| 1baed5e | Matthew Hoffman | 02 February 2022, 02:21:00 UTC | Remove saveActualWhen argument to mpas_stream_mgr_read() Having saving of the actualWhen time being optional could lead to confusion if one accesses the new mostRecentAccessTime attribute elsewhere. This commit makes it so the actualWhen time is always saved for all streams that are read. Hence the saveActualWhen argument is deleted. | 02 February 2022, 02:21:00 UTC |
| 91bfee5 | Matthew Hoffman | 17 November 2021, 22:22:54 UTC | Replace actualWhen with saveActualWhen This commit modified the previous commit by removing the actualWhen argument to the MPAS_stream_mgr_read() routine and replacing it with an optional argument saveActualWhen. The actualWhen argument was ambiguous when MPAS_stream_mgr_read was called in a way such that multiple streams were read - the actualWhen value returned came from the final stream read and could possibly be wrong for the other streams that were read. Given the previous commit added the mostRecentAccessTime attribute to the MPAS_stream_list_type type, the actualTime argument was somewhat redundant anyway. Now, instead of being able to have the actualTime returned as an argument, there is the option to have the actual time saved to the new attribute. It can then be retrieved from the stream cursor as needed. The saveActualWhen argument is optional because some streams do not contain xtime and trying to obtain ‘actual when’ in those cases will cause the reading of the stream to fail. Therefore, it is important to be able to not seek this information if possible. If the saveActualWhen argument is not provided to MPAS_stream_mgr_read(), its value defaults to false. This commit also changes the land ice core to stop using actualWhen and replace it with saveActualWhen. Neither the ocean nor seaice cores use actualWhen so no other changes are necessary. | 24 January 2022, 17:12:27 UTC |
| 91b290d | Matthew Hoffman | 17 November 2021, 18:11:42 UTC | Add mostRecentAccessTime attribute to streams This commit adds a mostRecentAccessTime attribute to all streams. For input, this corresponds to the time for which input was last read. For output, this corresponds to the time for which output was last written. Note that for output, there is an option to specify an output time that is not the current time; the value used here for mostRecentAccessTime uses the time actually sent to the file. This attribute is initialized to '9999-12-31_23:59:59' and will contain that value prior to the first access. | 24 January 2022, 17:12:16 UTC |
| 3523b2b | noel | 21 January 2022, 21:21:35 UTC | Merge branch E3SM-Project/ndk/machinefiles/PM-module-fix (PR #4742) For Perlmutter, remove a line to load environment module that is no longer needed | 21 January 2022, 21:21:35 UTC |
| 0329967 | Jon Wolfe | 21 January 2022, 20:05:23 UTC | Merge branch 'MALI-Dev/develop' (PR #4725) Update MALI version and Greenland mesh This merge improves support for a dynamic Greenland ice sheet in E3SM using MALI. This includes: * Updating the version of Albany used on Cori to allow velocity solver improvements * Update to the GIS 1km initial condition file * Removing unneeded land model warnings These changes have been tested in both IG and BG compsets and run for one year at 5 day timesteps and 5 day glc coupling intervals. Results were examined qualitatively and deemed to be reasonable and realistic. Other features not generally used in E3SM: * Change from using beta as basal friction field to muFriction * Improvements to calving and facemelting parameterizations that allow * for exploration of more sophisticated calving treatment (off in E3SM) * Separates a flood fill routine for general use (BFB under all configurations) * A new namelist option to restore thickness after advection needed for some idealized configurations (not used in E3SM) * Improvements and fixes to the subglacial hydrology model (not * currently used in E3SM) Bug fixes: * Effective viscosity calculation caused a divide by zero in some situations and is now fixed * Fix bug to ensure time-varying forcing is read on initial time * Missing error variables are fixed that led to improper error handling in some cases * Damage was not being advected - that is now fixed (damage evolution is not currently used in E3SM) [NML] [non-BFB] for configurations with MALI | 21 January 2022, 20:05:23 UTC |
| 411351f | Jon Wolfe | 21 January 2022, 20:00:25 UTC | Merge branch 'xylar/ocn/init/fix-60-vert-lev-phc' (PR #4729) Fix interface locations for 60-layer PHC grid The previous values were the layer centers, not the layer interfaces for all but the top layer interface. See MPAS-Dev/compass#298 for the bug report, since this issue affects standalone MPAS-Ocean (in init mode) and not E3SM directly. [BFB] | 21 January 2022, 20:00:25 UTC |
