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76615e5 Luke Van Roekel 17 November 2023, 22:10:43 UTC updates redi slope limiting in regions where the isopycnal slope is small, the horizontal redi term is tapered to zero 17 November 2023, 22:10:43 UTC
faac9f0 Wuyin Lin 17 November 2023, 17:04:20 UTC Merge branch 'quantheory:quantheory/fix-negative-snow_depth' (PR #6034) Move h2osno limiter to ensure positive snow depth In LakeHydrologyMod, when applying the effects of sublimation and dew to snow, the snow_depth variable is set using the h2osno variable before that variable is limited to positive values. This commit changes the order of those statements to ensure that snow_depth is not accidentally set to a negative value. It is important to note that in the existing code, only extremely small-magnitude negative values are typically produced, because of another limiter applied earlier in the code. Specifically, h2osno variable is set using h2osno(c) = h2osno(c) - qflx_sub_snow(p)*dtime and qflx_sub_snow is set using qflx_sub_snow(p) = min(qflx_evap_soi(p), h2osno(c)/dtime) Thus, h2osno can only be temporarily negative due to limited floating point precision, i.e. the fact that we can get a slightly negative output from h2osno(c) - (h2osno(c)/dtime)*dtime For this reason, this commit only produces roundoff-level changes in answers under typical conditions. It is also known that invalid values of snow_depth and snowdp are implicated in some rare model crashes (see #5798). The causes are unknown, but in at least one case involved exponentially growing negative snow depth. It is possible that this change will prevent such crashes; investigation is ongoing at the time of this commit. [non-BFB] Possible, only if negative h2osno occur during the course of a test. 17 November 2023, 17:04:20 UTC
3e1a1bd Wuyin Lin 17 November 2023, 17:02:15 UTC Merge branch 'quantheory:quantheory/gustiness-fixes-for-v3' (PR #5850) Fixes for multiple issues in gustiness calculations This is designed to fix the following issues: . Confusion between scalar and vector stress calculations #5834 . Incorrect calculation of gustiness #5835 . EAM's 'U10' output includes a gustiness enhancement #5836 . Possible double-counting of boundary-layer gustiness contributions over land #5837 The first of these was fixed by forcing ATM_SUPPLIES_GUSTINESS=TRUE for all EAM cases, and the second was fixed purely by rewriting the Fortran formulas. These two changes are climate changing, and will generally tend to reduce the impact of gustiness on the mean winds, i.e. mean wind speed will increase. The third fix is to the U10 diagnostic only, and will decrease the output U10. A value that has not been "fixed" in this way can be obtained by outputting the new history variable 'U10WITHGUSTS' from EAM. The final fix is to remove some double-counting between gustiness parameterizations in EAM and ELM. The fix can be "undone" by setting force_land_gustiness = .true. in the ELM namelist. Note that these fixes are only applied over land and ocean. At the request of sea ice developers, this tag also disables gustiness over sea ice completely. Fixes #5834 Fixes #5835 Fixes #5836 Fixes #5837 [CC] [NML] 17 November 2023, 17:02:15 UTC
d2ffe91 Wuyin Lin 16 November 2023, 20:26:59 UTC Merge branch 'wlin/atm/fix_tests_with_L80' (PR #6054) Fix tests incompatitle with L80 and restore tentative config options for SSP The PR fixes two sets of tests. . SSP tests with tentative fix from # 5965 stops working. The EAM%CMIP6 generic pattern match needs to be removed to have it work. This is due to the -vbs option that would be set if having the generic pattern match. The additive style of EAM configure option would then have no mechansim to disable vbs once set. . Update the vertical dimension for 3D variables that condidiag tests track. [BFB] Only the above mentioned tests will diff; and the the differences for these tests following this fix are due to #5996, and other went in on the same day. 16 November 2023, 20:26:59 UTC
7680d57 Gautam Bisht 16 November 2023, 19:29:27 UTC Merge branch 'hongyili/mosart/mosart-heat-fix' (PR #5940) Adding the initialization of a variable used in MOSART-heat; otherwise, the main-channel temperature will be overestimated. The change made only affects stream temperature, nothing else. Fixes #5941 [BFB] 16 November 2023, 19:29:27 UTC
