Minutes of the code management group meeting 2017-10-19

Code management group minutes

THIS AGENDA IS STILL A WORK IN PROGRESS

Teleconference Details

Thursday 19th October 2017, 10am - 12noon BST

• UK Landline: +44 (0)1223 761376 (x61376 from an internal University of Cambridge phone)
• Participant passcode: 146205

Present

Met Office:

Cambridge:

Leeds:

Reading:

Lancaster:

Edinburgh:

UEA:

NIWA:

CSIRO:

Apologies:

Minutes

Actions from the Last Meeting (LA)

Minutes of the code management group meeting 2017-07-14

One off actions

1. (ongoing) GM to check 8.4 versus 7.3 (and possibly vn8.4 vs 10.x) GLOMAP-mode code and report any missing bug fixes on the bugfix page.
2. (ongoing) FOC to incorporate Bug #35 and others into dry deposition work. FOC to draft document that will cover what the new deposition scheme will do
3. (ongoing) LA to migrate PUMA UM tickets to MOSRS - see table below
4. (new) ALL to check through this table and comment on whether the tickets needs to be ported or not. Deadline 2017-07-28
5. (new) LA to open tickets for all changes that still require a ticket
6. (ongoing) JM,BJ,NB to discuss incorporation of Nicolas' RADAER description into UKCA (or separate UMDP). JM to take lead.
7. (ongoing) FOC to open ticket + Bugfixes Table entry related to 'Unable to calculate tropopause' warnings
8. (ongoing) FOC to recommend at next Exec meeting a policy of allowing only CMG to (certify and) distribute any UKCA configurations for science purpose.
9. (new) LA (& others who are interested) to look into how to re-organise the UKCA panel (e.g. into sub-panels)
10. (new) LA to organise a follow-up meeting of interested parties on the UKCA panel re-organisation
11. (new) MD to collate all UKCA parameters into ukca_constants in advance of removing duplicates already available in the UM
12. (new) LA to add comments on rafeps into #368
13. (new) FOC to close #2358 (Delete 2D photolysis scheme in UKCA)
14. (new) MD to take ownership of #142 (Remove old emissions system from UKCA)
15. (new) FOC to take ownership of #2356 (Delete older dry deposition scheme in UKCA)
16. (new) FOC to take ownership of #1507 (Remove Backward Euler Standard Tropospheric Chemistry)
17. (new) AH to take ownership of #2373 (quick method for calculating wet volume redundant)
18. (new) LA to take ownership of #1505 (Clean up ukca_strat_update)
19. (new) JM to clarify with CJ regarding "Wet oxidation of SO2 in GLOMAP"
20. (new) ALL to note code which is redundant
21. (new) AH to scope out reducing repetition of mode definitions in GLOMAP
22. (new) OM to work on the chemistry scheme code restructuring for vn10.8
23. (new) LA to update Bugs table following discussion, closing tickets where appropriate
24. (new) FOC to send LA RAQ testing jobs information
25. (new) MD to set up TS2000 free-running nudged jobs at vn10.8
26. (new) LA to add UKCA wiki page on using UKCA on the Virtual Machine
27. (new) LA to create a doodle poll for October after the date of the vn10.9 code freeze

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. This should be a standard part of our working practice.
5. (ongoing - standing item) ALL to review and remove obsolete code

Redundant Code (LA for NS)

Redundant code

• Question: Should all schemes using the backward Euler solver be proposed for redundancy?

#	Description	Ticket	Remarks	Status	Owner
1	Old emissions code (that which uses ancil files)	#142	None	PROPOSED	Nick Savage
2	Old dry deposition scheme	#2356	None	PROPOSED	Nick Savage
3	ukca_volume_mode.F90 - quick method for calculating wet volume is not used since iwvolmethod is hard coded to equal 2.	#2373	None	Complete	Alan J Hewitt
4	2D photolysis	#2358	None	PROPOSED	Nick Savage
5	ukca_strat_update.F90 - relax_ozone	#1505	None	PROPOSED	Nick Savage
6	Backward Euler Standard Tropospheric Chemistry	#1507	None	PROPOSED	Nick Savage
7	Wet oxidation of SO2 in GLOMAP	None	None	PROPOSED	Colin Johnson

