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b5dd3db Balwinder Singh 07 September 2023, 05:41:52 UTC Intermediate deguuing files but it has full info needed for pergro 07 September 2023, 05:41:52 UTC
d115180 noel 29 August 2023, 17:38:28 UTC Merge branch E3SM-Project/ndk/machinefiles/remove-NERSC-server (PR #5900) Remove NERSC inputdata server 29 August 2023, 17:38:28 UTC
1f6314c noel 28 August 2023, 21:06:58 UTC remove NERSC inputdata server 28 August 2023, 21:06:58 UTC
640bb28 James Foucar 28 August 2023, 18:16:09 UTC Merge branch 'jgfouca/change_ocean_petsc_libs' into master (PR #5824) mpas-ocean: Do not link petsc unless USE_PETSC is on [BFB] 28 August 2023, 18:16:09 UTC
ac7c892 Jon Wolfe 28 August 2023, 16:21:39 UTC Merge branch 'philipwjones/mpas-ocean/sal-acc-fix' (PR #5874) Fix openacc data directive on non-existent ssh_sal array An openacc data transfer on the self-attraction ssh change was outside any conditional for SAL so was operating on a non-existent array if SAL is turned off. This mod changes the location of the data directive so it is within the compute SAL routine and only executed of SAL is turned on Fixes #5866 [BFB] 28 August 2023, 16:21:39 UTC
394fdb7 Jon Wolfe 25 August 2023, 16:03:07 UTC Merge branch 'cbegeman/ocn/fix-tendency-metadata' (PR #5883) Correct the units of active tracer tendencies The units of active tracer tendencies in the Registry should have an additional factor of m. The activeTracerTend's are divided by a factor of layerThickness when they are used in the code to update active tracers. This operation is also needed to evaluate tracer conservation from activeTracerTend output. [BFB] 25 August 2023, 16:03:07 UTC
4b00636 Gautam Bisht 24 August 2023, 20:00:45 UTC Merge branch 'lnd/fates-refactor' (PR #5849) This pull request changes the names of a number of FATES use statements and type names to be consistent with the associated FATES refactor. The FATES submodule pointer is updated as a results as well. [B4B] for non-fates tests 24 August 2023, 20:00:45 UTC
e33c20d Jon Wolfe 24 August 2023, 17:49:03 UTC Merge branch 'jonbob/scripts/update-ne30pg2-orrs18to6v3' (PR #5865) Update mapping and domain files for ne30pg2-oRRS18to6v3 Adds new domain and mapping files for the ne30pg2-oRRS18to6v3 resolution, as well as smoothed runoff between r05 and oRRS18to6v3 [BFB] for all tested configurations 24 August 2023, 17:49:03 UTC
ba85852 Peter Schwartz 23 August 2023, 20:33:33 UTC Merge branch 'bishtgautam/lnd/rename-clm-modules' (PR #5689) Renames clm_time_manager module as elm_time_manager. [BFB] 23 August 2023, 20:33:33 UTC
6aa22b1 James Foucar 21 August 2023, 16:27:57 UTC Merge branch 'jasonb5/cime/adds_testing_excludes' into master (PR #5812) CIME's archive configuration is used for determining which history files are compared during the COMPARE_PHASE of tests. There was a fix in CIME that corrected the generated regex that was used to search for these files. Since the fix additional active component history files are being matched and generating test failures as they are required for archiving but not for the COMPARE_PHASE of a test. This PR excludes these components from the COMPARE_PHASE of tests. This PR includes a CIME update: Changes: 1) jenkins_generic_job: Add flag for ignoring memleaks 2) Always use the BATCH_COMMAND_FLAGS argument. This allows users to alter with xmlchange and append with --append 3) Default to single-build in PEM tests 4) Adds the force-rebuild argument to create_test and cs.status. This argument will set the SHAREDLIB_BUILD_PHASE to PEND for all tests. 5) Do not re-invoke make on repeat case.build calls 6) env_batch: replace PROJECT arg with nothing if PROJECT not required - Adds --driver to query_config Deprecates --comp_interface for query_config Fixes driver_choices in create_test 7) Add support for MPASO_USE_PETSC 8) Better error for missing config_machines.xml file 9) Adds skip-submit argument to case.build 10) change method of detecting fv3 dycore in cam and path to libfv3.a 11) add which to find ncdump and an error message if not found 12) do not allow EXEROOT or OBJDIR or LIBROOT to be CASEROOT 13) Add flexible controls of GPU configuration 14) Removes DAE.ww3a.ADWAV from cime_developers 15) Fixes hist_files excluding components during actual compare Fixes: 1) Fix create_test --single-exe option 2) Fixes issue causing case context to exit early. This would result in ERROR: Cannot modify case, read_only... errors. 3) Fixes regex pattern used to match history files. Only considers .nc files when copying history files for a tests COMPARE_PHASE. Adds a new optional attribute exclude_testing for comp_archive_spec which allows a components history files to be archived but excluded from the COMPARE_PHASE of tests when active. 4) Fixes creating directory for input data 5) batch: improve the account remove and add support for slurm 6) Docker CI fixes [BFB] 21 August 2023, 16:27:57 UTC
