Minutes of the code management group meeting 2018-02-21

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Code management group minutes

Teleconference Details

Wednesday 21st February 2018, 10am - 12noon BST

  • UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
  • Participant PIN: 632944

Present

Met Office: John Hemmings (JH), Mohit Dalvi (MD, Fiona O’Connor (FOC), Marc Stringer (MS), Alan Hewitt (AH)

Cambridge: Luke Abraham (LA), Scott Archer-Nicolls (SAN)

Leeds: Graham Mann (GM), Mark Richardson (MR), Chris Dearden (CD)

Reading: Nicolas Bellouin (NB)

Lancaster: Michael Hollaway (MH)

Edinburgh:

UEA:

NIWA:

CSIRO:

Apologies: Oliver Wild, Ashok Luhar, Olaf Morgenstern, Fraser Dennison, Marcus Koehler, Matt Woodhouse

Not present:

Actions from this meeting

One off actions

  1. (ongoing) GM find best person to check 8.4 versus 7.3 (and possibly vn8.4 vs 10.x) GLOMAP-mode code and report any missing bug fixes on the bugfix page.
  2. (new) LA to follow-up with GM in 2 weeks time to progress this.
  3. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below.
  4. (ongoing) LA to open tickets for all changes that still require a ticket.
  5. (ongoing) FOC to open ticket + Bugfixes Table entry related to 'Unable to calculate tropopause' warnings, which will also address print statements.
  6. (new) FOC to open ticket to add flexibility to use the s30 tropopause.
  7. (ongoing) FOC to recommend at next Exec meeting a policy of allowing only CMG to (certify and) distribute any UKCA configurations for science purpose.
  8. (ongoing) LA (& others who are interested) to look into how to re-organise the UKCA panel (e.g. into sub-panels) & think about removal of namelist items.
  9. (ongoing) LA to organise a follow-up meeting of interested parties on the UKCA panel re-organisation.
  10. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details.
  11. (ongoing) JM to continue discussions with CJ regarding "Wet oxidation of SO2 in GLOMAP" and other issues regarding redundant code. GM to be kept informed.
  12. (ongoing) AH to scope out reducing repetition of mode definitions in GLOMAP.
  13. (new) FOC to upload workplan.
  14. (ongoing) LA and MD to talk offline about releases.
  15. (new) FOC to check with AS about best practice when science changes break KGO.
  16. (new) MD to correct column-call rose-stem tests when pressure-level age-of-air diagnostic bugfix is lodged.
  17. (new) LA to comment code regarding wet deposition of ozone inconsistencies.
  18. (new) LA to update open bugs table.
  19. (new) LA to re-jig tables as short-term and long-term plans.
  20. (new) MD/LA to set up free-running and nudged GA7.1+StratTrop TS2000ish timeslice, with instructions to make it transient.
  21. (new) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
  22. (new) LA to set up doodle-poll for the 2nd/3rd week of June, avoiding various meetings going on then.

Standing actions

  1. (ongoing - standing item) CMG to monitor list of bugs and circulate between group for owners.
  2. (ongoing - standing item) At CMG future meetings there should be included an appendix listing the open bugs. If a ticket is included it is not an open bug (as the owner of ticket is person doing lodging).
  3. (ongoing - standing item) ALL with access to keep monitoring ukca_bugs email list.
  4. (ongoing - standing item) ALL to think about if code changes will change KGO and let systems team know in good time, and remember to include the UKCA & SC0138 keywords to all UKCA tickets. This should be a standard part of our working practice. Note also the required keywords.
  5. (ongoing - standing item) ALL to note, review, and remove obsolete/redundant code
  6. (ongoing - standing item) ALL closed ticket owners to produce a summary of their change for the UKCA newsletter
  7. (ongoing - standing item) Code Owner to produce draft newsletter for CMG to approve.

