Minutes of the code management group meeting 2019-11-04
Teleconference Details
Monday 4th November 2019, 10am - 11.30am GMT
- UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
- Participant PIN: 311041
Met Office: AJH, MS, MG, NC, JH, VB, MD, JM
Cambridge: LA
Leeds: MR, WF, DG, KP
Reading: NB
Lancaster:
Edinburgh:
UEA:
NIWA: OM
CSIRO:
Apologies: FOC
Actions from this meeting
- (ongoing) LA to put
C_SPECIES
definitions in the Redundant Code table (short-term), and switch to useM_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 vn11.6. - (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) LA to contact AS/AJH and ask how best to proceed with removing the depreciated NetCDF attribute options. Do after GA8 is released as still required for GA7.
- (ongoing) ALL to read API document and look through new API code and send comments to JH
- (ongoing) GM (supported by KP/MY/AH) to make table on UKCA wiki documenting this. LA to email.
- (ongoing) LA to contact MH/OW regarding FastJX-GLOMAP coupling. Follow-up after UMvn11.5 is released. LA to check with FOC about who will do this.
- (ongoing) MD to update um_ukca_eg app to be more in line with UKESM1, and add a rigorous test.
- (ongoing) LA to add N48 Linux and update EXP test
- (ongoing) ALL to make changes to Testing Requirements for UKCA Code Changes wiki page as they see fit.
- (ongoing) MR & LA to talk offline regarding Chris Dearden's tickets.
- (ongoing) LA to contact AJH/GM offline regarding coupling StratTrop to GLOMAP-CLIM
- (new) DG to progress fix for bug #114. LA to check original email for details & update table. LA contact DG offline.
- (new) LA to add names against list of priorities.
- (new) MD to make vn11.5 AMIP release jobs and document on wiki
- (new) ALL to aid their vn11.6 tickets to um:#5249 to allow a commit order to be determined.
- (new) LA to arrange a Doodle poll for the week of the 13th January 2020.
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 LA with suggestions for next set of tutorials
Minutes
Actions from the Last Meeting (LA)
Minutes of the code management group meeting 2019-09-16
- (ongoing) LA to put
C_SPECIES
definitions in the Redundant Code table (short-term), and switch to useM_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 vn11.6.- Ongoing
- (ongoing) LA check MD's script for perpetual nudging.
- Closed
- MD to add to releases page. ERA-5 work on progress.
- (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
- MD has a draft page. will link when signed off.
- (ongoing) JM to find someone to progress ticket/bugfix for SO2 deposition. Will need to be on a switch for UKESM1. LA to follow-up with JM
- Closed
- Will be covered by core group. Still deciding on best strategy. May wait for new year.
- (ongoing) LA to contact AS/AJH and ask how best to proceed with removing the depreciated NetCDF attribute options. Do after GA8 is released as still required for GA7.
- Ongoing
- There is a group looking at NetCDF files in the Met Office. AJH to attend meeting.
- (ongoing) FOC to encourage Garry Hayman to start lodging JULES code piecemeal.
- Closed
- LA & JM attended teleconference with GH a few weeks ago and made these points.
- (ongoing) ALL to read API document and look through new API code and send comments to JH
- Ongoing
- Schedule is rather out of date. JH is still keen to have comments.
- (ongoing) GM (supported by KP/MY/AH) to make table on UKCA wiki documenting this. LA to email.
- Ongoing
- LA to email again.
- (ongoing) Those with access check ukca_bugs regularly via OWA until Outlook access is fixed.
- Closed
- (ongoing) LA to contact MH/OW regarding FastJX-GLOMAP coupling. Follow-up after UMvn11.5 is released.
- Ongoing
- LA to check with FOC about who will do this.
- (ongoing) MD to update um_ukca_eg app to be more in line with UKESM1, and add a rigorous test. Age-of-air to be added.
- Ongoing
- Age of air has been added. Main app to be added for 11.6. AJH could SciTech.
- (ongoing) LA to add N48 Linux and update EXP test
- Ongoing
- (ongoing) ALL to consider other rose-stem tests that could be included
- Closed
- Move to standing actions
- (ongoing) ALL to email LA with suggestions for next set of tutorials
- Closed
- Move to standing actions
- (new) LA to ask GF to add more details to ticket UM:#4913 to understand the problem (bug #109)
- Closed
- LA to update wiki pages and email GF & AJH
- (new) ALL to consider thinking about fixing bug #113 (see UM:#5119)
- Closed
- JH to take ownership
- (new) GM to email AH/KC regarding nitrate
- Closed
- (new) ALL to make changes to Testing Requirements for UKCA Code Changes wiki page as they see fit.