| c79d2b0 | James Foucar | 21 January 2022, 19:24:42 UTC | Merge branch 'singhbalwinder/machines/compy-typo-fix' into master (PR #4747) Fixes a typo in compy's intel cmake file This typo breaks model compilation in the debug mode on Compy Fixes #4746 [BFB] - Bit-For-Bit * origin/singhbalwinder/machines/compy-typo-fix: Fixes a typo in compy's intel cmake file | 21 January 2022, 19:24:42 UTC |
| 95a0076 | Balwinder Singh | 21 January 2022, 01:01:47 UTC | Fixes a typo in compy's intel cmake file This typo breaks model compilation in the debug mode on Compy Fixes #4746 [BFB] - Bit-For-Bit | 21 January 2022, 01:03:36 UTC |
| 203b02a | Matthew Hoffman | 20 January 2022, 19:38:43 UTC | Merge branch 'matthewhoffman/fix_cori_cmake_again' into develop This PR removes an inadvertent stray character. * matthewhoffman/fix_cori_cmake_again: Remove inadvertent stray character that was in previous PR | 20 January 2022, 19:38:43 UTC |
| 48ed1bb | Matthew Hoffman | 20 January 2022, 19:35:04 UTC | Remove inadvertent stray character that was in previous PR | 20 January 2022, 19:35:04 UTC |
| 7b97a89 | Peter Schwartz | 20 January 2022, 18:37:29 UTC | Merge remote-tracking branch 'glemieuxfork/fates-spmode-rgknox_cnp_base'(PR #4669) This pull request makes E3SM compatible with FATES API 17.0.0 which enables the use of the FATES satellite phenology mode (aka "sp mode"). While FATES SP mode is operating, the state variables of TLAI, TSAI, HTOP and WTCOL are manipulated (from the surface dataset files) in the native HLM PFT based index space. In this PR, we set up mapping from the FATES IFP space into the HLM P space in elmfates_interfaceMod.F90. Note that the TLAI, TSAI, and HTOP history outputs are updated with a logic check on use_fates_sp to substitute the HLM variable output with the relevant fates sp mode version of these variables, which are identified with the suffix _hist_patch. This PR also introduces FATES no competition mode (use_fates_nocomp), which along with fixed biogeography mode (use_fates_fixed_biogeog), are necessary dependencies for fates sp mode. Fixed biogeography has been enabled in the namelist definition (previously it was set as a stub). The SatellitePhenology procedure has been slightly refactored to represent that it accepts different filters depending on whether or not it is being called for FATES sp mode or ELM sp mode as the FATES sp mode implementation needs to have access to both the active and inactive soil filter. [nonBFB] FATES cases | 20 January 2022, 18:37:29 UTC |
| b396be8 | James Foucar | 20 January 2022, 17:43:33 UTC | Merge branch 'jgfouca/fix_mpas_cmake_missing_dep' into master (PR #4736) Fix missing dependency in one case of gen_f90_targets This bug was causing .F changes to not be reflected in rebuilds. Fixes #4341 [BFB] * jgfouca/fix_mpas_cmake_missing_dep: Fix missing dependency in one case of gen_f90_targets | 20 January 2022, 17:43:33 UTC |
| 4326367 | Balwinder Singh | 20 January 2022, 17:13:22 UTC | Merge remote-tracking branch 'mt5555/ninst-fixes' (PR #4654) Fix component namelist creation bugs when NINST>1 A few bug fixes when running with NINST>1, as is done in the E3SM nbfb test suite MPAS sea ice component should use NTASKS_PER_INST_ICE instead of NTASKS_ICE when determining which partition file to use Ensure ATM and LND put the initial conditions from all ensemble members into the inputdata file list Similar fixes should probably be applied to the MPAS ocean (NTASKS_PER_INST_OCN) and ensemble member inputdata parsing for both MPAS ocean and ice. Not done in this PR since we currently dont use this capability. fixes #4648, #4645 [BFB] * mt5555/ninst-fixes: fix component namelist creation bugs when NINST>1 | 20 January 2022, 17:13:22 UTC |
| e8cc524 | Jon Wolfe | 20 January 2022, 16:03:51 UTC | Merge branch 'jonbob/scripts/update-ocn-bgc' (PR #4686) Update BGC compsets to turn ocn bgc back on, add new ocn bgc init file Adds new ocn BGC files that are consistent with the current MARBL-based implementation. This allows the ocn BGC to be turned back on in BGC compsets. Fixes #4616 [non-BFB] only for BGC compsets | 20 January 2022, 16:03:51 UTC |
| 783a279 | Matthew Hoffman | 19 January 2022, 22:32:48 UTC | Merge branch 'matthewhoffman/fix_cori_cmake' into develop This was accidentally deleted in 66432b7. Note that I am restoring the version of this line currently on master that was updated Nov. 11, 2021, in ee9eabe. * matthewhoffman/fix_cori_cmake: Restore inadvertent deletion of FFLAGS from intel_cori-haswell.cmake | 19 January 2022, 22:32:48 UTC |
