Upstream merge #2826
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Upstream merge #2826
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it helps finishing and not crashing in land model we do not zero out in general, like call mct_aVect_zero(x2a) this is one instance in which this was essential to continue
instead of going by each tag we were missing anyway some fields that were set by stream routine that was the big miss init to 0 are not needed anymore, as everything is now set properly
set_moab_tag_from_av is defined now in seq_flds_mod it is used by data models run methods to set moab tags values (from AV attributes to moab tags) each field is set at a time, the vector data is allocated before the method and deallocated at the end of the loop data rof is involving now the same procedure as before data rof does not have a rof mesh defined on coupler side, me just transfer coupler data mbrxid is now only vertices; how is that affecting the rest of the tags ? need to pay attention to projection from other meshes to rof, and from rof to others
we do initialize mapper_Fi2a, for domain checking ? even if ice_c2_atm is false in that case, do not augment with moab data, because we do not want those projections
introduced at refactoring
Adds 0.25 deg ELM surface dataset for 1850 and 2010. These new surface datasets include the TOP subgrid solar radiation scheme parameters. Adds three new -res <r025_IcoswISC30E3r5 | ne120pg2_r025_IcoswISC30E3r5 | ne30pg2_r025_IcoswISC30E3r5. In these -res, MOSART is inactive because a mapping between MOSART at r025 and OCN at IcoswISC30E3r5 is omitted. Adds a fourth new -res r025_r025 for ELM+MOSART simulation. Includes linear and nonlinear maps for the following: ne120np4.pg2 (atm) and r025 (lnd) ne30np4.pg2 (atm) and r025 (lnd) [BFB]
…stream_04_11_24
* scream/master: (539 commits)
aerosol_optics - fixing name of variable: from tau_g_sw to tau_ssa_g_sw.
add doc for namelist variables for MAM4 optics input files
aerosol_optics - remove code.
aerosol_optics - fixing run time error; we need to use get_field_out("qc") instead of get_field_in("qc").
aerosol_optics - remove old comment.
aerosol_optics - remove aero_tau_forward from field manager.
Add fallow-arg-mismatch to mappy
aerosol_optics - remove old comment.
aerosol_optics - remove temporal variables from field manager.
aerosol_optics - fix typo.
aerosol_optics - rename: aero_tau_forward -> tau_f_lw .
aerosol_optics - remove aero from aero_tau_sw.
aerosol_optics - remove aero from aero_tau_ssa_sw.
aerosol_optics - remove aero from variable name.
Switch mappy over to new toolchain
aerosol_optics - removed duplicate variable.
aerosol_optics - from Updated to Required.
aerosol_optics - update comments.
aerosol_optics - update comments.
aerosol_optics - comment.
...
Enable conversion of the ADIOS BP output files to NetCDF during file close for tests. This is required for tests like ERIO tests that require the NetCDF output before the dependent conversion job (which runs after the current job completes) gets a chance to perform the conversion.
Add MOAB paths for ubuntu 22 machines at Argonne [BFB]
Add subgrid scale correction scheme and init mode test cases This pull request adds a subgrid scale correction scheme into MPAS-Ocean. It is currently meant only for single-layer, barotropic coastal flooding applications and is implemented as an mpaso standalone feature. The subgrid corrections introduced here account for the nonlinear relationship between ssh and grid-averaged wet volume per unit area in partially wet cells. These relationships are calculated as lookup tables from high-resolution (subgrid scale) bathymetry data. This lookup table calculation is done as a pre-processing step implemented in MPAS-Ocean init mode. Using the subgrid correction scheme increases the accuracy of the wetting/drying transition. It is especially advantageous at coarser resolutions, where it can increase model efficiency by reducing the level of resolution required to represent the effects of small-scale conveyances. Two test cases are also added: 1. A subgrid version of the existing parabolic bowl wetting and drying test case 2. A simulation of Buttermilk Bay, MA with idealized tidal boundary forcing [NML] [BFB] for all standard E3SM tests, mpaso standalone only
Adds I-compsets that include active BGC (CNP+RD+CTC), black carbon (BC), and subgrid topographic parameterization for solar radiation (TOP) in ELM. These I-Compsets use GSWP DATM forcing. The compsets are for 1850, 20TR, and 2000. [BFB]
… directive. ie, pm-cpu, pm-gpu, etc
Removes EAMxx from the main e3sm docs for while it remains under intense development.
