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

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Code management group minutes

Teleconference Details

Thursday 19th October 2017, 10am - 12noon BST

  • UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
  • Participant passcode: 146205

Present

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

Cambridge: Luke Abraham (LA), James Keeble (JK)

Leeds: Mark Richardson (MR)

Reading:

Lancaster: Michael Hollaway (MH)

Edinburgh:

UEA: Marcus Koehler (MK)

NIWA: Olaf Morgenstern (OM), Fraser Dennison (FD)

CSIRO:

Apologies: Oliver Wild (OW), Nicolas Bellouin (NB), Ashok Luhar (AL), Paul Griffiths (PG)

Not present: Graham Mann (GM), Scott Archer-Nicolls (SAN)

Actions from this meeting

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.
  2. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below.
  3. (ongoing) LA to open tickets for all changes that still require a ticket.
  4. (ongoing) FOC to open ticket + Bugfixes Table entry related to 'Unable to calculate tropopause' warnings.
  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.
  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.
  7. (ongoing) LA to organise a follow-up meeting of interested parties on the UKCA panel re-organisation.
  8. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details.
  9. (ongoing) JM to continue discussions with CJ regarding "Wet oxidation of SO2 in GLOMAP" and other issues regarding redundant code.
  10. (ongoing) AH to scope out reducing repetition of mode definitions in GLOMAP.
  11. (ongoing) MD to set up TS2000 nudged jobs at vn10.8.
  12. (ongoing) LA to add UKCA wiki page on using UKCA on the Virtual Machine.
  13. (new) LA to embolden all ALL actions in future meetings
  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.
  15. (new) LA to update Redundant code tables with above information
  16. (new) LA and MD to talk offline about releases.
  17. (new) LA to look into recording lectures at January 2018 training
  18. (new) LA to set-up doodle poll for sometime between 9th-28th February 2018.

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.
  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 2017-07-14

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. ongoing
  2. (ongoing) FOC to incorporate Bug #35 and others into dry deposition work. FOC to draft document that will cover what the new deposition scheme will do. close but leave in bugfixes table
  3. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below. ongoing - partially done
  4. (new) ALL to check through this table and comment on whether the tickets needs to be ported or not. Deadline 2017-07-28. closed
  5. (new) LA to open tickets for all changes that still require a ticket. ongoing
  6. (ongoing) JM,BJ,NB to discuss incorporation of Nicolas' RADAER description into UKCA (or separate UMDP). JM to take lead. closed
  7. (ongoing) FOC to open ticket + Bugfixes Table entry related to 'Unable to calculate tropopause' warnings. ongoing
  8. (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
  9. (new) LA (& others who are interested) to look into how to re-organise the UKCA panel (e.g. into sub-panels). ongoing - it may be possible to incorporate this into removal of namelist items.
  10. (new) LA to organise a follow-up meeting of interested parties on the UKCA panel re-organisation. ongoing
  11. (new) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM. ongoing. Ticket is open, MD to circulate.
  12. (new) LA to add comments on rafeps into #368. closed
  13. (new) FOC to close #2358 (Delete 2D photolysis scheme in UKCA). closed
  14. (new) MD to take ownership of #142 (Remove old emissions system from UKCA). closed and lodged
  15. (new) FOC to take ownership of #2356 (Delete older dry deposition scheme in UKCA). closed
  16. (new) FOC to take ownership of #1507 (Remove Backward Euler Standard Tropospheric Chemistry). closed
  17. (new) AH to take ownership of #2373 (quick method for calculating wet volume redundant). closed and lodged
  18. (new) LA to take ownership of #1505 (Clean up ukca_strat_update). closed and see below
  19. (new) JM to clarify with CJ regarding "Wet oxidation of SO2 in GLOMAP". ongoing: CJ raised some issues. JM to have follow-on discussions regarding redundant code.
  20. (new) ALL to note code which is redundant. closed and move to standing item. new action: LA to embolden all ALL actions in future meetings.
  21. (new) AH to scope out reducing repetition of mode definitions in GLOMAP. ongoing
  22. (new) OM to work on the chemistry scheme code restructuring for vn10.8. closed and lodged
  23. (new) LA to update Bugs table following discussion, closing tickets where appropriate. closed
  24. (new) FOC to send LA RAQ testing jobs information. closed
  25. (new) MD to set up TS2000 free-running nudged jobs at vn10.8. closed for free-running, ongoing for nudged.
  26. (new) LA to add UKCA wiki page on using UKCA on the Virtual Machine. ongoing
  27. (new) LA to create a doodle poll for October after the date of the vn10.9 code freeze. closed
  28. (new) MS to add bug in offline oxidants to bugfixes table.