Minutes

Actions from the Last Meeting (LA)

Minutes of the code management group meeting 2017-10-19

One off actions

  1. (ongoing) GM to check 8.4 versus 7.3 (and possibly vn8.4 vs 10.x) GLOMAP-mode code and report any missing bug fixes on the bugfix page.
    Action: GM to find best person to do this task.
    Action: LA to follow-up with GM in 2 weeks time to progress this.
  2. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below.
    Ongoing
  3. (ongoing) LA to open tickets for all changes that still require a ticket.
    Ongoing
  4. (ongoing) FOC to open ticket + Bugfixes Table entry related to 'Unable to calculate tropopause' warnings.
    There is already a ticket open, which will also incorporate managing print statements.
    Action: FOC to open ticket to add flexibility to use the s30 tropopause.
  5. (ongoing) FOC to recommend at next Exec meeting a policy of allowing only CMG to (certify and) distribute any UKCA configurations for science purpose.
    Ongoing
  6. (ongoing) LA (& others who are interested) to look into how to re-organise the UKCA panel (e.g. into sub-panels) & think about removal of namelist items.
    Ongoing
  7. (ongoing) LA to organise a follow-up meeting of interested parties on the UKCA panel re-organisation.
    Ongoing
  8. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details.
    Ongoing
  9. (ongoing) JM to continue discussions with CJ regarding "Wet oxidation of SO2 in GLOMAP" and other issues regarding redundant code.
    Ongoing
    GM asks to be kept informed about this.
  10. (ongoing) AH to scope out reducing repetition of mode definitions in GLOMAP.
    Ongoing
  11. (ongoing) MD to set up TS2000 nudged jobs at vn10.8.
    Closed
    Redundant now. A nudged version of the release job will be required.
  12. (ongoing) LA to add UKCA wiki page on using UKCA on the Virtual Machine.
    Closed
  13. (new) LA to embolden all ALL actions in future meetings
    Closed
  14. (new) FOC to arrange meeting between FOC, MR, MS, LA (& others who are interested) to sit down and decide a plan to move forward with OpenMP work, before new person starts.
    Closed
    Action: FOC to upload workplan
  15. (new) LA to update Redundant code tables with above information
    Closed (see new action below)
    Be careful regarding GLOMAP routines - see Item 1
  16. (new) LA and MD to talk offline about releases.
    Ongoing
  17. (new) LA to look into recording lectures at January 2018 training
    Closed
  18. (new) LA to set-up doodle poll for sometime between 9th-28th February 2018.
    Closed

Standing actions

  1. (ongoing - standing item) CMG to monitor list of bugs and circulate between group for owners.
  2. (ongoing - standing item) At CMG future meetings there should be included an appendix listing the open bugs. If a ticket is included it is not an open bug (as the owner of ticket is person doing lodging).
  3. (ongoing - standing item) ALL with access to keep monitoring ukca_bugs email list.
  4. (ongoing - standing item) ALL to think about if code changes will change KGO and let systems team know in good time, and remember to include the UKCA & SC0138 keywords to all UKCA tickets. This should be a standard part of our working practice. Note also the required keywords.
  5. (ongoing - standing item) ALL to note, review, and remove obsolete/redundant code
  6. (ongoing - standing item) ALL closed ticket owners to produce a summary of their change for the UKCA newsletter
  7. (ongoing - standing item) Code Owner to produce draft newsletter for CMG to approve.

Bugs/Bugfixes (LA)