| 43d5559 | Matthew Hoffman | 19 January 2022, 22:27:04 UTC | Restore inadvertent deletion of FFLAGS from intel_cori-haswell.cmake This was accidentally deleted in 66432b7db334187c8b49c07312e5d58682806e53. Note that I am restoring the version of this line currently on master that was updated Nov. 11, 2021, in ee9eabe95ba8d69e4f7667d006bf1fa417325a24. | 19 January 2022, 22:27:04 UTC |
| bfd9e0d | noel | 18 January 2022, 20:56:52 UTC | For PM, remove a line to load a module that is no longer needed. Only affects gpu builds. | 18 January 2022, 20:56:52 UTC |
| 528e96a | Gautam Bisht | 17 January 2022, 21:42:47 UTC | Merge branch 'singhbalwinder/atm/sfeng-cpl-BPRP-lnd-atm' (PR #4703) This PR adds two land-atmosphere compsets (1850 and 20TR). Smoke tests are also added for these compsets. [BFB] | 17 January 2022, 21:42:47 UTC |
| 5de0be0 | Mark Taylor | 14 January 2022, 17:34:18 UTC | Merge branch 'mt5555/tom_sponge_start' (PR #4723) Add a simplified sponge layer with namelist variable (tom_sponge_start) to set the starting layer This is needed to run at high resolution with the E3SM 72L configuration (72L sponge layer is too thin, it starts at the 1mb layer). 72L configurations will crash at NE256 and higher resolution without making the sponge layer thicker. It will also be useful for the SCREAM 128L configuration, where the sponge layer is most likely too thick (it starts at the 20mb layer) default: tom_sponge_start=0 (disabled). documentation: https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/2967798203/EAM+Top+of+Model+Sponge+Layer [BFB] | 15 January 2022, 17:03:14 UTC |
| b77e4b7 | Mark Taylor | 14 January 2022, 17:35:58 UTC | Merge branch 'brhillman/eam/fix-adjust-ps-scream' (PR #4717) Make setting of adjust_ps consistent with SCREAM repo. We want to allow adjust_ps=.false. for SCREAM, but retain adjust_ps=.true. for E3SM to remain BFB for v2. This change was originally made downstream in SCREAM, but causes conflicts between the two repos, and prevents EAM compsets from being BFB between the E3SM and SCREAM repos. Moving this change upstream, protected in an ifdef, allows the two repos to be consistent, and keeps EAM compsets BFB between the SCREAM and E3SM repos. This also sets the precedent for allowing changes upstream in E3SM that should apply only to SCREAM configurations, protected in ifdef SCREAM. To enable, we simply need to add the -cppdefs '-DSCREAM' flag to CAM_CONFIG_OPTS for SCREAM compsets. [BFB] | 15 January 2022, 17:01:56 UTC |
| 58826d8 | Mark Taylor | 14 January 2022, 17:32:27 UTC | Merge branch 'mt5555/imex-unit-tests' into master (PR #4731) turn on (during startup) IMEX test of analytic jacobian ( verify that it it agrees with numerical approximation) turn on (during startup) test of the A. Bradley tridiagonal solver [BFB] | 14 January 2022, 22:07:48 UTC |
| 8441102 | Jon Wolfe | 14 January 2022, 15:53:45 UTC | Merge branch 'jonbob/ocn/fix-bulk-forcing' (PR #4733) Make surfaceTemperatureFluxWithoutRunoff private in omp pragma This PR adds surfaceTemperatureFluxWithoutRunoff to an omp pragma to be private for a loop in the mpas-ocean routine ocn_surface_bulk_forcing_active_tracers. It was causing some tests to be irreproducible when run with threading on. Fixes #4732 [non-BFB] for some threaded tests | 14 January 2022, 15:53:45 UTC |
| ce6b973 | Gregory Lemieux | 13 January 2022, 22:02:59 UTC | Updating assignment to fates pft_areafrac If not using a surface dataset with topounits, only access the first index for the topounit dimension as max_topounit is defined in these cases to be one. Otherwise we uses the column type indexing. | 13 January 2022, 22:02:59 UTC |
| f6bb0c5 | Oksana Guba | 13 January 2022, 21:17:53 UTC | Merge branch 'origin/oksanaguba/homme/bubble-rjmods' into next (PR #4482) This fixes an oversaturated state in the moist bubble initialization. Also, qsat in initialization now depends on RJ or Kessler physics. [nonbfb] for 1 homme test, moist bubble. | 13 January 2022, 21:17:53 UTC |
| 75ec9db | James Foucar | 13 January 2022, 19:53:26 UTC | Fix missing dependency in one case of gen_f90_targets This bug was causing .F changes to not be reflected in rebuilds. [BFB] | 13 January 2022, 19:53:26 UTC |
