Jgfouca/upstream merge 2024 11 14 #3115
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compute rof lnd interaction only if rof_c2_lnd is true we were computing an unnecessary map always even if rof_c2_lnd is false (for most coupled cases it is true)
in case rof c2 lnd, we were not retrieving the the MPI group needed for comm graph computation, for same grid path we were retrieving it for intx only how come we never had samegrid land rof before ?
Enables two major changes to the parameterization that calculates LAI burial by snow: a) pulls stocking density and taper parameters that influence vegetation height from hard-wired values in biogeochem/VegStructUpdateMod.F90 to allow to be specified on the surface file (per main/pftvarcon) and b) updates the LAI burial by snow rate from Wang and Zeng, 2007 (linear burial) to form proposed by Liston and Hiemstra, 2011 (linear or non-linear) burial. The Liston and Heimstra (2011) formulation introduces two new parameters: 1) bendresist, which specifies how resistant branches are to bending under snow loading (1 = no bending, lim->0 branches bend very rapidly) and 2) vegshape, which specifies how the shape of the vegetation crown affects how rapidly it is buried by snow (1 = paraboloid; 2 = hemispheroid). These new parameters can also be specified on surface file.
Temporary change, pending merge of IM4 updates. IM4 removed a lot of the hard-coded tests that looked for particular pfts by their assigned number. this required modifying the helper function "woody" to be a non-binary (i.e., now 0 = herbaceous, 1 = woody tree, 2 = woody shrub), but this updated function isn't available to IM3 currently.
The taper array was being initialized incorrectly, leading to developer test failures. This moves the definition down further to be able to initialize correctly.
Adds a new exact restart test that uses new parameters in the param file for snow/vegetation interactions.
fixes an issue where using less than the maximum pfts set new parameters with non-physical values
…ing and continue (instead of failing) when input has month dimension and output does not.
… modern compilers (per Xylar)
Adding support for ADIOS builds that include support for BLOSC (lossless compression) in FindPIO cmake module
…6739) [BFB] * jgfouca/scream_downstream_2024_11_07: (182 commits) Add ghci-oci Workflows: reworked how to skip eamxx testing jobs Workflows: added more eamxx workflows Workflows: fix logic for eamxx jobs skipping Workflows: allow to generate ALL baselines at ones for eamxx EAMxx: Use the main branch of mam4xx. EAMxx: Add tracer_reader_utils.hpp to microphysics.hpp. EAMxx: Remove temporary CPP macro. EAMxx: Update description of dry aerosol particle diameters. EAMxx: Use a temporary branch for mam4xx to test changes in the photo table code. EAMxx: Move read utils files to readfiles folder. EAMxx: Refine linoz parameter handling and class member references Correcting data types for variables, refining comments, and updating YAML input configurations. Addresses review comments: adds doc strings, reverts scorpio file change and cleanup Adds emissions file for ne4pg2, removes qaerwat from the input.yaml for single process test Using mam4::utils::extract_stateq_from_prognostics to copy data from prog to state_q. Refactor: move allocation of views from the tracer data struct interface to helper code. Combine multiple NC file registrations into a single function call: setup_tracer_data. Using one data structure to store beginning, end, and output data sets. Retrieve dgncur_a, dgncur_awet, wetdens, and qaerwat from FM 1. Use the Scorpio interface to get altitude from vertical emission files. I was getting zeros or junk values when I employed the AtmInput class. 2. Add altitude_int as a member of the Altitude class. ...
Add ICOS30 wave mesh for E3SMv3. [BFB]
…11'(PR #6568) MOSART can be forced to crash if negative channel storage values are produced mainly due to round errors, when the channel storage is completely depleted in a single time step. The crashing was reported in several cases of E3SM fully coupled runs, where the kinematic waving routing method was invoked by default. Jon Wolfe was able to reproduce the crashing error in a low-res run and print out detailed information to identify the cause. In this fix, a numerical treatment has been implemented in the kinematic wave routing method, subroutine Routing_KW(), to ensure that any channel storage does not get completely depleted in a single time step. This treatment is physically reasonable as long as MOSART runs at a sub-daily time step. Jon Wolfe has tested this treatment in his low-res coupled run, and it helped avoid crashing. [non-BFB] for MOSART
- Recover ADIOS support - Load libfabric/1.15.2.0 module - Fix typos in configuration files
Update conditions for Southern Ocean ice and river runoff removal
This PR modifies the conditions for river and ice runoff removal in E3SM
cases. This changes the behavior of E3SM cases where data icebergs (DIB)
or ice-shelf melting (ISMF) were active and thus doesn't not affect
water cycle simulations.
