Minutes of the code management group meeting 2016-01-12
Mohit Dalvi (MD), Nick Savage (NS), Fiona O'Connor (FOC), Alan Hewitt (AH), Nicolas Bellouin (NB), Mark Richardson (MR), Colin Johnson, Paul Griffiths (PG), John Hemmings (JH)
Apologies: Luke Abraham (LA), Alex Archibald (AA), Jane Mulcahy (JM), Graham Mann (GM), Zak Kipling (ZK), Sandip Dhomse (SD)
Actions from this meeting
One off actions
1. (ongoing) GM check 8.4 versus 7.3 GLOMAP-mode code and report any bug fixes the bugfix page 2. GLOMAP-mode coupling to FJX. AA to see if Paul Griffiths can be asked to do this. 3. (ongoing) FOC to incorporate Bug #35 and others into dry deposition work 4. NS to co-ordinate migration of MetO UM tickets to MOSRS 5. FOC to find someone to co-ordinate migration of PUMA UM tickets to MOSRS 6. NS to continue with lodging ticket #368 quick fix. A proposed fix to the value of RAFEPS allowing just one line to have a scaling factor on a namelist has been developed but NS is concerned about implementing it it due to his lack of understanding the code. Implementation will be pending the next action. 7. LA to contact Oliver Wild regarding NR solver. In particular to ask advice on the use of the increased value of rafeps to prevent model failures. How safe is this, and is there a better solution? 8. FOC to check rafeps branch in recent GA7-type runs 9. (ongoing) Bug #38: GM to take on lodging this on the trunk 10. (ongoing) LA to check doc for NVOC factor and open ticket to remove it from code 11. (ongoing) Ben Johnson (BJ) to review OC biomass burning emissions units (#41 in bug table) and if this is now correct, close. 12. Bug #52: GM to take on lodging this on the trunk 13. MR to add link to twiki on bugfix page for Bug #53 (RADAER) 14. FOC to follow up with Irina (CRUM) about progress on time availability codes for UKCA chemistry timesteps 15. FOC to find owner for UM ticket #987 (Checks in UKCA iBVOC emissions to prevent duplication of online and offline emissions) 16. CJ to check status of Bug #53 and update table as appropriate 17. NS to update table for Bug #57. 18. NS to update table, open ticket and take ownership of Bug #58 (Blocking Mode 3 in FastJX) 19. CJ to follow up and update table for Bug #62 20. NS to review and update table for Bug #68 21. LA and FOC to resurrect GungHo-UKCA discussions with Mohamed Zerroukat 22. MD to let people know when Rose suites with StratTrop chemistry and based on the frozen GA7 physics are available 23. LA to follow up with CMS about copying in both LA and MD in all UKCA and nudging tickets raised with them 24. LA to arrange next CMG subject to date of next UKCA Exec
- (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) JM to continue to link/send powerpoint results (re: GA7.0), as new configurations released and link/put files on UKCA wiki.
- (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. This should be a standard part of our working practice.
- UK Freefone: 0800 9171956
- Participant passcode: 89264837 then #
- Actions from the last meeting (2015-09-18)
- GA7.0/UKESM1 update
- UKCA Rose suites at UMvn10.3
- Targets for vn10.4 code freeze
- Bugs reported to CMS
- Date of next meeting
Actions from 2015-09-18
# JM/GM to talk offline regarding improvements. CLOSED # JM to open ticket. JM to check which ticket this referred to. CLOSED # CJ to email LA re problems with SO2 diagnostics for emissions. Issues related to using ASAD diagnostics package. Now fixed - CLOSED # CJ to put branch on PUMA email CMG location of branch to check details. Fixed - 'CLOSED # GM check 8.4 versus 7.3 GLOMAP-mode code and report any bug fixes the bugfix page. Leave OPEN # GLOMAP-mode coupling to FJX. AA to see if Paul Griffiths can be asked to do this. Leave OPEN # Incorporate Bug #35 into dry deposition work - Federico Centoni (FC) wants to do some sensitivities. Other bugs encountered. Leave OPEN # ALL to migrate tickets over to the shared repository (MOSRS). Some people have done this, but not all ticket migrated yet. NS to co-orindate MetO tickets. FOC to find someone to co-ordinate PUMA tickets. # NS to continue with lodging ticket #368 quick fix. A proposed fix to the value of RAFEPS allowing just one line to have a scaling factor on a namelist has been developed but NS is concerned about implementing it it due to his lack of understanding the code. Implementation will be pending the next action. Leave OPEN # LA to contact