Open Bugs

# Description Ticket Owner Status/ Updates Comments from previous meeting Comments from this meeting
31 FP exceptions in asad_sparse_vars
or asad_spimjmp
#368 (MOSRS) Nick Savage leave open Close as not seen in a long time. However, it should be noted that this is a bit of a difficult routine that caused some issues with compiler flag changes, for example.
35 Error in labelling: Surface resistance <--> stomatal resistance ? MOSRS #1409 Fiona O'Connor leave open Leave open for planned JULES work.
57 Incorrect logic for DMS anciliaries required #756 (MOSRS) Nick Savage Possibly close: JM to check impact LA/SAN to contact JM
72 UKCA Dry Deposition: Surface resistance values
not set for some species
#1250 AlanJHewitt leave open AH investigating best way forward and will speak with JM. Some concern regarding breaking UKESM1 KGO. See action.
74 Bug in ukca_tropopause with definition of PV tropopause #1283 Steven Hardiman leave open Change ownership to FOC. Extend scope for print statements.
75 Bug in STE fluxes #1367 Fiona O'Connor leave open. still not sure what is going on Believed to be ENDGAME related. Will investigate following the release of UKESM1
87 Possible issues with YSTORE in UKCA_CHEMISTRY_CTL. UM#3245 Colin Johnson/
Luke Abraham
leave open LA to talk to CJ offline.
92 UMDP084 incorrectly labels 38-476 ("Liquid cloud fraction") with units "m-3". It is a pure fraction (in the range 0.0 to 1.0) and so has no unit. AH to take ownership.
93 Inconsistent surface resistance values for organic hydro-peroxide (rooh) UM#3793 AlanJHewitt ??? AH to take ownership and talk to GF
94 Data corruption in Age-of-Air (and possibly Passive O3) diagnostic on pressure levels UM#3718 Mohit Dalvi Found to be a halo issue in STASHmaster_A. Hope to close soon. Will also correct column-call rose-stem tests.
95 wet/dry deposition flags for ozone are not consistent AlanJHewitt ??? Close

Action: FOC to check with AS about best practice when science changes break KGO.

Action: MD to correct column-call rose-stem tests when pressure-level age-of-air diagnostic bugfix is lodged.

Action: LA to comment code regarding wet deposition of ozone inconsistencies.

Action: LA to update open bugs table.

Redundant Code (LA)

Code for deletion

# Description Ticket Remarks Status Owner Comments from this meeting
2 Old dry deposition scheme #2356 None PROPOSED Nick Savage Leave as-is
4 ukca_strat_update.F90 - relax_ozone #1505 None PROPOSED Nick Savage LA to take ownership
5 Backward Euler Standard Tropospheric Chemistry #1507 None PROPOSED Nick Savage FOC to take ownership
6 Wet oxidation of SO2 in GLOMAP None None PROPOSED Colin Johnson CJ/JM to discuss with GM
7 Updraft velocity #3668 Proposed in December 2017 PROPOSED Alan J Hewitt AH to investigate further
8 All backward Euler chemistry schemes None None PROPOSED Luke Abraham Note that this is only for the “hard-coded” BE schemes. Quite a lot of work would be involved, but good as a longer-term aim. Note problems for AQUM would need to be addressed first.

Depreciated code for future retirement

# Description Ticket Remarks Status Owner Comments from this meeting
1 Deprecated UKCA netcdf attribute options #2513 'emission_type', string type attributes no longer recommeneded. Need some time for most new code to adopt these DEPRECATED Nick Savage Not yet due to AQUM files
2 Deprecated calculation of updraft velocity #3668 'l_conv_tke', logical recommended true DEPRECATED Alan J Hewitt Remove as a duplicate of 7 above.

Action: LA to re-jig tables as short-term and long-term plans.

Note that GLOMAP changes should be discussed with Leeds.

UKCA Release Job (LA/MD)

Note that there are some differences in JULES between UKESM1 and GA7.1, notably in the number of surface types and whether or not this supports iBVOC emissions.

Decision: Free-running and nudged GA7.1+StratTrop TS2000ish timeslice, with instructions to make it transient.

Action: MD/LA to set this up.

Action: LA to create Wiki page on UKCA website for users to add details of configurations and input files.

Note that this page will need to be maintained by the users rather than centrally.

Highlights from vn11.0 (LA)

  • (LA) #3384: More rose-stem tests added (still in code review), including:
    • Column-call StratTrop with processor decomposition tests
    • GA7/GA-dev tests using NR solver with offline oxidants with processor decomposition tests when -S INTEGRATION_TESTING=true
    • Improvements to VM tests to remove dependency on MPI_TASKS and with processor decomposition tests when -S INTEGRATION_TESTING=true
  • (MS) OpenMP is added to all the main parts of UKCA which previously didn't have it, see #3185, #3450, #3501 and #3506 (still in code review)
  • (MS) Fix N-R offline oxidant configuration (it is broken at UM10.9 without this branch), see #3606
  • (AH FOC MS) #3109: Higher optimisation flags for UKCA (in code review).