b42f4d8 Balwinder Singh 18 August 2023, 22:15:28 UTC Merge remote-tracking branch 'mkstratos/mkstratos/fix-pgn-test'(PR #5872) Add micro_p3 to list of possible ptend names in physpkg Fixes missing field error when running PGN test ERROR: GET_MASTERLIST_INDX: attemping to output field s_micro_p3 not on master list Fixed by adding micro_p3 to the list of possible ptend field names. [BFB] * mkstratos/mkstratos/fix-pgn-test: Add micro_p3 to list of possible ptend names 18 August 2023, 22:15:28 UTC
032bd09 Andrew M. Bradley 18 August 2023, 19:30:27 UTC Merge branch 'ambrad/eam/rm-bld-DNC4' (PR #5854) EAM/HOMME: Remove -DNC=4 in bld/configure; NC is an unused symbol. It is believed that NC was used in HOMME long ago. In any case, it is not used any longer. Remove it from bld/configure. e3sm_developer passes on Chrysalis. [BFB] 18 August 2023, 19:30:27 UTC
dc14534 James Foucar 17 August 2023, 19:36:56 UTC Update CIME again 17 August 2023, 19:36:56 UTC
83dea76 James Foucar 17 August 2023, 19:34:38 UTC Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: Fix array shapes in where assignment statements in micro_p3_interface.F90 revert to explicit initialization due to complaint by nvidia compiler Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays Update WCYCL PE-layouts on Chrysalis Bugfix: rework P3_input_dim and P3_output_dim for hist_coord bug fix in crm_physics.F90 17 August 2023, 19:34:38 UTC
8d81d0b Wuyin Lin 17 August 2023, 14:41:50 UTC Merge branch 'wlin/atm/fix_where_assignment_shapes' (PR #5886) Fix array shapes in where assignment statements in micro_p3_interface.F90 Mismatch of array shapes in where assignment statements and where mask expression causing three diagostic variables, AQRAIN, ANRAIN, FREQR, to differ from one run to another when using gnu compiler. The declared shapes of the three arrays are the same as the array rain. While the scope could be narrowed with rain(:ncol,top_lev:) in the mask expression, the assignment statments for the three affected variables still use the full scope. Although test with other compilers, e.g., intel, does not report diff, the diagnostic output for these three variables are assumed to have also be affected. Fixes #5864 [NBFB] for tests that compare eam.h0 with diff in AQRAIN, ANRAIN and FREQR. The test results are otherwise not affected. 17 August 2023, 14:41:50 UTC
1161cf7 Wuyin Lin 16 August 2023, 19:14:30 UTC Merge branch 'wlin/atm/fix_p3_input_output_dims' (PR #5876) Bugfix: rework P3_input_dim and P3_output_dim for hist_coord The constant integer scalar and array in calling add_hist_coord to define P3_input_dim and P3_output_dim can cause type mismatch for some compilers, leading to invalid values of these two coordinate arrays in eam history output, along with randomness from one run to another. This behavior causes tests to be labelled diff although they are otherwise BFB. Fixes #5863 [BFB] for all actual test results. Some baselines (that compare eam.h#) may contain invalid values for P3_input_dim and/or P3_output_dim, and the tests would report diff. * origin/wlin/atm/fix_p3_input_output_dims: revert to explicit initialization due to complaint by nvidia compiler Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays Bugfix: rework P3_input_dim and P3_output_dim for hist_coord 16 August 2023, 19:14:30 UTC
b8b7519 Wuyin Lin 16 August 2023, 02:28:38 UTC Fix array shapes in where assignment statements in micro_p3_interface.F90 Mismatch of array shapes in where assignment statements and where mask expression causing three diagostic variables, AQRAIN, ANRAIN, FREQR, to differ from one run to another when using gnu compiler. The declared shapes of the three arrays are the same as the array rain. While the scope could be narrowed with rain(:ncol,top_lev:) in the mask expression, the assignment statments for the three affected variables still use the full scope. Although test with other compilers, e.g., intel, does not report diff, the diagnostic output for these three variables are assumed to have also be affected. Fixes #5864 [NBFB] for tests that compare eam.h0 with diff in AQRAIN, ANRAIN and FREQR. The test results are otherwise not affected. 16 August 2023, 02:28:38 UTC
8ada657 Wuyin Lin 15 August 2023, 15:50:26 UTC revert to explicit initialization due to complaint by nvidia compiler 15 August 2023, 15:50:26 UTC