| 92fe52f | James Foucar | 13 January 2022, 19:10:30 UTC | Merge branch 'azamat/perf-tests/add-e3sm-prod-perf-tests' into master (PR #4728) Extend e3sm_prod testing with throughput and memory checks 1) add XML variable TEST_MEMLEAK_TOLERANCE for Chrysalis 2) add e3sm_prod_bench no-IO test suite This helps detect throughput and memory regressions while integrating new features. [BFB] * origin/azamat/perf-tests/add-e3sm-prod-perf-tests: Extend e3sm_prod testing with throughput and memory checks | 13 January 2022, 19:10:30 UTC |
| f74c6d2 | Jon Wolfe | 13 January 2022, 16:01:39 UTC | Merge branch 'jonbob/test/add-cmpaso-debug' (PR #4734) Add SMS_D_Ld3.T62_oQU120.CMPASO-IAF to e3sm_integration This PR adds a new test SMS_D_Ld3.T62_oQU120.CMPASO-IAF to e3sm_integration as a follow-up to PR #4733, which was uncovered from running this test by hand. [BFB] | 13 January 2022, 16:01:39 UTC |
| a793e4f | Jon Wolfe | 12 January 2022, 21:13:38 UTC | Add SMS_D_Ld3.T62_oQU120.CMPASO-IAF to e3sm_integration | 12 January 2022, 21:13:38 UTC |
| c1e8a78 | Jon Wolfe | 12 January 2022, 20:43:37 UTC | Make surfaceTemperatureFluxWithoutRunoff private in omp pragma | 12 January 2022, 20:43:37 UTC |
| 974743b | Azamat Mametjanov | 11 January 2022, 01:46:58 UTC | Extend e3sm_prod testing with throughput and memory checks | 12 January 2022, 20:17:58 UTC |
| 5a230dd | James Foucar | 12 January 2022, 19:35:10 UTC | Merge branch 'jgfouca/cime_update_2022_01_11' into master (PR #4730) to b0ada2143def2bfc5f6d42941486d8264a52628a Changes: 1) Extend throughput and memory checking in baseline tests 2) Introduce a new compset naming convention which maintains backward compatibility and allows position independence. Fixes: 1) FUNIT needs CIME_NO_CMAKE_MACRO ON for now [BFB] * jgfouca/cime_update_2022_01_11: Update CIME submodule Update CIME submodule | 12 January 2022, 19:35:10 UTC |
| 7b2601b | Mark Taylor | 12 January 2022, 16:43:37 UTC | Merge branch 'mt5555/remove-deta' (PR #4724) Remove two unused variables. Causes roundoff level changes in some standalone HOMME tests due to change in loop structure and size of hyvcoord struct. [BFB] except for some standalone HOMME tests | 12 January 2022, 16:43:37 UTC |
| c657b6f | Jon Wolfe | 11 January 2022, 19:44:24 UTC | Merge branch 'alicebarthel/ocn/fix-ml-heat-budget' (PR #4715) Fix calculation of the ML-averaged Brunt-Vaisala frequency This PR is correcting isuues in the calculation of the mixed-layer-averaged Brunt-Vaisala frequency Changes included: * corrected last layer thickness to partial in bruntVaisalaFreqML calculation * fetch index_temp as best practice (instead of assuming index_temp=1) [BFB] | 11 January 2022, 19:44:24 UTC |
| e677e18 | James Foucar | 11 January 2022, 17:19:55 UTC | Update CIME submodule to b0ada2143def2bfc5f6d42941486d8264a52628a Changes: 1) Extend throughput and memory checking in baseline tests 2) Introduce a new compset naming convention which maintains backward compatibility and allows position independence. Fixes: 1) FUNIT needs CIME_NO_CMAKE_MACRO ON for now [BFB] | 11 January 2022, 17:19:55 UTC |
| 0bd5411 | Xylar Asay-Davis | 11 January 2022, 16:14:18 UTC | Fix interface locations for 60-layer PHC grid The previous values were the layer centers, not the layer interfaces for all but the top layer interface. | 11 January 2022, 16:14:18 UTC |
| d3dfb36 | Matthew Hoffman | 10 January 2022, 21:28:20 UTC | Merge branch 'jonbob/update_bld_files' into develop This merge makes the necessary changes to E3SM GLC bld files to properly add new namelist options to E3SM from recent branches. * MALI-Dev/jonbob/update_bld_files: Update bld files with outo-generated changes to match Registry | 10 January 2022, 21:28:20 UTC |
| bfdc5a2 | Mark Taylor | 10 January 2022, 16:14:50 UTC | re-enable imex unit tests | 10 January 2022, 16:14:50 UTC |
| 5ec00ed | Mark Taylor | 09 January 2022, 22:09:55 UTC | Merge branch 'mt5555/remap-options2' (PR# 4722) Remove obsolete/unused remap algorithms add q_alg=11 ( from @ambrad - more accurate, doesn't impose monotonicity at boundaries) added option to specify dynamics algorithm independently from tracer algorithm (from Jason Torchinsky summer intern project) q_alg=11 fixes long standing issue with noise in HOMME's internal gravity wave test cases [BFB] except for one HOMME test, which was modified to test the new code. | 09 January 2022, 22:09:55 UTC |
| d97bfd2 | James Foucar | 06 January 2022, 21:45:47 UTC | Update CIME submodule ... to bc80870bfa0b08d154e89b1fd46493cad1b39a02 Changes: 1) Split CESM configs out of repo 2) Adds enforcing code formatting to pre-commit 3) Refactor all CIME internal testing, split into smaller files and move to a more-logical dir 4) Cleanup Scorpio I/O performance data in the run directory 5) Remove documentation sections for pieces no longer included in CIME 6) Improve Macro.make generation Fixes: *) Loads of small fixes related to recent code churn. 1) Cleanup Scorpio I/O performance data in the run directory [BFB] | 07 January 2022, 22:43:12 UTC |
