Updating 219 from main. #426

bschroeter · 2024-10-18T02:58:52Z

Updating branch 219 from main.

📚 Documentation preview 📚: https://cable--426.org.readthedocs.build/en/426/

This is done so that: 1. We can create separate targets for the serial and MPI executable and only link against the MPI libraries when needed without relying on the MPI compiler wrapper. This lets us compile all executables (serial and parallel) with a single invocation of CMake. 2. We can use object libraries to compile the object files common to both serial and MPI builds. This saves compiling these object files for each executable (serial and MPI), reducing compilation time. Note: since compiler flags are the same across all targets, this change applies the flags globally to all targets in the current directory and below via [`add_compile_options`][add_compile_options]. [add_compile_options]: https://cmake.org/cmake/help/latest/command/add_compile_options.html

Flags for release and debug configurations for the GNU compiler were taken from build.ksh (CABLE-POP_TRENDY branch).

This pull request should follow after the CMake implementation (see #200). This change adds the following build system changes: - List source files in alphabetical order in CMakeLists.txt. The order of source files was previously chosen so that we could demonstrate binary equivalence in executables between the CMake build and the Makefile build. - Use [`find_package(MPI REQUIRED)`](https://cmake.org/cmake/help/latest/module/FindMPI.html) instead of specifying `mpif90` when invoking `cmake` for MPI case. This is done so that 1. We can create separate targets for the serial and MPI executable and only link against the MPI libraries when needed without relying on the MPI compiler wrapper. This lets us compile all executables (serial and parallel) with a single invocation of CMake. 2. We can use object libraries to compile the object files common to both serial and MPI builds. This saves compiling these object files for each executable (serial and MPI), reducing compilation time. - Portability fixes and improvements to build.bash. - Add `--compiler` flag to build.bash and GNU compiler support. - Add Matthias's configuration for example. Regression tests using [benchcab](https://github.com/CABLE-LSM/benchcab)* (bitwise comparison of model output via nccmp) show that model output is bitwise identical between the current branch and the main branch for serial and MPI model runs. *executables were built manually as benchcab does not yet support the recent build system changes (see related issue: CABLE-LSM/benchcab#258). Fixes #215  ---- 📚 Documentation preview 📚: https://cable--216.org.readthedocs.build/en/216/

Making CABLE available as a [spack](https://spack.io/) package allows us to test the model compiles successfully inside a continuous integration (CI) environment which gets triggered automatically on a pull request. This change adds the model build CI workflow developed by the ACCESS-NRI release team to compile CABLE offline via spack (see [build-ci](https://github.com/ACCESS-NRI/build-ci) for more details). This workflow compiles CABLE using the intel compiler. The CI for other compilers will follow after this pull request. Fixes #202  ---- 📚 Documentation preview 📚: https://cable--223.org.readthedocs.build/en/223/

# CABLE ground water hydrology work of Mengyuan Mu This pull request is part of integrating the ground water hydrology work of Mengyuan Mu into CABLE, which will take place in a sequence of pull requests. The actual integration project itself was completed back in September 2023. The current work involves just a gradual merge into the main branch. ## Description 1. A new SUBROUTINE GWspatialParameters is introduced in **src/offline/cable_parameters.F90** 2. This subroutine will eventually be called only once, from **src/offline/cable_input.F90**. I will add this call at the appropriate time, but for now the subroutine is inactive 3. Dependencies are introduced in **src/offline/cable_parameters.F90** and **src/offline/cable_define_types.F90** in order for the code to compile successfully (confirmed) 4. This pull request involves only code additions, no deletions or modifications of existing code were carried out (some minor typos I came across in existing comments were fixed) 5. *PLEASE* do not delete any of my in-code comments (tagged rk4417) for now. Once the integration of the ground water hydrology work is complete and its functionality is confirmed to reproduce the results obtained already outside of the repo, I will clean-up all of my comments in a single pull request. Deleting any of my comments now will just make it much more difficult for me to track down and fix any issues that might arise during this process.  ---- 📚 Documentation preview 📚: https://cable--224.org.readthedocs.build/en/224/

# CABLE ## Description gfortran could not compile the CABLE main branch, neither in release mode (-O3 -Wno-aggressive-loop-optimizations) nor in debug mode (-O -g -pedantic-errors -Wall -W -Wno-maybe-uninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan). The name `mland` was an ambiguous reference in the routine `landuse_allocate_mland` in landuse3.F90 because it is used via landuse_constant and defined in `landuse_allocate_mland`. I renamed it locally to `imland` in the routine. With this change, the release mode compiled. However there were plenty of 'Nonconforming tab character' and 'continued character constant' in the other files. I removed all that and now it compiles in release and debug mode. ## Type of change Please delete options that are not relevant. - [x] Bug fix - [ ] New or updated documentation ## Checklist - [x] The new content is accessible and located in the appropriate section. - [x] I have checked that links are valid and point to the intended content. - [x] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--221.org.readthedocs.build/en/221/