b9cdd88 Carolyn Begeman 29 June 2023, 16:34:50 UTC Correct the units of active tracer tendencies 15 August 2023, 14:13:14 UTC
2e3be1d Azamat Mametjanov 15 August 2023, 01:41:07 UTC Merge branch 'azamat/chrysalis/update-v3-wcycl-pes' (PR #5879) Update WCYCL PE-layouts on Chrysalis. [BFB] 15 August 2023, 01:41:07 UTC
2a4ef31 Wuyin Lin 14 August 2023, 20:15:19 UTC Change to use implicit loop to populate P3_input_dim and P3_output_dim arrays 14 August 2023, 20:15:19 UTC
31f1e12 Azamat Mametjanov 14 August 2023, 19:09:48 UTC Update WCYCL PE-layouts on Chrysalis [BFB] 14 August 2023, 19:09:48 UTC
6d5a875 Benjamin Hillman 14 August 2023, 18:06:03 UTC Merge branch 'whannah/mmf/surface-flux-bug-fix' (#5838) Fix a bug in which surface sensible and latent surface fluxes have been unintentionally swapped in the CRM interface. The impact of this fix will generally be small because these fluxes are currently only used to influence the internal CRM friction calculation. The application of suface fluxes in the PBL scheme outside of the CRM (in tphysac) are still correct, so there is no fundamental impact to the water mass or energy budgets. [non-BFB] for MMF cases. 14 August 2023, 18:06:03 UTC
b58039e Wuyin Lin 11 August 2023, 16:52:45 UTC Bugfix: rework P3_input_dim and P3_output_dim for hist_coord 11 August 2023, 16:52:45 UTC
b77febc Phil Jones 11 August 2023, 15:13:42 UTC fix openacc data directive on non-existent ssh_sal array an openacc data transfer on the self-attraction ssh change was outside any conditional for SAL so was operating on a non-existent array if SAL is turned off. This mod changes the location of the data directive so it is within the compute SAL routine and only executed of SAL is turned on 11 August 2023, 15:13:42 UTC
3ca0a18 Mike Kelleher 11 August 2023, 13:30:46 UTC Add micro_p3 to list of possible ptend names 11 August 2023, 13:30:46 UTC
40a5d80 Jon Wolfe 08 August 2023, 23:17:11 UTC Update mapping and domain files for ne30pg2-oRRS18to6v3 08 August 2023, 23:17:11 UTC
b8be65d Gregory Lemieux 31 July 2023, 17:33:20 UTC update fates type names for fates refactor 08 August 2023, 18:35:50 UTC
f7bb269 James Foucar 08 August 2023, 17:08:27 UTC Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: (114 commits) Make chemistry preprocessor processed files permanent for chemistry package superfast_mam5_resus_mom_soag, ridding use of -usr_mech_infile. Fixed cime submodule Update shell_commands for eam-chem_pp test with v3 chem_mech Update use_cases for BGCEXP_LNDATM_CNPRDCTC Rename ncdata file for SCM use cases Fix FIDEAL test - added back ideal_phys_option removed in MAM5 PR Fix issue when ZM is off and reset FAQP to use v2 config Update arm97 and generic SCM to use v3atm Remove prescribed volcanic aerosol and tracer specifier CH4 from v3atm use_case files Run exact-restart wcycl-debug test with 2 threads On pm-cpu only, make default compiler by Intel (from GNU) [bfb] fixes indexing bug in mpas cvmix interface Ensure seasaltaod gets fillvalue at nighttime add alternative impl for tro/str AODSO4 Reset non-default PSTRID to 1 Add back spa as chem package option Update pm-cpu intel compiler version Enable compset specific option for dust_emis_scheme Revert "Merge branch 'tangq/atm/lightning-NOx' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5806)" Add reference for dust emission scheme 2 ... 08 August 2023, 17:08:27 UTC
78a5ea1 noel 07 August 2023, 16:05:20 UTC Merge branch #5845 from E3SM-Project/ndk/machinefiles/pm-cpu-use-intel-by-default (PR #5845) On pm-cpu, change default compiler to Intel 07 August 2023, 16:05:20 UTC
915e929 Wuyin Lin 07 August 2023, 14:47:35 UTC Merge branch 'v3atm/eam/master_MAM5_wetaero_chemdyg' (PR #5781) Three climate changing features, consolidated compsets, and some code cleanup for EAMv3 Add remaining climate changing features for v3 atm. - Improve the aerosol wet removal parameterization (CC for both v2 and v3 compsets). Significantly reduce the aerosol loading overestimation and help decrease the overly strong aerosol radiative forcing. . Use vertical velocity from ZMmp to calculate the (previously prescribed) in-cloud supersaturation, Lagrangian timestep, and pdraft fraction. . Consider the cloud-borne aerosol detrainment. This makes cloud-borne aerosol evolution consistent with the convective cloud condensate. . Reorder the deep convection wet removal and stratiform wet removal as described in: Shan, Y., X., Liu, L., Lin, Z., Ke, Z., Lu (2021): An improved representation of in-cloud wet removal processes in a global climate model and impacts on simulated aerosol vertical profiles, J. Geophys. Res.