Minutes of the code management group meeting 2023-01-30

Code management group minutes

Teleconference Details

Monday 30th January 2023, 10.00am - 11.30am GMT

Meeting via Zoom - details have been emailed

Met Office: CH, MD, JH, FM, CN, MS, AJH

Cambridge: NLA

Leeds: DG, MR, GM

NIWA:

CSIRO:

Apologies: FOC, JW

Actions from this meeting

(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) GM/DG to update table on UKCA wiki documenting GLOMAP versions. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA.
(ongoing) NLA to feedback comments to JH on updated API document (reflecting the UMvn13.0 release) before it can be circulated.
(ongoing) Unprotected rose-stem options: MD to look at highorder_scheme.
(ongoing) Unprotected rose-stem options: AJH to look at i_mode_setup=6
(ongoing) ALL look at um:#6203 showing other unprotected rose-stem options and think about any code/settings they are interested in.
(ongoing) ALL to consider who is best to add a test for 2-D photolysis as part of Photolysis API changes. Could be part of box model tests.
(ongoing) NLA, AJH to identify owners for TropChem and StratChem items in the Desirable changes not Tested Table. AJH to arrange call with NLA. Should also update the UKCA UMDP to reflect which configurations are supported/widely used.
(new) AJH to check over list and see which have been completed.
(new) NLA to follow up with JM about UKESM2 package testing.
(new) DG - activation change/possible bug to implement.
(new) NLA to send Doodle poll for the middle to the end of March 2023

Actions from the Last Meeting (NLA)

Minutes of the code management group meeting 2022-11-16

(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
(ongoing) Monsoon users MASS data Management. Removal commands issued for ~550 umui jobs (total 175Tb). Still need to issue commands for other jobs. MD/NLA to discuss this with Monsoon by email and at next MMG
- MD - clarified that it will be one big project on new HPC, asked for ownership to be transferred to MD. MD will do another round this year chasing up old data.
- Close
(ongoing) GM/DG/MR to update table on UKCA wiki documenting GLOMAP versions. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA.
- Has been updated, need to give jobids/suite-ids. Currently mainly UMUI-based, need to work on putting back into latest version. Have had discussions between GM/DG/AJ. Also have updates to PSC.
- Remove MR from this action
- DG to make account on UKCA wiki and GM/DG to update table
(ongoing) NLA to feedback comments to JH on updated API document (reflecting the UMvn13.0 release) before it can be circulated.
- Ongoing - might be some minor updates, but comment on current doc
(ongoing) Unprotected rose-stem options: MD to look at highorder_scheme.
- Ongoing - have consolidated code changes
(ongoing) Unprotected rose-stem options: AJH to look at i_mode_setup=6
- Ongoing - not ready for UMvn13.2
(ongoing) ALL look at um:#6203 showing other unprotected rose-stem options and think about any code/settings they are interested in.
- Ongoing
(ongoing) ALL to consider who is best to add a test for 2-D photolysis as part of Photolysis API changes. Could be part of box model tests.
- Ongoing, API work is delayed
(ongoing) NLA, AJH to identify owners for TropChem and StratChem items in the Desirable changes not Tested Table. AJH to arrange call with NLA. Should also update the UKCA UMDP to reflect which configurations are supported/widely used.
- Ongoing
(ongoing) OM and AJ to discuss the modal dust scheme
- Have had some meetings. Changes ported from CLASSIC dust to modal dust
- Closed
(new) NLA to change standalone UKCA milestone as date will be missed.
- Closed
(new) NLA to send Doodle poll for mid-end January.
- Close

Standing actions

(ongoing - standing item) CMG to monitor list of bugs and circulate between group for owners.
(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).
(ongoing - standing item) ALL with access to keep monitoring ukca_bugs email list.
(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.
(ongoing - standing item) ALL to note, review, and remove obsolete/redundant code
(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.
(ongoing - standing item) Code Owner to produce draft newsletter for CMG to approve.
(ongoing - standing item) ALL to consider other rose-stem tests that could be included.
(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 KEYWORD FOR ALL UKCA CHANGES THIS RELEASE

Also see overview ticket um:#7094

NOTE: The UM requirement for LFric testing of all changes under UM:src/atmosphere, UKCA:src/science, and UKCA:src/control/core

Please also give any feedback on the UMvn13.2 release cycle to NLA to pass-back to UM Sys.

