Minutes of the code management group meeting 2019-01-25

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Code management group minutes

Teleconference Details

Friday 25th January 2019, 10am - 11.30am GMT

  • UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
  • Participant PIN: 471030

Present

Met Office: Alan J Hewitt (AJH) , Mohit Dalvi (MD), Mark Stringer (MS), Jane Mulcahy (JM), Maff Glover (MG), John Hemmings (JH)

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

Leeds: Chris Dearden (CD), Graham Mann (GM), Mark Richardson (MR), Hamish Gordon (HG), Masaru Yoshioka (MY)

Reading:

Lancaster: Ewa Bednarz (EB)

Edinburgh:

UEA:

NIWA: Olaf Morgenstern (OM)

CSIRO:

Apologies: Fiona O'Connor (FOC), Adrian Hill (AH), Nicolas Bellouin (NB), Ashok Luhar (AL), Kirsty Pringle (KP)

Actions from this meeting

One-off actions

  1. (ongoing) MY to check GLOMAP-mode code and report any missing bug fixes on the bugfixes page.
  2. (ongoing) GM/MY to arrange telecon with LA when MY starts.
  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 recommend at next Exec meeting a policy of allowing only CMG to (certify and) distribute any UKCA configurations for science purpose.
  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
  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.
  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.
  9. (ongoing) LA to make instructions as to make UM11.0 release job transient.
  10. (ongoing) NLA/MD make script for perpetual nudging (symbolic linking to existing files).
  11. (new )HG to send MD suite-id for L70 job that has nudging errors.
  12. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
  13. (new) LA to discuss with Leeds plans for a separate repository.
  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
  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.
  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.
  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.
  19. (ongoing) CH working on ticket/bugfix for SO2 deposition. Hopes to lodge vn11.4, will need to be on a switch for UKESM
  20. (ongoing) LA, JM, CEJ, SAN to discuss rate fixes offline and keep GM in loop.
  21. (ongoing) LA to contact AS/AJH and ask how best to proceed with removing the depreciated NetCDF attribute options.
  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
  23. (new) ALL to give feedback within 1 month on proposed PPFC changes.
  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.

Minutes

Actions from the Last Meeting (LA)

Minutes of the code management group meeting 2018-11-12

One-off actions

  1. (ongoing) MY to check GLOMAP-mode code and report any missing bug fixes on the bugfixes page.
    • ongoing
  2. (new) GM/MY to arrange telecon with LA when MY starts.
    • LA to do ASAP
  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.
    • ongoing
  6. (ongoing) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM and circulate details.
    • 20-year run in progress
    • AQUM, GA7, UKESM affected
    • Won’t be able to finish the tests in time for KGO change deadline. Need to discuss with Alistair and Paul Earnshaw.
    • Bump for vn11.4.
  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 vn11.3.
    • Bumped for vn11.4
  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.
    • ongoing
  9. (ongoing) LA to make instructions as to make UM11.0 release job transient.
    • ongoing.
    • Edinburgh want to do this and MD has done some instructions, will send to LA.
  10. (ongoing) NLA/MD make script for perpetual nudging (symbolic linking to existing files).
    • MD sent to LA, ongoing. LA to check.
    • Nudging doesn’t work in all configurations (e.g. L70). HG to send MD suite-id.
  11. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
    • ongoing
  12. (ongoing) MR to discuss with KP implications for GLOMAP in regards to a separate UKCA repository:
    • Feeling was that this was generally a good thing, but more thinking about GLOMAP is required. LA to talk with Leeds offline.
  13. (new) LA to forward NERC proposal to Leeds.
    • Closed
  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
    • LA to forward proposal to CEJ/JM
  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
    • bump to next CMG. Need to clear-out any data no longer required.
  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.
    • ongoing
    • NEW action, LA to make a separate telecon to consider actions to link 1, 2, 12, 14, 16 as a whole? LA to check with FOC/AH
  17. (ongoing) JM to do a catch-call ticket for GMED - (DONE, ticket here)
    • closed
    • Currently only has one change. AJH covering a lot of the others. Leave open for now. Will be for GA9.
  18. (ongoing) LN to l_fix_nh4no3_equilibrium in rose-stem and jobs and remove if necessary.
    • in progress, a ticket is open with AJH to Sci/Tech.
  19. (new) JM to open ticket and new bug for SO2 deposition.
    • Catherine Hardacre is working on this now. Hopes to lodge vn11.4, will need to be on a switch for UKESM
  20. (new) LA, JM, CEJ, SAN to discuss rate fixes offline and keep GM in loop.
    • ongoing. Could be large numbers of changes. Use the versioning system?
  21. (new) LA to contact AS and ask how best to proceed with removing the depreciated NetCDF attribute options.
    • ongoing
    • Jamie Kettleborough asked about NetCDF to AJH - there are differences between GLOMAP_CLIM and other UKCA NetCDF files, e.g. options for updating of files.
    • Copy AJH into email to AS.
  22. (new) MD to back-port STE fixes to UM11.0 suite.
    • closed
  23. (new) MD/LA to make up vn11.1 and vn11.2 configs similar to TS2000 and send-off 20-year AMIP runs to produce standard evaluation suite plots.
    • closed
  24. (new) LA to take ownership of ticket um:#4397(GA7 NR Offline test).
    • closed. No action taken for vn11.3
  25. (new) LA to send round Doodle poll for middle of January.
    • 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 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.
Leave open. Garry working on rewrite. Making progress.
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.
96 Output drydiam diagnostics where l_ukca_arg_act but not l_ukca_radaer UM:#3962 Alan J Hewitt The beginnings of a solution are found in vn11.0_ukca_drydiam_activate_wo_radaer. Leave open. AJH to take ownership - may be affected by reorganisation. This just limits options. Leave until code is reorganised. Closed as feature. This is currently a low priority fix.
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.
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
104 Incorrect value for Rc for SO_2 deposition to open water UM:#4635 Catherine Hardacre See above, covered already.
105 segmentation fault on ukca_plev_diags_mod.F90 UM:#4625 Michele Guidolin Under SciTech review NA Simple fix - new compiler found the bug.

