glemieux/fates

repository for the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

fates's Issues

Flesh out scientific unit tests documentation

Dummy issue 1

Refactor `bc_out%seed_out` to avoid passing this to `update_history_dyn`

As of NGEET@3a0c352, it is necessary to introduce a breaking change to the API for both the ELM and CLM host land models. Since we are calculating the seed_out in fates, there isn't any reason to pass this back through to fates from the API. This will avoid breaking the API for both HLM once the fates-side pull request is integrated into main.

Generate v0 LUH2 unified netcdf data files

Generate unified

Tasks

• Develop file name standard

Historic data

• Generate f45 historic file
• Generate f1.9 historic file

Tracking issue

This is testing tracking issues within a higher-level issue. This tracking issue is a "unit of work"

• #10
• #11
• #13

Review fates-sp mode calls to determine where decomposition calls can be avoided

Per discussion in ESCOMP/CTSM#1723 (comment), determine whether or not we actually need to pass values to the moisture scalars if we are running in sp mode (i.e. without decomposition). If so, generate new issue on ngeet org repo.

Different tracking issue test

This unit of work tracking issue will test adding the issues to be tracked in a different comment cell.

Clarify tutorial setup steps wrt making fresh clones

Hi Greg,

That was the intent, this command should be executed on the fresh clone. If the wiki was not clear on that, could you help correct it?
My guess is that the already existing clone is now out of date.

Originally posted by @rgknox in #5 (comment)

Dummy issue 2

Update seed dispersal code to accommodate multiple pfts

The current seed dispersal code only handles one pft for the seed dispersal run. This needs to be updated to account for all possible pfts to account for differences in pft spread.

Related thought for future update: based on references, how would we define a dispersal mode (i.e. wind, bird, etc) for the particular pft type?

• Update dispersal code to add a second dimension pft to the outgoing/incoming global seed variables
• Update the dispersal code to pass the access the neighborhood_type bound dispersal fraction
• Update parameter file to include parameter types for the kernel and code to read in the new data

Add this test issue from kboard

Dummy issue 4

Bareground patch refactor

This issue is a super task for the bareground patch refactor project

References:

• NGEET#775
• NGEET#973
• NGEET#911

Develop V0 LUH2 data processing tool and workflow

Adapt @ckoven's prototype python code to develop a FATES tool to process LUH2 data.

Tasks

• Convert Charlie's code to a module
• Develop calling script
• Generate conda environment file

Testing

• Test passing start/stop times to script
• Test on perlmutter
• Test on summit
• Test on cheyenne

fates tutorial: checkout_externals svn authentication error for ccsm

@rgknox and @ckoven, in section 0-5 of the tutorial I've hit an authentication error in trying to ./manage_externals/checkout_externals in the ~/FatesTutorial_Feb2019/ctsm> directory. It's asking for authentication and my UCAR password doesn't seem to work. Here's the output:

glemieux@cheyenne6:~/FatesTutorial_Feb2019/ctsm> ./manage_externals/checkout_externals 
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: cism, source_cism, clm, fates, ptclm, mosart, cime, rtm, 
Checking out externals: cism, clm, mosart, cime, rtm, 
Processing externals description file : Externals_CISM.cfg
Checking out externals: source_cism, Authentication realm: <https://svn-ccsm-models.cgd.ucar.edu:443> ccsm:models
Password for 'glemieux': ****************

Authentication realm: <https://svn-ccsm-models.cgd.ucar.edu:443> ccsm:models
Username: glemieux
Password for 'glemieux': ****************

Authentication realm: <https://svn-ccsm-models.cgd.ucar.edu:443> ccsm:models
Username: 
Password for '': 

ERROR: Failed with output:
    svn: E215004: Unable to connect to a repository at URL 'https://svn-ccsm-models.cgd.ucar.edu/cism/branch_tags/longer_var_list_tags/longer_var_list_n01_cism2_1_develop_n02'
    svn: E215004: No more credentials or we tried too many times.
    Authentication failed

ERROR: In directory
    /gpfs/u/home/glemieux/FatesTutorial_Feb2019/ctsm
Process did not run successfully; returned status 1:
    svn checkout --quiet https://svn-ccsm-models.cgd.ucar.edu/cism/branch_tags/longer_var_list_tags/longer_var_list_n01_cism2_1_develop_n02 /gpfs/u/home/glemieux/FatesTutorial_Feb2019/ctsm/components/cism/glimmer-cism
See above for output from failed command.
Please check the log file manage_externals.log for more details.

On a related note, am I correct in running the command from the ~/FatesTutorial_Feb2019/ctsm> directory? Re-reading the tutorial workflow from 0-4, it could suggest running the command from the ~/FatesTutorial_Feb2019/TestCloneSpace/ctsm> directory. Interestingly, running the checkout from the ctsm root in the TestCloneSpace directory works fine. Was the original intent of the tutorial to run from the TestCloneSpace directory and I misinterpreted it?