-Atmos, 126, e2020JD034173. https://doi.org/10.1029/2020JD034173. - Implement MAM5, which adds an additional stratospheric sulfate mode on top of the existing MAM4 aerosol scheme (CC) MAM5 is able to better represent the stratospheric sulfate aerosol and can work with both Simple chemistry (SC) and Full chemistry (FC). MAM5-SC is linked to chemUCI. - Fix the the aqueous chemistry bug where total condensate (liquid +ice) mass mixing ratio was used for the SO2 aqueous chemistry process. The problem is that only liquid water mass mixing ratio should be used here. The bug was found because P3 produces more ice mass which leads to a much larger sulfate production from aqueous chemistry compared to MG2. By working together with Dick Easter, we identified this problem and we also got confirmation from NCAR. - Add compsets with full v3atm configuration, and finalization of it. - Add consolidated v3 compsets and configurations based on v3alpha02. . The compset names, both the aliases and the longnames, retain the format used in V2. For example, F1850, F2010, F20TR have corresponding longnames of 1850_EAM%CMIP6.+, 2010_EAM%CMIP6.+ and 20TR_EAM%CMIP6.+. . The new physics and chemistry from v3atm, including chemUCI, Linozv3, MAM5, VBS-SOA, and ZM enhancements, do not appear in the compset names but are active after this PR. . The new physics and chemistry are indicated in the description of the compsets, and reflected in the new use_case files. . This PR will retire V2 compsets under the same names upon merging. . Additional changes are added to enable or fix nightly tests that will use the new code base along with the consolidated compsets. These include FIDEAL, FAQP, SCM, BGC, clubb-only, chem_pp. . Lightning NOx bugfix that was on this branch was reverted. A revert of revert should be done when v3alpha02 based runs are completed. . Make preprocessed files permanent for v3 chemistry package superfast_mam5_resus_mom_soag. . Some code clean-up. [CC] [NML] Fixes #5713 07 August 2023, 14:47:35 UTC
496e6d4 Andrew M. Bradley 03 August 2023, 18:45:20 UTC EAM/HOMME: Remove -DNC=4 in bld/configure; NC is an unused symbol. 03 August 2023, 18:45:20 UTC
b3454bb Wuyin Lin 03 August 2023, 18:27:57 UTC Make chemistry preprocessor processed files permanent for chemistry package superfast_mam5_resus_mom_soag, ridding use of -usr_mech_infile. 03 August 2023, 18:27:57 UTC
855bd01 Azamat Mametjanov 03 August 2023, 17:21:59 UTC Merge branch 'azamat/tests/superbfb-atm-wcycl' (PR #5717) Add initial superBFB tests for EAM and WCYCL The purpose of this suite is to make sure new code maintains bit-for-bit properties we demand of the model. These properties include: - exact restart: the model should be able to restart during a run with bit-for-bit identical results compared to a model which ran for the same total time without restarting. - MPI-task count invariance: The model should give the same answers between two runs that only differed by the number of MPI tasks used. - OpenMP thread count invariance: The model should give the same answers between two runs that only differ by number of OpenMP threads used. There is a suite for each major component model (`atm`, `ocn`, `ice`, `lnd`, `rof`, and fully-coupled `wcycl`). They cover the standard-resolution grids in both release/optimized and debug configurations. [BFB] 03 August 2023, 17:21:59 UTC
ea8b3b9 Jon Wolfe 03 August 2023, 15:56:23 UTC Merge branch 'vanroekel/ocean/fix-cvmix-indexing-bug' (PR #5842) Fixes indexing bug in mpas cvmix interface There is a small indexing error in the MPAS ocean interface to CVMix. It has only emerged in GPU configurations, but may emerge in cases where minLevelCell is not equal to 1 Fixes #5840 [BFB] 03 August 2023, 15:56:23 UTC
06d37b7 Wuyin Lin 03 August 2023, 12:17:24 UTC Merge branch 'mahf708:add_so4_aods' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5833) EAM: split AODSO4 into tropospheric and stratospheric components This small PR splits AODSO4 into its stratospheric and tropospheric components following previous (v2) practice. Note that there is already "stratospheric sulfate AOD" (from v3) that's not modified by this PR. This implementation has two distinct advantages over the current one from v3: 1) it follows the logic of previous implementation of speciated AODs; 2) it follows the naming scheme of the previous implementation and aligns it with the naming of burdens (SAODVIS vs AODSO4_STR, cf ABURDENSO4_STR). [BFB] 03 August 2023, 12:17:24 UTC
