https://github.com/E3SM-Project/E3SM

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ec9f4d4 add link flag 05 April 2024, 19:00:31 UTC
61a476c Merge 'oksanaguba/homme/sycl' of github.com:E3SM-Project/E3SM into oksanaguba/homme/sycl 05 April 2024, 18:44:28 UTC
5877bc5 cmake fix, new kokkos, more debug in remap 05 April 2024, 18:41:05 UTC
ce0cb7d fix linking error 11 March 2024, 15:48:29 UTC
48ad7f7 aot cache file 07 March 2024, 17:04:28 UTC
73081a3 Merge branch 'origin/master' into oksanaguba/homme/sycl all conflicts are about building kokkos, which i reverted to use standalone kokkos a while ago Conflicts: components/homme/CMakeLists.txt components/homme/cmake/HommeMacros.cmake components/homme/test/unit_tests/CMakeLists.txt components/homme/test_execs/share_kokkos_ut/CMakeLists.txt components/homme/test_execs/thetal_kokkos_ut/CMakeLists.txt 21 February 2024, 17:50:54 UTC
ccbccc1 Merge branch 'bartgol/cmake/use-hints-instead-of-paths' into master (PR #6218) Prefer HINTS to PATHS in cmake find modules For all the cmake find_XYZ utilities, there is a well defined ordered list in which CMake scans paths while searching. In this list, the paths passed via the argument HINTS appear early on. On the other hand, the paths passed via the argument PATHS appear quite late. After trying HINTS and before trying PATHS, CMake consider other options, among which we have: * system paths (e.g., /usr directory on linux) * cmake package registry (this is only for find_package, but can be quite annoying and hard to find, as we experienced with EKAT) CMake states that HINTS and PATHS should be used for different reasons. In particular, regarding HINTS it states that: These should be paths computed by system introspection, such as a hint provided by the location of another item already found. Hard-coded guesses should be specified with the PATHS option. However, the fact that PATHS is scanned after system folders makes its usage more complicated. Since HINTS and PATHS are treated in the same way (meaning, CMake grabs the paths contained in them, and just scan them), from the practical point of view, the difference between the two is just the fact that one is considered much earlier than the other. The alternative would have been to add NO_SYSTEM_PATH to the find_XYZ calls, but it comes with a drawback: if on some testing machine (a shared workstation, perhaps) we do have a valid installation of a tpl in the system paths, we would not pick it up. Using HINTS, we can still pick up the system install (leaving HINTS empty). Fixes #6217 [BFB] 19 February 2024, 17:56:14 UTC
feab339 Merge branch 'jgfouca/cime_update_2024_02_15' into master (PR #6243) ... to 662369b2b8e9f87993cad81bbe71638bfdefdc8a Fixes: 1) Updates to cprnc build system to fix various issues 2) Fix a string that should be raw 3) case.submit: Fix no-batch mode 4) fix issue getting correct parameters for job subgroups 5) jenkins_generic_job: Should probe branch of main src repo, not cime repo 6) check_input: If chksum is off, don't try to download_checksum_file 7) Fix .env_mach_specific.sh when unsetting env 8) Fix recursive call 9) Update initial conditions in PGN and TSC tests. 10) fix component-only (no coupler) testing. [BFB] 19 February 2024, 17:50:34 UTC
2413b32 Bring in more CIME updates Update to 12142ee0c0 cime6.0.218 Update initial conditions in E3SM PGN and TSC tests Fix standalone component (no coupler) testing. 19 February 2024, 02:20:02 UTC