a3a53ba Peter Schwartz 16 November 2023, 19:05:26 UTC Merge remote-tracking branch 'donghuixfork/donghuix/lnd/wetland-inundation-scheme' (PR #5974) In default, the infiltration rate is the same for the non-water surface and surface water storage within the grid cell. This assumption results in a significant underestimation of surface water because the infiltration in the surface water storage is not constrained. In this PR, we introduced a modified infiltration scheme to constrain the infiltration in the surface water storage. The infiltration rate in the surface water storage is smaller than the infiltration rate in the non-water surface. More details about this new scheme and corresponding evaluations can be found in the preprint: https://doi.org/10.21203/rs.3.rs-2733749/v1 The manuscript is still under review. The new infiltration scheme can be turned by adding use_modified_infil = .true. in user_nl_elm. We passed all the tests in e3sm_land_developer test suite. We also created a test for the simulation of surface water dynamics with the new infiltration scheme and calibrated parameter for NLDAS domain: surface_water_dynamics. This test was added into e3sm_land_developer test suite. [BFB] 16 November 2023, 19:05:26 UTC
a3ea386 jayeshkrishna 16 November 2023, 18:56:13 UTC Merge branch 'dqwu/machinefiles/upgrade-anlgce-ub18' (PR #6026) Recently, two ANL GCE nodes (compute-01 and compute-02) have been upgraded from Ubuntu 18.04 to 22.04. Create a new machine named anlgce-ub22 to replace deprecated anlgce-ub18. Also remove deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22. [BFB] * dqwu/machinefiles/upgrade-anlgce-ub18: Removing deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22 Adding support for two ANL GCE nodes that use Ubuntu 22.04 16 November 2023, 18:56:13 UTC
0908426 James Foucar 15 November 2023, 18:53:30 UTC Merge branch 'jgfouca/cmake_names_in_macros' into master (PR #6014) Use CMake variables/names in our cmake macros This should be the last major PR in CMAKE V2 effort. Changes Summary: * Macro structure changes * Add post-process step to set final values for a few items * Make cmake conversion more robust by storing pre-macro values and comparing instead of just looking at new variables * Change all macros to set variables that cmake knows about! This is a huge change with wide impacts * We no longer have to set flag properties on all files. This simplifies things but makes it hard to support e3sm_remove_flags so that feature has been removed. You should always be able to append flags to achieve the same effect as removing a flag. * Try to remove as much of the linker flag micromanagement as possible * We now default to cxx linker. Intel and PGI still have to use fortran unfortunately since our main function is in fortran * Remove as many non-cmake settings as possible from the macros * Add script for converting macros from the old style to new style * Upgrade the compare-flags tool to support parsing the e3sm.bldlog file. This is a tougher way to compare flags since you have to build the cases with -j 1, but it's more robust than looking at cmake internal files. * Remove lots of unneeded stuff from main cmake files (build_model and common_setup) * Remove unused old makefiles for COSP and MPAS * Move gptl build to cmake Testing: * mappy_gnu: e3sm_developer, with full flag compare on a couple big cases * anlgce: e3sm_developer builds * pm-cpu_intel: e3sm_developer, with full flag compare on one big case * chrysalis_intel: e3sm_developer, with full flag compare on one big case * summit: build one big case with pgigpu, ibmgpu, pgi [BFB] 15 November 2023, 18:53:30 UTC
10f1bac James Foucar 14 November 2023, 18:49:40 UTC Update upstream macros 14 November 2023, 18:55:59 UTC
42c41fc James Foucar 14 November 2023, 18:42:44 UTC Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: Homme/SL: Address a warning. Homme: Fix latitude in dcmip2016_test1_forcing. Minor updates to ELM tech doc. Homme: Add gllfvremap_planar_ut unit test. Homme(xx): Set up C++-vs-F90 standalone planar pg2 test. Homme: Add planar capability to gllfvremap_mod. Homme: Modify dcmip2016_test1_pg_forcing to handle planar case. Change minimum concentration and mass of sea ice velocity solution Add single missing variable to OMP private Use small pe layout for TSC test Add size 'S' pes for chrysalis ne4 tests 14 November 2023, 18:42:44 UTC
f4fef0b Andrew M. Bradley 14 November 2023, 17:24:11 UTC Merge branch 'ambrad/homme/dp-pg' (PR #6057) Homme(xx)/pgN: Add pgN feature to doubly periodic planar mode. * Add pgN feature to planar doubly periodic mode. * Add some standalone-hommexx infrastructure to support using the same unit-test exe in multiple tests. * Add an init-planar capability to Hommexx unit tests. * Add a unit test: gllfvremap_planar_ut, planar version of old gllfvremap_ut unit test. * Add a BFB test for F90/C++ dycore consistency in planar mode with pg2 physics grid. e3sm_developer passes on Chrysalis. Additional tests for GPU/EAMxx pass on various machines. [BFB] except for new tests in homme_integration 14 November 2023, 17:24:11 UTC