0cf98a8 Wuyin Lin 03 August 2023, 12:04:09 UTC Merge branch 'wlin/atm/v3compsets_alpha02' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5823) Consolidate v3 compsets with v3alpha02 configuration v3atm based simulations have been relying on a combination of physics/chemistry specific compsets and customized run scripts. The run scripts typically contain additional configuration options replacing physics, chem package, chemistry mechanism file, forcing files, and tuning options. In this PR, all the above are consolidated into compsets and the corresponding complete configuration options for the component (EAM). The v3alpha02 configuration is made default for the consolidated compsets. The compset names, both the aliases and the longnames, retain the format used in V2. For example, F1850, F2010, F20TR have corresponding longnames of 1850_EAM%CMIP6.+, 2010_EAM%CMIP6.+ and 20TR_EAM%CMIP6.+. The new physics and chemistry from v3atm, including chemUCI, Linozv3, MAM5, VBS-SOA, and ZM enhancements, do not appear in the compset names. The new physics and chemistry are indicated in the description of the compsets, and reflected in the new use_case files. This PR will retire V2 compsets under the same names upon merging. Additional changes are added to enable or fix nightly tests that will use the new code base along with the consolidated compsets. These include FIDEAL, FAQP, SCM, BGC, clubb-only, chem_pp. [BFB] for all equivalent v3 configurations that previously were controlled via run script. 03 August 2023, 12:04:09 UTC
da80625 Wuyin Lin 02 August 2023, 14:23:11 UTC Fixed cime submodule 02 August 2023, 14:23:11 UTC
a9af24b Wuyin Lin 02 August 2023, 04:32:14 UTC Update shell_commands for eam-chem_pp test with v3 chem_mech 02 August 2023, 04:32:14 UTC
97582a3 Wuyin Lin 02 August 2023, 03:36:31 UTC Update use_cases for BGCEXP_LNDATM_CNPRDCTC 02 August 2023, 03:36:31 UTC
550b65a Wuyin Lin 01 August 2023, 03:29:03 UTC Rename ncdata file for SCM use cases 01 August 2023, 03:29:03 UTC
f980751 Wuyin Lin 01 August 2023, 01:47:11 UTC Fix FIDEAL test - added back ideal_phys_option removed in MAM5 PR 01 August 2023, 01:47:11 UTC
4666e60 Wuyin Lin 31 July 2023, 12:28:35 UTC Fix issue when ZM is off and reset FAQP to use v2 config 31 July 2023, 12:28:35 UTC
c1bf918 Wuyin Lin 31 July 2023, 02:36:12 UTC Update arm97 and generic SCM to use v3atm 31 July 2023, 02:36:12 UTC
b58cc11 Wuyin Lin 30 July 2023, 03:50:50 UTC Remove prescribed volcanic aerosol and tracer specifier CH4 from v3atm use_case files 30 July 2023, 03:50:50 UTC
e6c4d78 Azamat Mametjanov 28 July 2023, 21:31:35 UTC Run exact-restart wcycl-debug test with 2 threads 28 July 2023, 21:31:35 UTC
4fb8edd Robert Jacob 28 July 2023, 17:59:14 UTC Merge branch 'mahf708/rad-diags-fix-AODs' (PR #5817) Make sure AODSS has a fillvalue at night like other OD variables. Technically, it is a bug fix PR, but it is BFB as the bug is in a diagnostic output, and not in anything used internally in the model. [BFB] Fixes #5822 Xref #4800 and #5816 (discussions that prompted this discovery) 28 July 2023, 17:59:14 UTC
782378c Gautam Bisht 15 May 2023, 22:30:56 UTC Removes CLM from module name 27 July 2023, 20:19:34 UTC
f439da9 noel 27 July 2023, 17:41:10 UTC On pm-cpu only, make default compiler by Intel (from GNU) [bfb] 27 July 2023, 17:41:10 UTC
45d843f noel 27 July 2023, 17:26:02 UTC Merge branch E3SM-Project/ndk/machinefiles/pm-update-modulesJul2023b (PR #5826) On pm-cpu and pm-gpu, update module version for craype and cray-mpich 27 July 2023, 17:26:02 UTC
7294b29 James Foucar 27 July 2023, 16:26:55 UTC Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: Instead of hard-coding the small value, set as a parameter. Check if unsat is also too small and treat like it's zero if so update comment in pelayout On pm-cpu, update one PE layout that impacts the ne120 test in the hires suite. Increase the partition count for both ocean and ice to use part files that exist. [bfb] Switch on high-frequency sea ice flux coupling as the default 27 July 2023, 16:26:55 UTC
c52162a Luke Van Roekel 27 July 2023, 13:09:50 UTC fixes indexing bug in mpas cvmix interface 27 July 2023, 13:09:50 UTC
a9b3b00 Walter Hannah 25 July 2023, 18:13:17 UTC bug fix in crm_physics.F90 25 July 2023, 18:13:17 UTC
522051b Jon Wolfe 25 July 2023, 18:12:57 UTC Merge branch 'proteanplanet/seaice/hfdefault' (PR #5813) Switch to high-frequency sea ice turbulent flux coupling as the default for all configurations Switches on high-frequency boundary layer coupling between the atmosphere and sea ice for all configurations of E3SM, where previously it was switched off for standard resolution without (EC30to60E2r2) and with (ECwISC30to60E2r1) ice shelves. [NML] for configurations with EC30to60E2r2 or ECwISC30to60E2r1 [non-BFB] for configurations with EC30to60E2r2 or ECwISC30to60E2r1 25 July 2023, 18:12:57 UTC
