Notes from NorESM CTSM Friday meetings. - NorESMhub/CTSM GitHub Wiki

Agenda for next meeting.

Priorities

  • 16pft dataset
  • megan PR
  • drydep code

Sept 20th

  • Think about what happens in FATES with 78pft surface dataset.
  • Thinking about FATES-SP runs. Ok?
  • Status of drydep issue
    • Rosie have made a draft version. Need to look up Wesely 1989 to understand how the season indexes should work, to correctly calculate this in Fates.
  • Regridding and plotting
  • Mariana have written info on: :
  • Timeline (hopefully):
    • New CTSM5.2 SE dataset (with corrected soil properties) available:
    • CTSM5.3 hopefully ready around end of next week
    • For now, we could do a short spin-up with fixed 5.2 surface data, to run coupled NorESM. (CAM-Nor people might want to look at this).
    • We probably need a couple of weeks before we can do i) CTSM5.3 simulations and ii) NorESM-FATES-Nocomp simulations. (Need to keep in mind that NorESM-FATES-SP probably also have problems with drydep)

Sept 13th

  • System updates
    • Matvey will test new modules on betzy on Monday.
  • Dust
    • New initial condition files (for CLM53) and surface datasets being made at NCAR with the new non broken surface datasets.
  • Spinup:
  • NorESM meetings will shift to being development meetings.
  • Fire code: need to write last part of fire emissions code. Maybe not required to make FATES NOCOMP work in coupled mode.
  • MEGAN
    • https://github.com/NorESMhub/fates/pull/8
    • FATES-SP mode produces VOC values presumably using ghost pft indices.
    • It is plausble that FATES NOCOMP mode will do the same thing, and produce the same erroneouosly mapped VOC emissions, in the absence of getting the MEGAN FATES code working.
  • Dry deposition
    • Drydep scheme needs 1) wesley vegetation type and 2) season index.
      1. Wesley vegetation type can be created by FATES
      1. Season is a strange beast. Need to look at the original paper to figure out how to calculate it. Potentially send the season index from FATES

Sept 6th

  • Action items and updates from NorESm2.5 meeting

    • NorESM2.5 code 'chill' at the end of the year.
    • means we need to prioritize outstanding chemistry coupling issues and nitrogen coupling.
    • There will be a spinup and calibration 'task team' lead by Jerry. Need to think about the 'equilibrium' state of FATES wrt LULUC.

  • Next step is to run a simulation which has FATES-SP and compare with the CLM51-SP simulations.

    • Alok will run this and Mariana will write an issue with instructions in it.
    • This will be 'out of the box' FATES per the latest NorESM-CTSM tag
    • AFTER that, Rosie to point to new FATES parameter file, assuming that nothing goes wrong.
    • AFTER that, we will check that we have all the most up to date snow schemes etc.

  • Discussion of dry deposition issue.

    • Next friday 13th we will do 9.30-11.30ish mini hackathon on this.

  • Status of fire and VOC PRs.

  • Dust emissions and surface file in SE vs FV

    • Marit to make issue on ESCOMP about the strange PCT_CLAY strangeness.

August 16th

  • Status of code after Betzy module debacle.
  • Status of FATES calibration and spin-up.
  • Recap of discussion of diagnostics package.
  • FATES Initial condition interpolation for SE grid

August 9th

June 28th

June 21st

  • Updates
    • Calibration
    • Trigrid update
    • Ada discussion r.e. august runs Configuration notes: noresm2_5_alpha03_v1 in my fork git clone https://github.com/mvertens/NorESM.git cd NorESM git checkout feature/noresm2_5_alpha03_v1

TRIGRID case: ./create_newcase --case /cluster/home/mvertens/noresm/test_nf1850oslo_trigrid --compset NF1850oslo --res a%ne30np4.pg3 _l%0.9x1.25_oi%ne30np4.pg3_r%r05_w%null_z%null_g%null_m%tnx1v4 --project nn9039k --run-unsupported

SE grid case: ./create_newcase --case /cluster/home/mvertens/noresm/test_nf1850oslo_trigrid --compset NF1850oslo --res a%ne30np4.pg3 _l%ne30np4.pg3_oi%ne30np4.pg3_r%r05_w%null_z%null_g%null_m%tnx1v4 --project nn9039k --run-unsupported

Status of the FATES code on the CTSM repo?

  • Discussion of Betty's PhD project.