| e7beed5 | Mark Taylor | 07 January 2022, 19:55:27 UTC | update unit test after q_alg=1,2 removal | 07 January 2022, 21:00:39 UTC |
| b3e8364 | Alice Barthel | 07 January 2022, 17:36:11 UTC | modified comment on partial thickness to clarify | 07 January 2022, 17:36:11 UTC |
| ccea41d | Mark Taylor | 07 January 2022, 16:41:32 UTC | remove unneeded reamp_alg argument from compute_ppm() | 07 January 2022, 16:41:32 UTC |
| 90de3b5 | Jon Wolfe | 07 January 2022, 00:37:47 UTC | Update bld files with outo-generated changes to match Registry | 07 January 2022, 00:37:47 UTC |
| 61214eb | Peter Schwartz | 06 January 2022, 22:28:44 UTC | Merge branch 'bishtgautam/lnd/mkmapdata' (PR #4602) The script that lists all the maps needed for creating a new ELM surface dataset is fixed to account for the name change of the land model to ELM ELM tools directory is reorganized by moving all tools from clm4_5 and shared directory to one-level up. The old directory structure was inherited from CESM in which tools supported two models (clm4_0 and clm4_5) with a common shared directory. [BFB] | 06 January 2022, 22:28:44 UTC |
| e7789f5 | Mark Taylor | 06 January 2022, 21:11:26 UTC | Merge remote-tracking branch 'mt5555/cleanup' (PR #4721) Remove a lot of obsolete code three minor bug fixes: lap_p_wk array dimension, Nthreads=-1 logic: only enable threads if HORIZ_OPENMP or COLUMN_OPENMP enabled parseE3.py typo [BFB] | 06 January 2022, 21:11:26 UTC |
| 72e8ca9 | Mark Taylor | 06 January 2022, 01:24:38 UTC | remove unused variables | 06 January 2022, 01:24:38 UTC |
| 4cc1136 | Matthew Hoffman | 05 January 2022, 22:06:09 UTC | Merge branch 'matthewhoffman/MALI/hydro_timestepper_update' into MALI-Dev/develop This merge make the hydro timestepper more verbose in the log and has the model die if the hydro adaptive timestep gets too small. It also ignores water thickness head in lakes in the channel model. A final commit adds an option (off by default) to allow higher sheet conductivity for water thickness in excess of the bump height. Also fixes bugs: * A bug in the mask initialization that prevented clean coldstarts from a previous hydro model state. * A bug that allowed hydropotential adjacent to the ocean to fall below sea level * A previous design choice that disabled water thickness diffusion across the grounding line * MALI-Dev/matthewhoffman/MALI/hydro_timestepper_update: Add option to have higher sheet cond. for water thickness > bump height Ensure hydropotential adjacent to ocean does not fall below sea level Allow water thickness diffusion across the GL/margin Adjust if statement for readability Calc mask before first use of it in hydro init Add location of CFL limitations to log file Have hydro timestepper print a lot more info while subcycling Make model err if SGH dt < 1 millisecond Ignore the water thickness head in the channel model Correct the hydro dt in the log file | 05 January 2022, 22:06:09 UTC |
| f055966 | Matthew Hoffman | 05 January 2022, 21:45:49 UTC | Merge branch 'stephenprice/glc/mali-updates' into MALI-Dev/develop This pull request updates support for conducting simulations with a dynamic Greenland ice sheet in E3SM using MALI. Updates include: * update Albany library path * update filename associated with GIS 1to10 km init. cond. * commenting out excessive land model warnings that degrade performance These changes have been tested in both IG and BG compsets and run for one year at 5 day timesteps and 5 day glc coupling intervals. Results were examined qualitatively and deemed to be reasonable and realistic. Solver performance was quite uniform throughout (linear and nonlinear iteration counts consistently below 20 and closer to ~10). An additional commit updating support for use of a 20 km resolution Greenland initial condition has been added. * MALI-Dev/stephenprice/glc/mali-updates: Update support for new Greenland 20km input file (now has muFriction and temperature interpolated from 1to10km input file). Update date format for new gis1to10km input file to YYYYMMDD format. Update date format for new gis20km input file to YYYYMMDD format. Make glc elev class warnings active again (commit number 42b5e7bf4b14117b952c324d7df6e1182aed9fe7 fixes the problem of excessive warnings for case where ice sheet upper surface and bed topography elevations are equal to one another). Update code so that ice sheet upper surface value passed to coupler is the max of either the ice