Minutes of the code management group meeting 2022-05-10

From UKCA

Code management group minutes

Teleconference Details

Tuesday 10th May 2022, 10.00am - 11.30am GMT

Meeting via Zoom - details have been emailed

Met Office: AH, AJH, MS, JH, CH, MD, NC, FM, MD

Cambridge: NLA, SAN

Leeds: DG, MR

NIWA:

CSIRO:

Apologies: AL

Actions from this meeting

Actions from the Last Meeting (NLA)

Minutes of the code management group meeting 2022-03-29

  1. (ongoing) NLA 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.
    • Ongoing
  2. (ongoing) Monsoon users MASS data Management. Removal commands issued for ~550 umui jobs (total 175Tb). List from Oxford still awaited. MD to contact PS again.
    • MD hasn’t heard back from PS. Gave deadline of end of June after which point data would be deleted.
    • Leave as ongoing until data is removed.
  3. (new) NLA to contact UKCA SMB and ask for feedback on setting a 'delete-by' deadline for Oxford MASS data.
    • Closed - fine to give "delete-by" deadline.
    • NEW ACTION: NLA to contact MR regarding the MASS replacement. There have been some announcements on Yammer
  4. (ongoing) GM (supported by KP/MY/AH) has made a table on UKCA wiki documenting GLOMAP versions. ALL to read, GM & others to update table.
    • Ongoing
    • Note that KP has left Leeds.
  5. (ongoing) JH to update API document to reflect the UMvn12.2 release
    • Ongoing - do for UM13.0 after the code freeze.
  6. (ongoing) Unprotected rose-stem options: MD to look at highorder_scheme.
    • Ongoing
  7. (ongoing) Unprotected rose-stem options: AJH to look at i_mode_setup=6
    • Ongoing
  8. (ongoing) ALL look at um:#6203 showing other unprotected rose-stem options and think about any code/settings they are interested in.
    • Ongoing
  9. (ongoing) DG/AH/GM to consider the code and lodging process for GLOMAP developments. DG working on porting code either from GLOMAP v8.0 or v8.2.
    • Ongoing
    • Code needs testing - DG now has access to the Met Office so will try running there.
    • This is just the first change, will progress others later.
  10. (new) NLA to reply to email thread regarding GLOMAP lodging after this meeting
    • Closed
  11. (ongoing) NC to add a test for 2-D photolysis as part of Photolysis API changes
    • Ongoing
  12. (ongoing) MR to discuss with AH, HG and update the CMG on any issues related to UKCA ancil creation in Nesting Suite
    • Closed
    • Have briefly discussed this. Currently using LAMPOS, which pre-dates ANTS.
  13. (ongoing) NLA, AJH to identify owners for TropChem and StratChem items in the Desirable changes not Tested Table. AJH to arrange call with NLA.
    • Ongoing
  14. (ongoing) JH,AH,AJH to update Mark (and possibly wider CMG) on LFric developments and UKCA aerosol code status. May want to talk with Simon Wilson at NCAS CMS who has a containerised version of LFRic.
    • Ongoing
    • LFRic is running on the ARC system, but driving data is needed.
    • Aerosol code has been ported to LFRic with offline oxidants, chemistry is a long way off.
  15. (ongoing) MD to take a look at EX1A issues (um:#6610). NLA to cc MD into email from Rich Gilham. MD to give update on the rose-stem failures on the EX1A HPC to email chain.
    • Closed
    • Found 2 issues: bit-comparability has been fixed, stability being worked on with MS, but have gotten close. The cause has not been found, but lowering the optimisation of the main solver routine is a usable work-around.
  16. (new) NLA to follow-up on the status of issues with GMED:#551.
    • Closed
  17. (new) MS to email Oliver Wild and NLA with chemical solver issues.
    • Closed
    • This didn't work. There are some issues with ARCHER2/EX1a & the new Cray compiler (which still uses Cray Fortran).
  18. (new) NLA to update categorisation list too from UKCA:#4 ticket.
  19. (new) NLA to add ukca_chem_master to list as the aim is to move to a file read for the chemical mechanism. Also consider doing a file read to tabulate the required diagnostic output.
    • Closed
  20. (new) SAN to contact JH about dependencies
    • Closed
  21. (new) NLA to send a Doodle poll round for mid-May avoiding EGU (23rd-27th May)
    • 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 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 for special occasions, e.g. to coincide with Composition-Climate Meeting.
  7. (ongoing - standing item) Code Owner to produce draft newsletter for CMG to approve.
  8. (ongoing - standing item) ALL to consider other rose-stem tests that could be included.
  9. (ongoing - standing item) ALL to email NLA with suggestions for next set of tutorials.

