2022 Software Engineering meeting notes - NGEET/fates Wiki

Current week meeting

June 27, 2022

Agenda

Upcoming meetings

  • FATES meeting: Thursday July 07, presenter TBD

PR status board (Pre-meeting synthesis)

  • #825 (Carbon Harvest) up next for integration

FATES crop discussion


Upcoming meetings

July 04, 2022

No meeting today due to July 4th federal holiday

July 11, 2022

Agenda

Upcoming meetings

PR status board (Pre-meeting synthesis)


Previous meetings

June 20, 2022

No meeting today in observation of Juneteenth federal holiday

June 13, 2022

Agenda

Upcoming meetings

  • FATES meeting: Thursday June 23 1100 PST, Marcos presenting
  • CESM Workshop this week: https://www.cesm.ucar.edu/events/workshops/2022/
    • No CTSM-FATES standup, CTSM software, or CLM meeting this week
  • E3SM Land/Energy NGD Monthly meeting canceled
    • Rosie asked where the notes meetings are held
  • No FATES software meeting next week (Monday June 20th): Juneteenth holiday
    • Next meeting: Monday June 27, 2022

PR status board (Pre-meeting synthesis)

  • #862/CTSM#1766 (patch count api update): Review in progress
    • Dry deposition discussion to be held between Erik and Ryan this week
      • Recommendation is to leave the dry deposition update for a future PR
    • Dynamic stoichiometry question [Ryan]: leaf-only or other organs in the future?
  • #863 (carbon allocation bug fix): Review complete, testing in progress
  • #856 (pft dimension mortality carbon fluxes): on deck

Walk-on topics

  • [Greg] E3SM software-centric meeting?
    • This came up in the context of Greg forgetting E3SM PR protocols and standards
    • Would be good to get heads up on upcoming infrastructure changes or impacts to elm
    • [Jennifer] agrees and recommends reaching out to Rob if there is a regular meeting
  • [Ryan] Next meeting main discussion will be on fates and crops
    • Ryan reported that Charlie would like to be able to collapse the crops into either C3 or C4
      • Some crop pfts are associated with irrigated or not irrigated
    • [Rosie] has anyone tried to have fates running with crops on a different landunit? Ryan is not sure.
    • [Greg] Erik has an action item to develop a matrix of the options for running fates/crops. This will be presented at the June 27 fates software meeting.
    • [Ryan] elm-fates crop coordination
      • [Jennifer] ELM crop model is based on CLM4.5 and being conducted by Beth Drewniak
        • Eva Lieungh is working on crop in elm as well using the FAN model
        • Phase 3 proposals being worked on currently, crops will be a part of this.
        • Jennifer will follow up on this to provide status update for June 27 meeting

June 06, 2022

Agenda

Upcoming meetings

  • FATES meeting: Thursday June 9 1100 PST, Xiangtao Xu presenting
    • Marcos to moderate as Charlie will be out due to vacation
    • Next meeting: Marcos offering to discuss defining pfts based on trait values
      • A number of people working on similar things, so maybe a good topic to get updates
  • DS4E meeting: Monday June 13 1200 PST
    • Alternate time for FATES software meeting?
      • Marcos to attend the DS4E meeting and report back at next fates software meeting. As such, regular fates software meeting time will be held
      • Adrianna, Jackie, and Charlie will be absent as well due to CESM workshop and vacation, respectively

PR status board (Pre-meeting synthesis)

  • Completed
    • #800 b4b PRs all integrated into single fates tag
      • #863 Carbon allocation bug to be integrated in near future
  • In progress
    • #862 parameter file under review
      • Ryan still trying to find non-b4b cause
    • #854/CTSM#1515 to be integrated after #862 and CTSM#1771
    • #788 crown damage module deconflicted but not yet merge back to PR branch
  • Up next (this week)
    • Carbon flux fix (#863) and mortality carbon flux pft update (#856)
      • Charlie notes that we should check that the length of the new history variables

Grass mortality disturbance discussion

  • Charlie confirmed this is a problem and has a PR fix in
    • This came up in the context of the California fire work
    • Aside: parallel disturbance #875 was not investigated in this context yet
  • The PR fix results in grasses can not cause canopy opening disturbances
    • fates_mortality_disturbance_fraction only applies to shrubs and trees now
    • Only disturbance with regards to grasses is due to fire (or future grass specific disturbances: e.g. grazing)
  • Related: some discussion about size of tree in creating a gap
    • [Marcos] degree of disturbance versus binary gap/no gap
    • currently fates only considers things in the canopy contributing to treefall mortality
    • Hank Shugart lab mentioned by Jennifer and Jackie with regard to potential future project
  • Decision: Move forward or further specific case tests?
    • Marcos to discuss