c336779 Jon Wolfe 14 November 2023, 17:08:44 UTC Merge branch 'jonbob/mpaso/fix-small-omp' (PR #6037) Add single missing variable to OMP private Adds one new variable to an OMP private directive in a recently modified routine. It doesn't appear to cause PET failures but still should be added. [non-BFB] potentially for threaded runs with active ocean 14 November 2023, 17:08:44 UTC
463a53e Robert Jacob 14 November 2023, 15:14:01 UTC Merge branch 'mkstratos/cime/nbfb-pes-change' (PR #6030) Adds a small (S) layout: 1 node per instance for the ne4 grid on chrysalis, to reduce the number of nodes requested for multi-instance tests Switches the TSC nightly test in e3sm_atm_nbfb to use this layout Nightly test node requests are reduced as follows MVK: 90 -> 30; TSC: 36 -> 12 Wall-clock times are increased by ~1.6x for TSC and ~2.6x for MVK [BFB] 14 November 2023, 15:14:01 UTC
ee14d67 Wuyin Lin 14 November 2023, 02:42:12 UTC Implement an adaptable index as pver in condidiag nml 14 November 2023, 02:42:12 UTC
8324c66 Andrew M. Bradley 13 November 2023, 22:09:45 UTC Homme/SL: Address a warning. 13 November 2023, 22:09:45 UTC
40efc90 Gautam Bisht 13 November 2023, 19:31:10 UTC Merge branch 'bishtgautam/lnd/fix-docs' (PR #6059) Updates the description of ELM technical documentation. [BFB] 13 November 2023, 19:31:10 UTC
375b69b Jon Wolfe 10 November 2023, 15:55:35 UTC Merge branch 'proteanplanet/seaice/vsolvelim' (PR #6050) Align minimum concentration and mass limits in MPAS-SeaIce This changes the minimum sea ice concentration and mass per unit area used to solve the sea ice momentum equation to 10^-11 and 10^-10, respectively, aligning the concentration cutoff with the value used in sea ice column physics. The values have been reduced from 10^-3 and 10^-2, respectively. The impact of this change is the removal of numerical diffusion in coupling to the ocean, thus sharpening the sea ice edge, and removing "shadow" fields in low-concentration sea ice mass, heat and salt fluxes with the ocean. This PR does not impact flux conservation between models, nor within MPAS-SeaIce [CC] 10 November 2023, 15:55:35 UTC
49e6d68 Wuyin Lin 10 November 2023, 00:54:41 UTC Change to use ne4pg2_oQU480 for WCYCL1850NS tests 10 November 2023, 00:54:41 UTC
6def04a James Foucar 09 November 2023, 23:18:59 UTC Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: Add muller machine Address few reviewer comments Second attempt at fixing bmatrix equation Fixes one more equation Fixes eqnarray for Github Changes how equations are defined Updates references Adds labels to equations and cross-references Adds mathjax.js for equation numbering add mkdocs-bibtex to pip install Initial commit of TOP parameterization documentation adds syntax highlighting Minor updates Adds notes on running e3sm land developer testsuite 09 November 2023, 23:18:59 UTC
63709e0 noel 09 November 2023, 17:46:46 UTC Merge branch E3SM-Project/ndk/machinefiles/add-machine-muller (PR #6061) Add muller -- small internal machine at NERSC with GPU nodes similar to pm-gpu 09 November 2023, 17:46:46 UTC
4951e07 Wuyin Lin 09 November 2023, 16:54:18 UTC Replace ne11_oQU240 WCYCL1850NS tests with ne4 09 November 2023, 16:54:18 UTC
7735241 noel 08 November 2023, 19:40:07 UTC Add muller machine 08 November 2023, 19:40:07 UTC
0b7cdf4 donghuix 08 November 2023, 05:10:25 UTC remove frac_h2osfc_act from output 08 November 2023, 05:10:25 UTC
50d641d Andrew M. Bradley 06 November 2023, 18:49:15 UTC Homme: Fix latitude in dcmip2016_test1_forcing. This is an old bug in the original forcing function. The physgrid variant, dcmip2016_test1_forcing, is fine. 07 November 2023, 20:09:52 UTC
1c3e9c3 Gautam Bisht 07 November 2023, 16:10:15 UTC Minor updates to ELM tech doc. Updates the description of ELM technical documentation. 07 November 2023, 16:10:15 UTC
9a1dca9 Gautam Bisht 07 November 2023, 16:01:50 UTC Merge branch 'bishtgautam/docs/lnd-baseline-notes' (PR #5978) Adds notes on explaining creating baselines and comparing against those baselines for the `e3sm_land_developer` test suite. [BFB] 07 November 2023, 16:01:50 UTC
ae74855 Wuyin Lin 07 November 2023, 03:39:34 UTC Add default IC (ncdata) for ne120np4 with L80 07 November 2023, 03:39:34 UTC