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).
    It was suggested starting a newsletter, tied to each MetUM release.
    new action: LA to collate list of users and produce draft newletter targetting vn11.0 release. CMG will approve prior to it being sent out.
    new standing action: ALL ticket owners to produce a summary for the newsletter.
  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. This should be a standard part of our working practice.
  5. (ongoing - standing item) ALL to review and remove obsolete code

Redundant Code (LA for NS)

Redundant code

Code Proposed for Deletion

# Description Ticket Remarks Status Owner
1 Old emissions code (that which uses ancil files) #142 None Completed Mohit Dalvi
2 Old dry deposition scheme #2356 None PROPOSED Fiona O'Connor
3 ukca_volume_mode.F90 - quick method for calculating wet volume is not used since iwvolmethod is hard coded to equal 2. #2373 None Complete Alan J Hewitt
4 2D photolysis #2358 None Do not remove code Fiona O'Connor
5 ukca_strat_update.F90 - relax_ozone #1505 None PROPOSED Luke Abraham
6 Backward Euler Standard Tropospheric Chemistry #1507 None PROPOSED Fiona O'Connor
7 Wet oxidation of SO2 in GLOMAP None None PROPOSED Colin Johnson
  • Question: Should ALL schemes using the backward Euler solver be proposed for redundancy?

It was agreed that this should be a long-term aim, targeting offline-oxidants first. OpenMP work will proceed around the column-call to ASAD to speed this up and make it competitive.

MS has OpenMP code that has not been lodged, for Fast-JX and current ukca_chemistry_ctl routine (using lat/lon slice in the call to ASAD).

new action: 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.

new action: LA to update Redundant code tables with above information

Depreciated Code

# Description Ticket Remarks Status Owner
1 Deprecated UKCA netcdf attribute options #2513 'emission_type', string type attributes no longer recomeneded. Need some time for most new code to adopt these DEPRECATED Alistair Sellar

This code should not be removed for legacy reasons.

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 vn10.x seems to be better leave open leave open
35 Error in labelling: Surface resistance <--> stomatal resistance ? MOSRS #1409 Fiona O'Connor folded into DD work leave open & see above leave open
57 Incorrect logic for DMS anciliaries required #756 (MOSRS) Nick Savage trivial. Might close as wontfix, but might want to do in RAQ leave open possibly close: JM to check impact
72 UKCA Dry Deposition: Surface resistance values
not set for some species
#1250 Alan Hewitt? leave open but there is a way forward leave open
74 Bug in ukca_tropopause with definition of PV tropopause #1283 Steven Hardiman Change ownership? Fix is separate from #75 leave open. FOC did try to lodge, but breaks KGO. Simple fix but with big changes. leave open
75 Bug in STE fluxes #1367 Fiona O'Connor could be endgame leave open. even with fix, these are still wrong leave open still not sure what is going on
87 Possible issues with YSTORE in UKCA_CHEMISTRY_CTL. UM#3245 Colin Johnson/
Luke Abraham
leave open leave open
88 Potential FastJX Scattering Bug UM#3261 David Wade/
Luke Abraham
In code review for vn10.9 leave open
FOC to send LA RAQ jobs information
close when ticket is closed
90 Extremely high/low NOy concentrations UM#3400
UKESM:#469
Mohit Dalvi/
Luke Abraham
In code review for vn10.9 close when ticket is closed

new action: MS to add bug in offline oxidants to bugfixes table.