Walk-on topics

  • Tom Powell email discussion: respiration parameter is off by an order of magnitude when tuning for Panama
    • Marcos thinks we should revisit the fates_base_mr_20 to make sure units are correct (gC/gN/s)
    • Ryan seeing similar issue with root respiration
      • Charlie and Jackie noted that lack of root data is likely causing a large amount of uncertainty
        • Thus it is a scientific result worth highlighting
      • FRED data set has good respiration data and has been workign to get BCI data included
        • Perhaps it has root respiration data now?
      • Also check out https://daac.ornl.gov/SOILS/guides/SRDB_V5.html
        • Ben Bond-Lamberty is associated with this
  • CESM Workshop
    • Marcos to supply a summary slide
    • Charlie to supply reduced complexity slide
    • Jackie will run the compiled slide deck past everyone that contributed
  • [Ryan] FATES hydraulics V2 coming soon
    • Includes fine roots biomass as prognostic variable (see ESS PI meeting slides for details)

May 30, 2022

No meeting due to federal holiday.

May 23, 2022

Agenda

Upcoming meetings

  • No FATES meeting this week due to ESS PI meeting
    • Next FATES meeting: Thursday June 9 1100 PST, Xiangtao Xu presenting
  • Aside: Charlie will be on vacation June 9-21

PR status board (Pre-meeting synthesis)

  • canopy_layer_tlai fix (828): testing complete, but looking into why some 1x1_brazil tests are b4b and others are not (on the first output step)
  • crown damage (788): Greg to review this week
  • parameter file update (862): ctsm-side pr (1766) created

Gridcell-to-gridcell seed dispersal meeting recap

  • Yanlan presented an overview of the work to date
  • Greg to develop improvements on the grid2grid code (current code based on Sam's prognostic beetles code)
    • Ryan asked if the changes would be applicable to other grid2grid spread disturbances
      • Yes, but performance will likely be an issue for the current land model pe layout scheme for fast disturbances (e.g. fire)
  • Charlie, Greg, Jennifer and Yanlan to start meeting every other week to track progress and discuss

fates patch count controls (pr 1766) feedback request

  • Companion to https://github.com/NGEET/fates/pull/862
  • Allows fates to dictate number of natveg patches. Also incorporates updatest to handle cfts.
  • Erik, Greg and Ryan to have meeting to discuss tomorrow
  • Related: what other dynamic fates + fates-sp mode combinations might be of interest? Moving from fates global flags to per column flag.
    • Ryan suggested running dynamic fates for non-crop pfts, but fates-sp for crops
    • Charlie also suggested regional dynamic fates, with everywhere else being fates-sp

Issue triage discussion items

  • Charlie, Greg, and Ryan walked through the issue board last week to triage and prioritize
    • We will conduct this as a regular every-other month meeting
  • Items to discuss
    • 303 - postponed for future discussion with Rosie
    • 311 - closed and transferred to fates-users-guide issue
    • 312 - still valid future goal, left open
    • 342 - postponed for future discussion with Rosie
    • 861 - move forward with proposed fix

Walk-on topics

  • No woody pft check on treefall disturbance?
    • Charlie ran into this when assessing California fire results. This means grasses will have impact on treefall disturbance rates. Should this be the case?
    • Marcos noted that there had been similar discussions about this in the past. Somewhat of a philosophical debate.

May 16, 2022

Agenda

Upcoming meetings

  • Next FATES meeting: Thursday May 26 1100 PST
    • Cancelled due to ESS meeting and CTSM training
    • June 9 presenter: Xiangtao Xu
  • Gridcell-to-gridcell seed dispersal discussion: Friday May 20 1530 PST
  • CLM meeting: Thursday May 19 1200 PST
  • CA FATES meeting: Thursday May 19 1300 PST
  • Note: E3SM meeting last week was canceled.

PR status board (Pre-meeting synthesis)

  • Cheyenne down last week so no regression testing conducted
  • Crown damage: added a new parameter and noted in the PR
    • PR needs deconflict and review, but should be good for regression testing
  • Crown fire (857): lots of discussion and testing
    • Jackie: Functionality testing shows it is working, but still needs to be assessed for correctness
  • Parameter file (862) updates
  • Carbon harvest (825): post-LULCC impact?
    • We decided that the harvesting rates could be decided by the fates side just needs review.
    • Check that we need a ctsm side PR

FATES LULCC recap and new board

  • Post-meeting recap:
    • FATES LULCC V1 discussion and presentation by Shijie
    • One action item prioritized from meeting: CTSM issue 1046
    • Jennifer to publish her meeting notes and will send out google doc with initial notes so that others may contribute
  • New project board started to transfer from fates board to organization beta project
    • Board is public, but currently only Jennifer and Greg have write access. Contact either for access.
      • Aside: organization-level beta projects provide more control over board access
    • Greg would like to use this board to help organize the work into potential milestones and set issue priority
      • Jennifer suggested using the notes as starting point to update project board
  • Jackie to talk to the Lawrences to conduct a set of complimentary cases to Shijie's presentation