235a708 Naser Mahfouz 18 July 2023, 02:19:41 UTC Ensure seasaltaod gets fillvalue at nighttime ` 25 July 2023, 15:39:42 UTC
760e08a Naser Mahfouz 25 July 2023, 15:25:27 UTC add alternative impl for tro/str AODSO4 25 July 2023, 15:25:27 UTC
5092025 Gautam Bisht 24 July 2023, 19:34:57 UTC Merge branch 'peterdschwartz/lnd/fix-o2-unsat-overflow' (PR #5828) Checks if o2_decomp_depth_unsat is too small to avoid triggering an overflow. Fixes #5767 [non-BFB] 24 July 2023, 19:34:57 UTC
77f1df9 James Foucar 24 July 2023, 19:29:15 UTC Remove --account flag for mappy since it doesn't use project tracking 24 July 2023, 19:29:15 UTC
58560f8 noel 24 July 2023, 18:49:44 UTC Merge branch E3SM-Project/ndk/machinefiles/pm-cpu-hires-pelayout (PR #5825) On pm-cpu, update one PE layout that impacts the ne120 test in the hires suite 24 July 2023, 18:49:44 UTC
f55cdaf James Foucar 24 July 2023, 18:49:00 UTC Merge remote-tracking branch 'origin/master' into jasonb5/cime/adds_testing_excludes * origin/master: (47 commits) add outputFieldName to ocean pointwise stats Remove dt from ocn_init_mct CPL: Fix format L spec for summit/ibmgpu compiler. Modified Registry comments of LTS vars add descriptions to LTS variables remove LTS namelist from E3SM build files Add LIBRARIES concept to mpas builds Modified dimension of LTS arrays Fix case of PETSC Fix ocean slibs Remove FindPETSc.cmake, the CIME one is fine updating fates pointer to tag: sci.1.66.2_api.25.5.0 (ema npp fix) removing references to temperature_vars in elm-fates interface updates after merge to master Cleaning up some unused variables Integrating changes from Mark Petersen's PR Added support for implicit bottom drag and vmix Added guard in LTS code Add new file to ocean cmake build Forgot to add a few line in LTS ... 24 July 2023, 18:49:00 UTC
db7d955 James Foucar 24 July 2023, 18:41:17 UTC Update CIME 24 July 2023, 18:41:17 UTC
4a3ba64 Azamat Mametjanov 24 July 2023, 15:50:18 UTC Reset non-default PSTRID to 1 24 July 2023, 15:50:18 UTC
9e83bea Wuyin Lin 22 July 2023, 04:39:25 UTC Add back spa as chem package option 22 July 2023, 04:39:25 UTC
4361928 Wuyin Lin 21 July 2023, 22:26:51 UTC Update pm-cpu intel compiler version 21 July 2023, 22:26:51 UTC
5c5a0d7 Peter Schwartz 21 July 2023, 21:40:14 UTC Instead of hard-coding the small value, set as a parameter. Decreased to 1.e-20 to avoid DIFFs in some tests 21 July 2023, 21:40:14 UTC
5244c09 Wuyin Lin 21 July 2023, 21:24:49 UTC Enable compset specific option for dust_emis_scheme 21 July 2023, 21:24:49 UTC
c0300fa Gautam Bisht 21 July 2023, 21:17:21 UTC Merge branch 'rgknox/lnd/fates-update-api' (PR #5802) This set of changes brings compatibility with FATES up to API 25.5. The main changes to the API update are a change to the FATES parameter file, and modifications to the coupling interface to enable communication with drought deciduous plants. [BFB] except for FATES 21 July 2023, 21:17:21 UTC
5c79ca4 Jon Wolfe 21 July 2023, 16:30:48 UTC Merge branch 'mark-petersen/ocn/fix-pointwise-stats' (PR #5820) Add outputFieldName to ocean pointwise stats The ocean pointwise stats analysis member has been broken because the field name is not communicated correctly to PIO for writing. Current use of pointwise stats results in an error. The problem was that for output streams the variable is named outputFieldName, rather than just fieldName, and the pointwise stats module never initiated outputFieldName. There is an additional field name here because the variable name for ssh, for example, becomes sshPointStats. This problem was found a year ago in the sea ice and corrected in #5160, but was not fixed in the ocean. Fixes #5510 [BFB] 21 July 2023, 16:30:48 UTC
e6513fd Peter Schwartz 20 July 2023, 22:22:09 UTC Check if unsat is also too small and treat like it's zero if so 20 July 2023, 22:22:09 UTC
9096f46 Andrew M. Bradley 20 July 2023, 17:14:09 UTC Merge branch 'ambrad/cpl/nlmaps-fix-format-ibmgpu' (PR #5821) CPL: Fix format L spec for summit/ibmgpu compiler. Fixes a build error in e3sm_gpuomp_next_ibmgpu. [BFB] 20 July 2023, 17:14:09 UTC
ba733c4 Jon Wolfe 20 July 2023, 16:45:50 UTC Merge branch 'jonbob/mpaso/driver-move-dt-retrieval' (PR #5777) Replace dt with 0.0 in ocn_surface_land_ice_fluxes_build_arrays call Currently the variable "dt" is used in subroutine ocn_init_mct in a call to ocn_surface_land_ice_fluxes_build_arrays before it has been set. This can cause errors in debug mode with some compilers. This replaces the variable with 0.0 in the argument list and removes dt from the routine, since it is not otherwise needed. Fixes #5772 [BFB] 20 July 2023, 16:45:50 UTC