sheet surface or 0 (sea level). Corrects excessive warnings regarding elevation classes below sea level. Undo additional commenting out of glc elev class warnings in nuopc driver (because e3sm does not regularly use this driver). Undo commenting out of glc elev class warnings in nuopc driver (since not regularly use by e3sm). Point to updated 20 km GIS input file for use in testing. Temporarily comment out warning lines associated with 1) glc dynamic runoff routing, 2) glc elev class 'too low' (below sea level). These warnings are so prolific that they very significantly impact coupled model performance. Note that this same warnings do NOT show up in IG cases. Update Greenland 1-to-10km initial condition filename information. Update path for Albany lib for cori-knl build. Remove path in file for unsupported cori-haswell build. | 05 January 2022, 21:45:49 UTC |
| 13f6b81 | Mark Taylor | 04 July 2021, 19:21:25 UTC | add simplified sponge layer including namelist option to specify sponge layer bottom/start | 05 January 2022, 20:24:29 UTC |
| ddebdcb | Mark Taylor | 04 January 2022, 23:44:32 UTC | improve 10/11 logic | 04 January 2022, 23:44:32 UTC |
| 22cc2f7 | Gregory Lemieux | 04 January 2022, 22:46:58 UTC | Updating to latest api 17 fates science tag In order to include the IBMfix branch tag commit, it is necessary to update to sci.1.49.2_api.17.0.0 at the least. Since the sci.1.15.0_api.17.0.0 tag is the last science update prior to a new api update, this one was selected. | 04 January 2022, 22:46:58 UTC |
| 60a5bdf | Jon Wolfe | 03 January 2022, 21:16:43 UTC | Update tests and testdefs to reflect new compsets and files | 03 January 2022, 21:16:43 UTC |
| 1ee0965 | Jon Wolfe | 03 January 2022, 19:40:47 UTC | Remove oEC60to30v3 eco option, since it will no longer work | 03 January 2022, 19:40:47 UTC |
| 29bb14f | Mark Taylor | 03 January 2022, 00:28:40 UTC | update unit tests for interface changes | 03 January 2022, 00:28:40 UTC |
| 745a96e | Mark Taylor | 02 January 2022, 23:48:57 UTC | check for ncl in runall script | 02 January 2022, 23:48:57 UTC |
| 3053da2 | Mark Taylor | 02 January 2022, 23:42:55 UTC | remove hypervis_power (more) | 02 January 2022, 23:42:55 UTC |
| de9d2d0 | Mark Taylor | 02 January 2022, 19:17:46 UTC | add vert_remap_u_alg option | 02 January 2022, 23:33:15 UTC |
| eba902c | Mark Taylor | 29 December 2021, 06:08:08 UTC | update test case to test q_alg=11 | 02 January 2022, 19:17:09 UTC |
| 4c6b9f9 | Mark Taylor | 28 December 2021, 00:38:58 UTC | update comments | 02 January 2022, 19:15:12 UTC |
| 740620f | Balwinder Singh | 01 January 2022, 22:33:40 UTC | Adds 20TR and 1850 tests for BGC | 01 January 2022, 22:33:40 UTC |
| 37c20c2 | Balwinder Singh | 01 January 2022, 22:21:21 UTC | Removes BPRP compset, adds Land-atm compsets and addresses comments [BFB] - Bit-For-Bit | 01 January 2022, 22:21:21 UTC |
| 790bc2c | Mark Taylor | 26 December 2021, 23:40:57 UTC | add remap alg option to SL code | 26 December 2021, 23:54:25 UTC |
| 9a8d580 | Mark Taylor | 21 February 2021, 16:22:59 UTC | reorg vertical remap code and add new options vert_remap_q_alg=0 unchanged vert_remap_q_alg=1 unchanged vert_remap_q_alg=2 removed vert_remap_q_alg=3 removed (it was identical to 1) vert_remap_q_alg=10 unchanged vert_remap_q_alg=11 new: q_alg=10 with out limiters, for research [BFB] | 26 December 2021, 23:35:10 UTC |
| 4849b2e | Mark Taylor | 24 December 2021, 23:37:06 UTC | typo in python parsing script | 25 December 2021, 14:23:57 UTC |
| 3ed833c | Mark Taylor | 24 December 2021, 23:36:46 UTC | fix wrong dimensions | 25 December 2021, 14:23:56 UTC |
| f56c25d | Mark Taylor | 24 December 2021, 22:50:48 UTC | remove extraneous lines from some CMakeLists.txt files These cmake files define macros that are used by other executables. The should only contain the setup macro and a call to createTestExec() Any other commands wont be run by the other executables | 25 December 2021, 14:23:56 UTC |
| d680cb8 | Mark Taylor | 24 December 2021, 22:49:45 UTC | add comments about EOS needing to return dpnh_i=1 at surface | 25 December 2021, 14:23:56 UTC |
| e8d6a19 | Mark Taylor | 24 December 2021, 22:49:13 UTC | remove obsolete HOMME_IMEX_MKLSOLVE code | 25 December 2021, 14:23:56 UTC |
| 3db07e8 | Mark Taylor | 20 April 2021, 16:34:15 UTC | dont run a state check when scale3=0 | 25 December 2021, 14:23:56 UTC |
| 7a1ab5f | Mark Taylor | 20 April 2021, 16:29:40 UTC | remove unused qn0 argument | 25 December 2021, 14:23:56 UTC |
| 07546bd | Mark Taylor | 20 April 2021, 14:02:56 UTC | remove hypervis_power restore correct var_coef behavoir remove hypervis power2 | 25 December 2021, 14:23:48 UTC |
