Minutes of the code management group meeting 2016-01-12

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Code management group minutes


Present

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

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) JM to continue to link/send powerpoint results (re: GA7.0), as new configurations released and link/put files on UKCA wiki.
  4. (ongoing - standing item) ALL with access to keep monitoring ukca_bugs email list.
  5. (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.

Teleconference Numbers

  • UK Freefone: 0800 9171956
  • Participant passcode: 89264837 then #

Agenda

  1. Actions from the last meeting (2015-09-18)
  2. GA7.0/UKESM1 update
  3. UKCA Rose suites at UMvn10.3
  4. Targets for vn10.4 code freeze
  5. Bugfixes
  6. Bugs reported to CMS
  7. LFRic
  8. A.O.B./D.N.M.
  9. Date of next meeting

Minutes

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

GA7.0/UKESM1 update

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

Met O:uab258
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.

Bugfixes

# Description Ticket Affected
Versions/
Config
Branch with fix Remarks
MetO NCAS
31 FP exceptions in asad_sparse_vars
or asad_spimjmp
#5616, #368 (MOSRS) #555 7.3:
CheT+Aero
MetO:
fcm:um_br/dev/fris/vn8.4_increase_rafeps
Puma:
fcm:um_br/dev/nhsavage/vn8.4_increase_rafeps
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:
fcm:um_br/dev/hadna/vn8.6_deactivate_volcanoes
Puma:
None
GM. To be Lodged
41 OC biomass burning emissions - incorrect
conversion. Assumes emissions as kg POM, but (new)
ancils are kg C
#6429 vn8.5: MetO:
fcm:um_br/dev/fpbj/vn8.6_ukca_mode_BBOC-POM_bugfix

Puma:
None
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:
vn10.2_ukca_acf_zero
Simple fix
lodged at vn10.3
65 qcl not correctly initialised
in ukca_calc_aqueous_6a
Part of #805 (MOSRS) UKCA run with
6A convection
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
NA vn10.0-10.2 UKCA
+ NetCDF
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
gas-radiative feeback
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
OPEN Jane Mulcahy
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
Tunings: vn10.2_ukca_asnow_rfrac_tune

Bugfix and Tunings backported to PUMA br at UMvn8.4.
Bugfix: fcm:um_br/dev/mdalvi/vn8.4_mphys_bugfix/src
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
UM#1355 UM10.2+ GLOMAP
with dust
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.

LFRic

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.

AOB

None

Date of next meeting

LA to arrange pending date of next UKCA Exec