Develop first draft of gridcell-to-gridcell seed dispersal

Project board: https://github.com/users/glemieux/projects/5/views/1

• https://github.com/glemieux/fates-tasks-notes/issues/19
• https://github.com/glemieux/fates-tasks-notes/issues/18
• https://github.com/glemieux/fates-tasks-notes/issues/23
• glemieux/E3SM#1
• https://github.com/glemieux/fates-tasks-notes/issues/50
• glemieux/E3SM#2

JOB_QUEUE ctsm script setting

@rgknox in the tutorial the 1x1 script has a setting JOB_QUEUE. How do I determine what to set here? Here's the script context:

# Configuration for CTSM on cheyenne
CIME_MODEL=cesm
MACH=cheyenne
COMP=I2000Clm50FatesGs
PROJECT=P93300041
JOB_QUEUE=R4231271

Looking through the Cheyenne user's guide on job submissions, it seems to suggest that you denote the nominal name for the queue (e.g. "regular"). That said I also saw on this page that using qcmd automatically starts the job on the "regular" queue:

Alternative - qcmd: For running resource-intensive tasks such as CESM and WRF builds or other compiles with three or more threads, CISL provides qcmd. This script starts a non-interactive job on a single batch node in the Cheyenne "regular" queue with a default wall-clock time of 1 hour.

Given this, what is the significance of the JOB_QUEUE setting in the script?

Attempt Julia-based driver for unit testing to compare again python-based driver

Dummy issue 5

Dummy issue 3

Do variables defined during type defintion within a module need to be specified as public?

For example in EDTypesMod.F90 the ed_cohort_type is defined. Do the variables defined for this type also need to be specified as public/private?

Relevant to NGEET#502.

Develop LandUse x PFT static data file tool

For the upcoming no-comp version of NGEET#1040, we need the landuse x pft mapping data from https://gdex.ucar.edu/dataset/188b_oleson/file.html and a tool to concatenate the data into a single file. Note that this data is already present on Cheyenne under /cesm_tools/clm5landusedatatool/CLM5_CURRENT_GEOG_DEG025/.

• Double check that this data is not already available in some other format.

Test out coverting a card to an issue and then tagging

This is me testing a project card to issue conversion. @rgknox and @ckoven you can see this yeah? I was thinking if I have any issues with the initial objectives, I'd record them here for posterity and ping you on them as necessary.

How do I determine which compsets and grid combos have been tested by CESM?

In running a ./create_newcase I received the following. I assumed that since the testsuite for this combo is available that this would be a good one to pick for me simple ./case.build but maybe not?

glemieux@cheyenne3:~/ctsm/cime/scripts> ./create_newcase --case /glade/scratch/glemieux/clmed-tests/mytestcase1 --compset I2000Clm50Fates --res 1x1_brazil --project P93300041 --compiler gnu
Compset longname is 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /gpfs/u/home/glemieux/ctsm/cime_config/config_compsets.xml
Compset forcing is 1972-2004
ATM component is  Data driven ATM  GSWP3v1 data set 
LND component is clm5.0:FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: (experimental)
ICE component is Stub ice component
OCN component is Stub ocn component
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is 
Pes     specification file is /gpfs/u/home/glemieux/ctsm/cime_config/config_pes.xml
Machine is cheyenne
Pes setting: grid match    is l%1x1|l%CLM_USRDAT 
Pes setting: grid          is a%1x1_brazil_l%1x1_brazil_oi%null_r%null_g%gland4_w%null_m%null 
Pes setting: compset       is 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV 
Pes setting: tasks       is {'NTASKS_ATM': 1, 'NTASKS_ICE': 1, 'NTASKS_CPL': 1, 'NTASKS_LND': 1, 'NTASKS_WAV': 1, 'NTASKS_ROF': 1, 'NTASKS_OCN': 1, 'NTASKS_GLC': 1} 
Pes setting: threads     is {'NTHRDS_ICE': 1, 'NTHRDS_ATM': 1, 'NTHRDS_ROF': 1, 'NTHRDS_LND': 1, 'NTHRDS_WAV': 1, 'NTHRDS_OCN': 1, 'NTHRDS_CPL': 1, 'NTHRDS_GLC': 1} 
Pes setting: rootpe      is {'ROOTPE_OCN': 0, 'ROOTPE_LND': 0, 'ROOTPE_ATM': 0, 'ROOTPE_ICE': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0, 'ROOTPE_ROF': 0, 'ROOTPE_GLC': 0} 
Pes setting: pstrid      is {} 
Pes other settings: {}
Pes comments: none
 Compset is: 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV 
 Grid is: a%1x1_brazil_l%1x1_brazil_oi%null_r%null_g%gland4_w%null_m%null 
 Components in compset are: ['datm', 'clm', 'sice', 'socn', 'mosart', 'cism', 'swav', 'sesp', 'drv', 'dart'] 
STOP:  
This compset and grid combination is untested in CESM.  Override this warning with the --run-unsupported option to create_newcase.

Generate LUH2 unified netcdf data files for future scenarios

This will likely be done post-v0 of the data processing tool issue #26. This is currently just a sketch of the tasks.

Tasks

• Download future scenarios from LUH2 site including "added_treecov" data sets
• Figure out how we want to handle added tree coverage data

Kanban board test issue

This is a test issue to practice using the Kanban board.