The build script currently does not support MPI builds with the GNU compiler on Gadi. This is due to the `intel-mpi` module being loaded when we should be using an MPI module that is compatible with the chosen compiler. This change loads the `openmpi` module when GNU compilation is enabled in the build script. Fixes #239  ---- 📚 Documentation preview 📚: https://cable--241.org.readthedocs.build/en/241/

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description Fixes #(285) Change Uber Quick guide instructions to run the testcase from src/offline/ since for now CABLE needs the namelists in the run directory. ## Type of change Please delete options that are not relevant. - [X] New or updated documentation ## Checklist - [x] The new content is accessible and located in the appropriate section. - [x] I have checked that links are valid and point to the intended content. - [x] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--286.org.readthedocs.build/en/286/

Case of mobile is not a major consideration here, comfort on a computer is more important

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description Increase the overall width of the page. This removes the large left and right margins and tend to improve the rendering of the tables throughout the documentation. You can link issues by using a supported keyword in the pull request's description or in a commit message: Fixes #(303) ## Type of change Please delete options that are not relevant. - [X] New or updated documentation ## Checklist - [X] The new content is accessible and located in the appropriate section. - [X] I have checked that links are valid and point to the intended content. - [X] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--305.org.readthedocs.build/en/305/

…-user-guide

# CABLE ## Description Added a table of physical constants and a table of mathematical constants to the user guide. Additional tables of constants can be added following the same pattern. Fixed missing/incorrect units in code and documentation. **It might be a good time at this stage to decide on the numerical value to use for the ice density: 910 from cable_soilparm.nml OR 921 from cable_phys_constants_mod.F90 ?** Interestingly another well known code uses 917. - [X] New or updated documentation  ---- 📚 Documentation preview 📚: https://cable--326.org.readthedocs.build/en/326/

Remove double summation of btran (#279) Require both changes.

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description Fixes #351. Move the definition of sum_rad_gradis and sum_rad_rniso out of the NITER loop in `define_canopy()` since these variables do not change in the loop. Having a quick comparison between the outputs before and after this commit [the effect is negligeable](#352 (comment)). Use `sum_rad_gradis` and `sum_rad_rniso` as calculated in define_canopy() everywhere in define_canopy(), dryLeaf() and wetLeaf(), instead of recalculating them sometimes. Move the initialisation of `canopy%DvLitt` and `canopy%kthLitt` to the top of `define_canopy()` since these variables are constant throughout the run. We also want these variables to be defined in all cases to avoid errors in function calls, but only used with `cable_user%litter` turned on. ## Type of change Please delete options that are not relevant. - [X] Bug fix ## Testing benchcab/me.org analysis: https://modelevaluation.org/analyses/anywhere/BPLvifw3DyARokYdg/s6k22L3WajmiS9uGv/CJGXP5GQWhGf3nH28/all Tested in benchcab the changes for DvLitt and kthLitt on their own. benchcab showed bitwise identical results when moving the initialisation compared to the previous implementation with the litter option on. Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--352.org.readthedocs.build/en/352/

# CABLE Add a subroutine to CABLE to ensure the consistency of ice points between soil and vegetation, related to #338. This branch will be used for the benchcab testing. Fixes #280 Fixes #338  ---- 📚 Documentation preview 📚: https://cable--349.org.readthedocs.build/en/349/

…ersion

# CABLE ## Description Following analysis in CABLE4 and discussion in #354 we should use total SW down in the call to `spitter` and apply the resultant `Fbeam` equally to the visible and near-infrared bands. The original intent (cable1.4) of spitter is to evaluate the fraction of SW down that is diffuse in nature - via the beam fraction `Fbeam`. This was evaluated once based on the total shortwave down. From CABLE2 onwards spitter was called twice - once for the visible and once for the near-infrared components. However the function itself was not adjusted - the result is that beam fraction is universally smaller than the original intent with unknown impacts on the model trajectory. This change set reverts the evaluation of `Fbeam` to operate on the total SW down and then applies `Fbeam` equally to the two radiation bands. This has been implemented as a bug fix, not on a switch. This change may require recalibration of the CABLE model (notably stomatal conductance parameters, leaf nitrogen exponential and any other parameters that impact GPP). Fixes #355 ## Type of change - [x] Bug fix - [ ] New or updated documentation ## Checklist - [x] The new content is accessible and located in the appropriate section. - [ ] I have checked that links are valid and point to the intended content. - [ ] I have checked my code/text and corrected any misspellings  ---- 📚 Documentation preview 📚: https://cable--357.org.readthedocs.build/en/357/