#	Description	Ticket	Remarks	Status	Owner
1	Deprecated UKCA netcdf attribute options	#2513	'emission_type', string type attributes no longer recomeneded. Need some time for most new code to adopt these	DEPRECATED	Nick Savage

Bugs/Bugfixes (LA)

Open Bugs

#	Description	Ticket	Owner	Status/ Updates	Comments from previous meeting	Comments from this meeting
31	FP exceptions in asad_sparse_vars or asad_spimjmp	#368 (MOSRS)	Nick Savage	vn10.x seems to be better	leave open
35	Error in labelling: Surface resistance <--> stomatal resistance ?	MOSRS #1409	Fiona O'Connor	folded into DD work	leave open & see above
57	Incorrect logic for DMS anciliaries required	#756 (MOSRS)	Nick Savage	trivial. Might close as wontfix, but might want to do in RAQ	leave open
72	UKCA Dry Deposition: Surface resistance values not set for some species	#1250	Alan Hewitt?		leave open but there is a way forward
74	Bug in ukca_tropopause with definition of PV tropopause	#1283	Steven Hardiman	Change ownership? Fix is separate from #75	leave open. FOC did try to lodge, but breaks KGO. Simple fix but with big changes.
75	Bug in STE fluxes	#1367	Fiona O'Connor	could be endgame	leave open. even with fix, these are still wrong
87	Possible issues with YSTORE in UKCA_CHEMISTRY_CTL.	UM#3245	Colin Johnson/ Luke Abraham		leave open
88	Potential FastJX Scattering Bug	UM#3261	David Wade/ Luke Abraham		leave open FOC to send LA RAQ jobs information

Standard Release jobs: What is required now to move UKCA recommended jobs up to GA7.1? (LA/CJ)

Strategy for next UKCA Release Job (LA)

There would technically be some differences between a GA7.1+StratTrop job and a UKESM1-AMIP job, mainly in the settings for iBVOCs and the primary marine organics. The community generally wants to have a job as close as possible to UKESM1.

A release strategy was considered where:

1. UKCA configurations are available across versions with the same science settings (e.g. similar to GA7.1)
2. Regression branches would be provided to allow for bit-comparison between UM versions to allow people to run the same science but at later versions - this would aid people in developing changes for the trunk
3. TS2000 free-running and nudged configurations will be provided and assessed at each UM version, without branches where possible. These will form the basis of the release and evaluation suite output will be provided from each run to allow for comparison to the previous UM version
4. Release jobs will not be updated once they have been released, instead users will be directed to the next model version for bugfixes etc.

A vn10.8 release is wanted for September for the new student intake.

MD to set-up jobs at vn10.8.

It was noted that UKESM1 jobs would be supported elsewhere.

Highlights from vn10.8 (LA)

vn10.8 UKCA tickets
UMPB May 2017 Highlight Report

• CJ: Water vapour feedback - This includes flux calculations of water production and loss available in stash, as well as a diagnostic which gives the change to q calculated at each timestep. (#1646 & #3123)
• LA: Quasi-Newton steps in Newton-Raphson solver - speeds up the model by ~2-3%. Will not bit-compare with runs without it however. (#2819)
• MR: OpenMP in UKCA_AERO_CTL - alternative method for passing array slices to sub processes, e.g. a(:,:,:,mode) had to be re-written a(1,1,1,mode) for the combination of Linux system SPICE and Intel ifort 12. (#1286 )
• MR: OpenMP in UKCA_AERO_CTL - a bespoke workshare had to be written due to ONE failure in rose stem. The formal method that used the default blocking of data failed. Again Linux and Intel 12. (#1286 )
• LA: 3 new UKCA rose-stem tests were added to the MetO XC40. This tests mirror the ones available on the VM, but run incredibly quickly. One has been added to the xc40_developer group - meto_xc40_n48_ukca_eg_omp_noios_gnu. (#2714)
  • Note: On the XC40 the _omp and _noomp jobs do not bit-compare, whereas they do on the VM. The version of the GNU compiler is different between these two sites - the XC40 uses GNU Fortran (GCC) 4.9.1 20140716 (Cray Inc.), whereas the VM uses GNU Fortran (Ubuntu 5.2.1-22ubuntu2) 5.2.1 20151010. The domain decomposition is different as well (4x4 on the XC40 vs. 1x{{MPI_TASKS}} on the VM). #3127 has been opened to investigate this.
• AJH: Radaer can be run from GLOMAP-mode climatology files (#288 )

