  
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* The corresponding CICE restart file is <code>xfxfhi.restart.2285-05-01-00000</code> - i.e. midnight on the first day of the month, the same as the UM.
  
   
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/home/ukca/comp_overides/hector_cce_7.3_asad_chem_diags
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=== 2. UM restart ===
  
   
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=Code Bugs and Bugfixes=
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* Copy your selected UM dump (e.g. <code>xfxfha.dac5510</code>) above to another directory. You may already have a <code>STARTDUMPS</code> directory defined in the UMUI, and may wish to copy it there.
  
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* Go to '''Start dump''': <br/> Model Selection -> Atmosphere -> Ancillary and input data files -> Start Dump <br/> ''You will need to alter the directory path and name of file to point to the start-dump you are interested in. You must then turn '''off''' the radio button '''Using the reconfiguation''' and make sure that the '''start-date''' (listed at the top of this panel) matches that in the dump file.''
  
   
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===Corrections to VN7.3_UKCA_CheM branch===
   
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'''The latest revision number is 9278.'''
   
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There have been four bugfixes to this branch, one correcting output units (revision 5887), one correcting conversion factors in any StratChem jobs (revision 6356), one correcting a bug win wet-deposition (revision 6791), and one fixing the <code>ukca_transform_halogen</code> routine (revision 9278) which affected the Total N tracer in Stratospheric Chemistry jobs. This also requires an update to the initialisation of this Total N tracer (tracer 4, 34004) - see [[Bugfixes#Total_N_tracer_initial_condition | below]].
   
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===Scenario script on PUMA===
   
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This script is located at <code>/home/ukca/bin/scenario</code>.
   
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This was giving incorrect values for CFC-11, CFC-12, and Methyl Bromide (CH3Br), the numbers being too high. This bug has been corrected as of 2011/10/18, but you should double-check your input scripts.
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== Useful Links ==
  
   
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=UMUI Bugs and Bugfixes=
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* [http://puma.nerc.ac.uk/trac/NEMOCICE PUMA NEMO/CICE page (login required)]
  
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==UMUI Panel Settings==
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===Total N tracer initial condition===
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The initial condition for the Total N tracer needs to be updated along with the fcm revision of the VN7.3_UKCA_CheM branch listed [[Bugfixes#Corrections_to_VN7.3_UKCA_CheM_branch | above]]. This file is in the same directory as the previous initial condition file, and is called <code>CheS_init_NOy.anc</code>. The UKCA UMUI jobs have been updated accordingly.
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===Lightning Emissions===
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Some jobs may be having issues with lightning NOx emissions. This will not affect all jobs, only those that take the section 0 prognostic cloud base height and cloud top height, rather than the section 5 diagnostic values (this can be checked in <code>ukca_setd1defs.F90</code> or in the UKCA STASH hand-edit). If you need the section 0 prognostics, please make sure following is set:
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Model Selection -->
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Atmosphere -->
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Scientific Parameters and Sections -->
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Section by section choices -->
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Section 5: Convection -->
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Continue (follow on window) -->
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"Apply time decay of convective clouds" = 0
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If this is not the case these two fields will be empty and there will be no lightning NOx produced by UKCA. This bug does not affect the VN7.3_UKCA_CheM branch, which uses section 5 diagnostics.
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==UMUI Hand-Edits==
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===RADAER update===
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There is an issue with the following hand-edits on PUMA:
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/home/ukca/hand_edits/VN7.3/std/radaer_indir1_on_l38.ed
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/home/ukca/hand_edits/VN7.3/std/radaer_indir1_on_l38_HECToR.ed
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/home/ukca/hand_edits/VN7.3/std/ukca_mode_cdnc_l38.ed
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The line
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&USE NAME="UPUKCA", LOCN=6
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should have been set to
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&USE NAME="UPUKCA", LOCN=1
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which has now been done. However, if a personal copy of this hand-edit has been taken, it will also need to be corrected. If you have not taken a copy of this hand-edit the correction will be applied the next time your job is processed.
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[[Category:Support]]

Revision as of 10:08, 7 September 2012

This page covers bug and bugfixes found in various UKCA branches or jobs. This page will be updated whenever a new bug/bugfix is found.

If you have any concerns, please contact Luke Abraham. If you think that you have found a bug, please report it to him, or alternatively you can add it to the bugfix talk page (or click on the discussion link above).

Compiler Bugs and Bugfixes

Cray compiler on HECToR XE6

Please also see advice from NCAS-CMS.

To allow the VN7.3_UKCA_CheM branch to compile, please include the following compiler file over-ride: 

/home/ukca/comp_overides/hector_cce_7.3_asad_chem_diags

Code Bugs and Bugfixes

Corrections to VN7.3_UKCA_CheM branch

The latest revision number is 9278.

There have been four bugfixes to this branch, one correcting output units (revision 5887), one correcting conversion factors in any StratChem jobs (revision 6356), one correcting a bug win wet-deposition (revision 6791), and one fixing the ukca_transform_halogen routine (revision 9278) which affected the Total N tracer in Stratospheric Chemistry jobs. This also requires an update to the initialisation of this Total N tracer (tracer 4, 34004) - see below.

Scenario script on PUMA

This script is located at /home/ukca/bin/scenario.

This was giving incorrect values for CFC-11, CFC-12, and Methyl Bromide (CH3Br), the numbers being too high. This bug has been corrected as of 2011/10/18, but you should double-check your input scripts.

UMUI Bugs and Bugfixes

UMUI Panel Settings

Total N tracer initial condition

The initial condition for the Total N tracer needs to be updated along with the fcm revision of the VN7.3_UKCA_CheM branch listed above. This file is in the same directory as the previous initial condition file, and is called CheS_init_NOy.anc. The UKCA UMUI jobs have been updated accordingly.

Lightning Emissions

Some jobs may be having issues with lightning NOx emissions. This will not affect all jobs, only those that take the section 0 prognostic cloud base height and cloud top height, rather than the section 5 diagnostic values (this can be checked in ukca_setd1defs.F90 or in the UKCA STASH hand-edit). If you need the section 0 prognostics, please make sure following is set: 

  Model Selection --> 
    Atmosphere -->
      Scientific Parameters and Sections -->
        Section by section choices -->
          Section 5: Convection -->
            Continue (follow on window) -->
              "Apply time decay of convective clouds" = 0

If this is not the case these two fields will be empty and there will be no lightning NOx produced by UKCA. This bug does not affect the VN7.3_UKCA_CheM branch, which uses section 5 diagnostics.

UMUI Hand-Edits

RADAER update

There is an issue with the following hand-edits on PUMA: 

 /home/ukca/hand_edits/VN7.3/std/radaer_indir1_on_l38.ed
 /home/ukca/hand_edits/VN7.3/std/radaer_indir1_on_l38_HECToR.ed
 /home/ukca/hand_edits/VN7.3/std/ukca_mode_cdnc_l38.ed

The line 

  &USE NAME="UPUKCA", LOCN=6

should have been set to 

 &USE NAME="UPUKCA", LOCN=1

which has now been done. However, if a personal copy of this hand-edit has been taken, it will also need to be corrected. If you have not taken a copy of this hand-edit the correction will be applied the next time your job is processed.

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