- Ongoing
- (new) MR & LA to talk offline regarding Chris Dearden's tickets.
- Ongoing
- (new) LA to contact AJH/GM offline regarding coupling StratTrop to GLOMAP-CLIM
- Ongoing
- (new) LA to send message to Paul Agnew regarding an AQUM representative to these meetings
- Closed
- (new) LA to send Doodle poll for early November.
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.
Bugs/Bugfixes (LA)
Open Bugs
# | Description | Ticket | Owner | Comments | 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. FOC to encourage Garry Hayman to start lodging JULES code piecemeal. |
|
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. LA to do with #103 Do for vn11.6. Quite a large ticket. |
Hope to progress for vn11.6 |
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 LA to do with #101 |
|
104 | Incorrect value for Rc for SO_2 deposition to open water | UM:#4635 | Catherine Hardacre | Got to be separate to #35, unless there is an idea of timelines. JM to find someone to progress bug #104. LA to follow-up with JM |
Core group to do in new year |
107 | Missing c_h2o conversion factor in offline_oxidants_be | um:#5118 |
Luke Abraham | Code is zq(:)=RESHAPE(q(:,:,k),(/theta_field_size/)) rather than zq(:) = RESHAPE(q(:,:,k),(/theta_field_size/))/c_h2o LA to take ownership and assess |
Do for vn11.6 |
108 | Incorrect stash processing of GLOMAP load*, conc* and plume_scav diagnostics | UM:#4909 | Mohit Dalvi | To be Lodged after 10.6 Do after CMIP6 runs are finished (after Jan 2020) |
Timeline still on track |
109 | Bug in dry deposition of CH4 for 13/17/27 tiles | UM:#4913 | Gerd Folberth | To be Lodged after 10.6 Gerd noted unusual CH4 output in CMIP6 runs. May need a rose stem test for H2 and CH4 drdydep code lodged at UM:#4157 Makes a huge difference to CH4. Needs testing. AJH or GF will do during vn11.4, progress for vn11.6. May need UKESM1 approval. Code is difficult to understand. AJH thinks GarryH is aware of this problem. LA to ask GF to add more details |
GF has emailed. LA to update wiki pages (see below) |
110 | UKCA solar-cycle routine does not pass NRUN-CRUN test | UM:#4828 | Luke Abraham | To be Lodged after 11.5 Have a solution. |
Solution is a bit tricky to check the logic correctly. |
111 | Cloud fraction array (cloud_frac) passed with wrong number of levels Array passed as (row_length, rows, :), so offset by 1 level under ENDGame |
Part of UM:#4822 | John Hemmings | Affects all ENDGame versions. To be Lodged for 11.5 Do as separate ticket after #4822 committed. MD #5009 testing |
Some issues with Code Owner approval. Will do for vn11.6 |
112 | delh2so4_chem is calculated incorrectly | UM:#5076 | Luke Abraham | To be Lodged for 11.6. Incorrectly "fixed" in UM:#3245 (Bug #87). All StratTrop+GLOMAP versions post vn8.2. Made worse post-vn11.4 if logical l_fix_ukca_h2so4_ystore is True. |
CEJ to SciTech |
113 | Latitude bugs affecting LAM configurations | UM:#5119 | John Hemmings | To be lodged for 11.6 ALL to consider thinking about fixing bug #113 (see UM:#5119) |
JH to progress |
114 | Bug in ukca_activate leading to droplet numbers being too high in the upper regions of continuous cloud columns Previously the number per m3 was replicated upwards from cloud base, but really this should be the number per kg of air to mimic what would happen in a rising air parcel (parcel expansion would lead to the number per m3 reducing with height as an air parcel rises, scaling with the air density). This is likely to make the largest difference for deep clouds where there are deep contiguous columns. |
DG has a vn10.8 branch, but changes are self-contained. See ticket um:#5233. ACTION: DG to progress ticket. LA to check original email for details & update table. LA contact DG offline. | |||
115 | Some UKCA-related variables accessed in other parts of UM remain undefined in non-UKCA configurations (Was: Suite that does not call GLOMAP mode setup) |
UM:#5151 | Alan J Hewitt | To be lodged for 11.6 | Niche use case found in BoM. AJH or MD may progress actual fix. Temporary fix is in place for vn11.6. |
116 | Problem with the "specific humidity change from UKCA" diagnostic (stashcode 50240) See information in UM:#4819 |
UM:#5164 | Needs further investigation. LA to have a look. JH to cc CEJ onto ticket. |
Update on bug #109 from GF
- At first we just activated CH4 dry deposition in UKESM1 without making any further code changes. In the ensuing test run 3/4 of the entire CH4 burden was lost from the atmosphere within the first year of the run. I narrowed down the issue to the logic that we built into surfddr to accommodate the various land tile options (9, 13, 17, 27) which resulted in some of the baseline parameters to be initialised to nearly infinity. But in case of CH4 these parameters have a different meaning: they are uptake rates. Consequently, the dry deposition velocity came out to nearly infinity as well at some gridboxes. Needless to say, that caused severe problems.