Targets for vn11.1 (and beyond) (LA)

PLEASE REMEMBER TO INCLUDE THE KEYWORDS: UKCA & SC0138

Tickets targeting vn11.1

# Description
#100 PM10 and PM2.5 diagnostics for MODE
#1250 UKCA dry deposition: surface resistance values not set for some species
#2689 Enable coupling of GLOMAP-MODE Aerosol to FAST-JX photolysis.
#2741 Addition of new diagnostic for the dry deposition flux of nitrogen
#2742 Addition of new diagnostic for the wet deposition flux of nitrogen
#2814 Allow UKCA Chemistry to work with aerosol climatologies
#2898 Input CO2 concentrations into UKCA when interactive CO2 is operational
#3028 Improve STASH section references related to UKCA components.
#3127 Investigate KGO differences in um_n48_ukca_eg app using GNU on the Cray
#3289 Removal of Backward Euler Std tropospheric chemistry
#3290 Removal of old dry deposition scheme using prescribed deposition velocities
#3292 Consolidate constant variables used by UKCA
#3367 Removing transport of peroxy radical tracers in Strattrop (CHeST)
#3547 Improve UKCA Lightning NOx scheme
#3718 Investigate issues with AGE-OF-AIR ON PRESSURE LEVELS (51-150)
#3726 rose stem testing for Section 54 - Activate
#3765 Continue to add functionality to use NetCDF GLOMAP-mode climatology fields to generate fields required by ACTIVATE
#3769 Time updating for glomap climatology
#3779 Improvements to the inline comments in ukca_option_mod
#3793 Consistant value of rooh for different number of tiles within ukca_surfddr

rose-stem tests (LA/AH)

When running rose-stem --group=ukca at the Met Office this runs (from vn11.0):

meto_xc40_aqum_eg  
meto_xc40_aqum_eg_glomap 
meto_xc40_aqum_eg_iau  
meto_xc40_aqum_eg_comp_check 
meto_xc40_aqum_eg_glomap_comp_check 
meto_xc40_ukca_eg_strattrop 
meto_xc40_ukca_eg_strattrop_columns 
meto_xc40_ukca_nudged  
meto_xc40_n96_orca025_mct_proto_ukesm 
meto_xc40_n48_ukca_eg_omp_noios_gnu (in developer)
meto_xc40_n48_ukca_eg_omp_noios_gnu_comp_check 
meto_xc40_n48_ukca_eg_noomp_gnu 
meto_xc40_n48_ga7_amip_2day_nrchem 
meto_xc40_n48_ga_amip_exp_2day_nrchem 
meto_linux_aqum_eg 
meto_linux_aqum_eg_glomap 
meto_linux_aqum_eg_noomp 
meto_linux_aqum_eg_glomap_noomp 
meto_xc40_n48_ga7_amip_2day (in developer)
meto_xc40_n48_ga7_amip_naming 
meto_xc40_n48_ga7_amip_2day_comp_check 
meto_xc40_n48_ga7_amip_10day 
meto_xc40_n48_ga7_amip_30day 
meto_linux_n48_ga7_amip_12hr (in developer)
meto_linux_n48_ga7_amip_12hr_comp_check (in developer)
meto_linux_n48_ga7_amip_naming 

Note that the developer tests are no longer run with the ukca group.

Processor decomposition tests are now included for ukca and GA7/GA-exp NR offline oxidants (when running with -S INTEGRATION_TESTING=true)

UKCA Training (LA)

AOB/DNM (LA)

Date of next meeting (LA)

The code review submission deadline for vn11.1 is 1st Jun 2018. This is an open release for most types of code changes.

Action: LA to set up for the 2nd/3rd week of June, avoiding various meetings going on then.