# CABLE ground water hydrology work of Mengyuan Mu This pull request is part of integrating the ground water hydrology work of Mengyuan Mu into CABLE, which will take place in a sequence of pull requests. The actual integration project itself was completed back in September 2023. The current work involves just a gradual merge into the main branch. Fixes #230 ## Description 1. cable_gw_hydro.F90 is replaced by its new version (drop-in replacement) 2. Dependencies are introduced in **src/offline/cable_parameters.F90**, **src/offline/cable_define_types.F90**, **src/science/soilsnow/cbl_thermal.F90**, and **src/util/cable_common.F90** in order for the code to compile successfully (confirmed) 3. *PLEASE* do not delete any of my in-code comments (tagged rk4417) for now. Once the integration of the ground water hydrology work is complete and its functionality is confirmed to reproduce the results obtained already outside of the repo, I will clean-up all of my comments in a single pull request. Deleting any of my comments now will just make it much more difficult for me to track down and fix any issues that might arise during this process.  ---- 📚 Documentation preview 📚: https://cable--231.org.readthedocs.build/en/231/

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description The creation of the call graphs (and others) by FORD in the API documentation was broken since moving to readthedocs. This should solve the issue Fixes #9 ## Type of change Please delete options that are not relevant. - [X] Bug fix ## Testing We do not build the graphs in the pull request preview of the documentation since it takes >3 min to build the doc with the graphs. This was tested in this fork: https://github.com/ccarouge/CABLE_test Result example in the documentation: https://cable-test.readthedocs.io/en/latest/api/proc/bgcdriver.html Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--399.org.readthedocs.build/en/399/

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description casaflux%frac_sapwood needs to be initialised to 1 for the correct calculation of casaflux%crmplant(:,wood) in casa_rplant when cable_user%CALL_climate is not true. This had been done in casa_inout at #274 but this subroutine is only used for offline simulations. This change does the initialisation, in casa_init_pk, for ESM1.5/ESM1.6 cases. Fixes #373 ## Type of change Please delete options that are not relevant. - [X ] Bug fix ## Checklist - [ ] The new content is accessible and located in the appropriate section. - [ ] I have checked that links are valid and point to the intended content. - [ ] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--374.org.readthedocs.build/en/374/

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description As described in #275, this change reinstates code that had been removed in 2022 with little justification. Reinstating the code provides consistency with ACCESS-ESM1.5 and also with relevant code in src_pop/core/biogeochem. Testing for a small sample of sites showed a large impact if this change was made alone. The related issue (#279) incorrectly calculates btran by summing over layers twice. This calculation is only used if the removed code in #275 is reinstated. Site tests with both changes showed only small differences. Change only impacts runs with CASA-CNP active. Also dealt with corrections to comment for subroutine avgsoil as noted in #279 and subroutine casa_coeffsoil (#277). Fixes #275, #277, #279. ## Type of change Please delete options that are not relevant. - [X ] Bug fix - [ ] New or updated documentation ## Checklist - [ ] The new content is accessible and located in the appropriate section. - [ ] I have checked that links are valid and point to the intended content. - [ ] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--372.org.readthedocs.build/en/372/

AM3 application specific see issue #370 Fixes #370 ## Type of change Hopefully will cover CM3 as well - [? ] New or updated documentation ## Checklist - [? ] The new content is accessible and located in the appropriate section. - [?] I have checked that links are valid and point to the intended content. - [ ] I have checked my code/text and corrected any misspellings  ---- 📚 Documentation preview 📚: https://cable--371.org.readthedocs.build/en/371/

The build-ci action has now been fixed (see ACCESS-NRI/build-ci#179). Fixes #408  ---- 📚 Documentation preview 📚: https://cable--409.org.readthedocs.build/en/409/

…odule, as gfortran provides a similar function that takes no arguments.

…g unused variables and arguments.

#375) # CABLE Thank you for submitting a pull request to the CABLE Project. ## Description Removed two ifdef ESM15 cases related to the use of xkpsorb. The ESM15 code option is inconsistent with how xkpsorb is input in the CABLE3 code. Fixes #283 ## Type of change - [X ] Bug fix ## Checklist - [ ] The new content is accessible and located in the appropriate section. - [ ] I have checked that links are valid and point to the intended content. - [ ] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--375.org.readthedocs.build/en/375/

…LE2.4/ACCESS-ESM1.5

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description This PR fixes compilation with gfortran. I also fixes several compiler warnings (mostly about unused variables) in the MPI master/driver modules. ## Type of change Please delete options that are not relevant. - [X] Bug fix ## Checklist - [x] The new content is accessible and located in the appropriate section. - [x] I have checked that links are valid and point to the intended content. - [x] I have checked my code/text and corrected any misspellings  ---- 📚 Documentation preview 📚: https://cable--410.org.readthedocs.build/en/410/