May 31st

Agenda

  • Updates
    • CICERO 'NextGenCarbon' project funded :)
    • calibration
    • trigrid
    • land use discussion
    • N cycle plans
  • Compsets discussion
  • Need to crate a protocol for NorESM3 coupled spinup. Perhaps in September. Both for :
    • the standard coupled model spinup
    • Emission-driven spinup
    • FATES spinup (with land use change)

May 24th

Agenda

  • Fire and BVOC code (Matvey doing coldstart temperature initialization for CTSM. Needed to make excess ice the default option.)
  • Calibration updates
  • BECCS v0 implementatioh. Does not pass balance check yet. https://github.com/rosiealice/ctsm/tree/BECCS_v0
  • Meeting with Charlie (and Ryan) on Wed at 5pm CET to talk about land-use spinup (& nutrients). -- Mariana, Ada and Mats gave talk to the CESM co-chairs meeting on Tuesday on NorESM plans.
  • Tri-grid and diagnostics. -- Mariana and Bill have done loads of work dealing with the complexities of the mapping, building on some previous work in E3SM.

May 3rd.

Agenda

Action:

  • Explore trigrid in CMEPS. Make sure it works
  • Test trigrid:
    • F compset, 2deg atm, 1deg land. Both FV
    • F compset, 1deg atm, 1deg land. Atm SE, land FV
    • F compset, 1deg atm, 1deg land. Both SE
    • B compset, 1deg atm, 1deg. SE/FV (atm/land). Check conservation

26 April

Agenda

  • Model calibration update
  • Discussion of ensemble diagnostics conversation with NCAR.
  • Update on to do list for NorESM.

Action- Rosie to arrange discussion on SE diagnostics package with Will, Daneiele, Mariana...

12 April

  • Matvey working on the ex cess ice in CTSM. The new lower (frozen) initial soil temperature breaks a FATES-hydro test which was previously passing but liekly would have failed in a longer test and exposes the inability of FATES-HYDRO to deal with totaly frozen soils, which we should probably fix independently. We can discuss this in the FATES SE meeting on Monday.

  • Report from the CMCC-NorESM meeting and follow-up items. (we didnt talk about this but the meeting was great and CMCC are still using CLM4.5/5 and so there are not any real imminent land related collaboration). There was discussion of how to have common github repos (ongoing), and how to do CMIP7 spinup, and how to do SE diagnostics.

  • Status of fire emissions coupling. Made PRs to both NorESM/ctsm and NorESM/fates branches. Still missing the part to deal with the emission species. Matvey will work on this potentially next week.

  • Status of MEGAN coupling, per https://github.com/NorESMhub/CTSM/issues/36

  • For the PRs to the FATES and CTSM main repositories, we should 1) wait for PRs to be accepted into the main FATES forks. 2) rebase onto the main FATES/CTSM repos. 3) Make new PR from branch into those repos.

  • CH4 NorESM doesn't have emission driven methane. But the reasons why seem to be that CH4 does not come out of the land, despite being calculated there. Mariana does not think that moving CH4 fluxes to the atmosphere might not be too difficult. Dirk might be doing interactive CH4 in NorESM as part of CN-coESM project. There are no hooks in mediator to accept it from the land, and no hooks in CAM to do with it so that would need fixing. In CLM5.2, wetland extent is going to be lower (from Will). Action is to email Dirk (Rosie). Zosia (CICERO) is potentially interested medium-term in using a fully coupled emissions-driven methane model and greater emission driven capacity is desirable. A coupled of people on the CLM side are also potentially interested in this.

  • Discussion of manage_externals change to git submodule. Possibly Matvey and/or Mariana to push back to NCAR on the need for community engagement on change tp basic workflow and dependency on external organizations system python settings.

March 2024

Meetings in March 2024, including 2 day hackathon, were dedicated to fire emissions coding. Project board link

Notes Meeting Feb 7th 2023

  • NorESM2.5 vs NorESM3: Fire emissions, bvoc's, nitrogen in FATES. Hackathon for fixing these issues before September?
    • Fire emissions plumbing next week (every two weeks friday 9:30-11:30)?
    • NorESMhub/fates branch and NorESMhub/CTSM branch for fire emissions development. Give Rossie/Kjetil rights to these.
  • NorESMhub/CTSM tag with FATES-two-stream parameter file: feature/two-stream. rosie's branch with two-stream on
  • INES interim meeting in September.
  • Frost mortality: low prior, no plant hydro for now.

