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

Code management group minutes

Teleconference Details

Monday 12th November 2018, 10am - 11.30am GMT

• UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
• Participant PIN: 232764

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), Scott Archer-Nicolls (SAN), Paul Griffiths (PTG)

Leeds: Chris Dearden (CD), Kirsty Pringle (KP), Mark Richardson (MR), Graham Mann (GM)

Reading:

Lancaster: Ryan Hossaini (RH), Ewa Bednarz (EB), Michael Hollaway (MH)

Edinburgh:

UEA:

NIWA: Olaf Morgenstern (OM)

CSIRO: Ashok Luhar (AL)

Apologies: Nicolas Bellouin (NB), Colin Johnson (CEJ)

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. (new) 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.
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.
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. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
12. (ongoing) MR to discuss with KP implications for GLOMAP in regards to a separate UKCA repository
13. (new) LA to forward NERC proposal to Leeds.
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
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
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. (ongoing) JM to do a catch-call ticket for GMED
18. (ongoing) LN to l_fix_nh4no3_equilibrium in rose-stem and jobs and remove if necessary.
19. (new) JM to open ticket and new bug for SO2 deposition.
20. (new) LA, JM, CEJ, SAN to discuss rate fixes offline and keep GM in loop.
21. (new) LA to contact AS and ask how best to proceed with removing the depreciated NetCDF attribute options.
22. (new) MD to back-port STE fixes to UM11.0 suite.
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.
24. (new) LA to take ownership of ticket um:#4397(GA7 NR Offline test).
25. (new) LA to send round Doodle poll for middle of January.

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 2018-09-05

One-off actions

1. (ongoing) MY to check GLOMAP-mode code and report any missing bug fixes on the bugfixes page.
   • MY starts in December for 4 months.
   • Action: GM/MY to arrange telecon with LA when MY starts.
2. (ongoing) LA to liaise with MY, and to chase MY and GM as to when this would be done.
   • 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.
   • 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.
   • Ongoing - will do at vn11.2
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.
   • AQUM tests will be straight-forward to check.
   • Action: LA to make a branch and progress for vn11.3
8. (new) AJH to open ticket and assign to himself regarding loops over imode+n and imode-n.
   • Ongoing - ticket opened UM:#4284.
   • Currently code is inflexible if add an extra mode. NB has similar ticket working on simplifications.
   • Discuss with GM offline.
9. (ongoing) MD/LA to talk about releases offline, and set up free-running and nudged GA7.1+StratTrop TS2000ish timeslice, with instructions to make it transient.
   • See agenda item below.
10. (new) NLA/MD make script for perpetual nudging (symbolic linking to existing files).
    • Ongoing.
11. (new) NLA to port suite to ARCHER.
    • Closed.
12. (ongoing) LA to create Wiki page on UKCA website for users to add details of configurations and input files.
    • Ongoing.
13. (ongoing) ALL to review output from vn11.0 release candidate(s).
    • Closed. OM commented that Stratosphere looked good. LA highlighted that Stratospheric NOy is now merely low-biased.
14. (new) MD to provide vn11.0 release candidate output again.
    • Closed.
15. (ongoing) FOC to circulate doodle poll for further emissions discussion to CMG for all to fill-in. That meeting to report to CMG
    • Closed. Report at next CMG.
16. (ongoing) MR to discuss with KP implications for GLOMAP in regards to a separate UKCA repository
    • Ongoing, with general agreement that this needs to be done and is a good thing.
    • Action: LA to forward NERC proposal to Leeds.
17. (new) NLA to contact CEJ (cc JM) about trace-gas convective plume scavenging and how this will be impacted (or impact) the repository work
    • Ongoing
18. (ongoing) LA to contact FOC, AH, MR, KP, ATA, Ken Carslaw, Philip Stier regarding taking the proposal for a separate code repository forward.
    • Closed. Generally positive feedback.
19. (ongoing) FOC to see what action can be taken from MASS, then put out an email for POCs from institutes.
    • Combine this in with action
    • AH & FOC will take joint responsibility, and are still working out what information they can get on current usage and users.
    • Roll discussion to next CMG.
20. (new) FOC/AH/MD to develop a strategy on MASS for discussion at next
    • Closed. Join with action above.
21. (new) FOC to contact Garry Hayman to highlight bug #35.
    • Closed.
22. (new) JM to take ownership of redundant code item #6 (Wet oxidation of SO2 in GLOMAP).
    • Closed.
    • Action: JM to open a ticket and add to redundant code table.
    • Keep GM/MY in the loop
23. (new) LN to document redundant code item #9 (Deprecated UKCA netcdf attribute options).
    • Closed - see below.
24. (new) JM to do a catch-call ticket for GMED
    • Ongoing
25. (new) LN to l_fix_nh4no3_equilibrium in rose-stem and jobs and remove if necessary.
    • Ticket open for vn11.3
    • Already used in GA series, so should be quick to close.
26. (new) NLA to do doodle poll for 90 minute meeting in first 2 weeks in November.
    • 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. See action.	Leave open. JM found bug in SO2 deposition, where there is an inconsistency when change tiles. Action: JM to open ticket and new bug.
87	Possible issues with YSTORE in UKCA_CHEMISTRY_CTL.	UM:#3245	Colin Johnson / Luke Abraham		Leave open. NLA to have another look. MS may have changed things with OMP changes.	Ongoing.
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. Leave open.	Ongoing. This just limits options. Leave until code is reorganised.
100	Negative concentrations of pvol_wat()	UM:#4383	Alan J. Hewitt	Work ongoing to lodge at vn11.3		In SciTech.
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. Action: LA, JM, CEJ, SAN to discuss offline and keep GM in loop.