HLM-FATES meeting recap

  • Outcome: it would be worthwhile to talk about surface roughness
    • Until there is a person identified it is on the backburner
    • Adrianna states she will do some review into this issue and coordinate with Ryan on his work from ED2
    • Specific topics to be discussed in clm or fates meetings (i.e. not a regular recurring meeting)
  • Related: FATES topics for CESM workshop
    • Will sent out email this morning encouraging participation
    • Jackie suggesting that Shijie present his LU work
    • Charlie will be out for the workshop
    • Rosie: Calibration cascade presentation
    • Highlights presentation idea
      • Adrianna, Jackie, Jessica, Marcos
        • Charlie will query CA fates attendees
    • Format will be the standard setup. Agenda is very preliminary and flexible.
      • Adrianna: FATES single point tutorial?

Walk-on topics

  • Cori issue: PIO errors
    • Jessica talked to Noel who is looking into it

May 9, 2022

Agenda

  • FATES meeting topics and presenters
  • Weekly synthesis of the PR Status Board: https://github.com/NGEET/fates/projects/7
  • Upcoming meetings
  • NGEET Github projects (beta) trial
  • Parameter file format (API) change tool demo/feedback, see 862
  • Walk-on topics

FATES meeting topics and presenters

  • Shawn Serbin to present this week
  • Marcos to follow up with Xuanlie about doing June fates meeting

PR status board (Pre-meeting synthesis)

  • 800 Carbon allocation bug fix: Marcos has closed and transfered to separate PRs
  • 862 Param file update: we will discuss this in later agenda
  • Erik merged ctsm pr to run fates-sp without soilbgc

Upcoming meetings

  • HLM-FATES meeting: Thursday 1PM PST/2PM MST
    • Agenda preview
      • Plan for long term coupling HLM-FATES
        • Process duplication (radiative transfer/albedo, roughness length and displacement height, photosynthesis, hydraulics)
        • What is being passed from FATES to HLM and how is HLM using this?
        • Case study: Roughness length and displacement height
      • Additional features: BVOC and dry dep, CLM-FATES nutrients, LCLUC
      • Broader context:
        • Where processes are duplicated (radiative transfer/albedo, roughness length, displacement height, photosynthesis, stomatal conductance, hydraulics)
        • What is being passed from FATES to HLM and how is HLM using this? (e.g. albedo)
  • LULCC meeting: Friday 9AM PST/10AM MST
    • Agenda preview
      • Cover Ryan's email thread on harvesting rates
      • Discussion of Shijie's mass based harvesting: https://github.com/NGEET/fates/issues/869
      • Ryan suggesting assessment of where we are and what needs to happen
        • Asked Marcos if he could overview ed2 development history
        • Charlie: What needs to be done to facilitate full global landuse CMIPs-like scenario? Charlie believes Peter is key for this.
      • For future meeting:
        • Bill Sacks: linking dynamic land use

NGEET github projects

  • FATES performance project: https://github.com/orgs/NGEET/projects/2
    • Purpose: Organize related issues and PRs into common view across organizations and repositories
      • performance issue came out of ctsm training effort that spawned a discussion culiminating in two main tasks (so far): hifrq history update and fates-sp mode not in soilbgc
  • FATES issue board: https://github.com/orgs/NGEET/projects/1
    • Purpose: Provide location to triage all FATES-related issues
      • Segragation of issues that are mainly discussion topics, issues that are requests for features, etc
      • Impetus was to setup a board similar to PR status for high-priority issues that we could review in this meeting
        • Perhaps review only monthly?
  • Questions:
    • Charlie: should we convert the existing repo-level?
      • Greg:

Parameter file change tool demo

  • Ryan has developed a tool to facilitate updates to be included in PR 862.
    • Uses xml to categorize type of change (e.g. variable add, variable change, etc)
    • Includes update to
  • Jennifer: do we want to have a prefix for each parameter?
    • Ryan: some things aren't directly associated with a specific module

Walk-on topics

  • LBL IT looking into ESMF installation and support

May 2, 2022

Agenda

FATES meeting topics and presenters

  • List update status
    • Shawn Serbin will present on May 12

Project Board (Pre-meeting synthesis)