Tickets (NLA)

Tickets on MOSRS:


PLEASE REMEMBER TO USE THE UKCA AND blocks:6717 KEYWORDS FOR ALL UKCA CHANGES THIS RELEASE

Please add a suggested commit order to um:#6794

NOTE: The UM requirement for LFric testing of all changes under src/atmosphere

Please also give any feedback on the UMvn13.0 release cycle to NLA to pass-back to UM Sys.

For the DOG: Note that the UM doesn't work on Apple Silicon (M1) chips, so running the VM on new Macs isn't possible.

MR highlighted that new Fortran may not allow named do loops

Update on UKCA API redesign (JH)

Documents:

No major updates this release. Current API ticket will remove remaining UM dependencies. There will then be a handful of UM modules that UKCA is still dependent on. It should soon not be dependent on other repos and will be virtually self-contained.

UKCA Developments over 2022 (NLA)

Meetings:


Tickets:


Current code structure

MS asked about the Hybrid configuration. This change shouldn’t affect it or any other configurations.

ACTION: NLA to make branch for licence & CLA to exist on trunk, make templates with questions from 6th April email. AH to review branch.

Progress with Priorities (NLA)

ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD: CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

The current priorities are:

# Description Owner Desirable for UKESM2? Status Comments from this meeting
1 UKCA API John Hemmings (main) No UKCA API work is progressing (AJH). Radaer API on hold until after GA7 port to LFRic. Functionality of RADAER in LFRic will work without an API although it will be preferable to update this in future.
2 Review UKCA tests to cover all requirements Luke Abraham / Mohit Dalvi Will cover these in a table in future for review.
3 Updates/fixes to GLOMAP routines YES AH asked about the stratospheric changes from a UKESM2 context, and whether there is any help for these.
4 Standalone UKCA configurations Luke Abraham/Scott Archer-Nicholls ExCALIBUR work progressing.
Aim to remove UKCA from UM trunk at vn12.3.
5 Emissions flexibility Mohit Dalvi
6 Separare UKCA repository Luke Abraham Separate UKCA trac environment set-up on MOSRS here, will hold UKCA code on completion of current ExCALIBUR project.
Aiming for vn12.3.
7 Non-API LFRic work, e.g. Porting science functionality etc. Alan J Hewitt No Porting calculation of CDNC from GLOMAP Climatology aerosols complete.
I will pass required elements of ukca_radaer to ukca_radaer_band_average (um:#5957)
Porting calculation of fields in radaer_band_average to be passed to Socrates underway(lfric:#2488)
Includes RADAER, need to use imode_setup=8
RADAER now callable from LFRic, can do GA-type comparisons from LFRic to UM. JH to put UKCA into LFRic soon - working in an SCM configuration (GLOMAP with offox) - needs more testing. A lot more work to do, possibly until end of 2021.
AJH has tickets going in for 12.1 that would cover all of the basic GA7 but with climatological aerosol. JH tickets will do the prognostic alternative. JH currently has an LFRic-SCM configuration with prognostic aerosol.
JH now has UKCA working in proto-GAL7 (LFRic) config. Needs to couple with convection & plume scavenging.
Convection & plume scavenging has been done.
8 RADAER API Alan Hewitt (main) No Radaer API on hold until after GA7 port to LFRic.
Functionality of RADAER in LFRic will work without an API although it will be preferable to update this in future.
Not clear if RADAER will work independently of UM in single column mode.
AJH and AH and JH and Ben Johnson and NB need to work out if desirable and practical to run independent of UM.
9 RADAER optimisation NO AJH highlighted that there have been some discussions about this - a few people interested in this (James Manners, AH, Ben Johnson, AJH). Have had someone looking to see if something could be changed to make it faster to make a trimmed-down version with less calculations for e.g. NWP.
10 Dry deposition and Jules tiles YES If Jules adds extra tiles for UKESM2 we may need to hard code options in dry deposition (like in um:#1761)