Agenda for the Feb 2nd meeting

  • FATES and Nutrients moved to norESM3?
  • Outcome of frost mortality discussion.
  • Update on coupled FATES-SP testing strategy.
  • Update on Adrianna's parameters.

Notes 26th January 2024

Suggested compsets and parameter files for coupled simulations (to be filled in, pointing to separate tags in NorESMhub/FATES):

  • FATES-SP twostream with default parameters.

  • FATES-SP new configuration/parameters (Rosie and Adrianna)

  • FATES-NOCOMP existing parameterization from Jessie (with or without the modifications to leaf layers). Needs to be spun up (1850, transient etc.)

  • FATES-NOCOMP/CN.

  • FATES-NOCOMP/CN with land use.

  • FATES with nutrient coupling goals for NGEE/FATES and NorESM (timeline, demand ...)

Agenda

  • CTSM/FATES tags woth TwoStream tests
  • Frost hardening mortality PR.
  • FATES SP calibration from Adrianna, before emulator/based parameter calibration:
    here
  • For reference, here are the TRENDY ILAMB outputs

Notes from the NorESM meeting (25 jan 24)

  • Defining configuration for the first tests of NorESM2.5. Waiting for some OsloAERO tunings from NCAR. Mariana has some issues with restarts in 1850.
  • We need to define a configuration in FATES for testing.

Hierarchy of FATES complexity runs.

  1. FATES-SP twostream with default parameters. The twstream model is turned on in the parameter file by changing the fates_rad_model variable to "2"
  2. FATES-SP new configuration/parameters (Rosie and Adrianna)
  3. FATES-NOCOMP existing parameterization from Jessie (with or without the modifications to leaf layers). Needs to be spun up (1850, transient etc.)
  4. FATES-NOCOMP/CN. CAN WE MAKE THIS PART OF NORESM3?
  5. FATES-NOCOMP/CN with land use.

Summary of Spectral Element diagnostics

  • SE runs do not work in the normal diagnostics package.
  • xESMF can be used in python to plot data, but isn`t part of a running diagnostics package yet.
  • Tri-grid capacity can in principle run atmosphere on SE and land on FV but this is scientifically wierd.
  • Keith O is using an old NCL diagnostics package with FV coupled versions to debug the CLM5.1 coupled issues (effort is mostly around snow and albedo and shrubs).
  • The existing diagnostics package is actually a bit hard to integrate into an efficient workflow as it needs to be moved outside the HPC firewall to view the results and that can be clunky.
  • Adrianna Foster (NCAR) and Jessie Needham (LBL) have been running ILAMB on ensembles of FATES. This does not as far as I know run with SE grids, but is useful in terms of hitting the available benchmark data.
  • Best approach might be to 1) operationalize the ILAMB approach and 2) test whether it can run with SE output and 3) discuss SE diagnostics with NCAR and 4) create nimble skeleton plotting tool for FATES output to assess the realistic workflow requirements.

Notes 19th January 2024

  • NorESM AMIP run with SE NorESM
  • Same but with FATES
  • Diagnostics for SE. CAM diagnostic package with xESMF by Jessie (but it's slow).
    • Use Keith NCL scripts
    • Output at 1 degree at run-time
      • Loose relationships within a gridcell for land variables
    • Run on different grids for the atmosphere and land.
      • More runtime
      • Changing coupling variables when regriding. ATMxLND will not be as straightforward as in 1to1
    • Make a package out of CAM package for CLM.

Notes from 12th January 2024.

As soon as two stream tag is in at ESCOMP.

  • Mariana will do 2deg 10-20-year FateNoComp and BgcCrop degree runs with NorESM2.5-dev - CAM on the finite volume grid on the piControl.
  • First, offline spinup with CPL history from CMIP6. 2deg FV resolution. Use DATM forcing from CMIP6 and run 100 years forcing CLM/FATES nocomp with the DATM forcing. Will see how well the plants are evolving. Need to ask Dirk for location of forcing files for piControl.
  • Rosie will provide the parameter file tag. Make a tag on NorESM-tage for checking out the new parameter file.
  • Make a CTSM tag that corresponding to the two-stream tag at ESCOMP.
  • Make another tag of the one above which points to fates tag Rosie will provide.
  • Make a NorESM tag to point to CTSM tag above.