0ea3bcf Gautam Bisht 20 July 2023, 16:20:49 UTC Merge branch 'peterdschwartz/lnd/fix-overflow' (PR #5780) If o2_decomp_depth_sat is too small, there's a very large (negative) exponentiation that must be computed that is flagged by overflow checks. Fixes #5767 [BFB] 20 July 2023, 16:20:49 UTC
c369f8b Mark Petersen 18 July 2023, 19:54:27 UTC add outputFieldName to ocean pointwise stats 20 July 2023, 13:54:04 UTC
b2a972f Wuyin Lin 20 July 2023, 05:12:43 UTC Revert "Merge branch 'tangq/atm/lightning-NOx' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5806)" Reverted to maintain the code base for the v3alpha02 configuration. This reverts commit f662a077d272ac55bfac904b0d75aa88a836674b, reversing changes made to 1f6ee31fcafcf41c8b595efb186982963a00400d. 20 July 2023, 05:12:43 UTC
b3ede3e Wuyin Lin 20 July 2023, 05:09:27 UTC Add reference for dust emission scheme 2 20 July 2023, 05:09:27 UTC
46dddb1 noel 19 July 2023, 23:07:18 UTC On pm-cpu and pm-gpu, update module version for craype and cray-mpich Proactive syncing with machine default versions. Does not fix or cause any issue. [bfb] 19 July 2023, 23:07:18 UTC
bb1977f noel 19 July 2023, 23:03:47 UTC update comment in pelayout 19 July 2023, 23:03:47 UTC
d973f0f noel 19 July 2023, 22:58:54 UTC On pm-cpu, update one PE layout that impacts the ne120 test in the hires suite. Increase the partition count for both ocean and ice to use part files that exist. [bfb] 19 July 2023, 22:58:54 UTC
7bea487 James Foucar 19 July 2023, 22:40:54 UTC mpas-ocean: Do not link petsc unless USE_PETSC is on [BFB] 19 July 2023, 22:40:54 UTC
f31dac6 Wuyin Lin 19 July 2023, 19:17:26 UTC Consolidate v3 compsets with v3alpha02 configuration v3atm based simulations have been relying on a combination physics/chemistry specific compsets and customized run scripts. The run scripts typically contain additional configuration otions replacing physics, chem package, chemistry mechanism file, forcing files, and tuning options. In these PR, all the above are consolidate into compsets and the corresponding complete configuration options for the component (EAM). The v3alpha02 configuration is made default for the consolidate compsets. The compset names, both the aliases and the longnames, retain the format used in V2. For example, F1850, F2010, F20TR have corresponding longnames of 1850_EAM%CMIP6.+, 2010_EAM%CMIP6.+ and 20TR_EAM%CMIP6.+. The new physics and chemistry from v3atm, including chemUCI, Linozv3, MAM5, VBS-SOA, and ZM enhancements, do not appear in the compset names. The new physics and chemistry are indicated in the description of the compsets, and reflected in the new use_case files. This PR will retire V2 compsets under the same names upon merging. [BFB] for all equivalent v3 configurations that previously were controlled via run script. 19 July 2023, 19:17:26 UTC
c06548c Gautam Bisht 19 July 2023, 18:53:28 UTC Merge branch 'tktesfa2014/lnd/fix_lunit_restart_error' (PR #5385) The changes in this branch have fixed an error related to the land unit fraction coming from the model restart file. [BFB] would be non-BFB for transient runs with topo units but there are none of those. 19 July 2023, 18:53:28 UTC
8e7bb6b Naser Mahfouz 18 July 2023, 02:19:41 UTC Ensure seasaltaod gets fillvalue at nighttime 19 July 2023, 15:59:15 UTC
48662e7 Xylar Asay-Davis 19 July 2023, 08:02:38 UTC Remove dt from ocn_init_mct We don't want to accumulate land-ice mass and heat during init, so we call `ocn_surface_land_ice_fluxes_build_arrays()` with `dt=0`. 19 July 2023, 08:02:38 UTC
bc781ef Andrew M. Bradley 19 July 2023, 02:58:02 UTC CPL: Fix format L spec for summit/ibmgpu compiler. 19 July 2023, 02:58:02 UTC
e41d49b Jon Wolfe 18 July 2023, 19:05:33 UTC Merge branch 'gcapodag/mpaso/lts' (PR #5460) Add Local Time-Step Capability to MPAS-Ocean Included a local time-stepping (LTS) method for the barotropic ocean that uses an operator splitting approach of the fast and slow tendencies. The slow tendencies are advanced with an explicit Euler step whereas the fast ones are advanced with an LTS method of order three based on a strong stability preserving RK method. The scheme is overall first order accurate in time. The tendencies for the fast modes are implemented ad-hoc for LTS in a way that allows us to avoid the use of multiple blocks as in our initial implementation. At this point, LTS is being added as an MPAS-Standalone feature. LTS was created for ICOM-related coastal inundation studies in ocean standalone mode, and only runs efficiently for single layer simulations. It doesn’t make sense to use LTS for layered-ocean simulations, which includes all E3SM climate simulations. LTS only provides substantial speed-ups for single layer simulations because it does not yet take advantage of barotropic/baroclinic splitting. For layered-ocean simulations, the split time-stepping schemes are more efficient. [BFB] - not used in E3SM 18 July 2023, 19:05:33 UTC
