Minutes of the code management group meeting 2019-04-01

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Code management group minutes

Teleconference Details

Monday 1st April 2019, 10am - 11.30am GMT

  • UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
  • Participant PIN: 166147

Present

Met Office: Mohit Dalvi (MD), Alan J Hewitt (AJH), Marc Stringer (MS), Lucy Neal (LN), John Hemmings (JH), Fiona O'Connor (FOC), Maff Glover (MG), Jane Mulcahy (JM), Adrian Hill (AH)

Cambridge: Luke Abraham (LA), Paul Griffiths (PTG)

Leeds: Mark Richardson (MR), Hamish Gordon (HG), Kirsty Pringle (KP), Dan Grosvenor (DG), Masaru Yoshioka (MY), Chris Dearden (CD)

Reading:

Lancaster: Ewa Bednarz (EB)

Edinburgh:

UEA:

NIWA: Olaf Morgenstern (OM)

CSIRO: Ashok Luhar (AL)

Apologies: NB, SAN

Actions from this meeting

One-off actions

  1. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below.
  2. (ongoing) LA to open tickets for all changes that still require a ticket.
  3. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details and progress for vn11.4
  4. (ongoing) LA to put C_SPECIES definitions in the Redundant Code table (short-term), and switch to use M_SPECIES instead. Talk with JH about AQUM tests and requirements. Note that there will be problems with exoplanets and >100km top configs where M_air not constant. LA to make a branch and progress for vn11.4.
  5. (ongoing) NLA/MD make script for perpetual nudging (symbolic linking to existing files).
  6. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
  7. (new) LA to discuss with Leeds plans for a separate repository.
  8. (ongoing) FOC to see what action can be taken from MASS, then put out an email for POCs from institutes. FOC/AH/MD to develop a strategy on MASS for discussion at next CMG as a data clear-out is required.
  9. (ongoing) CH working on ticket/bugfix for SO2 deposition. Will need to be on a switch for UKESM
  10. (ongoing) LA to contact AS/AJH and ask how best to proceed with removing the depreciated NetCDF attribute options.
  11. (new) FOC to encourage Garry Hayman to start lodging JULES code piecemeal.
  12. (new) LA to progress bug #87 on a switch.
  13. (new) JM to find someone to progress bug #104.
  14. (new) ALL to read API document and send comments to JH.
  15. (new) AH to talk to UM Systems Team.
  16. (new) LA to email UKCA vn11.4 developers regarding potential vn11.5 UKCA release and ask for feedback.
  17. (new) ALL to send any comments regarding proposed emissions changes to FOC within next 3 weeks before work will start.
  18. (new) JM to approach SW regarding model dust
  19. (new) FOC to approach AJ regarding stratospheric aerosol updates
  20. (new) LA to email GM and ask how GLOMAP would differ from how it is in other models (e.g. CTM, IFS etc.)
  21. (new) LA to send list to UKCA SMG
    1. UKCA API
    2. Review UKCA tests to cover all requirements
    3. Bug #87 (YSTORE/H2SO4)
    4. Updates/fixes to GLOMAP routines
    5. Standalone UKCA configurations
    6. Emissions flexibility
    7. Separare UKCA repository
    8. Chunking of chemistry solver
    9. ACTIVATE optimisation
    10. FastJX-GLOMAP coupling
    11. NaNs found with new schemes turned on (bug #106)
    12. CSIRO dry-deposition work
    13. Fixes for chemistry rates and ASAD (bugs #101 & #103)
    14. Rc fixes for water (bug #104)
    15. UKCA STASHmaster PP-codes
    16. Removal of redundant code
  22. (new) LA to circulate details of rose-stem ticket
  23. (new) LA to send round Doodle poll for first 2 weeks of June.
  24. (new) AJH and MD to chase up issues with ukca_bugs mailing list.