Notes from 4th January 2024 meeting

Issues to make FATES operational for NorESM2.5

  • Init_interp issues. Will NorESM spin-up different resolutions independantly?
  • Ways to visualize spectral element (ask Keith).
  • CMORization for FATES variables.

FATES gantt chart

Project board for NorESM-FATES lives on the NorESM repo here

Notes from 24th November 2023.

CLM-FATES is three times slower than CLM51 after 35 years. Mariana to make the FBG true for the timing test. This should improve timing. We discusses the sunderlying setup for NOCOMP mode in light of the potential to improve the speed with fewer cohorts etc. link to charlie's slide deck here

Notes from November 17th 2023

  1. Issue in call t_start() in CNDriver
  2. Compset for use_fates_nocomp
  3. Output for performance testing:
    • Runs with standard output + PFS tests
    • Fates hist PR
    • Output for spinup: FATES_VEGC, LAI +???
  4. CTSM5.2 project CTSM5.2 branch
  5. Timeline for CTSM6.0 and CESM3:
    • Preliminary: Winter 2024: includes CTSM5.2, Matrix CN, Dust emissions, Tillage ...
    • Code freeze: Summer 2024
    • Tunning: Winter - pre-tunning, Summer: actual tunning.
  6. ILAMB and diagnostics, PPE diagnostics. NorESM tunning: which diagnostic package to use?
  7. Landuse and preproc tools for mksruf_*

Notes from November 10 2023

  1. Performance Test for FATES. Use the current out of the box. Need to define the compset, tag resolution etc. Will wait for the restart bug to come into CTSM. Issue here
  2. INES2 - need to clearly state what will happen without more funding.
  3. Need to decide whether FATES tags live inside the NorESM repo or the NGEET repo.

Notes from 3 Nov 2023.

  1. Issue with input data disk space. Do we want to be testing etc on Fram as well as Betsy? Fram mostly used for offline land configurations. Do we need coupled model to be tested there? Mat and Mariana to discuss Betsy vs Fram usage. UiO people mostly using Betsy with release tags. Other developers using Fram. NorESM-3alpha is current development branch.

  2. Discussion with Betty on MIMICS+

  3. Next steps with FATES once restart bug is fixed.

  • Wait until the radiation scheme and the bugfix for FATES restart are available to do performance tests. Do these with NOCOMP at nominal 1 degree resolution (also FV 2 degree). FATES performance should spin up in 20 years - also verify this.

  • Spin-up script sorted for FATES. Issue added to project board

  • Need for N cycle to be linked from FATES to CTSM. Plan to do the CTSM side changes on the NorESM branch, .

Notes from Oct 27 2023

  1. Discussion of Fram CESM compilation issues. Discussion here
  2. Restart bug for FATES.
  3. NES2 proposal

Notes from 29 Sept 2023

Discussion of FRAM:

  1. Discussion with Greg and Ryan on FATES NOCOMP bug will happen on friday at 5pm
  2. INES2 land model work package in preparation. Rosie & Heiko leading WP2. Please get in touch if you want to discuss anything.
  3. Adele Zaini will start PhD on Oct 16th working on BVOCs in NorESM/CTSM/FATES
  4. Interesting discussion of modularity on ILMF forum. Model parameterization forum on Oct 10th.
  5. New progress on calibration of tree allometry and respiration in FATES (Jessie Needham and Adrianna Foster). Much healthier boreal forest! (was a big bias in last weeks calibration).
  6. Need to decide on he CTSM version for NorESM2.1. The current tag is v5.0.14

Notes from 22 Sept 2023

  1. We have created this board to track issues with FATES that need to be completed for the sake of the coupled NorESM FATES_NOCOMP

  2. @rosiealice gave a talk on the latest calibration efforts which are looking good. here

  3. We will have a meeting about the NOCOMP restart bug next week. Greg will organise the time.

  4. New updated issue on fire emissions logic: https://github.com/NGEET/fates/issues/1088

  5. We had a CLM meeting on theESCOMP CTSM-FATES tasks board , which are heavily parallel with our board. The notes should be in the minutes (but are not yet..

  6. INES2 planning underway. WP2 (land) and WP4(coupling) most relevant here.

Actions:

  • Rosie to send Mariana restart dataset . Mariana will run a restart test.
  • Add issue to the board to cover nutrient calibration