Add Pressure Gradient design document #225
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…ARY_PATH and revert previous work-around
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…3SM-Project#7143) This was a bug where I was passing around StridedLayout views to functions expecting LayoutLeft. Only caught in the PM-GPU nightlies and by PR E3SM-Project#6916, so I will ensure those pass before merging. [BFB]
Coupler: Add nlmaps_atm2srf_conserve option to nonlinear maps. To solve the problem of non-0 SUM-column wrain,wsnow values in the water budget tables, add a feature to the nonlinear-maps module to explicitly make the atmosphere-to-surface conservation error 0. Enable this feature by setting nlmaps_atm2srf_conserve = .true. in drv_in. See the module documentation in seq_nlmap_mod.F90 for details about the algorithm. Modify the existing nlmaps test to cover this feature; the code path when this feature is off is also covered in this test. Note: Because of the order of the call to cime_run_calc_budgets2 and the call to the atmosphere component, this PR alone won't make the wrain budget line show 0 in the SUM column. Instead, the ATM value from the previous instantaneous table matches the sum of the rest of the columns for the current table, which is not true without this PR. Testing: On Chrysalis, e3sm_developer passes, ERS_Ld3.ne30pg2_r05_IcoswISC30E3r5.WCYCL1850.allactive-nlmap diffs as expected, and SMS_Ld1.ne30pg2_r05_IcoswISC30E3r5.WCYCL1850.allactive-wcprod_1850 passes. [NBFB] for ERS_Ld3.ne30pg2_r05_IcoswISC30E3r5.WCYCL1850.allactive-nlmaps; otherwise BFB. [NML] for new option nlmaps_atm2srf_conserve in drv_in
Filter out some more noise in the optional diagnostics. This noise comes from the lack of area consistency between atmosphere and surface in this configuration due to eps_fraclim. This fixes a POSTRUN_SCRIPT failure on pm-cpu.
…(PR E3SM-Project#7137) Bump tj-actions/changed-files from 45 to 46
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Add new GLC grid: mpas.gis4to40km This is a medium resolution Greenland grid for MALI. It will eventually replace the gis20km grid for testing. It is the first MALI Greenland grid to extend far enough into the ocean to ensure overlap with MPAS-Ocean meshes, which is needed for the in-development OCN-GLC thermal forcing coupling used for Greenland fjords. E3SM grids are added that include this mesh paired with the other component grids for the suite of v3 BG, IG, and GG cases currently being used, as well as a GG case at ultra-low-res for rapid testing. [BFB] for all currently tested configurations
Also keep baselines in a mach-specific path
…so that we can directly use namelist variable instead of using negation
…M-Project#7116) Re-enabled I/O post processing that was disabled in the CIME workflow. Users can enable conversion of ADIOS output files (in BP file format) to NetCDF by setting the environment variable 'SPIO_ENABLE_ADIOSBP2NC_CONVERSION' to 1 [BFB]
…ter (PR E3SM-Project#7130) Re-enable consistency checks for EAMxx tests Instead of skipping them entirely, do them for the buildnml call that happens during the RUN phase. This give ERS test a chance to set the correct values of REST_N etc. [BFB]
…or-FPE-in-open (PR E3SM-Project#7144) For pm-cpu: adjust LD_LIBRARY_PATH to use Cray system settings after Feb18th NERSC maintenance made CPE changes
Co-authored-by: Mark Petersen <[email protected]>
Co-authored-by: Carolyn Begeman <[email protected]>
Coupler: Adjust error detection in POSTRUN_SCRIPT nlmaps_check.py Filter out some more noise in the optional diagnostics. This noise comes from the lack of area consistency between atmosphere and surface in this configuration due to eps_fraclim. This fixes a POSTRUN_SCRIPT failure on pm-cpu. [NBFB] for one test on pm-cpu
HOMME fortran init code refactor: important code hidden in print_cfl() is extracted into a new routine, dss_hvtensor dss_hvtensor improves HV results by making the HV coefficients smooth accross elements. It also does a bilinear projection of the coefficients within each element to minimize oscillations in the tensor coefficieints.
Update modules on alcf polaris. Also, - update queues - use cray wrappers for serial-gnu - update cmake for gnugpu builds - add eamxx cmake machine file - run small eam and mpas-o cases on 1 polaris node - add MOAB_ROOT env-var Fixes E3SM-Project#6422 [BFB]
… datm stream years
Previously, the file had the datestamp associated with the geometry used to create the masks (which still needs to be retained with suffix `mg` for mask geometry) but now it also has the creation date: ``` RRSwISC6to18E3r5_mocBasinsAndTransects20210623mg.20250205.nc ```
…#7141) EAMxx: Using top_lev from namelist. Update the interface to pass the 'top_lev' parameter to ndrop. The value of the top_lev parameter can be changed using the namelist variable top_level_mam4xx. See also PR 414 in mam4xx. [BFB] * odiazib/ndrop_top_lev: EAMxx: move top_lev. EAMxx: Using top_lev from namelist.