8e31009 Andrew M. Bradley 18 July 2023, 17:41:51 UTC Merge branch 'ambrad/cpl/nlmap' (PR #5691) See seq_nlmap_mod.F90 header doc for objective, usage, and method. Add an ERS test to e3sm_integration that, using a testmod, exercises all supported nonlinear maps, outputs diagnostic data (using a namelist option), and runs a POSTRUN_SCRIPT to check that the diagnostics values are good. e3sm_integration passes on Chrysalis but with namelist diffs. [BFB] except for the new e3sm_integration test ERS_Ld3.ne30pg2_r05_EC30to60E2r2.WCYCL1850.eam-nlmaps [NML] for essentially all tests 18 July 2023, 17:41:51 UTC
7fcb742 James Foucar 18 July 2023, 16:46:00 UTC Merge branch 'jgfouca/fix_cmake_module_path' into master (PR #5785) Cmake build system: Fix CMAKE_MODULE_PATH Make a new area to put E3SM cmake modules (components/cmake/modules). Append this dir to CMAKE_MODULE_PATH. Also, append the correct CIME dir to CMAKE_MODULE_PATH. It will come after the E3SM module dir so E3SM will take precedence. Fix MPAS use of SLIBS. Fixes #5783 [BFB] * jgfouca/fix_cmake_module_path: Add LIBRARIES concept to mpas builds Fix case of PETSC Fix ocean slibs Remove FindPETSc.cmake, the CIME one is fine Cmake build system: Fix CMAKE_MODULE_PATH 18 July 2023, 16:46:00 UTC
18645df Jason Boutte 17 July 2023, 21:49:54 UTC Adds testing excludes 17 July 2023, 21:49:54 UTC
df9725e Andrew M. Bradley 17 July 2023, 19:04:44 UTC Merge branch 'ambrad/eam/fix-real-indices' (PR #5805) EAM: Fix use of real(r8) rather than integer in index arrays. Fixes index type to be integer, as intended. e3sm_developer passes on Chrysalis. [BFB] 17 July 2023, 19:04:44 UTC
dd4b05e Peter Schwartz 17 July 2023, 18:56:54 UTC Merge branch 'bishtgautam/lnd/fix-units' (PR #5705) Corrects the units of time-averaged solar fluxes. Fixes #5704 [BFB] 17 July 2023, 18:56:54 UTC
0e8ca45 Peter Schwartz 17 July 2023, 18:56:06 UTC Merge branch 'bishtgautam/lnd/restart'(PR #5699) In ELM restart file, the cohort dimension is only defined when FATES is turned on. This code modification allows ELM to write elm.rh0 when hist_empty_htapes=.true. is set in user_nl_elm. Fixes #5694 [BFB] 17 July 2023, 18:56:06 UTC
25f1726 James Foucar 17 July 2023, 14:55:56 UTC Merge branch 'sarats/machines/remove-cnl-cmake' into master (PR #5745) Remove CNL specific CMake macros Removing CMake macro file used on old Cray supercomputers using Catamount OS. Updated OS entry for OLCF machines. If any other machines are still reliant on any flags in the deleted macro file, suggest moving those to specific compiler_machine.cmake macro file. [BFB] 17 July 2023, 14:56:32 UTC
64bd85c Sarat Sreepathi 17 July 2023, 03:48:48 UTC Frontier/Crusher: AMD compiler add NETCDF paths 17 July 2023, 03:48:48 UTC
47712cc Giacomo Capodaglio 16 July 2023, 21:41:13 UTC Modified Registry comments of LTS vars 16 July 2023, 21:41:13 UTC
f662a07 Wuyin Lin 15 July 2023, 22:04:19 UTC Merge branch 'tangq/atm/lightning-NOx' into v3atm/eam/master_MAM5_wetaero_chemdyg (PR #5806) Fix lightning NOx emission bug During v3atm aerosol-chemistry integration, "NO" was removed from the external foring list of chemistry mechanism files ending in _vbs.in. This means that the lightning NOx emissions won't be used by the simulations using these mechanisms. This PR corrects this bug. [non-BFB] 15 July 2023, 22:04:19 UTC
1817433 Mark Petersen 14 July 2023, 19:18:48 UTC add descriptions to LTS variables 14 July 2023, 19:34:37 UTC
8b9c493 Mark Petersen 14 July 2023, 18:53:11 UTC remove LTS namelist from E3SM build files 14 July 2023, 18:53:11 UTC
110bd91 Peter Schwartz 13 July 2023, 21:27:22 UTC Merge branch 'jayeshkrishna/elm/add_missing_levleaf_dim'(PR #5748) Adding missing fates_levleaf dim, which is used for defining the fates_levleaf variable This PR is non-BFB for FATES tests. [non-BFB] 13 July 2023, 21:27:22 UTC
5825ba7 James Foucar 13 July 2023, 19:30:42 UTC Add LIBRARIES concept to mpas builds Use target_link_libraries(comp PUBLIC libs) to ensure libs gets added to the e3sm link line. 13 July 2023, 19:30:42 UTC
130668c Giacomo Capodaglio 13 July 2023, 18:39:08 UTC Modified dimension of LTS arrays From 5 to 3. 13 July 2023, 18:39:08 UTC
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