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…uild * upstream/master: (194 commits) Everything working now Fixes for mpi-serial on mappy Revert "Merge remote-tracking branch 'liho/liho745/river/bug-fix-7792c63' (PR E3SM-Project#6313)" Get mappy working again with RHEL9 Bump DavidAnson/markdownlint-cli2-action from 16 to 17 Log PIO buffer size limit for default case Update sim_year_range in 20thC_transient.xml Updates cprnc version to match the new compiler version Add LND_FRC_DUST_MBL to elm.h0 for wcprod mods Reset sim_year_range to 1850-2015 in namelist_defaults for flanduse_timeseries Updates the long_name adjust artifacts to reflect recent edits update ghci container to restore gh/ci Enables output of land fraction used in dust mobilization update compy intel compiler Adjust PEs for MPAS dev-tests on Anvil Reduce test lengths Update CIME submodule with a new fix commit bug fix for N balance error due to spval value for land use simulation Explicitly set dust_emis_scheme=2 for MMF ...
Brings in new remote for yaml-cpp
Crucial to get new remote for yaml-cpp
…er/update-haero-ekat Update ekat submodule in haero submodule of scream
* origin/master: Update ekat submodule in haero submodule of scream Update EKAT submodule
…er (PR E3SM-Project#6596) For pm-cpu, upgrade Intel compiler to `2023.2.0` as well as other modules for Intel only
Update EKAT and Haero submodules. Crucial to get new remote for yaml-cpp. [BFB]
…rebuild upstream merge 20240919: Get mappy working again
This adds compsets and new output variables to facilitate the E3SM and E3SM-MMF contributions to phase 1 & 2 of the radiative-convective equilibrium model inter-comparison project (RCEMIP). NOTE: in the original RCE compsets there was a slight error in the value of constant_zenith_deg being off by 1/100. This difference is inconsequential, but I wanted to fix it here to ensure consistency with the other RCEMIP models. [non-BFB] - only for RCE cases because of updated constant_zenith_deg value
…ject#6621) harden eamxx/prod testmod makes the ERS eamxx/prod test compare outputs in all files, requiring pulling a bugfix from the scream repo. [BFB]
Signed-off-by: Jason Boutte <boutte.jason@gmail.com>
tested on perlmutter compiled with "gnugpu" compiler environment
Changes needed for spot/aurora: sycl kokkos spaces, temporary TP changes (TP init will be sorted out later), switch booleans to ints in F<-->xx interfaces. see E3SM-Project#6569 for the original branch/history. [bfb]
Add data land capability for moab driver; case tested: --res r05_r05 --compset RMOSGPCC standard data moab model, mainly adapt from data ocean implementation major change: Initialize all factors set by MOAB area correction init routine to 1.0. It affects all models, but it seems that some values were not initialized for data land case. On chrysalis, with intel compiler, it actually complained about non initialized values when applying correction factors. The compressing file errors seen during development were caused by non-ascii characters in the log files. Those were caused by an uninitialized mapper, for which we were still creating a MOAB map. It was never used, it is fixed properly now, the moab map is not computed anymore. [BFB]
…/mam4_constituent_fluxes_fix Automatically Merged using E3SM Pull Request AutoTester PR Title: MAM4xx: Fix of mam4_constituent_fluxes_standalone_np1 PR Author: odiazib PR LABELS: AT: AUTOMERGE, bugfix, AT: PRE-TEST INSPECTED, EAGLES, MAM
…/eamxx/mpi-abort-on-exception Automatically Merged using E3SM Pull Request AutoTester PR Title: Call MPI_Abort in CIME runs when an exception is thrown inside EAMxx PR Author: bartgol PR LABELS: AT: AUTOMERGE, AT: Skip weaver, AT: Skip v1 Testing, code usability, MPI
…with_moab_fields_rebase_var EAMXX uses a different implementation of the atmosphere model, compared to EAM, and moab driver needs to be extended to support a coupled case case tested is --compset F2010-SCREAMv1-MPASSI --res ne4pg2_oQU480 --driver moab this case uses mpas sea ice, CICE is not yet supported by MOAB the implementation follows similar strategy compared to the rest of the models Atmosphere mesh in moab has 4 different instances, similar to EAM, corresponding to coarse spectral mesh ( size 6nene), fine quad mesh (corresponding to GLL quad mesh, size 6nene* (np-1)* (np-1) ) pg2 FV type mesh (size 6nene* pg2 * pg2) point cloud corresponding to mct simplified vertex grid. On the coupler side, we still use just the pg2 FV type mesh, used for intersection and coupling with other models
MALI update to fix issues from earlier PR causing sporadic test failures Including a variable that was deactivated in the globalStats stream caused sporadic failures during the second run of some ERS tests on several platform/compiler combinations. That variable is now only included when MALI is using Albany. Also updates a namelist default that had been missed but does not change answers. Fixes E3SM-Project#6600 [NML] for configurations with MALI [BFB]
…3SM-Project#6633) * Adds dane/ruby queue definitions * Updates dane/ruby cmake macros * Updates dane/ruby machine definition to use slurm and new modules * Removes lc_slurm
…rtmgp_to_default_kokkos Flip rrtmgp to default to kokkos
…SM-Project#6709) Add overrun qos for pm-cpu/pm-gpu
…6705) Update chicoma-cpu gnu and nvidia builds Following the recent DST, this merge updates the module files and environment variables on LANL machine Chicoma-CPU. We note that these updates work well for gnu and nvidia compilers but not yet for intel, which we are continuing to work on. A separate update will be needed to address Chicoma-GPU as well. An environment variable has also been added to the MPAS standalone framework to accommodate overriding the library path for standard c++ on Chicoma. [BFB] for all E3SM testing
Fix for seed initialization that caused C:N an C:P ratios to diverge for some grid cells in transient simulations. Fixes E3SM-Project#6368 [non-BFB]
Update Cmake machine config for Aurora Cleanup certain warnings related to headers and Intel compilers Linking Fortran/C++/SYCL with CXX linker (-fortlib) instead of Fortran language for SYCL builds. Since Fortran linking with SYCL is no longer supported (link is in the PR).
…CH_MODE-software (PR E3SM-Project#6703) For pm-cpu, remove libfabric work-around of setting `FI_CXI_RX_MATCH_MODE=software`
Fix a bug in VBS SOA gas-aerosol partition calculation In subroutine mam_soaexch_vbs_1subarea in components/eam/src/chemistry/modal_aero/modal_aero_amicphys.F90 The calculation of p0_soa_298 is not correct. Temperature of 298 K should be used instead of ambient temperature This fix has very small impact on global mean climate. Fixes E3SM-Project#6474. [non-BFB] All tests with active E3SMv3 atm configurations that enable vbs soa are affected.
Add ability for MALI to create separate logs from each processor Adds a new variable config_create_all_logs_in_e3sm to MALI that allows users to choose to get a separate log file from each processor [NML] for configurations with MALI [BFB]
Add appropriate flags for MKL -mkl for older Intel MKL modules -qmkl for newer oneMKL modules -mkl is deprecated with newer oneMKL library leading to linking issues referring to the MKL functions
The stem:leaf allocation variable can go negative without this limiter, which can cause negative stem carbon pools. Fixes E3SM-Project#6591 [non-BFB]
Conflicts: components/homme/CMakeLists.txt components/homme/src/test_src/dcmip16_wrapper.F90
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