168957c Merge branch 'mahf708/idp/e3sm-gh-ci-cime-tests' (PR #6231) Adds the first batch of 7 tests to run on public CI resources during PR submission. Tests are SMS, SMS_D, ERS, ERP, REP, PET, PEM using F2010 and ne4pg2_oQU480. Tests are run with _P4 because CI resources are limited to 4 virtual CPUs for now. [BFB] 16 February 2024, 23:28:43 UTC
30c0bb6 Bring in recursion fix 16 February 2024, 21:03:03 UTC
be225c0 Update CIME submodule ... to 662369b2b8e9f87993cad81bbe71638bfdefdc8a Fixes: 1) Updates to cprnc build system to fix various issues 2) Fix a string that should be raw 3) case.submit: Fix no-batch mode 4) fix issue getting correct parameters for job subgroups 5) jenkins_generic_job: Should probe branch of main src repo, not cime repo 6) check_input: If chksum is off, don't try to download_checksum_file 7) Fix .env_mach_specific.sh when unsetting env [BFB] 15 February 2024, 21:39:26 UTC
a97c668 Merge branch 'bishtgautam/lnd/fix-elm-qian-test' (PR #6219) Adds namelist options to disable the creation of crop landunits in qian-1948 testmod Fixes #6192 [BFB] 13 February 2024, 22:13:45 UTC
e1993ad fix cprnc.out path: run/*.cprnc.out 13 February 2024, 18:53:01 UTC
6fe30be correct path of cprnc.out 13 February 2024, 17:45:48 UTC
80d065e catch artifacts more explicitly 13 February 2024, 15:19:45 UTC
0ad53bb Merge branch 'xyuan/polaris' (PR #6115) Add ALCF Polaris to E3SM machines. [BFB] 13 February 2024, 02:53:55 UTC
900ad7c remove unnecessary tests and rework logic 13 February 2024, 02:32:21 UTC
7876df5 add first patch of gh ci cime tests 11 February 2024, 19:09:10 UTC
5886da6 Merge branch 'jgfouca/fix_prov_git_config' into master (PR #6227) Provenance: do not crash if config_src does not exist Just skip that file. This should help with containerized E3SM. Fixes #6225 [BFB] 09 February 2024, 16:47:08 UTC
bbd32de Provenance: do not crash if config_src does not exist Just skip that file. This should help with containerized E3SM. [BFB] 08 February 2024, 22:40:13 UTC
abe7218 Merge branch 'xylar/mpas-framework/fix-cray-cray-openmp' (PR #6193) Fix OpenMP support for MPAS standalone builds with cray-cray A -fopenmp (rather than a -homp) flag seems to be needed for OpenMP on Frontier. For MPAS component standalone builds only -- does not impact E3SM [BFB] 08 February 2024, 18:38:04 UTC
2ce007f cache file 08 February 2024, 03:21:43 UTC
24f9f32 Fixes a I1850ELMCN test Adds namelist options to disable the creation of crop landunits. Fixes #6192 [BFB] 08 February 2024, 01:05:33 UTC
50485d0 Merge branch 'gcapodag/mpaso/wd' (PR #6074) Add wetting and drying capability to local time-stepping scheme This PR adds a wetting and drying capability to the local time-stepping (LTS) scheme for the barotropic ocean already available in master. The PR also adds several improvements for the LTS scheme not related to wetting and drying like for instance the upwind option for the layerThickEdgeFlux and inline tidal boundary conditions needed to run the drying slope test case from Compass. A separate PR on Compass will include drying slope, dam break, and parabolic bowl test cases for LTS. [BFB] - MPAS-Ocean standalone only 07 February 2024, 20:13:46 UTC
67abd00 Merge remote-tracking branch 'glemfork/lnd/fates-api-readparams-refactor' (PR #6027) This PR refactors the elm-fates interface to avoid having fates call elmfates_interfacemod. FatesReadParameters has been moved from the aforementioned module into FATES and takes in an HLM-provided fates_param_reader_type to read the parameters from disk. The existing SetFatesGlobalElements1 method now takes in an optional fates_param_reader_type. Upcoming PR's will modify the HLM's to construct and pass in instances of fates_param_reader_type (which will basically call the HLM-side ParametersFromNetCDF method), and then remove the old code path. This work is ported from ESCOMP/CTSM#2198 and is associated with NGEET/fates#1096 Fixes #6029 [BFB] 07 February 2024, 19:30:33 UTC