0dd0883 Peter Schwartz 06 November 2023, 20:00:22 UTC Merge branch 'bishtgautam/doc/top-parameterization'(PR #5980) Adds the technical documentation for parameterization of the topographic solar radiation. [BFB] 06 November 2023, 20:00:22 UTC
e1a1356 Andrew M. Bradley 02 November 2023, 02:55:00 UTC Homme: Add gllfvremap_planar_ut unit test. 06 November 2023, 18:41:40 UTC
804b3b9 Andrew M. Bradley 02 November 2023, 01:30:07 UTC Homme(xx): Set up C++-vs-F90 standalone planar pg2 test. 06 November 2023, 18:40:45 UTC
4b54afa Andrew M. Bradley 01 November 2023, 20:44:19 UTC Homme: Add planar capability to gllfvremap_mod. 06 November 2023, 18:40:02 UTC
206a093 Andrew M. Bradley 31 October 2023, 23:42:31 UTC Homme: Modify dcmip2016_test1_pg_forcing to handle planar case. 06 November 2023, 18:39:26 UTC
336123b Wuyin Lin 03 November 2023, 23:05:43 UTC Fix tests incompatitle with L80 and restore tentative config options for SSP 03 November 2023, 23:05:43 UTC
bc35c3b James Foucar 03 November 2023, 20:59:01 UTC Fixes for fortran linking 03 November 2023, 20:59:01 UTC
fe1b459 James Foucar 03 November 2023, 20:43:46 UTC Fixes for pgi 03 November 2023, 20:43:46 UTC
f9c0795 Andrew Roberts 03 November 2023, 18:30:50 UTC Change minimum concentration and mass of sea ice velocity solution 03 November 2023, 18:30:50 UTC
435ce72 James Foucar 03 November 2023, 18:04:25 UTC Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: (156 commits) Avoid calling add_default when no generic values present for gw_convect_hcf and hdepth_scaling_factor Reset hdepth_scaling_factor for MMF config Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier to allow use of rough topography Make "column_package" the default column_physics_type for BGC Add build-namelist default for chemdyg vertical indicies Add namelist definitions of UCIgaschmbudget_2D_L* remove unnecessary chemdyg settings in user_nl_eam for tests remove default chemdyg vertical indices in F90 code Add default chemdyg vertical indices in xml Update default chemdyg vertical indices in xml Update bld files to match Registry changes, using automated scripts Move some description changes from bld files to Registry Homme: Fix config.h comment style. Homme: Distinguish between F90 and C++ in HOMMEXX_ENABLE_GPU symbol use. Homme: Comment out two builds that aren't used in ctests. Hommexx: Fix issues related to qsize=0. Hommexx: Remove redundant HOMMEXX_ENABLE_GPU definition. Homme: Fix potential bad access to an array. Homme: Add USE_MPI_RUN_SCRIPT to standalone system. Homme(xx)/SL: Add SL-transport feature to doubly periodic mode. ... 03 November 2023, 18:04:25 UTC
19bd6d5 James Foucar 03 November 2023, 17:47:35 UTC Allow fortran linking if we have to 03 November 2023, 17:47:35 UTC
1df0c3b Wuyin Lin 03 November 2023, 17:28:51 UTC Merge branch 'wlin/atm/new_settings_qbo_kpom_hvref' (PR #6043) Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier The following settings are changed or added . hdepth_scaling_factor is halved to improve QBO . New mam_pom file with modified hygroscopicity to reflect the tuning of kPOM = 0.04, for v3 configurations . Additional optional hv_ref_profiles value for use with rough topography (which is not used by default) [NBFB] All tests involving EAM except for FIDEAL, FDPSCREAM, and MMF [NML] a modified parameter value and an updated input file 03 November 2023, 17:28:51 UTC
6a8c964 Wuyin Lin 03 November 2023, 17:26:51 UTC Merge branch 'tangq/atm/chemdyg-L80' (PR #6032) Implement default chemdyg vertical indices automatically adjust to L80 or L72 The L80 configuration #5996 will require a different default set of chemdyg vertical indices of namelist variables. This PR will automatically pick the correct chemdyg indices for L80 or L72, so the chemdyg budget diagnostics will be correct regardless of the vertical level setting. [BFB] [NML] new nml variables for control output for chemdyg 03 November 2023, 17:26:51 UTC
b658327 Wuyin Lin 03 November 2023, 17:24:53 UTC Merge branch 'zyuying/atm/fix-CLD_CAL_TMP' (PR #6011) Bug fix for output of COSP lidar simulator CLD_CAL_TMPICE and CLD_CAL_TMPLIQ are given the wrong values for liquid and ice in the interface code. The dimension for the variables with “_TMP” should be temperature instead of height (cosp_ht). Add a coordinate “cosp_temp” and change the long_name for “_TMP” variables. Fixes #6002 Fixes #6010 [BFB] for all tests except for cosp meta data and a new cosp_temp coordinate variable. 03 November 2023, 17:24:53 UTC