  • Quick updates:
    • Recent integrations: Logging clean up (729) integrated
    • 1643: mimics fates testing ongoing
    • Smaller PRs prioritize for this week: 828, 849, 854, 856
    • 788: Crown damage module moved to review
      • Jessica created ctsm branch
    • 857: Sam likely getting back to working on active crownfire this week
  • 851: Discussions with Chongang
    • Greg to reach out to Chongang via the email for the task list that I missed
  • 825: LULC discussion set for Friday May 13
    • Email discussion resulted in consensus
    • API branch needs PR (or incorporate into 862, see below)
  • 862: Parameter file updates
    • Some discussion on what will go in, but Ryan getting feedback
    • Ryan's questions:
      1. Do we want max cohorts per patch or use as hardcoded constant (https://github.com/NGEET/fates/issues/853)
        • clm needs a max some we need to have something to pass it
        • Rosie: Instead of max cohorts per patch do max cohorts per pft?
          • I.e. pft specific parameter. Charlie remembering that we were worried it was too complex a change.
          • Rosie: Just do a check instead of putting in parameter file
      2. Should we do a deep dive on organizing how we name things (i.e. ground lables)?
        • E.g. fates_fire_crowndepth -> fates_allom_fire_crowndepth
          • Also discussed what things should be switched
        • Make sure to include a transformation list
        • Jackie: Should we have a larger, long-term discussion about what to remove?
          • I.e. what was added for development, but now given tuning and hypothesis outcomes could be removed?
          • Greg: Should we start an issue to discuss this?
          • Ryan: Noted that this relates to determining what things we allow in a parameter file in the first place
        • Marcos: semi-deciduous parameter dependency on hypothesis
        • Jessie: Number of damage bin to default to be changed to 2
          • Charlie: what about adding a meta-data note stating what this is used for?
        • Add another attribute for meta-data
          • Naming: Mode or use case
          • Adrianna: What about adding an attribute to the variable to identify the grouping (in lieu of in the name)?
            • Consensus is that we should do both meta-data and namespacing
          • Jackie/Adrianna/Greg: have a stable/development attribute?
          • Perhap we could also include other information like hlm
          • Add an entry into the user's guide in coordination with run modes
      3. Should we add Shijie and Jessie's API changes?
        • 862 and eventual ctsm api needs to come in before 788 and 825
        • Adrianna: Offered to standardizing unit descriptions. Ryan to let her know when ready and then she will update.
        • Consensus is that its probably ok as long as the amount of work for each API isn't too large
  • Related:

NUOPC/ESMF issues

Walk-on Topics

  • CLM meeting: CTSM tutorial discussion
    • It may also have a discussion of surface roughness length

April 25, 2022

Agenda

FATES meeting topics and presenters

  • Hui Tang still on docket for this week
  • Charlie started list for future meeting planning

Project Board (Pre-meeting synthesis)

  • MIMICS coupling completed with ctsm5.1.dev091
  • #792 Logging is ready for testing
  • Ryan to start working on PR to wrangle the next paramfile update: https://github.com/NGEET/fates/issues/799
  • Harvest carbon status request from Jennifer
    • Jackie: we were talking about discussing this within the broader LULC discussion
      • Jackie will send out email this week to get the discussion going
      • Charlie doesn't want use regular fates meeting (so find different date than May 12 idea)

Performance and timing discussion

  • Discussion of fates timing in general and fates-sp mode specifically. Based on notes from Brian and calculation
  • Charlie: In fates-sp mode should we not run soil bgc?
    • Erik: I think we can turn this off?
    • Charlie: is dyn_subgrid supposed to be on as well?
      • David: yes, it can be on regardless of soil bgc
  • Charlie: hifrq_hist update
    • cost is remapping from cohort to ecosystem level every time step
    • Ryan: split into two groups site level and cohort level; add logic to select one or the other
    • Charlie: Break up associate statement and add if use_fates_sp logic
    • David: Why is this expensive for fates-sp if there is only one cohort per patch?
  • David: is this the bulk of fates cost? What about timing regular fates?
    • Adrianna: can we add timing to fates?
      • Ryan/Greg: yes we should be able to do this (perf_mod)
        • Erik: this should be the same from elm and clm
    • Dave will run f45 for non-sp mode comparison
  • Next steps
    • Jackie: Make issue and make sub issues
      • Ryan to file issue for fates wrap hifrq refactor
    • BGS shutoff
      • Ryan: edbgc wrappers need to be dealt with in clm_drv

Walk-on topics

  • Nitrogen coupling of ctsm-fates
    • David: identified as main deliverable for CESM3. What resources do we have for this?
    • Ryan: Will need pair programming; estimating half-year of implementation
      • Very difficult to estimate
      • Rosie: Mechanics versus tuning
        • David: Just asking about mechanics
      • Ryan: elm required a bunch of cleanup to facilitate this
        • EDBGC dyn file doesn't exist in elm

April 18, 2022

No notes recorded

April 11, 2022

Agenda

FATES meeting topics and presenters

Adrianna will present this week Jackie feedback:

  • Heard back from Sean Serbin
    • Wants to give a talk in the Fall about SW site
  • Gordon agreed to give talk on multi-layer canopy work
    • Will discuss with Ryan; Marcos will participate in discussion as well
    • Not available until mid-May at the earliest
  • Jennifer asking after focused land cover, land use model discussion.
    • Planning still in process via email.
      • Jackie will check with folks on NCAR side
      • From E3SM: Alan, Shijie, maybe Ben
    • Tentatively schedule for Thursday May 12
  • Rosie sent out email on Mar 28 for Hui to present 4 weeks (i.e Apr 28)

Action item: Create a calendar or spreadsheet to populate the list of presenters

Project Board (Pre-meeting synthesis)

  • #800 - ID of answer changing parts of the code are still in progress
    • Aside: Charlie asking if we've ever done the check to see what if any impact small noise in initial conditions has on output
    • Ryan and Marcos recommending splitting this PR into answer chaning and non-answer changing sections
      • Will need additional reviewers
  • #850 (CTSM #1643) - CTSM side is under active review.
  • #849 - Ryan to check in with author about scope of tests if any.
    • Ask Brad to review
    • Potentially, conduct a unit test "sanity check" against the previous range of values.
  • #851 - Feedback provided regarding transpiration error
    • Team would like to have further discussion with Chongang
  • #584 - Active crownfire starting back up. Greg, Jackie and Sam to discuss tomorrow
    • Feedback portion is not yet complete
  • #769 - Ryan looking towards working on this in near future
  • #788 - Still working on canopy too full issues. Greg to help debug.
    • Things taking too long, seems like its in the promotion/demotion scheme
      • Using the default scheme from the BCI parameter files.
        • Charlie recommends trying to use the opposite issue

Parameter file update

  • 12 new parameters not inluding another minimum of 4 parameters forthcoming from Jennifer
  • Ryan to create PR list
  • Discussion on when to add parameter
    • At minimum, new parameter shouldn't change answers without out some sort of discussion
    • Add section to develper's guide to for style guide on parameter file
    • Add user's guide section that discusses good first steps
      • Add to reference section additional meta-data for parameter file. Will require curation
  • How can we buffer a new user with what are relevant parameters

SIF discussion

  • Relevant to Gordron/Ryan/Marcos discussion above
  • We need to have a higher-level discussion about radiation prior to this. Tabled for later.

Walk-on topics

  • No topics

April 4, 2022

Agenda

FATES meeting topics and presenters

  • Team brainstormed a number of individuals. Ryan will email out potential list to include Charlie and Rosie to get there feedback.
  • Discussed using the dedicated fates Thursday time to access as focus conversation topics that might not be of interest to everyone

Project Board (Pre-meeting synthesis)

  • #847: Integrated and tagged
  • #800: Marcos to remove out-of-scope phenology-code from the PR
  • #825: Greg deconflicted and Shijie merged. Need to continue discussions; Ryan sent email to coordinate time.
  • #CTSM 1643: Added to board. This needs a FATES-side PR.
  • #788: Jessica is working through canopy too full errors.

CESM3 meeting preview discussion

  • Team asked Adrianna and Jackie for throughts on FATES within the context of CESM3
    • This conversation segued into the FATES updates question from Erik (see below)

CTSM software meeting FATES reporting

  • Related: Greg floated the idea of a broad quarterly FATES newsletter. Received
  • Related to CESM3 discussion
  • Related: E3SM methodology for tracking tasks to larger goals? Using Atlassian tools.
  • Adrianna and Jackie: User's stories, Agile framework, Epochs & Initiatives, clickup
  • Use this meeting to frame the report backs for the upcoming ctsm

Walk-on topics

  • CTSM training (May 25 and 26, 9am to noon)
    • Some discussion on how we can support this for FATES training
    • Overlaps with DOE ESS PI meeting

March 28, 2022

Agenda

FATES meeting topics and presenters

  • Adam is interested, but declined due to schedule conflicts
  • Current plan is to hold office hours this week
  • Potential future talks ideas:
    • PPE plans from Adrianna
    • Norway group: Rosie to follow-up.
    • ED2 improvements for comparison: Marcos to follow-up.
    • Ask Peter to give LULC status update: Jackie to follow-up.

Project Board (Pre-meeting synthesis)

  • #847: Greg to integrate (and update baselines)
  • #800: Ryan running some additional test cases by increasing LAI capacity allowable
  • #825: Ryan to double check units and Greg to deconflict
    • Discussion of the harvesting logic
      • Job of the host to tell FATES to harvest
      • ELM wants to read in smoothed
        • We asked Shijie to make it agnostic
      • Eventually FATES will allow HLM to dictate harvesting everyday
        • We need an update to the disturbance code to allow all types in a given day to
      • Next steps: Continue discussion on the github thread
        • Why does ELM want smoothing?
        • Should we give a time bounds for the harvesting interval?
          • CTSM crop model does something similar
  • #828: Merge in Ryan's branch commits to remove unnecessary LAI and continue discussions about LAI calculation method
    • Methodolgy of assessing what is in canopy 'above' for future PR
      • Currently looking at instantaneous LAI
      • Ryan suggesting a time-averaging idea
  • #824: Greg has access to Summit now. Will attempt to replicate issue this week.
  • #801: Status update on work to date
    • What are the user controllable parameters that the community would like to see?
      • Related: Jessica and Marcos have updates as well (see issue #799)
    • This PR will be superseded by a rebased version of the PR branch

Unit check for soil metric potential

March 21, 2022

Canceled: No pressing topics to discuss and some members out on vacation.