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 None 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
14 Remove temporary logical l_fix_nh4no3_equilibrium
Introduced at UM:#646
UM:#4382 Already accepted to GA9/AQUM/MOGREPS/rose-stem
Logical l_fix_nh4no3_equilibrium just needs removing.
PROPOSED Medium-term Pedro Molina-Jimenez See LN temporary logical 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.

New Action: All to consider these redundant routines.

UKCA Release Job (LA/MD)

Targets for vn11.3 (and beyond) (LA)

See details of the 29th October 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 vn11.3 deadline please bump your ticket to vn11.4 or hopefully.

Tickets targeting vn11.3

UM vn11.3 code review submission deadline is 8th Feb 2019. SOCRATES/JULES/GCOM/CASIM/FFPP/KGO by 1st Feb 2019.

# Description
UM:#2689 Enable coupling of GLOMAP-MODE Aerosol to FAST-JX photolysis.
UM:#3292 Consolidate constant variables used by UKCA
UM:#3367 Removing transport of peroxy radical tracers in Strattrop (CHeST)
UM:#3611 Make diagnostics selection compliant with method of listing chemistry
UM:#3779 Improvements to the inline comments in ukca_option_mod
UM:#3840 Add extra UKCA tests to NCI rose stem
UM:#3959 RO2-Permutation Chemistry
UM:#3997 Retire temporary logical l_fix_improve_drydep
UM:#4020 Improved calculation of ozone dry deposition to ocean - surface resistance term
UM:#4058 UKCA-INFERNO coupling
UM:#4111 Add GLOMAP PM diagnostics to rose-stem tests
UM:#4145 Retire temporary logical l_fix_ukca_impscav
UM:#4201 Verify use of qsmin in UKCA plume scavenging diagnostics
UM:#4221 Optimisation of GLOMAP_CLIM
UM:#4225 Sulphur diagnostics are incomplete in the UKCA strattrop mechanism.
UM:#4231 Adding Common Representatives Intermediate (CRI) mechanism
UM:#4245 Retire temporary logical l_fix_ukca_h2dd_x
UM:#4288 Extend GLOMAP_CLIM rose stem testing to new compilers e.g. ifort & gfortran
UM:#4357 Replace glomap_clim_n48.nc in rose-stem/app/um_n48_glomap_clim (& n96)
UM:#4375 Implement cache-blocking loop in UKCA to optimise the chemistry solver
UM:#4382 Retire temporary logical l_fix_nh4no3_equilibrium
UM:#4481 Impose top-boundary conditions for upper-atmosphere species
UM:#4522 Change DMS non-stoichometric chemistry (OH addition reaction) in Strattrop mechanism
UM:#4549 Optimise GLOMAP_CLIM by refactoring code
UM:#4562 Bug-fix convergence check of maximum rate error in asad_spimpmjp
UM:#4598 Update to ASAD iteration counter in UKCA to include failed attempts at convergence
UM:#4612 CASIM-UKCA coupling interface and minimal changes to UKCA to enable convection-permitting runs

Use of PP codes in UKCA STASHmaster_A entries

We have been asked to look at retiring PP codes if this is possible. This should be able to be achieved by setting them to 0 in the STASHmaster_A if we do not make use of them.

  • cf-python - no issues assuming that a STASH code is present
  • Xconv - the PP code is used to define the NetCDF variable name of the field, meaning all UKCA variables would be field0, field0_1, field0_2 etc.
  • Xancil - the PP code is assumed to be the name of the field and is used to automatically choose which variable from the NetCDF file to put into the requested ancillary field. This would mean that any UKCA ancillaries made using Xancil must have the variables MANUALLY chosen.
  • AQUM - don't believe that PP codes are used, but any issues would show-up in rose-stem tests, and additional downstream tests could be done as well to be sure.

New Action: All to give feedback within 1 month

AOB/DNM (LA)

newline functionality

Date of next meeting (LA)

New Action: LA to send Doodle poll for end of March/beginning of April