6bf384e Wuyin Lin 03 November 2023, 17:20:46 UTC Merge branch 'whannah/atm/add-L80-support' (PR #5996) Add L80 support for v3 Modify default configurations to use a new 80 layer vertical grid, mainly for enhancing the QBO in E3SMv3. Since this PR touches many compsets and tests I took the opportunity to clean up how the configurations are specified and delete some unused compsets. New atmosphere initial condition files (i.e. ncdata) have been added for ne4, n30, and ne120 grids, but only for cases with realistic topography. The process of creating new initial conditions for idealized compsets like aquaplanet and RCE was complicated by the new aerosol/chemistry options, so these configurations will continue to use the v2 settings, including L72, and will be updated later. [non-BFB] [NML] 03 November 2023, 17:20:46 UTC
4f4f6fa Wuyin Lin 03 November 2023, 17:18:30 UTC Merge branch 'mingxuanwupnnl/atm/fix_VBS_SOAG_DryDep' (PR #5962) Fix gas dry deposition for VBS SOAG gas species This PR fixes the issue on dry deposition of VBS SOAG gases. Dry deposition for VBS SOAG gas species, namely SOAG0, SOAG15, SOAG24, SOAG35, SOAG34, SOAG33, SOAG32, SOAG31, is now included in shared seq_drydep_mod.F90 and namelist drydep_list. Fixes #5963 [CC] [NML] 03 November 2023, 17:18:30 UTC
1fa7ef7 Gautam Bisht 02 November 2023, 18:22:07 UTC Address few reviewer comments 02 November 2023, 18:22:07 UTC
4d44ecd James Foucar 01 November 2023, 21:21:47 UTC gptl build fixes 01 November 2023, 21:21:47 UTC
8771928 James Foucar 01 November 2023, 20:29:38 UTC Turn on verbose makefiles for gptl 01 November 2023, 20:29:38 UTC
94d6a36 James Foucar 01 November 2023, 19:07:07 UTC Remove last uses of e3sm_remove_flag in Depends files 01 November 2023, 19:07:07 UTC
3872f4c Jon Wolfe 01 November 2023, 18:42:27 UTC Merge branch 'jonbob/seaice/fix-bgc-column-physics-type' (PR #6036) Make "column_package" the default column_physics_type for BGC With icepack now the default seaice column physics package, we need to make "column_package" the default when seaice BGC is on until it's completely supported in icepack. [non-BFB] only for BGC configurations with active seaice (which are currently broken) 01 November 2023, 18:42:27 UTC
8af0c4f Wuyin Lin 01 November 2023, 17:22:12 UTC Avoid calling add_default when no generic values present for gw_convect_hcf and hdepth_scaling_factor 01 November 2023, 17:22:12 UTC
253dd26 James Foucar 01 November 2023, 16:11:40 UTC We haven't used Makefiles to build cosp in years 01 November 2023, 16:11:40 UTC
73b395a James Foucar 01 November 2023, 15:52:40 UTC More fixes to sharedlibs 01 November 2023, 15:52:40 UTC
a4c868a James Foucar 01 November 2023, 15:27:12 UTC More fixes to buildlib.kokkos and post_process.cmake needs to not blow away things set up by the project command 01 November 2023, 15:27:12 UTC
ae2d6d4 Wuyin Lin 01 November 2023, 03:02:38 UTC Reset hdepth_scaling_factor for MMF config 01 November 2023, 03:02:38 UTC
1ab9633 Wuyin Lin 01 November 2023, 02:39:03 UTC Add settings to re-tune QBO, kPOM, and additional hyperviscosity modifier to allow use of rough topography 01 November 2023, 02:39:03 UTC
3af01f9 James Foucar 31 October 2023, 22:08:04 UTC Revert "Not sure we keep this" This reverts commit c0a92a2214b0a2019c0cc24630aff1c441ba4590. 31 October 2023, 22:08:04 UTC
81d80e0 James Foucar 31 October 2023, 22:03:37 UTC Cleanup kokkos sharedlib build wrapper 31 October 2023, 22:03:37 UTC
9e6f04e James Foucar 31 October 2023, 21:50:12 UTC Remove FFLAGS_NOOPT concept 31 October 2023, 21:50:12 UTC
db42f2a Benjamin Hillman 31 October 2023, 21:43:50 UTC Merge branch 'whannah/mmf/fix-gw-heating' (#5982) Previously the MMF heating tendency used for the convective gravity wave parameterization included the effect of radiation. This moves the calculation so that radiative heating can be removed at all levels. [non-BFB] for all MMF tests 31 October 2023, 21:43:50 UTC
bb4ec51 Jon Wolfe 31 October 2023, 19:15:12 UTC Add single missing variable to OMP private 31 October 2023, 19:15:12 UTC
f92ce02 Jon Wolfe 31 October 2023, 18:40:38 UTC Make "column_package" the default column_physics_type for BGC 31 October 2023, 18:40:38 UTC
cdfebee James Foucar 31 October 2023, 18:34:58 UTC Clean up deoptimization a bit 31 October 2023, 18:34:58 UTC
198c7b8 James Foucar 31 October 2023, 17:13:35 UTC Fixes for free/fixed and macro exp 31 October 2023, 17:13:35 UTC
abe445e Andrew M. Bradley 31 October 2023, 16:44:42 UTC Merge branch 'ambrad/homme/dp-sl' (PR #6013) * Add semi-Lagrangian transport feature to planar doubly periodic mode. * Add a BFB test for F90/C++ dycore consistency. * Fix some C++ dycore issues related to qsize=0. * Add a bit of infrastructure to make running standalone tests on Summit much easier. Passes e3sm_developer and homme_integration on Chrysalis. Passes new BFB test on Ascent. [BFB] except for new tests in homme_integration 31 October 2023, 16:44:42 UTC