| c7a8708 | Mark Taylor | 20 April 2021, 13:45:28 UTC | dont try to turn on horiz/vert threads if no compiler support remove unecessary if statement in nu_div/nu logic remove unused namelist variable | 24 December 2021, 21:47:02 UTC |
| 962e16e | Gregory Lemieux | 23 December 2021, 23:41:45 UTC | adding fates satellite phenology test | 23 December 2021, 23:41:45 UTC |
| b076971 | Gregory Lemieux | 23 December 2021, 22:08:02 UTC | Merge branch 'master' into fates-spmode-rgknox_cnp_base | 23 December 2021, 22:08:02 UTC |
| dd244ac | Benjamin R. Hillman | 23 December 2021, 21:03:02 UTC | Make adjust_ps consistent with SCREAM Make setting of adjust_ps consistent with SCREAM repo. We want to allow adjust_ps=.false. for SCREAM, but retain adjust_ps=.true. for E3SM to remain BFB for v2. This change was originally made downstream in SCREAM, but causes conflicts between the two repos, and prevents EAM compsets from being BFB between the E3SM and SCREAM repos. Moving this change upstream, protected in an ifdef, allows the two repos to be consistent, and keeps EAM compsets BFB between the SCREAM and E3SM repos. This also sets the precedent for allowing changes upstream in E3SM that should apply only to SCREAM configurations, protected in ifdef SCREAM. To enable, we simply need to add the -cppdefs '-DSCREAM' flag to CAM_CONFIG_OPTS for SCREAM compsets. [BFB] | 23 December 2021, 21:03:02 UTC |
| 679cebf | Oksana Guba | 23 December 2021, 18:39:55 UTC | Merge branch 'origin/oksanaguba/homme/xx-ttype9' into master (PR #4682) Adding ttype9 and dcmip2012 tests 2.1, 2.2, and 3 to the bfb suite. Converting some of the tests to ttype9. Not yet added is a limiter call between ttype9 stages. There will be another PR to move limiter from CaarFunctorImpl and to verify it is bfb with F code. [nonbfb] for homme bfb suite for theta-fhs3 (now with ttype9) and new baselines for theta-fdc tests. | 23 December 2021, 18:39:55 UTC |
| 7e954ba | Robert Jacob | 23 December 2021, 18:36:19 UTC | Merge branch 'wlin/atm/update_ftest_ena_twp_rrm' (PR #4655) F2010 is being used in extra coverage test suite for enax4v1 and twpx4v1, and the tests failed to proceed. Change to use compset F2010-CICE as no mpas mesh has been configured to work with these two atm RRM meshes. [BFB] | 23 December 2021, 18:36:19 UTC |
| 80a67f0 | Jon Wolfe | 23 December 2021, 15:59:37 UTC | Merge branch 'mark-petersen/lanl-scratch3' (PR #4716) Update LANL scratch3 to scratch4 LANL /lustre/scratch3 will be decommissioned January 4, 2022. All data should now be written to /lustre/scratch4. This updates the machine files for LANL grizzly and badger. [BFB] | 23 December 2021, 15:59:37 UTC |
| a3b22b9 | mark-petersen | 22 December 2021, 22:29:30 UTC | Update LANL scratch3 to scratch4 LANL /lustre/scratch3 will be decommisioned January 4, 2022. All data should now be written to /lustre/scratch4. | 22 December 2021, 22:29:30 UTC |
| 78b2f4d | Gregory Lemieux | 22 December 2021, 07:08:09 UTC | Reinstating p indexing accidentally removed This line was accidentally removed during an update | 22 December 2021, 07:08:09 UTC |
| acc9bbe | James Foucar | 22 December 2021, 01:09:06 UTC | Merge branch 'jgfouca/use_lmod_modules_for_mappy' into master (PR #4714) Use lmod modules for mappy [BFB] | 22 December 2021, 01:09:06 UTC |
| 5fd19d6 | James Foucar | 22 December 2021, 01:05:17 UTC | Use lmod modules for mappy | 22 December 2021, 01:05:17 UTC |
| 6528b78 | Azamat Mametjanov | 21 December 2021, 21:52:10 UTC | Merge remote-tracking branch 'mt5555/slurm-bindings' (PR #4712) Update some srun settings for HOMME tests Recent upgrades on Anvil/Chrysalis require setting the -c option to avoid poor performance when running with threads. Now that scripts set -c, remove hardcoded -c options on Cori. Also - fixed CPRNC path for Anvil/Chrysalis (they were swapped) - updated CPRNC path on Cori (it was using an ancient version that couldn't parse newer output files) - fixed CMAKE to pass MPI options to the limiter_ut test. srun hangs on Compy without --mpi=pmi2 On compy, HOMME machine file compy.cmake changed to a link, linked to compy-intel.cmake [BFB] | 21 December 2021, 21:52:10 UTC |
| 46b5c6b | Wuyin Lin | 21 December 2021, 15:03:54 UTC | Merge branch 'wlin/atm/diags_tropopause_cpp' (PR #4713) New algorithm for determining tropopause and additional diagnostic output Add a new algorithm for determining tropopause: cold point parabolic. Output at additional levels in the stratosphere are also added. While the new algorithm is enabled during runtime, no additional variables are saved by default. [BFB] | 21 December 2021, 15:03:54 UTC |