# CABLE Thank you for submitting a pull request to the CABLE Project. ## Description In casa_delsoil the evaluation of casaflux%Pleach had two versions, one specific to ESM1.5 (selected via an ifdef) and the alternat for all other cases. Following the code through, the ESM1.5 version had a hard-wired value (1.e-4) for casaflux%fPleach. casaflux%fPleach is filled from xfPleach which is read in from the pftlookup file. The ESM1.5 specific code can be safely removed with no change to the output if xfPleach is set to 1.e-4 in the pftlookup file. Note that there are versions of the pftlookup with xfPleach = 5.e-4. I am not aware of when/who set it to this value and whether it is considered to be better/more realistic. Fixes #278 ## Type of change Please delete options that are not relevant. - [X] Code clean-up ## Checklist - [X ] The new content is accessible and located in the appropriate section. - [ ] I have checked that links are valid and point to the intended content. - [X ] I have checked my code/text and corrected any misspellings Please add a reviewer when ready for review.  ---- 📚 Documentation preview 📚: https://cable--422.org.readthedocs.build/en/422/

ccarouge and others added 30 commits November 28, 2023 15:22

write review guidelines - Fixes #186

ff709c7

Remove 'Nonconforming tab character'

8ff8a98

Remove 'Nonconforming tab character'

77fa660

Remove 'Nonconforming tab character' and 'continued character constant'

563906f

Remove 'Nonconforming tab character' and 'continued character constant'

ec74353

Removed 'extra tokens at end of #ifndef directive'

a30cbd3

Name 'mland' was an ambiguous reference

7b8d0e3

List source files in alphabetical order

c0ce0e4

Portability fixes and improvements to build.bash

0369c4e

Add --compiler flag and GNU compiler support

93ac165

Flags for release and debug configurations for the GNU compiler were taken from build.ksh (CABLE-POP_TRENDY branch).

Add Matthias's configuration for example

29d8b26

Introduce SUBROUTINE GWspatialParameters

ba007d5

Replace cable_gw_hydro.F90 with its new version

fba0e4a

(#285): run testcase from within src/offline/ for now.

81b8795

(#186): additions to review guidelines

87c9592

(#186): formatting

3ab8f45

(#186): revised text

5d7b808

(#186): few more edits

8d73f90

(#186): simplify language (review)

d8b5538

Update content of pft_params.nml options under User Guide

38e2a64

Auto refresh MathJax on page load

400f550

(#303): increase max width.

21195f6

Case of mobile is not a major consideration here, comfort on a computer is more important

ccarouge and others added 29 commits August 8, 2024 11:57

Merge branch 'main' into 325-add-a-table-of-physical-constants-to-the…

1239fec

…-user-guide

Always initialise canopy%DvLitt and canopy%kthLitt

fe0b80e

Reinstate dry and cold stress (#275)

fdcb99f

Remove double summation of btran (#279) Require both changes.

Correction to comments as #277 and #279

7bd295b

(#338) - Add namelist option for ice consistency.

4db0469

(#338) - Update doc

6ed2afc

(#351) - correct reference for DvLitt and kthLitt

06bd3af

Initialise casaflux%frac_sapwood=1 for use in casa_rplant (#373)

6f22bdd

(#338) - Add new namelist option to cable.nml

57a343d

Remove ESM15 case as inconsistent with current input of xkpsorb (#283)

03f924e

Merge branch 'main' into 230-replace-cable_gw_hydrof90-with-its-new-v…

1dd3724

…ersion

(#9) - Install graphviz for readthedocs

aad87bc

Update build-ci version (#409)

8f62897

The build-ci action has now been fixed (see ACCESS-NRI/build-ci#179). Fixes #408  ---- 📚 Documentation preview 📚: https://cable--409.org.readthedocs.build/en/409/

Fix compilation with gfortran: use the abort defined in cable_abort_m…

66e717a

…odule, as gfortran provides a similar function that takes no arguments.

Cleanup of mpi drivers by addressing some compiler warnings, includin…

d0e1995

…g unused variables and arguments.

Removed ESM15 version with hard-wired parameter, #278

183df1f

User guide edit to pftlookup table to note xfPleach hard-wired in CAB…

d0688cb

…LE2.4/ACCESS-ESM1.5

bschroeter merged commit 0911f96 into 219-implement-init_wetfac-as-per-access3-jules Oct 18, 2024
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Updating 219 from main. #426

Updating 219 from main. #426

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Updating 219 from main. #426

Updating 219 from main. #426

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