a27115e Jon Wolfe 31 October 2023, 16:35:06 UTC Merge branch 'proteanplanet/ocean/pslv' (PR #5999) Fixes PMSL coupling between ocean and atmosphere This fixes a major bug in E3SM by replacing an incorrect coupling of PBOT (pressure in the mid-bottom atmospheric layer), with PSLV (atmosphere model sea level pressure) in the ocean-atmosphere coupled fields. The consequences of this PR are widespread: It was diagnosed from intermittent crashes that have been experienced in the Mediterranean Sea, it changes widespread pressure fields experienced on all ocean surfaces, and fixes sea ice biases. This pull request only affects B-cases. In G-cases, PBOT and PSLV are currently identically set to pressure at mean sea level, thus a reason why this bug has previously gone undetected. Reference to PBOT has been completely removed in the sea ice coupling code as part of this PR to avoid future confusion, because it is was not being used. [CC] for B-cases 31 October 2023, 16:35:06 UTC
d18c6e9 Jon Wolfe 31 October 2023, 16:30:04 UTC Merge branch 'eclare108213/seaice/icepack-integration' (PR #5958) Initial icepack integration Installs Icepack in E3SM. This PR includes MPAS-seaice changes necessary to run Icepack in equivalent physics configurations as the original column package code. The entire Icepack repository is installed as a submodule linked from the main branch of E3SM’s Icepack fork. Some minor changes were made to the original column package code for consistency with Icepack during testing. Icepack replaces colpkg as the default column physics package in this PR. Fully coupled E3SM v3alpha trigrid with Icepack physics is statistically compatible with the 100-year control at the 99% confidence interval. Icepack is thoroughly and promptly documented in its git repository (the source code is in icepack/doc/). [NML] [CC] 31 October 2023, 16:30:04 UTC
5330bd8 James Foucar 31 October 2023, 16:25:40 UTC Better way to handle free/fixed fortran 31 October 2023, 16:25:40 UTC
522cd9f Jon Wolfe 31 October 2023, 15:59:39 UTC Merge branch 'erinethomas/mpas-si/reduce_flux_iterations' (PR #5921) Reduce number of sea ice flux iterations from 10 to 5 The current number of iterations to calculate sea ice fluxes is excessive. Convergence of atm-sea ice fluxes is reached within a few iterations, therefore, the default value for the number of iterations should be reduced from 10 to 5. [NML] [non-BFB] 31 October 2023, 15:59:39 UTC
18b455d James Foucar 31 October 2023, 15:37:05 UTC Fixes for using cmake vars 31 October 2023, 15:37:05 UTC
c05d008 Sean Patrick Santos 30 October 2023, 22:05:06 UTC Move `h2osno` limiter to ensure positive snow depth. In `LakeHydrologyMod`, when applying the effects of sublimation and dew to snow, the `snow_depth` variable is set using the `h2osno` variable before that variable is limited to positive values. This commit changes the order of those statements to ensure that `snow_depth` is not accidentally set to a negative value. It is important to note that in the existing code, only extremely small-magnitude negative values are typically produced, because of another limiter applied earlier in the code. Specifically, `h2osno` variable is set using ``` h2osno(c) = h2osno(c) - qflx_sub_snow(p)*dtime ``` and `qflx_sub_snow` is set using ``` qflx_sub_snow(p) = min(qflx_evap_soi(p), h2osno(c)/dtime) ``` Thus, `h2osno` can only be temporarily negative due to limited floating point precision, i.e. the fact that we can get a slightly negative output from ``` h2osno(c) - (h2osno(c)/dtime)*dtime ``` For this reason, this commit only produces roundoff-level changes in answers under typical conditions. It is also known that invalid values of `snow_depth` and `snowdp` are implicated in some rare model crashes (see #5798). The causes are unknown, but in at least one case involved exponentially growing negative snow depth. It is possible that this change will prevent such crashes; investigation is ongoing at the time of this commit. [non-BFB] 30 October 2023, 22:05:06 UTC
f2e04d4 James Foucar 30 October 2023, 19:26:17 UTC Updating compare-flags to look at logs 30 October 2023, 19:26:17 UTC
7f5b078 James Foucar 30 October 2023, 16:10:57 UTC Clean up some logic in build_model 30 October 2023, 16:10:57 UTC