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 2019-01-25

  1. (ongoing) MY to check GLOMAP-mode code and report any missing bug fixes on the bugfixes page.
    • closed
  2. (ongoing) GM/MY to arrange telecon with LA when MY starts.
    • closed
  3. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below.
    • ongoing
  4. (ongoing) LA to open tickets for all changes that still require a ticket.
    • ongoing
  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.
    • closed
  6. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details and progress for vn11.4
    • ongoing
  7. (ongoing) LA to put C_SPECIES definitions in the Redundant Code table (short-term), and switch to use M_SPECIES instead. Talk with JH about AQUM tests and requirements. Note that there will be problems with exoplanets and >100km top configs where M_air not constant. LA to make a branch and progress for vn11.4.
    • ongoing
  8. (ongoing) AJH to open ticket and assign to himself regarding loops over imode+n and imode-n UM:#4284. Currently code is inflexible when adding modes. AJH to discuss with GM offline.
    • closed
  9. (ongoing) LA to make instructions as to make UM11.0 release job transient.
    • closed - MD created and will link on Wiki.
  10. (ongoing) NLA/MD make script for perpetual nudging (symbolic linking to existing files).
    • ongoing - LA to check MD script
  11. (new )HG to send MD suite-id for L70 job that has nudging errors.
    • closed
  12. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
    • ongoing
  13. (new) LA to discuss with Leeds plans for a separate repository.
    • ongoing
  14. (ongoing) NLA to contact CEJ (cc JM) about trace-gas convective plume scavenging and how this will be impacted (or impact) the repository work, and LA to forward proposal to CEJ/JM
    • closed - JH and CEJ to consider offline.
  15. (ongoing) FOC to see what action can be taken from MASS, then put out an email for POCs from institutes. FOC/AH/MD to develop a strategy on MASS for discussion at next CMG as a data clear-out is required.
    • ongoing - FOC & AH have agreed on split of institutes
  16. (ongoing) JM to take make a UM ticket for redundant code item #6 (Wet oxidation of SO2 in GLOMAP). Keep GM/MY in the loop.
    • closed
  17. (new) LA to make a separate telecon to consider actions to link various GLOMAP actions as a whole
  18. (ongoing) LN to l_fix_nh4no3_equilibrium in rose-stem and jobs and remove if necessary. AJH to Sci/Tech.
    • closed
  19. (ongoing) CH working on ticket/bugfix for SO2 deposition. Hopes to lodge vn11.4, will need to be on a switch for UKESM
    • ongoing - won't make vn11.4
  20. (ongoing) LA, JM, CEJ, SAN to discuss rate fixes offline and keep GM in loop.
    • closed
  21. (ongoing) LA to contact AS/AJH and ask how best to proceed with removing the depreciated NetCDF attribute options.
    • ongoing - will also need to consider LFRic at some point as well
  22. (new) ALL to check whether unused functions, subroutines, modules listed under redundant code 19 are still required, see vn11.3_remove_redundant_UKCA_code
    • closed - AJH to send to SciTech ASAP
  23. (new) ALL to give feedback within 1 month on proposed PPFC changes.
    • closed - set to 0 for new STASH items
  24. (new) LA to send round Doodle poll for March/April.

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 meetings Comments from this meeting
35 Error in labelling: Surface resistance <--> stomatal resistance ? UM:#1409 Fiona O'Connor Leave open. Garry Hayman started work in offline JULES.
Still ongoing. JM found bug in SO2 deposition, where there is an inconsistency when changing tiles. Making progress.
Leave open. GH gave update, has done a lot of work. Concerned it might not be bit-reproducable, but could be solvable. Encouraging to lodge existing. Resistances done as metadata. Not clear as to timescales.
ACTION: FOC to encourage Garry Hayman to start lodging JULES code piecemeal.
87 Possible issues with YSTORE in UKCA_CHEMISTRY_CTL. This may mean than there is no H2SO4 because of this, with impacts on GLOMAP aerosols. Need to also select the correct products in chemistry_ctl. Combination of two different bugs - see r61958_vn10.8_cos_mmr_value_so2_2 UM:#3245 Luke Abraham Leave open. NLA to have another look. MS may have changed things with OMP changes.
Original fix didn't consider everything. LA to progress for vn11.4, Catherine Hardacre to do for vn11.0/vn11.1. Test for AerChemMIP. Leeds have vn11.2 branch. Use versioning system and apply for column.
ACTION: LA to progress bug #87 on a switch.
101 Errors in reaction rates and diagnostics UM:#4466 Luke Abraham / Scott Archer-Nicolls There is a need to conserve science config for UKESM1, so changes need to be on a flag.
Colin has been looking at DMSO, as this is not currently used in StratTrop but is in Offline.
Might be able to merge the rate with CEJ changes, but best to leave the diagnostic issues as a separate change.
LA, JM, CEJ, SAN to discuss offline and keep GM in loop.
Use versioning system. Talk about further offline.
Keep ongoing.
103 Incorrect indexing of tmprc array: ASAD_SPIMPMJP UM:#4562 Scott Archer-Nicolls Breaks KGO - affects solver convergence. In practice doesn’t make a huge difference, but should go into vn11.4, but does change KGO. UKESM1 - small change might be OK - get in touch for advice - might be able to test with UKESM1 AMIP only. Check with Oliver Wild Could be rolled-up with #101
104 Incorrect value for Rc for SO_2 deposition to open water UM:#4635 Catherine Hardacre See above, covered already. Got to be separate to #35, unless there is an idea of timelines.
ACTION: JM to find someone to progress bug #104.
106 NaNs appearing when new UKCA science is turned on UM:#4397 Luke Abraham in progress

