Merge ctsm1.0.dev113 tag into fates_main_api #1231
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…CL to calculate corners for other cases
Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See ESCOMP#884 for details.) Also, some minor fixes from Bill Sacks: - Resolves ESCOMP#203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in ESCOMP#1019) - Resolves ESCOMP#930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves ESCOMP#1021 - Changes SSP test to only do symlink if needed
…uld be used for FATES
Deallocate memory after running init_interp Many of the pointer arrays in init_interp were not being deallocated when init_interp finished. This was a particular problem because some of these arrays were allocated for the full global source grid on each processor, so the memory use was significant. This tag fixes this issue. This issue is documented in ESCOMP#1010 and ESCOMP#1032. Resolves ESCOMP#1032 (Memory isn't deallocated in some of the init_interp code)
Add LILAC
Add LILAC: The Lightweight Infrastructure for Land-Atmosphere
Coupling. This infrastructure consists of two major pieces:
(1) A lightweight coupling infrastructure built on top of ESMF that
makes it easier for atmosphere models to call CTSM directly, rather
than using the hub-and-spoke architecture that is used by CESM.
(2) A set of python-based tools for building CTSM and creating its
runtime inputs when running in an atmosphere model via
LILAC. Although these tools are built on top of cime, details of the
create_newcase / case.setup / case.build process are hidden from the
user, because many of the aspects of this workflow don't make sense
in the LILAC context.
So far we have used LILAC to couple CTSM to WRF. There are plans to use
the same infrastructure to couple CTSM to other regional atmosphere
models.
Documentation of LILAC is provided in
https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html
(though there are still some missing sections), as well as in various
presentations on the wiki
(https://github.com/ESCOMP/CTSM/wiki/Presentations).
There have been many contributors besides myself to the development,
testing and documentation of LILAC; chief among them being Mariana
Vertenstein, Negin Sobhani, Joe Hamman, Sam Levis, Mike Barlage and Dave
Lawrence.
Add LILAC
Add LILAC: The Lightweight Infrastructure for Land-Atmosphere
Coupling. This infrastructure consists of two major pieces:
(1) A lightweight coupling infrastructure built on top of ESMF that
makes it easier for atmosphere models to call CTSM directly, rather
than using the hub-and-spoke architecture that is used by CESM.
(2) A set of python-based tools for building CTSM and creating its
runtime inputs when running in an atmosphere model via
LILAC. Although these tools are built on top of cime, details of the
create_newcase / case.setup / case.build process are hidden from the
user, because many of the aspects of this workflow don't make sense
in the LILAC context.
So far we have used LILAC to couple CTSM to WRF. There are plans to use
the same infrastructure to couple CTSM to other regional atmosphere
models.
Documentation of LILAC is provided in
https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html
(though there are still some missing sections), as well as in various
presentations on the wiki
(https://github.com/ESCOMP/CTSM/wiki/Presentations).
There have been many contributors besides myself to the development,
testing and documentation of LILAC; chief among them being Mariana
Vertenstein, Negin Sobhani, Joe Hamman, Sam Levis, Mike Barlage and Dave
Lawrence.
Bring in changes from release-clm5.0.31-releas-clm5.0.34 except for the documentation updates, SSP 2100-2300 extension, manage_externals update, and externals update. Changes were brought in using patch, and removing the changes that were unneeded.
…an apparant change to answers even for cases that dont' run past 2005
…so that clm4_5 answers can be the same
Add new SE (Spectral Element) grids: ne30np4.pg2, ne30np4.pg3, ne30np4, ne60np4, ne120np4, ne120np4.pg2, ne120np4.pg3,
ne0np4CONUS.ne30x8, ne0np4.ARCTIC.ne30x4, ne0np4.ARCTICGRIS.ne30x8
Add new datasets for them, some new tests, and add support for their creation.
Also add some new initial condition (IC) files for 1979, 2000, and 2013 for use when coupled to CAM
The process for picking initial condition files was improved so that there can be more than one year that matches
and it will do the best to pick the best match. Also added the possibility for 1982 and 2013 simulation years for
specific grid matches.
Also update cime to a newer version that supports these new grids. And update CMEPS (and hence add in fox, CDEPS)
to latest used on the nuopc_dev branch. Testing with nuopc wouldn't work without this update. The cime version updates
the tables for dry-deposition and changes answers for dry-deposition when it's turned on.
…lated, add f09 and f19 clm5_0_cam6.0 1979 SP finidat files needed for CAM
…for f19 and clm5_0_cam6.0, use st_year for date for finidat file only if a transient simulation
Update cime so default end year for GSWP3 forcing is 2013 and change prevyr default for vcmax/jmax
I sometimes find myself wanting to check what options I provided to run_sys_tests after the fact. This change records this information in the SRCROOT_GIT_STATUS file.
Updates sources of surfacedata and land use time series in tools/contrib
I think this may be important to avoid errors and/or wrong behavior in some edge cases where we have < 0.5% cover of glacier and/or lake, and other cases. See ESCOMP#1118 for detailed thoughts Resolves ESCOMP#1118
Some bit-for-bit changes needed for the Perturbed Parameter Ensemble work
Some bit-for-bit changes needed for the Perturbed Parameter Ensemble work
glemieux
changed the title
|
All fates suite tests PASS b4b with some exceptions. The cime tag has been updated to cime5.8.32 resulting in some of the test comparison failures for the NLCOMP check. The other failures appear to be due to updates to the default namelists in commit 5021749 and 6837e11. This PR pulls in an update to the testlist grids from |
glemieux
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FATES API update
ekluzek
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Dec 19, 2020
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@glemieux I don't know of a good way to review this update. The changes are large enough that it's hard to really validate they are right, without my more of less doing the same update and comparing it to yours. So I think I'll just approve it as it is. Unless there's something in particular you'd like us to look at. Or if we can think of another way to verify and update like this.
|
@ekluzek the The only other thing that might be specifically worth reviewing is the commits I made in 1e15627 clear conflicts. |
glemieux
added
the
PR status: ready
I ran this test on the @rgknox I think this is ready to integrate. |
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Description of changes
This PR brings the fates_main_api branch up to date with ctsm1.0.dev113 tag.
Specific notes
This effort is undertaken with the goal of approaching parity with CTSM master/main so as to eventually create fates api PRs directly to the main branch. Another update will likely follow shortly assuming changes do not unveil any major changes to FATES answers.
Some simple fixes were made in the merge to account for refactoring of CNFireFactoryMod.F90.
Contributors other than yourself, if any: @ekluzek
CTSM Issues Fixed (include github issue #): None
Are answers expected to change (and if so in what way)?
Any User Interface Changes (namelist or namelist defaults changes)? No
Testing performed, if any:
aux_clmsuite outputs: Completefatessuite outputs:g17grid:/glade/u/home/glemieux/scratch/clmed-tests/fma-merge-ctsm1.0.dev113.fates-sci.1.43.2_api.14.2.0-ctsm1.0.dev113-C1e156277-F5534a940g16grid for b4b check:/glade/u/home/glemieux/scratch/clmed-tests/fma-merge-ctsm1.0.dev113-g16.fates-sci.1.43.2_api.14.2.0-ctsm1.0.dev113-C1e156277-F5534a940NOTE: Be sure to check your coding style against the standard
(https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review
the list of common problems to watch out for
(https://github.com/ESCOMP/CTSM/wiki/List-of-common-problems).