Oliver Wild regarding NR solver. In particular to ask advice on the use of the increased value of rafeps to prevent model failures. How safe is this, and is there a better solution? Leave OPEN. FOC to check rafeps branch in recent GA7-type runs. # Bug #38: GM to take on lodging this on the trunk. leave OPEN # JM to contact Alistair Sellar and check on criticality of bug #38 (volcanic emissions) for UKESM1. DONE - Alastair believes GM has more urgent things to do for UKESM1 but ticket to remain OPEN. # LA to check doc for NVOC factor and open ticket to remove it from code. Leave OPEN # FOC to raise with Ben Shipway (as well as MH from previous LFRic meeting) regarding when aerosols will be needed for LFRic. Done - no requirement for an interactive aerosol scheme in the current phase of porting physics. # FOC to raise with David Walters about aerosol climatologies for LFRic. Done - no timeline as to when this functionality is required but DW would like to see UKCA-GungHo coupling being tackled proactively and not retrospectively as was done for ENDGame. # FOC to follow up about Rose stem on MONSooN. Done' - MR has used it! # JM to put the branch to fix nucleation diagnostics in the microphysics on the bug fixes wiki together with a list of changes need to aerosol tunings. Done # JM to prepare some slides on the impact of the bug in the microphyics on aerosol and upload to this wiki. Done # NB and James to look at the impact of the bug in the microphyics and the tunings needed to go with it on performance in a GA4 job. Done # NB to add branch for GA4 job to UKCA wiki bug fixes table. Done - post T/C # NS to add owner and CLOSED/OPEN columns in bugs table. Done # Ben Johnson (BJ) to review OC biomass burning emissions units (#41 in bug table) and if this is now correct, close. Leave Open # NS to investigate issues with aerosol surface area (#52) and find more suitable owner for ticket. Done - GM now new owner # MR to provide information on his fixes to RADAER files on the bugs table (#53). MR to add link to twiki on bugfix page # JM to investigate current status of netCDF files in coupled jobs (#66). CLOSED # NS to open ticket to capture issue with time availability codes for UKCA chemistry timesteps. Talk to Jane about her requirements and issues. See if CRUM team will take on the work. Irina (CRUM) looking into it. FOC to follow up # NS if issue with output of NTPs on pressure levels not resolved before lodging the code, open a ticket to investigate further after 10.3. Fixed - CLOSE # FOC to open a doodle poll for December and 2nd Week January. Done
GA7 now frozen NRUN/CRUN bit comparability now achieved
Targets for UMvn10.4 code freeze
NS noted that for the UMvn10.4 code freeze, there is no ticket limit. Therefore, the deadline is a hard deadline i.e. if your ticket is not in code review by the ticket deadline, it will not make UMvn10.4. It was also noted that if tickets miss UMvn10.4, the only other opportunity for code changes targeted for inclusion in UKESM1 is UMvn10.5.
Jane (by email) also requested that when people refer to tickets, can they be explicit in which type of tickets e.g. GA ticket, UM ticket, UKESM1 ticket etc..
UM ticket #987: FOC to find owner
UKCA Rose suites at UMvn10.3
Two suites available based on GA6136#19 (latest GA7 physics) with StratTrop chemistry and GLOMAP-mode aerosols
PUMA:uab396 (ported by Jeremy Walton)
Archiving working okay for both suites
NB - Post meeting note Please note that GA7 has now been frozen and Mohit will update suites accordingly. Action on MD to circulate message when these are available.
|Branch with fix||Remarks|
|31||FP exceptions in asad_sparse_vars
|#5616, #368 (MOSRS)||#555||7.3:
|Paused pending LA discussion with Oliver Wild|
|35||Error in labelling: Surface resistance <--> stomatal resistance ?||#6417||#653||7.3:||None||Awaiting input from Federico Centoni|
|38||Missing logical for volcanic so2 emissions.||#6418||#656||MetO:
|GM. To be Lodged|
|41||OC biomass burning emissions - incorrect
conversion. Assumes emissions as kg POM, but (new)
ancils are kg C
|To be lodged|
Need to determine which ancils
are POM vs C. BJ to review.
|46||Inconsistent use of wet_levels and model_levels
in UKCA_AERO_CTL 1-D arrays
|None||All versions||None||Impact if wet_levels/= model_levels, but |
this option has never been supported for New Dynamics or ENDGAME and
wet_levels has been retired by #425 for 10.3.