Strategy for next UKCA Release Job (LA/MD)

MD has a free running TS2000 job, and is adding a nudging job. However, many users are requesting an AMIP job. While aerosol emissions are transient, chemical emissions are decadal means. It was noted that um:#3400 could be used as a potential AMIP base-job, but is still using climatological emissions. CMIP6 time-varying emissions still some weeks away.

new action: LA and MD to talk offline about releases.

Highlights from vn10.9 (LA)

PLEASE REMEMBER TO INCLUDE THE KEYWORDS: UKCA & SC0138

vn10.9 UKCA tickets
UMPB September 2017 Highlight Report

  • Removal of old emissions system #142
  • Correct NaCl density using temporary logical #2405
  • Solar-cycle in photolysis #2587
  • Make number of aerosol components flexible #2788
  • AQUM fixes for ammonium nitrate #2986 & #3174
  • Improvements to compiler settings #3109
  • Column-call for NR solver #3209
  • FastJX bugfix #3261
  • Fixes to rose-stem #3267
  • Re-organisation of NR chemistry listings #3326
  • Fix NAt PSC sedimentation #3400 (see below)

"Highlight": NOy events

See um:#3400 and UKESM:#469.

A big thank-you goes out to all who were involved with tracking this down and fixing it.

Targets for vn11.0 (and beyond) (LA)

  • Update from CSIRO: We have almost finalised the oceanic ozone dry deposition parameterisation work and at some point will need some guidance as to if and when this can be incorporated into the Trunk. See point 2 from the last meeting.

Tickets currently targeted for UM11.0 in Trac

Ticket Summary Owner Comments from this meeting
#100 PM10 and PM2.5 diagnostics for MODE johnhemmings
#1250 UKCA dry deposition: surface resistance values not set for some species alanjhewitt
#1703 Update appropriate UMDPs with regard UKCA-mode aerosol and interactions janemulcahy
#2086 Time updating for glomap climatology alanjhewitt
#2134 UKCA-GLOMAP Nx1 PE set-up does not bit-compare with others mohitdalvi
#2532 Review of option codes associated with UKCA burden diagnostics when running with BE solver fionaoconnor
#2689 Enable coupling of GLOMAP-MODE Aerosol to FAST-JX photolysis. michaelhollaway
#2741 Addition of new diagnostic for the dry deposition flux of nitrogen fionaoconnor
#2742 Addition of new diagnostic for the wet deposition flux of nitrogen fionaoconnor
#2814 Allow UKCA Chemistry to work with aerosol climatologies lukeabraham
#2898 Input CO2 concentrations into UKCA when interactive CO2 is operational colinjohnson
#3025 Add functionality to use NetCDF GLOMAP-mode climatology fields to generate fields required by ACTIVATE alanjhewitt
#3028 Improve STASH section references related to UKCA components. mohitdalvi
#3127 Investigate KGO differences in um_n48_ukca_eg app using GNU on the Cray lukeabraham
#3289 Removal of Backward Euler Std tropospheric chemistry fionaoconnor
#3290 Removal of old dry deposition scheme using prescribed deposition velocities fionaoconnor
#3292 Consolidate constant variables used by UKCA mohitdalvi
#3367 Removing transport of peroxy radical tracers in Strattrop (CHeST) scottarchernicholls
#3384 Add UKCA processor decomposition tests to rose-stem lukeabraham

Tickets currently targeted as Hopefully

Training (LA)

UKCA Training January 2018

Registration deadline: 3rd November!

new action: LA to look into recording lectures

AOB/DNM (LA)

Date of next meeting (LA)

vn11.0 Code Review deadline is the 9th February 2018, to released on (or before) 28th February 2018.

new action: LA to set-up doodle poll for sometime within these three weeks.

Doodle poll: https://doodle.com/poll/hk5xdqwna39uzuuq