11 FastJX-GLOMAP coupling YES UMvn10.8 branches exist - see ticket UM:#2689
Note: FastJX rates also need updating - potential for code as well as input-file changes
12 Cloud-J
13 Fixes for chemistry rates and ASAD (bugs #101 & #103) Luke Abraham YES #101 still open, #103 completed (necessary for GC5 ticket GMED:#551)
Issues on EX1A.
Closed - see also UKESM:#841 for UKCA package ticket
14 Rc fixes for water (bug #104) UKESM Core Team YES Lodged at UMvn11.7 in ticket UM:#5167
15 CH4 deposition fixes (bug #109) Gerd Folberth YES Closed
16 UKCA STASHmaster PP-codes Luke Abraham Verification system makes some use of existing PP-codes. New items should have a PP-code of 0 and verification team will use STASH items for these if required.
17 Removal of redundant code ALL No Parked whilst GA7.0 is a protected suite.
18 GLOMAP-CLIM API refresh Alan J Hewitt No Parked until science functionality around GLOMAP aerosols ported to LFRic.
19 N48L85 configuration
20 ACTIVATE optimisation TBC A quick win here is to reduce nwbins in namelist ( see um:#4740 ).
Parked for now.
There does not seem to be resource to look at this at present.
21 Stratospheric Ozone improvements James Keeble/Luke Abraham YES
UKESM:#729
Work ongoing, covered in ticket UM:#5641.
Note: FastJX rates also need updating - potential for code as well as input-file changes
See also UKESM:#841 for UKCA package ticket
22 Solar cycle in photolysis Luke Abraham YES
UKESM:#732
Some code lodged at UMvn10.9 (UM:#2587) but needs bugfixing. This work has stalled in ticket UM:#4828 (bug #110).
UM:#4828 lodged for UMvn12.2.
See also UKESM:#841 for UKCA package ticket
23 Deposition updates from CSIRO YES
UKESM:#730
UKESM:#739
Code lodged in UM:#4020 (UMvn11.4, oceanic dry deposition) and UM:#5713 (UMvn11.8, Lightning NOx updates).
See also UKESM:#841 for UKCA package ticket

Bugs/Bugfixes (NLA)

Open Bugs

# Description Ticket Owner Comments Comments from this meeting
35 Error in labelling: Surface resistance <--> stomatal resistance ? UM:#1409
um:#5751
Fiona O'Connor/Garry Hayman 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.
FOC to encourage Garry Hayman to start lodging JULES code piecemeal.
LA to email GH, cc JM
JM to email GH
GH adding improvements via UM:#5751
GH targeting 12.2
um:#5751 was in code review for UMvn12.2 but failed to progress - aiming for early in vn12.3 release cycle.
Should be lodged for vn12.3. Will be put into UKESM2.
In Code Review for UM13.0
124 H2 and N2 cannot be set for RCP and WMOA1 scenario routines UM:#5620 Mohit Dalvi Values are hard-wired in the code and cannot be changed without a branch
Will be handled at UM11.8
At least for the next version
Keep open
128 Bug in UKCA stratospheric chemistry diagnostics UM:#5839 Luke Abraham pre-UMvn10.0. The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics
May be best to lump #101.
NLA to contact JM
Should be fixed for UKESM2
Biggish ticket for 12.2 with bug fixes.
See if can be done for 12.3
135 The SO2 dry deposition improvements added under #5167 do not work for Convection permitting configurations (e.g Nested suite) and fail due to absence of Convection diagnostics. um:#6433 The error message could be turned to a warning and related fields initialised to zero
136 There appears to be a bug in some Section 51 diagnostics. 6598 51996 and 51999 are fine.
51921 and 51922 are broken.
Other fields unknown.
Problem uncovered during 6358
May just linger. Should we take the broken ones out?
138 Missing dry deposition settings in ukca_aerod for RA13NO3, RA16NO3 and RA19NO3 for CRI-Strat v2. um:#6626 Garry Hayman Discovered in um:#5751.
Should be being fixed in um:#5751 (for UMvn12.3)
139 Several rose-stem failures on the new EX1A HPC um:#6610 Mohit Dalvi Also impacts use of gmed:#551.
This has LFRic impacts, but LFRic are currently testing with GAL7. At GAL9, could cause significiant issues.
MD to take a look at EX1A issues (um:#6610). NLA to cc MD into email from Rich Gilham.
Stability & bit-comparison issues.
MD to give update on the rose-stem failures on the EX1A HPC to email chain.
Have fixes