|49||UKCA emissions: incorrect number,
un-initialised slots in all_emissions()
|#381 (MOSRS)||All UKCA||Example fix here (MOSRS)||To be lodged at vn10.2 as |
part of #805 (MOSRS)
|50||ukca_solve_coagnucl failures||#319 (MOSRS)||UKCA-GLOMAP||Example fix here (MOSRS)|| Mainly a workaround |
To be lodged
|51||Units of wetland emissions||#571 (MOSRS)||All versions||Example fix here (MOSRS)||Wetland emissions misinterpreted as |
gridbox mean rates rather than a land
fraction rate - Lodged at UM10.1 as part of the
UKCA bugfix_package under ticket #564 (MOSRS)
|52||surface area array so4_sa in ukca_main with L_ukca_sa_clim true setting so4_sa to zero if CLASSIC is off||#609 (MOSRS)||UKCA with l_het_psc||Needs further investigation. NS to look into this and find more appropriate owner.|
|53||UKCA RADAER namelists aren't read on the Cray||#577 (MOSRS)||RADAER, some platforms only||Change to input files, not code||lodged at UM10.1. MR to update this with his changes to make this work at earlier UM versions. Ben Johnson to discuss with UM systems/collaboration teams and ask for best approach to making available.|
|54||Offline oxidants Chemistry:
Diagnostics not properly initialised
|#659 (MOSRS)||Offline Chem||None yet||to be lodged at UM10.3|
|55||Use of trigonometric variables e.g. f3_at_u
not consistent with ENDGame
|#658 (MOSRS)||All UKCA||vn10.2_ukca_bugfixes_package||Basic fixes included in #805 to be lodged for 10.3|
|56||Array size issues with UKCA tracers when using EG limited area models||#682 (MOSRS)||ENDGAME UKCA LAMs||MOSRS: vn10.1_ukca_eg_array_dims||Fixed at 10.3|
|57||Incorrect logic for DMS anciliaries required||#708 (MOSRS)||UKCA jobs not using
CLASSIC but without DMS in chemistry
|MOSRS: vn10.1_aqum_eg_fixes||Model stops with message about |
missing input. NS. In progress. Very minor, only affects jobs without CLASSIC which have no DMS in mechanism.
|58||Fastj-X runs on patches all in dark||None yet||UKCA jobs using FastJ-X||None yet||May not be a bug, but if |
so line should be deleted not commented out
|59||Mismatch in levels while reading
CDNC from D1 under ENDGame
|#704 (MOSRS)||EG-UKCA vn9.0+
with Indirect effects
|MOSRS: vn10.0_fix_cdnc_lev||To be lodged at UM10.3 in #805|
|60||Model failure with PrStatus_Diag||#784 (MOSRS)||UKCA on Cray||MOSRS: vn10.2_ukca_prstat_diag_fixes||To be lodged at UM10.3 in #805|
|61||MPI BCAST bug in NetCDF emiss code||#782 (MOSRS)||vn10.1 UKCA
with Netcdf emiss
|MOSRS: vn10.2_ukca_netcdf_bcastbug||To be lodged at UM10.3 in #805|
|62||Inconsistency in aero_surf area used in
heterogeneous reactions routine. Het rates to be placed in the UM dump file if a job is to be restarted
|(MOSRS)||UKCA+ het||To be lodged. CJ|
|63||Inconsistency in timestep/ interval
calculation for BE-Offline scheme
|#774 (MOSRS)||All BE Offline||vn10.2_ukca_repair_interval||To be lodged at vn10.3|
|64||Very low cloud fraction values
can cause failures in Fastj/jx
|#757 (MOSRS)||Any||Simple fix:
|Simple fix |
lodged at vn10.3
|65||qcl not correctly initialised
|Part of #805 (MOSRS)||UKCA run with
|MOSRS: vn10.2_ukca_bugfixes_package||To be lodged at UM10.3 in #805|
|66||Crash in NetCDF emissions and oxidants routines
when using NetCDF-4 libraries
|MOSRS: vn10.2_ukca_readnc_offline_fix||Automatically fixed as part of #282. Only affects coupled model versions. JM to follow up|
|67||Error in indexing of Radiative gases array.
Radiation sees MMR of the wrong ('next') species
|#1150||All EG-UKCA with
|MOSRS: vn10.2_grgas_addr_fix||Lodged at UM10.3||CLOSED||Marc Stringer (UKESM)|
|68||HO2 heterogeneous loss rate 1st order(?)||No ticket||No ticket||Strat-Trop and Tropisop with l_ukca_trophet=TRUE||None||This may be correct||OPEN||Nick Savage|
|69||Inconsistency between aerosol size and mmr/Nd.
wetdp and drydp not recalculated after aerosol remoding
|#1089||ALL UKCA- GLOMAP.||MOSRS UM10.2: vn10.2_ukca_wetdp_drydp_recalc_bug
[MOSRS UM10.3: vn10.3_ukca_wetdp_drydp_calc_fix
|Leads to unphysical large spikes
in AOD. Believe UM7.3 jobs may be
unaffected but haven't checked.
