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Bring changes on release-clm5.0 branch to master #883

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merged 98 commits into from
May 2, 2020

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ekluzek
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@ekluzek ekluzek commented Jan 10, 2020

Description of changes

Brings changes on release-clm5.0 branch to master. Most of release-clm5.0.13 to release-clm5.0.30.

Specific notes

Contributors other than yourself, if any: none

CTSM Issues Fixed (include github issue #):

Fixes #873 -- Release clm5.0.12 changes
Fixes #871 -- don't check for valid resolution for CESM cases by default
Fixes #836 -- add izumi as a place that can run tools tests
Fixes #831 -- add namelist tint_algo settings for input streams
Fixes #817 -- Have clm4_5 use the same ndep file as clm5_0 for 1850
Fixes #809 -- mkmapdata using an old version of intel
Fixes #804 -- mksurfdata option
Fixes #791 -- fix threading for prescribed LAI and soil-moisture
Fixes #786 -- allow use_init_interp for a branch
Fixes #746 -- Some CLM45 configurations use CLM50 initial conditions files
Fixes #741 -- C13_HR, C13_NBP, FPI values result in numeric conversion not representable error (changes answers)
Fixes #734 -- Isotope historical files off of NetCDF-4
Fixes #716 -- 2 degree CMIP6WACCMDECK needs Carbon isotopes off
Fixes #707 -- Missing mapping files for hirespft
Fixes #673 -- Ice shelf wetland fix in mksurfdata_map can lead to glacier+lake > 100% on surface datasets (changes surface dataset creation)
Fixes #653 -- To save disk on fsurdat files use zwt0 on finindated file
Fixes #629 -- Remove unused fields from surface datasets
Fixes #624 -- QSNOEVAP history output incorrect
Fixes #621 -- Fully remove rcp in place of only ssp_rcp
Fixes #608 -- Odd (blocky) spatial patterns in generic crop leafc for BGC simulation when initialized from BGC-Crop
Fixes #589 -- Existence of content in the lai_streams namelist makes it confusing to users
Fixes #557 -- no-anthro compset and options
Fixes #553 -- More robust mksurfdata_map logic for determining where to put wetlands
Fixes #547 -- Add conus_30_x8 grid as valid option for CTSM and mksurfdata_map
Fixes #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers
Fixes #544 -- Transient cases are matching wrong IC file
Fixes #533 -- Add -no-anthro option to mksurfdata
Fixes #276 -- Tests for pre_alpha/pre_beta
Fixes #262 -- hirespft option to mksurfdata.pl
Fixes #175 -- Set stream_year_first_urbantv/last for CLM4.5
Fixes #150 -- mksurfdata code cleanup

Are answers expected to change (and if so in what way)? Yes

Some of the namelist defaults change.

Any User Interface Changes (namelist or namelist defaults changes)? Yes

Testing performed, if any: will run regular testing

ekluzek and others added 30 commits July 1, 2019 16:16
… and resolving rejected differences by hand, make sure the build-namelist unit tester runs
…rcp, fix bgc_spinup tests for sp and suplnitro
…m array that is a 1D array, so you have to account for the number of levels in the index for it. Still need to get a 3D GSMAP to get this to work
…e file, and 3D grids don't allow mapping, so set mapping to none
…n without bounds errors, but dies with soil balance problem
dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960

Bug-fix to prevent the model from aborting when running with fewer soil
layers than lake layers; not to imply that this was not a bug when the
model wasn't aborting. It was.
…n, add a couple more namelist tests for it, also check if streams are off, but streams namelist items are used
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ekluzek commented Apr 29, 2020

I got two finidat files in place
that now get the last tests to pass...

ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic
LII_D_Ld3.f19_g17_gl4.I2000Clm50BgcCrop.cheyenne_intel.clm-glcMEC_spunup_1way
SMS_Ld2_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic_interp
SMS_Lm1.f10_f10_musgs.I1850Clm50BgcCropCmip6waccm.cheyenne_gnu.clm-basic

Update cime to latest in cesm2.2 beta tag (cesm2_2_beta04)
Fix two small issues that had gone on the release-clm5.0 branch.
Update manage_externals (to manic-v1.1.8)

NOTE: Part of the reason for updating cime, was because of some problems
Mike Mills was having on cheyenne with inputdata files being deleted out
from under him before setting up his cases. We think system issues were
interacting with issues with cime putting in place zero length
missing files for the version of cime he was using. Those issues went
away with a cime update, so we hope updating to a newer cime version here
will help prevent those issues for CTSM users.

cime updates:

some cleanup from the last maint-5.6 update
Add ne5np4.pg4 grid.
case.setup: Add --keep option
Add omip as option to DATM_CO2_TSERIES
@ekluzek ekluzek added PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete and removed PR status: work in progress labels Apr 29, 2020
@ekluzek ekluzek added this to the cesm2.2.0 milestone Apr 29, 2020
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ekluzek commented Apr 29, 2020

Regular testing has passed as expected.

ekluzek and others added 20 commits April 29, 2020 10:56
…s now can, fix a difference that didn't get in from the release branch that wasn't allowing the code to compile in mkglcmecMod
…nial as well as PtVg and high resolution PFT raw datasets
@ekluzek ekluzek merged commit 8265b77 into ESCOMP:master May 2, 2020
@ekluzek ekluzek deleted the rel2master branch May 2, 2020 04:28
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