Redundant Code (LA)

Code for deletion

PLEASE REMEMBER TO EDIT THE ORIGINAL REDUNDANT CODE TABLE AND NOT THIS PAGE

# Description Ticket Remarks Status Timeframe Owner Comments from previous meetings Comments from this meeting
2 Old dry deposition scheme UM:#2356 None PROPOSED Medium-term Nick Savage
4 ukca_strat_update.F90 - relax_ozone UM:#1505 None PROPOSED Medium-term Luke Abraham
5 Backward Euler Standard Tropospheric Chemistry UM:#1507 None PROPOSED Medium-term Fiona O'Connor
6 Wet oxidation of SO2 in GLOMAP UM:#4475 None PROPOSED Medium-term Colin Johnson JM to look at this re: UKESM1 c.f. offline GLOMAP. JM to take ownership.
7 Updraft velocity - l_conv_tke UM:#3668 Proposed in December 2017. Approval being sought for GA series (likely GA8). PROPOSED Medium-term Alan J Hewitt / Ian Boutle
8 All backward Euler chemistry schemes None 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 that problems for AQUM would need to be addressed first. PROPOSED Long-term Luke Abraham
9 Deprecated UKCA netcdf attribute options UM:#2513 'emission_type', string type attributes no longer recommeneded. Need some time for most new code to adopt these. Still used in AQUM files. DEPRECATED Medium-term Nick Savage AQUM are addressing the files. Have gone from operational jobs, have ticket to remove from rose-stem. LN to document. These have been removed from AQUM.
AQUM work has been done.
10 ASAD families chemistry None Families chemistry has not been used for many years (since at least UM6.1. It is likely that it no longer works if turned on, and it complicates the code making other developments harder DEPRECATED Short-term Luke Abraham
11 Dry deposition 9 PFT option None The 13 PFT option has been adopted for UKESM1.
The 9 PFT option is possibly not being used at all.
Proposed in June 2018.
PROPOSED Long-term Alan J Hewitt
12 Remove explicit C_SPECIES constants and calculate these from M_SPECIES and the mass of air None Will have wide-ranging rose-stem KGO breakages PROPOSED Short-term Luke Abraham
13 Remove temporary logical l_fix_nacl_density
Introduced at UM:#2405
UM:#3490 Requires AMIP testing and a GMED ticket
Could be accepted to GA9
PROPOSED Medium-term Jane Mulcahy See JM GMED action
15 Remove temporary logical l_fix_ukca_impscav
Introduced at UM:#1421
UM:#4145 Approval being sought for GA series (likely GA9)
GMED:#402
PROPOSED Medium-term Alan J Hewitt See JM GMED action
16 Remove temporary logical l_fix_improve_drydep
Introduced at UM:#1250
UM:#3997 Approval being sought for GA series (likely GA9)
GMED:#393
PROPOSED Medium-term Alan J Hewitt See JM GMED action
17 Remove temporary logical l_fix_ukca_h2dd_x
Introduced at UM:#4157
UM:#4245 Approval being sought for GA series (likely GA9)
GMED:#410
PROPOSED Medium-term Alan J Hewitt See JM GMED action
18 Remove temporary logical l_fix_neg_pvol_wat
Introduced at UM:#4383
UM:#4416 Approval being sought for GA series (likely GA9)
GMED:#421
PROPOSED Medium-term Alan J Hewitt
19 Remove MODULEs/SUBROUTINEs/FUNCTIONs
within UKCA not called within the UM:

SUBROUTINE asad_dealloc_chemdiag
FUNCTION cd_findspeciesloc
SUBROUTINE asad_lin_diagnostic
MODULE asad_emissn_mod and SUBROUTINE asad_emissn
FUNCTION prcount
MODULE asad_inemit_mod and SUBROUTINE asad_inemit
MODULE asad_inhet_mod and SUBROUTINE asad_inhet
MODULE asad_inphot_mod and SUBROUTINE asad_inphot
SUBROUTINE asad_mod_final
MODULE asad_ycn_mod and SUBROUTINE asad_ycn
MODULE quanto1d_mod and SUBROUTINE quanto1d
SUBROUTINE activmkpdf
MODULE ukca_fixedsb_mod and SUBROUTINE ukca_fixedsb
SUBROUTINE deallocate_radaer_struct
SUBROUTINE ukca_relax_ozone
UM:#4512 Not called within UM
Need to decide whether any should be kept

vn11.3_remove_redundant_UKCA_code
DEPRECATED Short-term Alan J Hewitt All to look at subroutines not being called.