| 9ffdb63 | Wuyin Lin | 21 December 2021, 00:12:04 UTC | New algorithm for determining tropopause and additional diagnostic output Add a new algorithm for determining tropopause: cold point parabolic. Output at additional levels in the stratosphere are also added. While the new algorithm is enabled during runtime, no additional variables are saved by default. [BFB] | 21 December 2021, 00:12:04 UTC |
| fa890d1 | Mark Taylor | 19 December 2021, 20:23:18 UTC | tweaks to pass MPI arguments to unit test | 19 December 2021, 20:23:18 UTC |
| 1d7b57c | Balwinder Singh | 19 December 2021, 15:21:59 UTC | Merge branch 'singhbalwinder/machines/sooty-mach-update' (PR #4668) Updates PNNL- Sooty's machine files to use PIO2 and other module changes Some recent machine files updates by Phil Rasch to run E3SM v2 on PNNL cluster Sooty. * singhbalwinder/machines/sooty-mach-update: Updates machine files to use PIO2 and other module changes | 19 December 2021, 15:21:59 UTC |
| 89ef6be | Mark Taylor | 18 December 2021, 20:34:11 UTC | thread bindings for knl and haswell, update cprnc path | 18 December 2021, 20:34:11 UTC |
| d3a4a5c | Gregory Lemieux | 18 December 2021, 01:06:58 UTC | sum the weights for nat veg across all topounits for a given gridcell | 18 December 2021, 01:06:58 UTC |
| 004d15e | noel | 17 December 2021, 19:52:52 UTC | Merge branch E3SM-Project/ndk/machinefiles/correct-small-pelayout-knl-ne120pg2 (PR #4705) After recent PR, correct PE layout for "S" size of ne102pg2 F cases using CICE | 17 December 2021, 19:52:52 UTC |
| 9c0c5b3 | Gregory Lemieux | 17 December 2021, 18:24:53 UTC | adding endrun call after lai check | 17 December 2021, 18:24:53 UTC |
| 8ab5faf | Gregory Lemieux | 17 December 2021, 18:22:35 UTC | updating to latest api 17 fates param file | 17 December 2021, 18:22:35 UTC |
| b5525f3 | noel | 17 December 2021, 17:46:39 UTC | Merge branch E3SM-Project/ndk/machinefiles/perlmutter-env-update (PR #4710) Update module environment for Perlmutter | 17 December 2021, 17:46:39 UTC |
| a445407 | Mark Taylor | 17 December 2021, 17:31:44 UTC | anvil/chrysalis threading and cprnc fix fixes to standalone HOMME: correct cprnc paths for anvil, chrysalis add cores-per-task srun option (otherwise HOMME threading tests have terrible performance) | 17 December 2021, 17:31:44 UTC |
| 60ec507 | Jon Wolfe | 16 December 2021, 19:51:01 UTC | Merge branch 'akturner/seaice/kstrength_constant_bug' (PR #4702) Removed Cf from sea ice constants The sea ice parameter Cf (config_ratio_ridging_work_to_PE) was incorrectly set in both constants and shared parameters in the column package, so that changing config_ratio_ridging_work_to_PE had no effect. Removed Cf from constants. Fixes #4701 [BFB] (Unless config_ratio_ridging_work_to_PE changed) | 16 December 2021, 19:51:01 UTC |
| d02413b | jayeshkrishna | 16 December 2021, 17:47:46 UTC | Merge branch 'dqwu/anlgce/downgrade-netcdf-lib' (PR #4706) Some E3SM cases run on the ANL GCE nodes with the netcdf4p type and NetCDF 4.8.1 might return NC_EHDFERR from nc_enddef(). So switching back to NetCDF 4.8.0, an older but more stable release. For consistency on GCE nodes, we downgrade the serial version of the NetCDF lib to 4.8.0 as well. [BFB] | 16 December 2021, 17:47:46 UTC |
| 4af5914 | wadeburgess | 16 December 2021, 16:10:07 UTC | Merge pull request #4708 from E3SM-Project/wadeburgess-patch-1 Edit sandiatoss3 to change 'gpfs1' to 'gpfs' | 16 December 2021, 16:10:07 UTC |
| e778eaf | wadeburgess | 16 December 2021, 15:20:18 UTC | Edit sandiatoss3 to change 'gpfs1' to 'gpfs' | 16 December 2021, 15:20:18 UTC |
| cc97cda | dqwu | 15 December 2021, 21:41:45 UTC | Downgrading NetCDF lib from 4.8.1 to 4.8.0 for ANL GCE nodes It has been confirmed that some E3SM cases run on ANL GCE nodes with netcdf4p type and latest NetCDF 4.8.1 might return NC_EHDFERR from nc_enddef(). An issue has been created for NetCDF developers to fix. Before this issue is fixed in newer releases of NetCDF, we have to switch back to NetCDF 4.8.0, an older but more stable release. For consistency on GCE nodes, we downgrade the serial version of the NetCDF lib to 4.8.0 as well. | 15 December 2021, 21:41:45 UTC |
| c8d23d2 | jayeshkrishna | 15 December 2021, 21:20:03 UTC | Merge branch 'dqwu/anlgce/add-mpilib-mpi-serial' (PR #4665) Define NETCDF_PATH for E3SM to use a serial NetCDF lib installed on anlgce when mpilib is set to mpi-serial. This fix is required to run SMS_D_Ln9_Mmpi-serial.f19_g16_rx1.A, a cime_developer test that uses mpi-serial. [BFB] | 15 December 2021, 21:20:03 UTC |