…oject#7197) First round of name convention enforcing in namelist_defaults_eamxx.xml and YAML files. Related to E3SM-Project#7179 Avoid arbitrary capitalization of param names, use only when it really makes sense (like T for temperature). Full list of XML renames: * Scorpio -> scorpio * Type -> type * Averaging Type -> averaging_type * Group -> group * Sequential -> sequential * Moisture -> moisture * BfbHash -> bfb_hash * cldFraction -> cld_fraction * Filename -> filename * MPI Ranks in Filename -> mpi_ranks_in_filename * ML* -> ml_* * testOnly -> test_only * Frequency -> frequency * Ckh -> coeff_kh * Ckm -> coeff_km * srf_emis_specifier_for_DMS -> srf_emis_specifier_for_dms * srf_emis_specifier_for_SO2 -> srf_emis_specifier_for_so2 YAML renames: * Remove mpi_ranks_in_filename * column_conservation_checks_fail_handling_type Warning/Fatal -> warning/fatal * disable_diagnostics and theta_hydrostatic_mode, False->false * GLL -> gll * PG2 -> pg2 * None -> none (physics_grid_rebalance) * Homme -> homme * All average_type values should be lowercase * Max Snapshots Per File -> max_snapshots_per_file * Fields -> fields * Physics -> physics * Field Names -> field_names * Mesh Free -> mesh_free * Restart -> restart. Restart Run -> restart_run * Point Grid -> point_grid * Checkpoint Control -> checkpoint_control * Sub Name -> sub_name * Grid Name -> grid_name. IO Grid Name -> io_grid_name * SurfaceCouplingImporter -> surface_coupling_importer * Dynamics -> dynamics * physics gll -> physics_gll. physics pg2 -> physics_pg2 [BFB]
) Add new SOwISC12to30E3r4 ocean and sea-ice mesh Alternative version of the Southern Ocean Regionally Refined (SORRM) mesh. This mesh has resolution that is: * 12 km around Antarctica * 30 km elsewhere In contrast to SOwISC12to30E3r3, this mesh uses ice-sheet and bedrock topography from the MALI E3SM-Project#6884 mesh and initial condition. It also uses a new type of sea-surface salinity (SSS) restoring (MPAS-Dev/compass#883) in G-cases. The mesh is with Ice-Shelf Cavities (wISC) around Antarctica and has 80 vertical layers. Its longname is SOwISC12to30kmL80E3SMv3r4 [BFB]
…roject#7213) Update icepack with negative silicate bug fix Icepack BGC bug fix for silicate limitation, which was mistakenly wrapped in an if statement for iron tracers that caused negative values. Fixes E3SM-Project#7127 [non-BFB] only with active BGC, BFB otherwise.
Update new freshwater_tracers test to only require one year of JRA data A new stealth test added by PR E3SM-Project#7087 did not limit the amount of JRA data necessary for testing. This PR fixes that by adding a new testdef and having the new test use that. [BFB]
…7224) Port ensure pylib eamxx stuff to newer python pkg_resources is gone as of py 3.12. Use packaging.version instead if possible. [BFB]
ZM cleanup - create zm_transport module Create a new module to contain methods for the ZM tracer and momentum transport methods. [non-BFB] only on pm-cpu gnu. * whannah/eam/zm-cleanup-05: Remove momtran, convtran2 from physpkg remove debug print statement from zm_transport.F90 Add new fields to physpkg remove unused chunk identifier add line return at end of file bug fix for zm_transport_momentum misc bug fixes initial creation of zm_transport module
…ject#7199) EAMxx: Replacing temporary views with the emaxx buffer. I modified the mam4::buffer to be utilized across all mam4 processes by making the number of buffer.scratch processes dependent on the layout. These variables are specifically designed for the ncol x nlev layout. For other layout types, I introduced buffer.temporary_views, which is a 1D view. To configure buffer.temporary_views, I implemented the methods get_len_temporary_views and init_temporary_views in each process. Additionally, I did not replace views that need to be reset to zero each time run_impl is invoked. [BFB] * odiazib/emaxx/mam4_buffer: EAMxx: Fixing the typo from temporal to temporary. EMAxx: clang-format EMAxx: Fixing the failing test by using views instead of buffer_. EAMxx: Remove buffer.work and move the temporal views size inside buffer_size. EAMxx: Using buffer_ to set temporal views in wetscav. EAMxx: Using buffer_ to set temporal views in optics. EAMxx: Using buffer_ to set temporal views in microphysics. EAMxx: Using buffer_ to set temporal views in dry deposition. EAMxx: Using buffer_ to set temporal views in ACI. EAMxx: Utilizing the buffer within the ACI intefface. EAMxx: Modifying the mam4xx buffer to set the number of scratch files.
…Project#7229) For backwards remap in PhysicsDynamicsRemapper, use Kokkos::AUTO for choosing team size instead of machine specific ifdefs. Fixes E3SM-Project#7200: an Aurora fail where team size was too large. [BFB]
Merge E3SM `master` into Omega `develop`
…to-polaris-0.7.0 Update locations for metis/parmetis to Polaris 0.7.0
- changed macros to have a clearer verb-first name - updated documentation
Adds a new omega error handler
Add tridiagonal solvers
Co-authored-by: alicebarthel <[email protected]>
Add EOS design document
sbrus89
requested review from
alicebarthel,
katsmith133,
mark-petersen,
mwarusz,
philipwjones,
vanroekel and
xylar
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This PR adds the design document for the pressure gradient module for Omega-1.
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