River runoff:
Previous behavior: never removed
New behavior: removed when atmosphere is not active and ice shelf melt
fluxes are on
Ice runoff:
Previous behavior: removed when DIB is on and atmosphere is active
New behavior: removed when DIB is on
[NML] when DIB or DISMF are active
[BFB] when DIB and DISMF are inactive (all WC configurations)
[non-BFB] when DIB or DISMF are active
Adding preliminary support for ADIOS output compression and updating to SCORPIO v1.6.6 (which includes patch to support the new I/O type to use for data compression) Modifying CIME config and scripts to support writing ADIOS output files with data compression. A new I/O type is added to support writing output in ADIOS BP file format with data compression. However users would need to move to SCORPIO master to write ADIOS output with data compression Note: Writing ADIOS output with data compression is now supported in SCORPIO master but is not included in SCORPIO v1.6.6. A future release of SCORPIO will include this feature [BFB]
Set default config_check_ssh_consistency for oQU240wLI to false Change the default config_check_ssh_consistency setting for oQU240wLI to false, to avoid confusing warnings/errors from tests with this grid. Otherwise we end up with log.ocean.err files complaining about: ERROR: Warning: Sea surface height outside of acceptable range (20m). In general, mpaso sets config_check_ssh_consistency to false for grids with ice shelf cavities, but this one was missed. [NML] for configurations with oQU240wLI [BFB]
This PR updates the machine and compiler files for Frontier (Nov. 2024), including the following: * Recovery of ADIOS2 support * Loading of the libfabric/1.15.2.0 module * Correction of typos [BFB] no baseline for Frontier yet.
…merge_2024_11_14 * upstream/master: (219 commits) Set default config_check_ssh_consistency for oQU240wLI to false Update machine and compiler files for Frontier Adding support for ADIOS builds with BLOSC fix formatting of changed md files update pam to match new p3 signature Add ghci-oci change the coupling period of MOSART to be half hour in land river two-way coupling to avoid time step mismatch increase time for wav tests and increase processor count for PEM test Updating to SCORPIO v1.6.6 clean up seq_map_map line for Sw2o remove wav to ocean flux remapping remove WAV2OCN_FMAPNAME remove white space remove flux wave to ocean remapping (will be done in later PR) cleanup whitespace correction to langmuir mixing logic for LandIce Mask. trim down wav dev test suite add B case ICOS test to wav_developer test suite remove seq_map_map call for wave to ocn fluxes (no fluxes coupled yet) remove wav-atm, wav-ice coupling (for future PR) ...
Merge ProtectionsYour pull request matches the following merge protections and will not be merged until they are valid. 🟢 Enforce checks passingWonderful, this rule succeeded.Make sure that checks are not failing on the PR, and reviewers approved
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bartgol
reviewed
Nov 14, 2024
components/eamxx/CMakeLists.txt
Outdated
| @@ -200,6 +200,9 @@ option(SCREAM_MPI_ON_DEVICE "Whether to use device pointers for MPI calls" ON) | |||
| option(SCREAM_ENABLE_MAM "Whether to enable MAM aerosol support" ON) | |||
| set(SCREAM_SMALL_KERNELS ${DEFAULT_SMALL_KERNELS} CACHE STRING "Use small, non-monolothic kokkos kernels for ALL components that support them") | |||
| set(SCREAM_P3_SMALL_KERNELS ${SCREAM_SMALL_KERNELS} CACHE STRING "Use small, non-monolothic kokkos kernels for P3 only") | |||
| message("JGF DEFAUL_SMALL_KERNELS is ${DEFAULT_SMALL_KERNELS}") | |||
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Was this meant to be just some debugging stuff?
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Yes, whoops! Let me remove that
bartgol
previously approved these changes
Nov 14, 2024
mahf708
reviewed
Nov 14, 2024
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jgfouca
added
CI: automerge
bartgol
approved these changes
Nov 15, 2024
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Noting that the automerge feature of mergify worked (after not working for a long time). The merge commit is correctly formatted according to the mergify specs: |
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@bartgol why did the tests not run tho? |
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mergify(bot), good bot! |
That is a very good question. The output of pre_process_pr shows "No relevant files touched by this PR", which is obviously not true, given the changes in components/eamxx. Perhaps I need to crank up the stuff I print in that action (e.g., the list of changed files, the patterns, the matches), so we can debug when stuff like this happens. Ah. I executed the commands that the pre_process_pr job does, and indeed, there's no eamxx file listed: I wonder if the rest API is only returning the first X files. This list contains 30 files. Such a round number... Edit: indeed, I changed to and now I got 100 files. Still less than the actual number, so I think there's an upper limit. Which means we need to revisit the pre_process_pr logic... :/ See #3117 |
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@dqwu Asked for this. This should be one of the last upstream merges.