Redundant Code (NLA)

Code for deletion

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

  • The NG-Composition Project Board has agreed to use the Redundant code table as the Technical Debt Log for UKCA as part of that project. This has highlighted the issue that some areas of code are not listed as being redundant, but are also not tested/used routinely and are not in any rose-stem tests, for example 2D photolysis and the TropIsop and Strat chemistry schemes. We have been asked to review this code and list untested code which is still desirable to be included for testing, and to ensure that other areas of code are listed for deletion.
# Description Ticket Remarks Status Timeframe Owner Comments from previous meetings Comments from this meeting
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.
Still needed for CTM. Relevance for standalone code and later coupling to CTM.
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.
From AS: In the ancil ticket linked from #2513 (https://code.metoffice.gov.uk/trac/ancil/ticket/782) it says that GA7 depends on the old format files, and as far as I know this is still true. In the 3-step timeline suggested, we haven't reached step 2 unfortunately. That ticket was about ensuring GA8 did not use the old attributes. I believe that GA8 is due for release in the next few months (it has been a very long time coming), so UM vn11.5 may be the last version at which GA7 is supported. Do you mind waiting a bit longer?
AJH to follow-up with LA
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
21 Remove code behind L_use_stratclim from ukca_fastjx_mod
Introduced prior to MOSRS
UM:#4854 This could either be properly included via a namelist or removed from the UM PROPOSED Medium-term Alan J Hewitt LA contact OW about progressing FastJX-RADAER work
Ties in with API work. MD/NC to take a look, can be removed. Do as part of API.
Relevant person take ownership as part of API work
NC to take ownership as part of his work
22 Remove temporary logical l_fix_ukca_input_meoh_emiss
Introduced at UM:#3031
UM:#4848 Approval being sought for GA series (likely GA9)
GMED:#461
PROPOSED Medium-term Mohit Dalvi
24 Remove ability to use of Cambridge 2D model data from ukca_stratf.F90 PROPOSED Neal Carr Need to confirm from wider community for possible tropospheric configs and other choices for top-bdy
25 Change from using ukca_chem_master.F90 to a file-read for the chemical mechanism PROPOSED Short-term Luke Abraham Current chem_master module has compiler issues with that require changes to optimisation level on some compilers. A file read would be more flexible and would allow the mechanism to be more easily changed not requiring UM/UKCA code tickets.

Desirable Science not tested

PLEASE REMEMBER TO EDIT THE ORIGINAL SCIENCE NOT TESTED TABLE AND NOT THIS PAGE

See also the complete list of unprotected rose-stem options

# Description Ticket Remarks Owner
1 Use of tropospheric (2D) look-up table photolysis Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring NC
2 TropIsop chemistry configuration May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations.
3 Strat chemistry configuration Useful for stratospheric studies, particularly with a high model top.

Round (virtual) Table of current activities, plans

Person Activity
NLA Submitted a proposal for the NERC training call.

A.O.B. & D.N.M. (NLA)

AH noted that in LFRic the SCM capability is there but the test cases aren’t. It would be good to have a think about what to do about test cases. If people want to get used to LFRic, this configuration could be a good way in to the system.

AJH & others were looking forward to the repository work being completed and usable!

Date of next meeting (NLA)

ACTION: NLA to send a Doodle poll for the next meeting in mid-July