3a4451b Prefer HINTS to PATHS in cmake find modules In the list of paths searched by CMake, the content of the HINTS arg appears early on, while the content of PATHS is down the list. In particular, between HINTS and PATHS in that list there are - system paths - cmake package registry These can cause system installation of a tpl or previous installation of a tpl to be picked up instead of the passed PATHS arg 07 February 2024, 17:15:12 UTC
075645f Merge branch 'jgfouca/smp_present_is_gone' into master (PR #6216) SMP_PRESENT is gone, use BUILD_THREADED A few more of these have slipped in. [BFB] 06 February 2024, 23:30:17 UTC
93120a4 SMP_PRESENT is gone, use BUILD_THREADED A few more of these have slipped in. [BFB] 06 February 2024, 23:08:53 UTC
1e5c47f Merge branch 'ambrad/cpl/fix-6199' (PR #6200) CPL: Fix uninitialized variable. This code is used in checking the maps at initialization. [BFB] 06 February 2024, 20:00:42 UTC
6607537 Merge branch 'liho745/river/bug-fix-417902b' (PR #6146) A bug in RtmMod.F90 has been causing a floating-point error, related to Tunit%rlen, when the land-river two-way coupling is invoked. This PR fixes that bug based on a branch off the commit, 417920b, where the bug was introduced into the master. [BFB] Fixes #5540 06 February 2024, 19:45:45 UTC
02192fe Merge branch 'ndk/machinefiles/add-muller-cpu-muller-gpu' (PR #6154) Initial add of 2 machines that are similar to perlmutter -- muller-gpu =~ pm-gpu, muller-cpu =~ pm-cpu. I can use these machines to test software stack changes before we use them on permutter. Only handful of nodes on each. Also, for one conus test (only tested in scream), I reduced the number of nodes needed for pm-gpu/muller-gpu. [BFB] 06 February 2024, 18:09:24 UTC
1fa0cfa Disable gpu env-vars in cpu runs; append cuda path to link flags 06 February 2024, 04:05:34 UTC
37db2c1 Merge branch 'tizhou/mosart/budget_table' (PR #6092) Adding global water budget tables to rof log file. The budget tables include a net water fluxes table and a water states table at the end of each month and year. Resolves #6024 [NML] 02 February 2024, 22:05:01 UTC
4cc2ced Merge branch '/iulian787/remove_shr_dependency' (PR #6168) mpas framework should not depend on driver-moab/shr mpas ocean cannot be built in standalone mode with MOAB, because of this [BFB] 01 February 2024, 19:46:04 UTC
827493c CPL: Fix uninitialized variable. This code is used in checking the maps at initialization. The fix is BFB. 01 February 2024, 19:15:48 UTC
43d7472 update fates external for API31 refactor 01 February 2024, 18:07:46 UTC
b8fe865 refactor elmfates api to avoid calling hlm-side procudures this also updates fates submodule to sci.1.68.3_api.31.0.0 01 February 2024, 18:02:17 UTC
318d612 Merge branch 'lnd/fates-testmod-update' (PR #6018) This pull requests updates the ed_update_site call in elmfates_interfacemod to pass a flag for when this procedure is called during restart. This update should be coordinated with NGEET/fates#1098, which addresses the long duration exact restart issue NGEET/fates#1051. Additionally this pull request resolves #5548 by expanding the fates regression test coverage to include more run mode options for fates at a variety of resolutions and runtimes. [non-BFB] for FATES Fixes #5548 01 February 2024, 17:33:14 UTC