70b4126 Wuyin Lin 30 October 2023, 13:08:02 UTC Merge branch 'wlin/lnd/extra_surfdata_with_top' (PR #6008) Update surfdata with TOP for ne4np4/ne4pg2 simyr1850 and ne30np4_simyr2010 The surfdata with TOP is needed for ne30_oECv3.F2010 and ne4_oQU240.WCYCL1850NS tests. The surfdata for ne4pg2_simyr1850 is also updated. Fixes #6007. [BFB] No other tests are affected. [NML] fsurdat changed for above mentioned test grids/compsets combinations 30 October 2023, 13:08:02 UTC
8189158 Wuyin Lin 30 October 2023, 13:05:25 UTC Merge branch 'whannah/atm/add-hdepth_scaling_factor' (PR #5985) Merge branch 'whannah/atm/add-hdepth_scaling_factor' into next (PR #5985) Add hdepth scaling factor for convective gravity waves Adds a namelist variable "hdepth_scaling_factor" for the convective gravity wave scheme that will be needed for tuning the QBO in v3. The default value of 1 will retain the current behavior. [BFB] [NML] new nml variable hdepth_scaling_factor for all tests involving eam 30 October 2023, 13:05:25 UTC
f94e7e3 dqwu 26 October 2023, 20:40:17 UTC Removing deprecated CMake macro ZLIB_PATH for anlgce/anlgce-ub22 Recently, the dependency on CIME/Tools/Makefile has been removed for SCORPIO and we no longer need CMake macro ZLIB_PATH for anlgce or anlgce-ub22. 28 October 2023, 02:24:23 UTC
7d29f0b dqwu 26 October 2023, 18:39:00 UTC Adding support for two ANL GCE nodes that use Ubuntu 22.04 Create a new machine named anlgce-ub22 for two ANL GCE nodes that have recently been upgraded from Ubuntu 18.04 to 22.04. This change also replaces the deprecated machine anlgce-ub18. 28 October 2023, 02:24:21 UTC
50924a3 Qi Tang 27 October 2023, 22:20:23 UTC Add build-namelist default for chemdyg vertical indicies 27 October 2023, 22:20:23 UTC
696c8a6 Qi Tang 27 October 2023, 22:13:21 UTC Add namelist definitions of UCIgaschmbudget_2D_L* 27 October 2023, 22:13:21 UTC
7f9228a James Foucar 27 October 2023, 21:39:24 UTC Merge remote-tracking branch 'origin/master' into jgfouca/cmake_names_in_macros * origin/master: (41 commits) Ascent needs to use static hdf5 libs Don't change submodule Reorg csm_share Depends Clean up csm_share depends files a bit Add missing variable to omp directive Add missing variable to omp directive Update CIME submodule Fix a few things I missed Update new mapping files to use updated algotihms and naming convention For NERSC machines only, update to latest AMD compiler Add some modules to remove before loading what we want. Set default as config_Redi_quasi_monotone_safety_factor=0.9 Set E3SM default to config_Redi_use_quasi_monotone_limiter=true Remove RediKappaScaling creation and initialization Update bld files to match Registry changes Make bld files consistent with Registry changes Fixed OpenMP changes redi namelist options fixes build errors Changes redi tapering and slopes add domain to RK4 subroutine ... 27 October 2023, 21:39:24 UTC
f76c5f8 James Foucar 27 October 2023, 21:37:41 UTC Progress 27 October 2023, 21:37:41 UTC
0ec006d James Foucar 27 October 2023, 21:21:53 UTC Merge branch 'jgfouca/ascent_fix' into master (PR #6028) Ascent needs to use static hdf5 libs The ibm linker chokes on the .so's due to the non-standard suffix. FindHDF5 for some reason does not use the symlinks which have a normal suffix. [BFB] 27 October 2023, 21:21:53 UTC
a8b7065 Michael Kelleher 27 October 2023, 21:12:05 UTC Use small pe layout for TSC test 27 October 2023, 21:12:05 UTC
f501def Michael Kelleher 27 October 2023, 21:10:59 UTC Add size 'S' pes for chrysalis ne4 tests 27 October 2023, 21:10:59 UTC
1107d6b James Foucar 27 October 2023, 20:50:59 UTC Progress 27 October 2023, 20:50:59 UTC
9d94967 Qi Tang 27 October 2023, 20:44:59 UTC remove unnecessary chemdyg settings in user_nl_eam for tests 27 October 2023, 20:44:59 UTC
d4f5a99 Robert Jacob 27 October 2023, 20:27:42 UTC Merge branch 'sbrus89/wav/ww3_test_fix' (PR #5274) Correct an error in the compset name for the WW3 extended coverage test. Reduce the amount of data downloaded. [BFB] new test 27 October 2023, 20:27:42 UTC
6f5d3b7 Qi Tang 27 October 2023, 20:19:35 UTC remove default chemdyg vertical indices in F90 code 27 October 2023, 20:19:35 UTC
81f00b5 Qi Tang 27 October 2023, 20:17:28 UTC Add default chemdyg vertical indices in xml 27 October 2023, 20:17:28 UTC
eef6af3 Qi Tang 27 October 2023, 20:14:00 UTC Update default chemdyg vertical indices in xml 27 October 2023, 20:14:00 UTC
4d78ed5 James Foucar 27 October 2023, 20:03:31 UTC Ascent needs to use static hdf5 libs The ibm linker chokes on the .so's due to the non-standard suffix. FindHDF5 for some reason does not use the symlinks which have a normal suffix. [BFB] 27 October 2023, 20:03:31 UTC