To be Lodged at UM10.3
|70||Age-of-air only configuration does not work at UM10.3||part of #1171||UM10.3 Age-air-only||MOSRS: vn10.3_ageair_and_minor_fixes||Lodged at UM10.3||CLOSED||Mohit Dalvi|
|71||Minor bugs flagged up by rigorous compilation flags:
dust_flux: array not allocated if L_dust=False, but passed regardless to ukca_new_emiss_ctl
soil_layer_moisture: first dimension=0 if no land on PE.
advt(): variable used in loop over total tracers when size is jpctr (=chem_tracers).
nldepx: out-of-bounds with Offline oxidants scheme. Size of array
should be 6+jpspec, based on information from ASAD developer.
|#1171||UKCA+NetCDF emiss||MOSRS: vn10.3_ageair_and_minor_fixes||Lodged at UM10.3||CLOSED||Mohit Dalvi|
|72||UKCA Dry Deposition: Surface resistance values
not set for some species
|#1250||UM7.3+||None yet||To be Lodged||OPEN||Alan Hewitt?|
|73||UKCA-GLOMAP: MDT< MDTMIN warnings from GA6+ runs||#1251||UM7.3+||None yet||To be Lodged||CLOSED||Graham Mann|
|74||Bug in ukca_tropopause with definition of PV tropopause||#1283||UM10.3||MOSRS: vn10.3_ukca_tropopause_amendment||To be Lodged, but still a work in progress||OPEN||Steven Hardiman|
|75||Bug in STE fluxes||#1367||ENDGame?||No branch and needs investigating||To be lodged||OPEN||Fiona O'Connor|
|76||Scale Lightning emissions||#1310||UMvn7.3+||vn10.2_scale_lightning_nox works but scaling is to be added as namelist variable for lodging purposes||To be lodged||OPEN||Steven Hardiman|
|77||Bug in microphysics process rates used by GLOMAP which leads to process rates being ~O(10) times too low and hence too small aerosol removal. The aerosol removal has to be tuned in response to this bugfix||bugfix: #367 Tunings: #854||GA4 + Configs [tunings applied in GA7 development +)||Bugfix: vn10.2_mphys_bugs_improvements
Bugfix and Tunings backported to PUMA br at UMvn8.4.
Tuning: fcm:um_br/dev/j.mollard/vn8.4_scav_bugfix_with_JMscavimpr/src [revision 20160]
|Both Lodged from UM10.3||CLOSED||Jonathan Wilkinson/Jane Mulcahy|
|78||GLOMAP dust bugs:
1. Mapping of bin->mode emissions
2. incorrect STASH options codes
|vn10.3_ukca_dust_diag_emis_fixes||To be lodged at UM10.3||OPEN||Stephanie Woodward|
|79||Aerosol Impaction scavenging bugs:
1. Incorrect use of Conv Frac (FC)
2. Total (conv+dyn) precip rate applied separately for convective as well as dynamic scavenging (double counting)
|??||vn7.3+ GLOMAP||vn10.3_ukca_impscav_fix||To be lodged at UM10.3||OPEN||Stephanie Woodward|
Bug #50: Mohit has branch with workaround. Filter value in Graham's branches are different
Bug #52: Now open with GM
Bug #53: Done? Action on CJ to check and update table as appropriate
Bug #57: With NS. Occurs when CLASSIC off and no DMS ems. Not high Priority. Action on NS to update table
Bug #58: Action on NS to update table, open ticket and take ownership (Blocking Mode 3 in FastJX)
Bug #62: CJ to follow up and update table
Bug #68: NS to review and update table
Bug #69: In Sci/Tech review with GM
Bug #73: Close - Refer to Mohit's UM ticket #1332
Bugs Reported to CMS
A few months ago, a problem was reported to CMS which was related to nudging. It took a month before MD (nudging code section owner) was contacted, who was aware of the problem and had a fix for it. To avoid this situation arising in the future, MD and FOC are proposing that all UKCA and nudging tickets raised with CMS are copied to both LA and MD. Action on LA to follow up with CMS.
No real progress to report. Matthew Hort is attempting to secure some resource within the MetO. John Pyle is planning to approach Rowan Sutton once FOC prepares a one-page summary of UKCA coupling workplan (UKCA Exec action on FOC). Discussions between LA, FOC and Ben Shipway to be resurrected although Ben will be replaced by Mohamed Zerroukat.
Date of next meeting
LA to arrange pending date of next UKCA Exec