66752a8 Set E3SMinput project paths and 1:1 MPI-to-GPU affinity 01 February 2024, 04:07:19 UTC
a54948b Array initialization 31 January 2024, 22:51:40 UTC
38f3165 Re-added FATES specific initialization for fire calculation. Moved from col_cf_setvalues to col_cf_zero_forfates_veg 31 January 2024, 22:30:16 UTC
359013d Update gnugpu, nvidia and nvidiagpu cmake and modules 31 January 2024, 04:10:22 UTC
104a202 Merge branch 'jonbob/coupler/fix-infodata-format' (PR #6167) Fix format for nlmaps_exclude_fields in seq_infodata_print The format for printing out nlmaps_exclude_fields in seq_infodata_print is currently F0I (for an integer value) but the variable is a character array. This type mismatch causes a failure when the seq_infodata_print subroutine is called, from cime_comp_mod.F90 when info_debug > 1. This PR uses a formatting suggested by Andrew Bradley to more elegantly print out this array. Fixes #6165 [BFB] 30 January 2024, 18:48:02 UTC
c589892 Merge branch 'jgfouca/adjust_frontier_macros' into master (PR #6194) Adjust gnugpu_frontier.cmake macro Fixes SHAREDLIB build errors [BFB] 30 January 2024, 16:13:30 UTC
d6b1807 Add `-fopenmp` for OpenMP support with cray-cray 30 January 2024, 12:37:13 UTC
d0b7d53 Adjust gnugpu_frontier.cmake macro Fixes SHAREDLIB build errors 29 January 2024, 20:50:28 UTC
3e727e0 Merge branch 'dependabot/github_actions/actions/setup-python-5.0.0' (PR #6191) Bump actions/setup-python from 4.7.0 to 5.0.0 [BFB] 29 January 2024, 17:48:41 UTC
74a78e7 Update paths and modules, add gnu config 27 January 2024, 09:16:35 UTC
4edde11 Update paths and queues 27 January 2024, 09:16:35 UTC
bd072a2 Update Polaris config 27 January 2024, 09:16:21 UTC
6f8bd21 add polaris machine 27 January 2024, 09:15:01 UTC
dbe7276 persist-credentials: false 26 January 2024, 20:52:18 UTC
c012a65 Bump actions/setup-python from 4.7.0 to 5.0.0 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.0 to 5.0.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4.7.0...v5.0.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 26 January 2024, 20:50:03 UTC
7f3280f Merge branch 'jgfouca/scream_downstream_merge' into master (PR #6153) Downstream merge of scream/eamxx fork into E3SM The build system fixes on the fork are needed for E3SM. Also updates E3SM with latest version of eamxx. Merge remote-tracking branch 'scream/master' into jgfouca/scream_downstream_merge Updates submodules: * ekat * haero * mam4xx EAM updates: * Consolidate shoc_Ck nml settings * New iop_coriolis nml setting (for nudging) * initialize IOP information on the first restart time step * SHOC updates * Add wet/dry qv_sat (saturation mixing ratio), old qv_sat is still available for backwards compatibility * P3 updates (scream version only) This PR now includes #5925 : Update the YAKL submodule, and update PAM submodule to work with the YAKL update. [YAKL] [BFB] - (except for SCREAM/EAMXX and MMF2 cases) 26 January 2024, 20:48:02 UTC
0c8b36d Fix Homme Cmake, EKAT subm update changed the EkatBuildKokkos module 26 January 2024, 20:03:05 UTC
b00c52c Merge branch 'mahf708/ipd/dependabot' (PR #6163) With this, dependabot will perform dependency checks on things we use inside GitHub Actions at a configurable frequency (for now, weekly). If there are updates, it will issue a PR requesting reviews from members (for now, Luca and Naser) and assigning the PR to an integrator (for now, Rob). [BFB] 26 January 2024, 06:19:35 UTC