0326442 noel 27 October 2023, 20:02:33 UTC Merge branch from E3SM-Project/ndk/machinefiles/pm-cpu-update-aocc2 (PR #6003) Clean up modules on all NERSC machines; update AMD on pm-cpu/alverez 27 October 2023, 20:02:33 UTC
b2ea1c3 James Foucar 27 October 2023, 16:06:16 UTC Merge branch 'jgfouca/csm_share_no_makefile' into master (PR #6025) CSM_share: no cime/Tools/Makefile The CSM_share build is very similar to how we build our main components, except it was being driven by the CIME/Tools/Makefile. This PR changes it to use our CMake build_model function. A few minor tweaks were needed, the main problem was with the Depends files. The CSM_share build cannot use our standard Depends system due to the likelihood that the Depends file will modify flags for files that CSM doesn't know about, which is currently an error. Instead, the CSM depends files are moved to E3SM/share, which is a bit unfortunate since it is not consistent and also makes them non-customizable within a case. On the plus side, this allows us to get rid of our last remaining Makefile-style Depends files. [BFB] 27 October 2023, 16:06:16 UTC
6e70c30 James Foucar 26 October 2023, 21:42:19 UTC Don't change submodule 26 October 2023, 21:42:19 UTC
b64b5d6 James Foucar 26 October 2023, 19:20:18 UTC Reorg csm_share Depends 26 October 2023, 19:20:18 UTC
0b367fb Jon Wolfe 26 October 2023, 19:19:47 UTC Merge branch 'vanroekel/ocean/change-redi-slopes-and-limiter' (PR #5947) Improve slope calculation and fix slope limiting for redi mixing In current MPAS code, slopes are altered directly, e.g. when S > Scrit it is set to zero. Griffies et al 1998 (Appendix C) equates this to slope clipping. The correct approach is to taper the redi kappa coefficient for each individual flux instead. The cross terms ("term2" and "term 3") end up being identical as they are d/dz(kappa S grad phi) so tapering kappa or S are identical. However for the vertical it is d/dz(kappa |S|^2 d phi / dz) so tapering S is different from tapering kappa. Also term 1 (laplacian diffusion) was not being tapered with slopes creating a cross isopycnal flux in steeply sloping regions. These issues are fixed here. In addition a new slope calculation from @dengwirda is introduced to prevent the slopes from getting very large when grad phi or d/dz(phi) get small. This function limits the slope to be between -1 and 1. [NML] [CC] 26 October 2023, 19:19:47 UTC
510fca6 Jon Wolfe 26 October 2023, 19:11:43 UTC Merge branch 'vanroekel/ocean/fix-richardson-number-calculation' (PR #5946) Fixes MPAS-Ocean Richardson number calculation This changes the calculation of the gradient and bulk richardson numbers to utilize the normal and tangential velocities to avoid the factor of two issue and also fixes a number of places where the loop was over maxLevelCell and should have been to maxLevelEdgeTop. [NML] [CC] 26 October 2023, 19:11:43 UTC
4d48d07 Jon Wolfe 26 October 2023, 19:06:26 UTC Merge branch 'mark-petersen/ocean/redi-flux-limiter' (PR #5945) A quasi-monotone flux limiter for isopycnal diffusion (Redi) This PR addresses a range of issues concerning the isopycnal diffusion operator (Redi): * Updating the use of the triad slopes in one of the Redi fluxes. * Correcting the implementation of the Redi fluxes. * Adding a new new quasi-monotone flux limiting strategy that attempts to prevent the development of non-monotone tracer values. [non-BFB] [CC] 26 October 2023, 19:06:26 UTC
c98976b James Foucar 26 October 2023, 18:32:08 UTC Clean up csm_share depends files a bit 26 October 2023, 18:32:08 UTC
e8e45c2 James Foucar 26 October 2023, 18:05:22 UTC Merge branch 'master' into jgfouca/csm_share_no_makefile * master: Update CIME submodule Fix a few things I missed 26 October 2023, 18:05:22 UTC
9d100e4 Jon Wolfe 26 October 2023, 18:04:23 UTC Merge branch 'xylar/mesh/add-ecwisc30to60e3r2' (PR #5927) Add new ECwISC30to60E3r2 ocean and sea-ice mesh Long name: ECwISC30to60L64E3SMv3r2 This mesh is a new eddy closure (EC) mesh with ice-shelf cavities (wISC) that has: * 30 km resolution at the equator * 60 km resolution at mid latitudes * 35 km resolution near the poles This mesh is a candidate for the E3SM v3 (E3) low res mesh. It is revision 2 (r2) of the mesh. (Revision 1 had incorrect bathymetry and coastline around Greenland.) All new supporting files have been staged on the inputdata repo [BFB] 26 October 2023, 18:04:23 UTC
52b0551 Elizabeth Hunke 26 October 2023, 17:27:54 UTC Merge pull request #45 from eclare108213/jonbob/seaice/update-bld-files Move comments to Registry and update bld files to match 26 October 2023, 17:27:54 UTC
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