UKCA API redesign

JH has been working on redesigning the UM-UKCA interface to remove the model specific coupling. His proposed design document can be found here:

JH described where this was heading in terms of design. It would allow UKCA to couple to other models independent of the UM. There is a provisional list of tickets in the appendix of above document. The first “standalone” code version hopefully by UM11.6. Diagnostics more problematic, similarly with plume scavenging. Some initialisations taken outside of UKCA main. All bit-compares and shouldn’t affect results. Yet to hear back from UM Sys.

ACTION: ALL to read API document and send comments to JH.

Potential closed release for vn11.5.

ACTION: AH to talk to UM Systems Team.

ACTION: LA to email UKCA vn11.4 developers regarding potential vn11.5 UKCA release and ask for feedback.

Emissions

The minutes of the UKCA emissions discussion can be found here:

Please see the document for further details.

The aim is to remove restrictions, and implement tracking_id and add a pop-up warning to remove prescribed files. This should also improve functionality for vertical profiles/emissions.

ACTION: ALL to send any comments regarding proposed emissions changes to FOC within next 3 weeks before work will start.

GLOMAP telecon

on 2019-03-12 LA, JH, GM, & MY met and discussed various GLOMAP actions. MY has made great progress in creating vn11.0 branches of developments made at earlier versions, and work has been ongoing to validate the changes at vn11.0 with the equivalent functionality at earlier versions.

There was one action:

It was suggested to lodge changes separately, and also to check with Cat Scott to check whether code is up-to-date with latest literature (e.g. with SOA). MY is now working on something else, so cannot work on this further. We could ask Steph Woodward to look at Dust and perhaps Andy Jones could look at Stratospheric aerosol.

ACTION: JM to approach SW

ACTION: FOC to approach AJ

ACTION: LA to email GM and ask how GLOMAP would differ from how it is in other models (e.g. CTM, IFS etc.)

Priorities for the next year

Following the first meeting of the UKCA Science and Management Group on 2019-03-22 at the Met Office, this group has been asked to supply a list of priorities for the next year. The provisional list below could serve as a prompt for the discussion.

  1. UKCA API
  2. Review UKCA tests to cover all requirements
  3. Bug #87 (YSTORE/H2SO4)
  4. Updates/fixes to GLOMAP routines
  5. Standalone UKCA configurations
  6. Emissions flexibility
  7. Separare UKCA repository
  8. Chunking of chemistry solver
  9. ACTIVATE optimisation
  10. FastJX-GLOMAP coupling
  11. NaNs found with new schemes turned on (bug #106)
  12. CSIRO dry-deposition work
  13. Fixes for chemistry rates and ASAD (bugs #101 & #103)
  14. Rc fixes for water (bug #104)
  15. UKCA STASHmaster PP-codes
  16. Removal of redundant code

ACTION: LA to send list to UKCA SMG

ACTION: LA to circulate details of rose-stem ticket: um:#4397

Use of PP codes in UKCA STASHmaster_A entries

Update from Jamie Kettleborough:

[W]e met last week – and one of the meeting attendee’s thinks that UKCA pp codes are used in the MO verification system.  We’re following up to try to understand.
 
I think this doesn’t affect the policy of assigning new UKCA diagnostics pp codes a value of 0, but it could mean we should leave current diagnostics as is.

UKCA Suites (LA/MD)

Targets for vn11.4 (and beyond) (LA)

See details of the 7th March UM Developers and Owner's Group.

PLEASE REMEMBER TO:

  • INCLUDE THE KEYWORDS: UKCA & SC0138.
  • ASSIGN THE TICKET AFTER ITS CREATION. NO TICKETS SHOULD BE LEFT AS NEW.

If you do not think that you will make the vn11.4 deadline please bump your ticket to vn11.5 or hopefully.

UM vn11.4 code review submission deadline is 31st May 2019 for ALL ticket types.

AOB/DNM (LA)

Date of next meeting (LA)

ACTION: LA to send round Doodle poll for first 2 weeks of June.