4f0d0ca Merge branch 'hkang/ocean/pm-gpu-fix' (PR #6116) Fix bugs in OpenACC directives: - Change an openacc directive in mpas_ocn_diagnostics.F to avoid getting stuck on pm-gpu. Fixes E3SM-Project/E3SM#6127 [BFB] 26 January 2024, 02:52:03 UTC
f6f79a2 Merge branch 'trhille/mali/develop-231220' (PR #6126) Update MALI version to include higher-order advection and time integration This merge includes numerous updates to MALI The major updates include: * Higher-order, flux-corrected thickness and tracer transport. * Three strong stability-preserving Runge-Kutta time integrations schemes (a two-stage, second-order scheme; three- and four-stage third-order schemes) Minor updates include: * Earlier update of clock within time step * Prevent unrealistic calving into holes within an ice shelf * Change default start and stop times to avoid unpredictable I/O behavior * Higher-order grounding-line flux calculation * Several small bug fixes [NML] - only for cases with MALI [BFB] 25 January 2024, 22:41:26 UTC
fd65dbe Merge branch 'bishtgautam/lnd/v3-compset' (PR #6108) The following compsets are updated to change ELM's mode from SP to active BGC mode with TOP solar parameterization: F1850 F20TR F2010 WCYCL1850_chemUCI-Linozv3 WCYCL1850_chemUCI-Linozv3-mam5 WCYCL20TR_chemUCI-Linozv3-mam5 WCYCL1850-4xCO2 WCYCL1850 WCYCL1850-1pctCO2 WCYCL20TR WCYCL1850NS [CC] [non-BFB] but v3 sims already using these by runscript. [NML] 25 January 2024, 22:38:05 UTC
3dd1cf4 Fix MOAB compile issues 25 January 2024, 21:14:52 UTC
1708b46 Set pam subm to latest master 25 January 2024, 17:32:26 UTC
2140ebc Increase gator pool size for pm-cpu 25 January 2024, 16:54:00 UTC
373ebcd Bring in latest PAM branch 24 January 2024, 22:36:29 UTC
738c2a5 forgot a define 24 January 2024, 21:02:08 UTC
097de56 remove seq_flds dependency for mpas_moabmesh mpas framework should not depend on driver/shr this was a mistake 24 January 2024, 20:45:27 UTC
dc6c743 Updates the logic to create crop landunits The value of `use_top_solar_rad` is also included in the logic to create crop landunits. 24 January 2024, 19:37:55 UTC
95c0a58 Another update to PAM to fix build errors on mappy 24 January 2024, 19:35:58 UTC
e832fb5 Merge branch E3SM-Project/ndk/machinefiles/pm-gpu-nvidiagpu-fix (PR #6166) For pm-gpu, add module gcc-mixed/11.2.0 for nvidiagpu builds. 24 January 2024, 19:12:32 UTC
11b76e0 Use more elegant printing of nlmaps_exclude_fields from Andrew Bradley 24 January 2024, 17:08:49 UTC
09da5ec Merge remote-tracking branch 'abag/abagusetty/yakl-submodule-update' into jgfouca/scream_downstream_merge * abag/abagusetty/yakl-submodule-update: Update PAM for build fixes Update PAM to work with YAKL updates Fix YAKL fortran interface build [YAKL] update yakl to latest tip [YAKL] update YAKL submodule 24 January 2024, 16:38:33 UTC
f370642 Update PAM for build fixes 23 January 2024, 23:45:17 UTC
1a92065 fix a bug for reservoir storage calculation and logic update 23 January 2024, 22:57:44 UTC
cc84546 Fix format for nlmaps_exclude_fields in print_seq_infodata 23 January 2024, 17:57:39 UTC
492c1eb For pm-gpu, add gcc-mixed/11.2.0 for nvidiagpu builds. 22 January 2024, 22:46:57 UTC
d8951c0 set fates testmods to be single threaded 22 January 2024, 19:42:20 UTC
43b642d Updates the definition of WCYCL1850-WW3 22 January 2024, 19:26:34 UTC
46b599c add dependabot for github actions 20 January 2024, 18:44:12 UTC
caa81ca Add EAMxx component to master list Add EAMxx component to master list and change order 19 January 2024, 22:29:29 UTC
8cd5447 Change EAMxx site name for docs Change EAMxx site name for docs to match simple string used in other models 19 January 2024, 22:28:44 UTC