Message from UM Sys - please take care when considering keywords. It is important to get these correct for the Code Review process.

AJH ticket ukca:#7/um:#6630 will clash with everything - will ask to do last.

Difficulties with LFRic cycle, versioning, and when they release.

AJH will work out clashes on Code Review day.

Update on UKCA API redesign (JH)

JH - current improves interface for non-UM builds. Turning deposition & lumping on & off, reducing the number of input fields. Have also revamped the diagnostic output debugging input fields, now covers all required input fields. Will do automatically without having to duplicate logic, and can change also change the timestep when you get the output, e.g. for fields with a diurnal cycle etc., or have issues later in the run. Should be able to do in the UM too. Next priority is to implement the diagnostic handling system outside of the UM (not individual diags, just top-level functionality).

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.	Updated testing coverage on Linux and can run 1x1 decomposition
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. See UKCA Box Model page
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. UKCA removed from UM at UMvn13.0 - see UKCA repo
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. AJH - some of this has been done or is in progress.
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) Aerosol Dry Deposition will be considered in the JULES context once the gas-phase changes have been committed.	Completed for UM13.1
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

Action: AJH to check over list and see which have been completed.

Action: NLA to follow up with JM about UKESM2 package testing.

Bugs/Bugfixes (NLA)

Open Bugs

#	Description	Ticket	Owner	Comments	Comments from this meeting
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 Tested it quickly - N2 is used from namelist but not obvious, but H2 needs further testing
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 Nice to do ASAP, but if just diagnostics might be able to do at a later time.
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? MD has opened a ticket to see which ones fail and which ones work
140	Heaviside Function cannot have multiple level sets	um:#6816		The Heaviside function needed to scale UKCA pressure-level diagnostics is valid only for a single set of pressure levels from Stash requests. If some Sec 51/52 diagnostics are requested on say 19 pressure-levels and the same/ different ones on 36 pressure-levels, the Heaviside field in output will be applicable to only one of these. May be able to request multiple Heaviside functions
141	The area variable used for units conversion of GLOMAP primary emission diagnostics (38-20X) is calculated erroneously in LAMs (or with rotated pole).			Fix is to use the surf_area variable used for other calculations. Impact on concerned diags in Global runs being assessed MD assessing impact. MD has a fix, calculates 3D and passes it via API
143	Error in print statements from UKCA_TRACERS_COPY_FROM_UM			The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber.
144	interchangeable use of specific humidity and water vapour mixing ratio	#6813		UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket #6660 (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected.	JH doesn’t think it’s complicated but not particularly trivial either.
145	all_ntp not explicitly dimensioned in UKCA_MAIN	Possible fix here		all_ntp not being dimensioned explicitly in ukca_main1-ukca_main1.F90. Highlighted in NCAS CMS ticket https://cms-helpdesk.ncas.ac.uk/t/nested-ukca-suite-on-archer2/604 raised by Paul Field. Grenville Lister has found the cause and implemented a possible fix https://code.metoffice.gov.uk/trac/um/changeset/110132/main/branches/dev/grenvillelister/vn12.0_all_ntp_fix
147	Missing products in Sec-50 diagnostics: Mismatch in ukca_chem_master and asad_flux_dat 50-092 STRATOSPHERIC OH LOSS (B153) Products for (OH + H2) changed under scheme v121 but not reflected in asad_flux_dat 50-123 STRAT O3 LOSS: HO2 + NO3 (B61) Product O2 not available for StratTrop After chem v121/ always		Luke Abraham	NLA to take a look

Action: DG - activation change/possible bug to implement.

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
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.

A lot of changes tied up with GA6/7. May be taking GA6 away soon. GA7 is tied to UKESM1, but should be able to remove once UKESM1.1 paper is published.

AJH may be able to remove 9 PFT option, but it might be better to do when removing other dry-dep temporary logicals.

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	Remarks
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
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
DG	Now working for UKESM team

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

Date of next meeting (NLA)

Action: NLA to send Doodle poll for the middle to the end of March 2023