Minutes of the code management group meeting 2020-05-05
Teleconference Details
Tuesday 5th March 2020, 10am - 11.30am GMT
Meeting via Zoom - details have been emailed
Met Office: CH, FM, MG, MS, MD, JH, NC
Cambridge: LA
Leeds: MR, DG
Reading:
Lancaster:
Edinburgh:
UEA:
NIWA: OM
CSIRO: AL
Apologies: AH, 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) ALL to consider Monsoon users MASS data plan and feedback to FOC. Please also include suggestions for local points of contact. AH/FOC to assign people following feedback
- (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) JH to update API document and ask for further feedback on this when completed
- (ongoing) GM (supported by KP/MY/AH) to make table on UKCA wiki documenting this. LA to email. See GLOMAP versions. LA to email GM
- (ongoing) LA to add N48 Linux and update EXP test
- (ongoing) LA to contact AJH/GM offline regarding coupling StratTrop to GLOMAP-CLIM
- (ongoing) DG to progress fix for bug #114. LA to check original email for details & update table. LA contact DG offline
- (new) LA to contact GF about bug #109 (Bug in dry deposition of CH4 for 13/17/27 tiles)
- (new) LA to update MOSRS links in Bugfixes table and include HG's bug
- (new) LA to send round Doodle Poll for the first 2 weeks of July.
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 2020-03-20
- (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) ALL to consider Monsoon users MASS data plan and feedback to FOC. Please also include suggestions for local points of contact. LA to check with FOC on progress
- Ongoing. Will try to assign POCs in coming weeks
- (ongoing) AH/FOC to assign people following feedback
- Closed. Fold-in with above action
- (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
- (ongoing) JH to update API document and ask for further feedback on this when completed
- Ongoing. LA to send feedback ASAP
- (ongoing) GM (supported by KP/MY/AH) to make table on UKCA wiki documenting this. LA to email. See GLOMAP versions. LA to email GM
- Ongoing. LA to chase GM
- (ongoing) FOC will contact OW regarding FastJX-GLOMAP coupling
- Closed. Code branch provided and being examined. In progress.
- (ongoing) LA to add N48 Linux and update EXP test
- Ongoing
- (ongoing) LA to contact AJH/GM offline regarding coupling StratTrop to GLOMAP-CLIM
- Ongoing
- (ongoing) DG to progress fix for bug #114. LA to check original email for details & update table. LA contact DG offline.
- Ongoing. Work progressing, needs more testing and long runs. LA to update with MOSRS ticket
- (ongoing) JM to send informal email to GH with updates, cc LA (re: Dry Deposition Bug #35)
- Closed. Progress is being made, aiming to work in offline JULES first prior to full interactive UM runs.
- (new) LA to email Maff Glover, AJH, & MR about Bug #117 (um:#4954) and ask for an opinion.
- Closed. Not a bug.
- (new) LA to open a ticket for Bug #119, cc JM, NC (Incorrect calculation for gridbox area - only affects GLOMAP-mode diagnostics)
- Closed. um:#5506
- (new) MD to take on the ticket for Bug #120 (nr_steps warning message)
- Closed. Committed.
- (new) FM to forward Ben Drummond email about Dry Deposition to AJH & JM
- Closed. Have had a few exchanges. No need for a ticket, Ben has a branch.
- (new) Relevant person take ownership of Redundant Code #21 (L_ukca_stratclim) as part of API work
- Closed. NC has taken ownership.
- (new) LA to follow-up with João Teixeira for the exp test with Inferno.
- Closed. Should progress for vn11.7
- (new) JM to point out various papers describing set ups with their acronyms.
- Closed. MR to forward to LA for inclusion on Wiki.
- (new) LA to arrange WebEx for the next meeting.
- Closed.
- (new) LA to make Doodle Poll over the weeks of the 27th April to 15th May.