Targets for vn10.9 (and beyond) (LA)

Tickets currently targeted for UM10.9 in Trac

Ticket	Summary	Owner	Comments from this meeting
#100	PM10 and PM2.5 diagnostics for MODE	johnhemmings
#1250	UKCA dry deposition: surface resistance values not set for some species	alanjhewitt
#1703	Update appropriate UMDPs with regard UKCA-mode aerosol and interactions	janemulcahy
#2086	Time updating for glomap climatology	alanjhewitt
#2301	Improve the handling of emissions from explosive volcanoes in UKCA/GLOMAP	--
#2373	Removed redundant code for calculating wet volume	alanjhewitt
#2382	rose stem app for Section 54	alanjhewitt
#2405	Test and implement sea-salt density change	colinjohnson
#2532	Review of option codes associated with UKCA burden diagnostics when running with BE solver	fionaoconnor
#2587	Adding solar variability to photolysis scheme	fraserdennison
#2689	Enable coupling of GLOMAP-MODE Aerosol to FAST-JX photolysis.	michaelhollaway
#2741	Addition of new diagnostic for the dry deposition flux of nitrogen	fionaoconnor
#2742	Addition of new diagnostic for the wet deposition flux of nitrogen	fionaoconnor
#2814	Allow UKCA Chemistry to work with aerosol climatologies	lukeabraham
#2898	Input CO2 concentrations into UKCA when interactive CO2 is operational	colinjohnson
#3025	Add functionality to use NetCDF GLOMAP-mode climatology fields to generate fields required by ACTIVATE	alanjhewitt
#3028	Improve STASH section references related to UKCA components.	mohitdalvi
#3109	PE decomp reproducibility for UKCA, with higher optimisation flags	matthewglover
#3127	Investigate KGO differences in um_n48_ukca_eg app using GNU on the Cray	lukeabraham
#3209	column-call UKCA Newton-Raphson solver	lukeabraham
#3267	Fix UKCA NRUNvsCRUN test (CRUN running full 2-days)	mohitdalvi

• Michael Hollaway: I currently have a test version of the code working that uses RADAER to pass the aerosol optical properties to FAST-JX. This runs at UM-UKCA 10.6.1. I am currently working on testing the code with different MODE setups and then will work on going through the required steps to get the code into the trunk at 10.9 (sci/tech review, code review, etc). All being well the updates should hopefully be ready for 10.9 (fingers crossed).

Highlights/Targets from CSIRO

1. Matt W. has incorporated a primary marine organic aerosol emission parameterisation into GLOMAP (included in the trunk from UMvn10.6).
2. We are close to finishing further work on parameterisation of ozone dry deposition to the ocean (work so far reported in the ACP paper, 17, 3749-3767, 2017). I have communicated with Gerd Folberth (MO) as to the process to put the new parameterisation into the trunk once our studies are finished.
3. A CSIRO project with Melbourne University has started which aims to have an ACCESS coupled model with UKCA CheST configuration at UM10.6 and GA7.1 (main ACCESS components are UM atmos + MOM ocean + sea ice + CABLE land surface + UKCA).
4. ACCESS-CM2 coupled model is being tested for aerosols (including dust, at GA7.1).

Virtual Machine (LA)

UM Virtual Machine Guide - Note: this will be superseded by UMPB X10 from vn10.8 onwards.

LA - to write up UKCA specific VM instructions on the UKCA wiki.

Training (LA)

UKCA Training January 2018

Date of next meeting (LA)

LA to create a doodle poll for October after the date of the vn10.9 code freeze

Poll for 6th-27th October 2017