Comments from CEJ:

The Sulphur cycle has been in the spotlight because of cooling in the UKESM1 historical runs.   One reason for this may be that the Strattrop mechanism has no DMSO and hence an unrealistic SO2 production from the DMS + OH addition reaction.   This is stated as DMS + OH => SO2 + MSA without any product yields which is clearly wrong.  As DMSO is still a tracer still I propose we reinstate the OH addition reaction as DMS + OH => 0.6SO2 + 0.4DMSO + MeOO as before and have the DMSO + OH reaction reinstated (DMSO has dry + wet deposition too).  I will do a branch for this, and also another to add diagnostics for the sulphur cycle reactions which are missing and for the marine source of OC which needs to be budgeted too.

Adding the DMSO reaction reduces the SO2 burden by around 4 %.   There are also some corrections to the SO2 dry deposition to make.

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. Action: LA to contact AS and ask how best to proceed.
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

UKCA Release Job (LA/MD)

Release Job UM11.0

See previous comments under actions from the last meeting.

ATA -- I have had a look at the Chemistry evaluation output. In general vn11 looks good to be released. As with other release versions I think it is important that we probably summarise a number of "features" of the model output. For example, the O3 STE is very low. I know Mohit has recently fixed the diagnostic and it would be good if this fix could be added and new output generated to confirm that the STE is so low. The other bits of the budget however look fine. The methane lifetime is a bit too short. But the age of air looks good relative to SF6. etc etc.

Action: MD to back-port STE fixes.

Note that UKESM1 release will be at vn11.1 or vn11.2 - this is still TBD.

It was decided to advertise the UM11.0 suites ASAP, by sending to the UKCA training/lecturers list as well as the CMG.

Action: 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.

At future UM releases an equivalent configuration will be made and tested, making an list equivalent to the GA table across versions. Similarly, GA8 versions will be made when available.

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.

Tickets targeting vn11.3

UM vn11.3 code review submission deadline is 7th Feb 2019. SOCRATES/JULES/GCOM/CASIM/KGO by 31st Jan 2019.

#	Description
UM:#2689	Enable coupling of GLOMAP-MODE Aerosol to FAST-JX photolysis.
UM:#3127	Investigate KGO differences in um_n48_ukca_eg app using GNU on the Cray
UM:#3292	Consolidate constant variables used by UKCA
UM:#3367	Removing transport of peroxy radical tracers in Strattrop (CHeST)
UM:#3779	Improvements to the inline comments in ukca_option_mod
UM:#3959	RO2-Permutation Chemistry
UM:#3997	Retire temporary logical l_fix_improve_drydep
UM:#4001	Magic numbers in ukca_setup_chem_mod.F90
UM:#4020	Improved calculation of ozone dry deposition to ocean - surface resistance term
UM:#4024	Triggering of i_ukca_dms_flux by l_sulpc_so2
UM:#4131	Enable use of ASAD Backward-Euler solver with UKCA offline oxidants chemistry
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:#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:#4383	Calculation of wts() masswaterkg() mdwat() pvol_wat()
UM:#4397	Rose stem test for i_ukca_chem=54

Owner for 4397

Ticket um:#3606 made fixes to allow the Newton-Raphson Offline Oxidants scheem to work, but there is currently no rose-stem test for this configuration to protect it. Ticket um:#4397 has been created for this, but currently does not have an owner.

Action: LA to take ownership.

AOB/DNM (LA)

• Note that from vn11.2 the UKCA GUI panel has changed. Care should be taken with the sort-key to ensure that new items are added after the one they are triggered from.

• UKCA training is 8th-10th January in Cambridge. This is just the practicals.
  • https://www.ncas.ac.uk/en/introduction-to-ukca-course
  • Lectures from last year are available on this wiki.

Date of next meeting (LA)

Action: LA to send round Doodle poll for middle of January.