March 14, 2022

Agenda

FATES meeting topics and presenters

  • Charlie to reach out to Adam about FATES meeting on March 31

Project Board (Pre-meeting synthesis)

  • CTSM #1681 going through re-test
  • E3SM #4777 under review
  • #825 next steps being discussed via email
  • #800 discussion
    • This PR is tripping the LAI explosion issue (#844) at year 16
      • Master branch does not show the issue
    • Should we proceed as normal and integrate (PR is passing regression tests)?
    • Charlie: How do we explore the hypothesis that the PR is just unlucky?
      • Increase number of leaf layers until it passes the long case test
      • Ryan: Has a test that is running to cap the LAI
    • slamax provenance
      • Elise
    • Nominally tree should trim to reduce lai
    • Charlie: This is a long standing problem
      • CLM4 creataceous runs was getting huge lai as well
      • Allowing leaves thiness to approac infinty is problematic and allows much higher LAI
    • Charlie: Sergei and Elena use a memory term similar to what Ryan is proposing
    • Ryan to run sensitivty analysis to assess how this is performing
      • Code update is based on Greg's PR #828. We will likely expand the scope of that PR to include this.
  • #788: Jessie is having issues getting Lawrencium and the nuopc update
  • #768: Jennifer and Ryan to meet after this meeting to discuss next steps

Walk-on topics

  • #843: Adrianna to make change and test

March 7, 2022

Agenda

FATES meeting topics and presenters

  • Adrianna: volunteered to present allometry work for next meeting
  • Marcos: maybe Adam could present reproduction work in two weeks. Charlie to reach out.

Project Board (Pre-meeting synthesis)

  • #831: coming in next with a minor api change ctsm PR
    • Last time we update the parameter file was API 16.1
    • Jessica asked how to incorporate parameter file update for her #788
      • Ryan pointed to issue #799 that will get its own PR soon
  • #824: Summit request denied. Emailed ORNL for explaination.
  • E3SM #4777 needs to be brought upto API 22 now. Ryan to work on it soon.
  • #800: Review and testing this week. Ryan to handle.
  • #825: Email sent to Shijie to confirm the plan from last comment.
    • Will need porting of e3sm changes to ctsm side change to provide testing.
  • #788: Jessica is implementing a reviewer request which is resulting in the code breaking due to a weird bug.
    • Failure at ~70 years. Restarting from that point allows run to continue for another decade or so before another repeat failure.
      • Maybe memory leak or un-initialized variables?
  • #801: Drought deciduous needs to be brought up to date
  • #768: Jennifer has a few other parameters to add to issue #799
    • Ryan and Jennifer to connect offline to scope out the necessary refactor

Diffusion radiation angle granularity

  • Issue #841 to be included in future PR. Discussion delayed until later date.

Re-visit respiration issues

  • Ryan suggested making this a topic for a future FATES meeting.
    • Review Shinwan's view on the topic

Readthedocs.org membership payment

  • Should we reinstate paying for the readthedocs membership to remove community ads?
    • Consensus is yes, pay to remove the ads.

Walk-on topics

  • Adrianna: Scientific unit tests
    • Would they help illuminate specific issues, e.g. radiation balance issues?
    • How do we know to set for the module level inputs? E.g. Dummy cohorts/pacthes?
      • Charlie: MAAT (Anthony) test bed (R scripts) useful here?
    • Ryan has some stuff built up, e.g. for allometry.
    • Greg: For infrastructure code might be worth it to keep an eye on interactive fortran project: https://lfortran.org/
  • Ryan: Should we spend time moving to a different radiation model instead of Norman?
    • Would be a significant effort.
    • Jackie: Is there benefit from adopting some of two-stream (clm) model concepts?