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
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. LA to email GH, cc JM JM to email GH |
|
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 Bump for vn11.7 LA may be able to progress. Versioning has been done separately. Another issue was added to this recently, to do with formation of H2O - may have an impact |
Some CRI fixes needed too. May not be able to progress for vn11.7 |
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 Bump for vn11.7 |
|
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 Planned for vn11.7. JM to check for clashes with Steve Rumbold. Will add to vn11.7 group ticket. Guang Zeng at NIWA to review ddep resistances. JM to check with GZ about a new ticket for this. Code is complex and hard to read with temporary logicals |
Ticket closed, will be fixed in um:#5167 owned by MS. Nearly ready for approval |
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 Bump for vn11.7 May be OK to lodge for vn11.7, but correction is hard-wired in postprocessing scripts. JM to check whether a later version is needed |
Bump to a later version |
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) Only impacts emission driven runs. |
LA to check with Gerd about this issue |
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. |
Currently testing. May not make vn11.7. |
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. |
um:#5233 | DG has a vn10.8 branch, but changes are self-contained. See ticket um:#5233. DG to progress ticket. LA to check original email for details & update table. LA contact DG offline. LA to discuss with DG offline to see about progressing |
LA to update with MOSRS ticket, may make vn11.7 | |
119 | Incorrect calculation for gridbox area - only affects GLOMAP-mode diagnostics | um:#5506 | Calculation of volume appears correct, but area is not. This calculation is missing the factor fv_cos_theta_latitude so will not cause area to tend towards zero at the poles. It also seems to use an unnecessary approximation to the latitude difference (based on sinv_latitude ) which may break down at high latitudes. The calculation should perhaps be consistent with subsequent volume calculation but without the delta_r factor. This will likely only affect diagnostics calculated in ukca_emiss_diags_mode , where it is used to convert from kg/m2/s to mol/gridbox/s, although it is also printed out in ukca_aero_ctl . JH spotted. Just diagnostic affected. LA to open a ticket. cc JM, NC |
LA to update with MOSRS ticket | |
120 | nr_steps warning message - eg um_n48_ga_amip_exp | UM:#5505 | Perhaps this should have a clean fail rather than warning? There may be a lot of rose-meta and code changes to allow nr_steps to be set in niche cases. Some chemistry schemes seem to need an NRSTEPS value when they shouldn’t. MD to take on the ticket. |
Closed - lodged | |
122 | O(1D) is calculated incorrectly as a steady-state species Only affects the diagnostic. Values are a factor of 3 too large |
UM:#5525 | Luke Abraham | Currently in code review | Closed - lodged |
There is also a bug from HG that needs to be included in this table.
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:#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 |
Update on UKCA API redesign
4 API tickets targeted at vn11.7:
- um:#4948 Handling of Configuration Data for UKCA API
- um:#5128 Reference Data Handling for new UKCA API
- um:#5488 UKCA API changes: Reference data handling: aerosol SAD
- um:#5554 Refactor offline oxidants input for revised UKCA API
Mohit and Neal are working on tickets to change the handling of reference data from sequential files. These data will now be read and interpolated outside UKCA and passed in to UKCA namespace in the same way as other environmental driver fields using the ukca_set_environment API routine.
Input of offline oxidant data from NetCDF files will be treated similarly but this ticket is likely to be bumped to vn11.8. John is working on configuration data handling, focussing on the data (primarily namelist data) currently provided by ukca_option_mod. This module will become a UM-side module and all configuration variables will be passed to UKCA via the ukca_setup argument list. Within UKCA, they will be held in derived type structures ukca_config and glomap_config and accessed from there instead of from ukca_option_mod. The resulting ticket is quite large, affecting over 100 UKCA modules (mostly with minor changes), so unfortunately will have a high potential of causing merge conflicts. There are a small number of associated structural changes including splitting up the validation of configuration inputs between UM-specific checks that will be done outside UKCA and the remaining UKCA checks that will be done internally.
There remains a large amount of interface work to be done which will inevitable spread over a number of future UM release cycles. Once the revised design document is available, John would like to encourage people to send in their comments and also have a look at the tasks remaining and consider whether there are any that they might like to get involved with to help speed up the process.
Progress with Priorities (LA)
The current priorities are:
# | Description | Owner |
---|---|---|
1 | UKCA API | John Hemmings |
2 | Review UKCA tests to cover all requirements | Luke Abraham / Mohit Dalvi |
3 | Updates/fixes to GLOMAP routines | |
4 | Standalone UKCA configurations | Luke Abraham |
5 | Emissions flexibility | Mohit Dalvi |
6 | Separare UKCA repository | Luke Abraham |
7 | Non-API LFRic work, e.g. I/O, diagnostics etc. | |
8 | RADAER optimisation | |
9 | FastJX-GLOMAP coupling | |
10 | Cloud-J | |
11 | Fixes for chemistry rates and ASAD (bugs #101 & #103) | Luke Abraham |
12 | Rc fixes for water (bug #104) | UKESM Core Team |
13 | CH4 deposition fixes (bug #109) | Gerd Folberth |
14 | UKCA STASHmaster PP-codes | Luke Abraham |
15 | Removal of redundant code | ALL |
16 | GLOMAP-CLIM API refresh | Alan Hewitt |
17 | N48L85 configuration | |
18 | ACTIVATE optimisation |
UM11.7 Tickets
See here for UM vn11.7 tickets on MOSRS.
PLEASE REMEMBER TO USE THE UKCA KEYWORD FOR ALL UKCA CHANGES
NOTE: New requirement for LFric testing
of all changes under src/atmosphere (MD)
PLEASE ADD YOUR UKCA TICKETS TO GROUP TICKET um:#5495
REMEMBER TO "BUMP" TICKETS TO A LATER VERSION (OR "HOPEFULLY") IF IT WILL NOT MAKE THE VN11.7 DEADLINE OF 22ND MAY 2020
The UM Systems Team have highlighted potential issues about how the working will be in the current conditions. They may have to bump some non-urgent tickets.
AOB/DNM (LA)
Date of next meeting (LA)
LA to send round Doodle Poll for the first 2 weeks of July.