Add e3sm_cryo_developer test suite This merge adds data iceberg (DIB) and data ice-shelf melt flux (DISMF) files for the oQU240wLI mesh. It then uses these files in tests added to a new e3sm_cryo_developer test suite. [BFB]
semoab_mod.F90 file is moved from components/eam/src/dynamics/se folder to components/homme/src/share folder. It belongs naturally there, as it involves just grid routines from homme base code also, it should prepare for SCREAM-moab connection later on fix also some complaints about non-allocated arrays when there are no cells on some dynamic tasks (when number of tasks is larger than number of spectral cells in homme) [BFB]
Several ANL GCE nodes have recently been upgraded from Ubuntu 20.04 to 22.04. This PR updates the configuration of machine anlgce-ub22 to include these newly upgraded nodes. [BFB]
Add distinct passive tracer background vert diffusivity Add capability to specify a different background vertical diffusivity for passive tracers than is used for active tracers. [NML] [BFB]
ERS.f09_f09.IELM.elm-lnd_rof_2way in the test suits results in negative channel water storage in MOSART. This was raised in PR #6313. The reason is that f09_f09 uses different spatial resolutions in ELM and MOSART. This is problematic for land river two-way coupling, which requires the same grid in ELM and MOSART. This PR changed f09_f09 to r05_r05 for the land river two-way test, and there is no negative main channel storage. [BFB]
… #6313) Enforces MOSART to stop when there is negative channel storage for any tracer. The e3sm_mosart_developer tests all passed at Compy BFB. Fixes #6302 [BFB]
…-directive (PR #6402) For NERSC machines (including pm-cpu, pm-gpu) remove `exclusive` slurm batch directive
- Adds support for hourly ERA5 forcing (ELMERA5) and the 6 hourly ERA5 forcing (ERA56HR) from 1979-2021. - Adds tests for the new compsets. [BFB]
This PR will take time to integrate, I'm opening it so I can keep track of what I check.
e3sm_integration:
chrysalis (intel): all PASS
pm-cpu (intel) 127 PASS and 1 DIFF: SMS_Ld2.ne30pg2_r05_IcoswISC30E3r5.BGCEXP_CNTL_CNPECACNT_1850.pm-cpu_intel.elm-bgcexp (which is currently consistently failing in the e3sm_integration_next_intel nightly build)
e3sm_developer:
pm-cpu (gnu): 75 PASS and 1 DIFF: ERP_Ld3.ne4pg2_oQU480.F2010.pm-cpu_gnu
homme_integration:
chrysalis (intel): PASS
pm-cpu (gnu): builds PASS, stuck in Q for run, so I cancelled it. pm-cpu is not tested in nightlies anyways
eamxx testing (from eamxx repo, with a few additional commits for eamxx)
v1 (CIME)
chrysalis (intel): 10 PASS (all scream v1) 5 DIFF (all scream v0)
pm-cpu (gnu): 3 PASS, 1 DIFF
frontier PEND
ascent: no longer part of eamxx nightlies
pm-gpu (gnugpu): 7 PASS, 5 DIFF. All DIFF are in debug mode, while all non-debug builds pass. I'm trying to understand what's the catch.
standalone
mappy (gnu): all PASS
weaver (gnu+cuda): all PASS
[BFB]
Upgrading to SCORPIO v1.6.3 and adding support for the
new rearranger, PIO_REARR_ANY.
SCORPIO v1.6.3 includes the following enhancements/fixes,
* Support for standalone EAMXX/SCREAM builds
* A new rearranger, PIO_REARR_ANY
* Fixes for ADIOS to NetCDF conversion tool hangs/crashes in certain
scenarios
* Fixes for ultra high res simulations using the SUBSET rearranger
* Support for reading ADIOS BP files and updates to the BP to
NetCDF conversion tool to integrate with CIME/E3SM
* Adding a SCORPIO CMake package during install
* Support for new CDF5 types in the C interface
* Support for pio_set_fill()
* Fix for performance issues while writing large output files
(hang during enddef() call)
* Fix for issues writing/reading ADIOS string attributes
* Misc bug fixes
[BFB]
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Bring in recent upgrade of ekat/kokkos submodule from e3sm.