February 28, 2022

Agenda

Project Board (Pre-meeting synthesis)

  • #831 recap
    • Rosie doesn't believe that the albedo bug she is working on is related to the parameters
    • Jackie noted that there are differences discussed in the paper between the supplement (which is used by clm) and the averages presented in some of the main tables. It might be worth reviewing how this affects the ILAMB results.
      • Adrianna offered to handle this
    • Jackie to ask Shawn Serbin to provide his insight into the source paper based on his work
  • #838 update
    • This generated a discussion on how to mitigate technical debt
  • #788 status update: Jessica noted that she's ready to start testing

Walk-on Topics

  • #837 issue status update: Albedo bias (Rosie)
    • Still seeing high bias with the test case (1x1_brazil)
    • Comparison to CLM-bigleaf isn't entirely informative given the difference between the way CLM and fates handles this
    • If stems are removed from fates there is still a high albedo bias
    • Radiation balance check might be relevant to the testing
    • Not related to multiple canopy layers as Rosie is testing in SP mode (single canopy layer per patch)
    • Aside: To enable Issues in github for your personal fork of fates, click the checkbox under "General" section in "Settings" tab.
  • FATES_FRACTION rename (Adrianna)
    • Discussion about rolling this into an upcoming PR
  • Charlie has a PR bug fix forthcoming
  • History variable indexing and IO discussion
    • How much time is taken up by the output calculation and IO
    • How much time is the hi-freq output taking up in calculation and IO operations? What about instantiating a flag for setting different levels of output
      • Charlie to look to see if we have an issue already and bump it up the list. Otherwise he will
    • Aside: Is there a better way to setup and allocate fates variables? Discussion about Adrianna's hashmap idea.
  • Charlie proposed discussing the Thursday fates meeting topic setting/speaker recruiting in this meeting
    • We gave it a try for this coming Thursday
      • One topic will be to do a walk through of the User's Guide to advertise it and solict feedback in the form of github issues
  • TSS meeting report back

February 21, 2022

No meeting due to President's Day holiday

February 14, 2022

Agenda

Project Board (Pre-meeting synthesis)

  • #766 Hydro picard ready and waiting on next ctsm tag
  • #833 NoComp + disturbance testing passed as expected
  • #831 optical properties double check in progress
    • Adrianna presented ILAMB comparison between FATES spmode master param file and the new optical parameters
      • GPP and Upwelling is worse
      • Adrianna will posted the results link and context for further discussion
        • This spurred a general discussion on how we want to benchmark with ILAMB going forward
  • #824 Summit account requested
  • #836 frost mortality scheme drafted
    • Check in with Marius

Updates to FATES documentation

  • Namelist options clarification
    • The links to the different section of the wiki and tech-notes are good. Just need to expand these to modes that don't have coverage and flesh out some of the ones that currently do as well.
  • Autobuilding of PRs through Read The Docs server enabled on fates-docs and fates-users-guide
    • Integrated with github. Will block merge button if failing. Notifies defined email list of failure.
  • FATES User's guide
    • Good initial feedback and suggestions. Greg will transfer this to the NGEET repo once the wiki pages have been converted.
    • Started up a new page titled "Notable Differences" for comparison against big leaf (and other) models.
      • Greg asked for and encouraged contribution to this page. The focus should be on broad differences, with links to specific documentation for details (i.e. tech-note, clm user's guide, etc.)
    • Greg to update user's guide configuration to utilize markdown to speed up wiki conversion process

Walk-on topics

  • Discussion of ILAMB specific flux variables for grid cell averaging
    • Can we conducting the necessary averaging calculation in ILAMB (i.e. post-processing) rather than in the model code?
      • Per Adrianna, yes this is possible.
        • ILAMB can conduct a confrontation using a ‘derived’ variable
        • There are still some calculations that FATES does not currently conduct that might not be derivable.
      • Charlie noted that this would help avoid divergence between HLMs.
        • Jackie noted, in support, that ILAMB isn't HLM specific either
      • Aside: Is it possible to output time-invariant data in just the first timestep? Charlie thinks CLM can do this.
        • Adrianna believes so. Will ask Erik. Uncertain if this is pulled straight from dataset or passed through model.
        • Doing this for fates would help cut down on storage for certain things.
      • Short discussion of using ILAMB as development tool for scientific comparsion between tags
  • Drought decidous flickering issue question wrt #801
    • Charlie was reminded of the issue working on #833. Does Marcos' #801 fix this?
      • Marcos: Unfortunately, no.

February 7, 2022

Agenda

Project Board (Pre-meeting synthesis)

  • #766/CTSM#1592 - waiting on next ctsm devtag
    • Ryan will incorporate this into the API 21 FATES-ELM update
  • #831 - do we want to conduct additional science tests for the update optical parameters?
    • Conduct an assessment using ILAMB
      • This spurred discussion about incorporating an ILAMB test for each answer changing PR. The team agreed that this would be a good practice to adopt.
      • Adrianna to create an issue to track this and take point on this
  • #800 - Ryan brought up idea to adapt this PR to coordinate the simplified model using parteh
    • We agreed to push forward with this PR as is and conduct the leaf organ priority
  • #824 - IBM compiler issues
    • Greg to attempt to replicate in community, local version of IBM compiler. Will attempt to get summit account in parallel.
    • Marcos suggests adding test to check if the pointer is actually allocated/associated prior to the deallocation
  • #825 - Charlie will review
  • #833 - Charlie just submitted this to get nocomp and disturbance working together
    • Should be ready for review and testing
  • #788 - Still in progress
  • #768 - Jennifer will merge this up to match Ryan's nutrient branch work
    • Anthony has a paper that is coming out soon that we'd like to use for this hypothesis