5c757a2 Restore backwards compatible qv_sat 19 January 2024, 21:51:44 UTC
258d61b Revert "eam/micro_p3.F90 was using qv_sat, which is gone." This reverts commit 423bc742c27102793dead19bfdbca451e91753ca. 19 January 2024, 21:49:43 UTC
d0e9a4f Revert change that was not meant for eam physics 19 January 2024, 21:42:47 UTC
6fbe2c6 change conditional on action run 19 January 2024, 21:37:49 UTC
595999b need CIME in e3sm dosc for params gen 19 January 2024, 21:27:51 UTC
5fb7d64 rename gh-pages and generate params 19 January 2024, 21:25:37 UTC
ede5796 Change test grid for wcprod suite except for SSP & NARRM 19 January 2024, 19:22:05 UTC
8fe3157 Update default settings for v3 wcycl land config 19 January 2024, 19:14:53 UTC
0549495 Unset elm's finidat for wcprod test suite 19 January 2024, 19:01:43 UTC
5ec189b Only do eamxx github actions when PR is labelled with EAMxx 18 January 2024, 20:57:46 UTC
9eba6d6 Merge branch '/bishtgautam/lnd/fix-fan-setup' (PR #6151) If use_fan = .true. in user_nl_elm, add settings for the FAN model in lnd_in. Fixes #6152 [BFB] 18 January 2024, 20:57:37 UTC
423bc74 eam/micro_p3.F90 was using qv_sat, which is gone. The scream version of micro_p3 appears to use qv_sat_dry wherever qv_sat was being used before, so I just replaced all occurances of qv_sat with qv_sat_dry. 18 January 2024, 19:56:28 UTC
9cc027f more changes for muller-cpu and muller-gpu machine 18 January 2024, 17:53:07 UTC
97a5c31 Downstream merge of scream/eamxx fork into E3SM The build system fixes on the fork are needed for E3SM. [BFB] Merge remote-tracking branch 'scream/master' into jgfouca/scream_downstream_merge * scream/master: (1060 commits) typo forbid using weighted nudging from coarse data in scorpio interface, only access array when it is not empty return early in layout check to avoid segfault EAMxx: set initial timestamp for rrtmgp active gases in fvphys init layer EAMxx: in scorpio output, only track avg cnt for fields that are outputed EAMxx: ensure accum fields are fully inited before I/O runs EAMxx: make FieldLayout::invalid() return something different from a 0d layout EAMxx: remove unused (and buggy) FieldLayout constructors EAMxx: fix expected prop check output in unit test EAMxx: add timing of pre/post/conservation checks EAMxx: avoid pointless sync to host in FieldWithinIntervalCheck EAMxx: avoid pointless work in FieldWithinIntervalCheck EAMxx: print prop check msg when field is repaired Improve error messages in perturb() Assume geo data is synced to host Add comment for SKIP_BLAS Skip blas instead of hardcoding blas_libraries Improve comment on linker Use plain ftn as linker ... 18 January 2024, 17:17:33 UTC
7835327 Updates the definition of WCYCL1850NS 17 January 2024, 21:47:27 UTC
057f1f8 Merge branch 'peterdschwartz/lnd/remove-initializations' (PR #6058) Every model timestep, the vegetation and column fluxes are set to zero for the CNP variables. This took up roughly 1/3rd of the time for the Ecosystem model time, and this PR reduces that by over half. [BFB] 17 January 2024, 20:59:37 UTC
dc26875 Fixes ELM namelist for with active FAN model If `use_fan = .true.` in `user_nl_elm`, add settings for the FAN model in `lnd_in`. 17 January 2024, 20:04:24 UTC
9af3b1e Add new modules to landice.cmake 16 January 2024, 16:15:40 UTC
2a5e068 Make bld files consistent with Registry changes 16 January 2024, 16:15:40 UTC
90a2790 col_cf%nee needs to be zero'd every time step for BGC coupled runs. 16 January 2024, 01:04:47 UTC
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