- I am also not quite happy with the way the todo list is determined. The way its done now means that we have uptake to vegetation in places where there is no vegetation (a bit complicated to explain in just a few words). Its not a huge problem, though, but I’d like it to be discussed at some point in time.
- More critical in my mind is the fact that something is wrong with the initialisation of variables. I added a whole lot of per-PFT diagnostics to the model to analyse the dry deposition code. Setting the deposition rates to zero in surfddr at the very end of the routine should produce diagnostic output that shows deposition rates on PFTs to be zero. However, for quite a number of PFTs and all species the diagnostics are not empty. I don’t understand this and while it doesn’t seem to have an impact on the gridbox deposition velocity (as far as I could tell) I would like to understand this weird behaviour.
- Surfddr is essentially unreadable for people who are new to and/or unfamiliar with UKCA and dry deposition, but we know this already. It took me the best part of two weeks to fully understand the flow of the routine.
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. 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? |
|
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:#4875 | 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 | |
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 |
Update on 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 thanks ALL for their patience during closed release. 3 major tickets have gone in. Environment fields and tracers are set. UKCA can be interrogated for what it needs. Tracer mapping done by UM. MD did the emissions. Outstanding work: diagnostics and UM calls within UKCA. Configuration variables & other inputs need to be handled differently - e.g. shared modules from UM.
Will be work outstanding for multiple release cycles. Certain things that need to be done for LFRic are done as a priority. Talk to Adrian about standalone code. There will still be work outstanding after 11.6. Diagnostics less of an issue for LFRic. Offline-Oxidants+GLOMAP the priority.
Progress with Priorities (LA)
The current priorities are:
- UKCA API
- Review UKCA tests to cover all requirements
- Fix for c_h2o in Offline-Oxidants (bug #107)
- Updates/fixes to GLOMAP routines
- Standalone UKCA configurations
- Emissions flexibility
- Separare UKCA repository
- ACTIVATE optimisation
- FastJX-GLOMAP coupling
- Cloud-J
- Fixes for chemistry rates and ASAD (bugs #101 & #103)
- Rc fixes for water (bug #104)
- CH4 deposition fixes (bug #109)
- UKCA STASHmaster PP-codes
- Removal of redundant code
- GLOMAP-CLIM API refresh
- N48L85 configuration
AJH has some thoughts on ACTIVATE optimisation. Would like to refactor so don’t get a science change.
JM pointed out that there are no names by the list of priorities.
ACTION: LA to add names to priorities.
UM11.6 Tickets
See here for UM vn11.6 tickets on MOSRS.
PLEASE REMEMBER TO USE THE UKCA KEYWORD FOR ALL UKCA CHANGES
Steve Rumbold will work on additional SO2 dry dep for vn11.6.
ACTION: MD to make vn11.5 AMIP release jobs and document on wiki
AOB/DNM (LA)
LA: UM Developers and Owners Group meeting later today - Might have another situation where there are a lot of tickets for vn11.6. Should we consider producing an order for UMsys? Might depend on how many tickets are going. Could propose a ticket order page.
Follow-up - this was raised at the UM DOG. Ticket um:#5249 has been created for this purpose.
ACTION: ALL to aid their vn11.6 tickets to um:#5249 to allow a commit order to be determined.
AJH - UM ticket on last release for changing argument list. Associated LFRic ticket. Going along quite well. Should have climatology functionality within LFRic. Don’t want to port CLASSIC.
Date of next meeting (LA)
ACTION: LA to arrange a Doodle poll for the week of the 13th January 2020.