FATES wiki updates

  • Tabled for next week

FATES User's guide

  • Greg will attempt to consolidate the wiki into read-the-docs as a starting point
  • Rosie noted that CICE consortium README page is nice and might be good structure to adapt

Subset single point function

  • Team agreed that zeroing out the lake, urban, glacier and wetland percentages is correct. Ryan noted that tower sites usually don't consider these things as part of their inventory.

Single pft SP mode issue

  • Push on with PR to address crops or split out the code relevant to the order of operations fix?
    • Greg will test out the latter option
    • Or we could remove the crop related param file changes and just repurpose the PR as the fix to #728

FATES AD Spinup report

  • Ryan noted that investigation on why accelerated decomp is not working with clm-fates is ongoing but slow due to other commitments
    • We're not broadcasting the spinup flag when fates is on
  • Charlie volunteered to take a look at this as well

January 24, 2022

Cancelled due to NCAR LMWG meeting

January 24, 2022

Agenda

  • Weekly synthesis of the PR Status Board: https://github.com/NGEET/fates/projects/7
  • E3SM FATES API Updates
  • Planning CLM-FATES surface roughness science discussion
  • Discuss ways to facilitate new user simulations and generate more scientifically supported configurations
  • Walk-on topics

Project Board (Pre-meeting synthesis)

  • SP mode is now in ELM. (are the ERS fixes in?)
  • Ryan will submit new PR now to E3SM for FATES API 21 (merge in Greg’s Changes)
  • Picard Hydraulics PR: (needs minor changes: SRL and loop cosmetic fixes in the new Solver) - Greg and I are going to team up on this. No more review necessary, just implementing review comments
  • Marcos’ allocation algorithm - this is a bug fix PR, so we are prioritizing this now, along with 829 and 828 (Josh’s bug and minor update to calculating TLAI)
    • Marcos' new capability will eventually need a regression test.
    • Charlie: Maybe we should add a conservation check on individuals to help catch errors like Josh's mortality crisis?

E3SM FATES API Updates

  • Ryan and Greg are working with Teklu to add an E3SM-FATES-TOPO test on the 4x5
    • Jennifer: Doing this will also exercise precipitation downscaling

CLM-FATES surface roughness

  • Meier is using Monin-Obukhov
  • Ryan: roughness calculation is an 'emergent' assemblage in fates at the canopy-level (patch) and not tied into pft
    • Charlie: counter-point that roughness can be based on pft shape (shape of indiv crown)
    • Ryan: we should do a review of the literature to see if there is a way to do better to use the structural information
  • Jackie was suggesting we have a discussion in a fates science call
    • The consensus seems to be this would need a dedicated person to explore this issue

Facilitating and engaging new users

  • FAQ documentation
    • Rosie: Perhaps we could create a survey for CLM-LMWG to help populate/refine a FATES FAQ
    • Greg: In the FAQ it might be helpful to include a "Noteworthy Differences" section to compare the general model type (i.e. versus gap models) and the specific implementation (e.g. versus big-leaf). See this example from Julia language docs.
    • Marcos: We should highlight which hypothesis we can analyze with fates that are difficult in others (e.g. selective logging)
  • Workflows
    • Jackie: Getting things into ILAMB framework will help
    • Rosie/Marcos: May have more opportunity to conduct benchmarking using additional workflows
    • Adrianna: BCI usermods and fates for NEON
  • Training
    • Jackie: TSS FATES specific tutorial would be helpful, but will need dedicated support

January 10, 2022

Agenda

E3SM FATES API Updates

  • Junyan is going to be doing simulations in the Chesapeake bay region for fates hydro and will want to use sp mode as well
  • Updating to API 20:
    • Ryan adopted a method for how elm calculates snow fraction for the bc_in%fcansno
    • Charlie: ctsm folks wrote a paper when they updated the canopy snow cover.
      • Ryan to write email asking about this.

API changes inbound with updates to hydraulics

  • Ryan updated the group on hydraulics update. CTSM side update has been approved by Greg

PR status board

Walk on topics

  • FATES ILAMB support discussion
    • We discussed having an audit of what we currently pass to the hlm (prognostic versus diagnostic)
      • What additional values do we need/want to send to be included for ILAMB?
    • Adrianna and Ryan to team up after LMWG meeting (Jan 31 to Feb 4) to work on this