| d3c302b | Andrew M. Bradley | 20 October 2023, 01:16:36 UTC | Hommexx: Remove redundant HOMMEXX_ENABLE_GPU definition. This symbol was being defined in both Hommexx_config.h and config.h. The distinction between these two is subtle but definite. The first is for symbols used only in the Hommexx code. The second is for symbols used in both Hommexx and Homme, the latter including Homme dycores built for BFB testing with Hommexx. Since the symbol is redundantly defined (leading to a preprocessor warning about this), one must be removed. It's used in Homme, so the Hommexx_config.h.in instance should be removed. | 24 October 2023, 01:01:56 UTC |
| f46aa31 | Andrew M. Bradley | 20 October 2023, 00:53:13 UTC | Homme: Fix potential bad access to an array. | 24 October 2023, 01:01:56 UTC |
| e6a628d | Andrew M. Bradley | 19 October 2023, 21:49:39 UTC | Homme: Add USE_MPI_RUN_SCRIPT to standalone system. On exotic machines, none of the MPI run lines in testing-utils.sh work. Rather than adding more to that script, add a new CMake variable, USE_MPI_RUN_SCRIPT, that points to a run script. Use this new feature to get CTest working on Summit/Ascent. | 24 October 2023, 01:01:56 UTC |
| 8942c1d | Andrew M. Bradley | 05 October 2023, 20:39:25 UTC | Homme(xx)/SL: Add SL-transport feature to doubly periodic mode. Runs in F90 and C++ dycores with a new BFB test to verify consistency. | 24 October 2023, 01:01:56 UTC |
| 6174a70 | Azamat Mametjanov | 26 September 2023, 00:05:58 UTC | Merge branch 'azamat/machines/add-init-snan-intel-debug' (PR #5801) Initialize arrays and scalars to signaling NaNs for Intel in debug mode Add `-init=snan,arrays` to Intel's debug-compile flags. Also, initialize EAM's and ELM's uninitialized arrays, which were flagged by compiler's run-time checks. [BFB] | 26 September 2023, 00:05:58 UTC |
| b9b3764 | Azamat Mametjanov | 25 September 2023, 23:58:43 UTC | Add ncol in aero_model.F90 for pm-cpu intel | 25 September 2023, 23:58:43 UTC |
| 4653e61 | James Foucar | 25 September 2023, 18:48:30 UTC | Merge branch 'jgfouca/cime_update_2023_09_21' into master (PR #5944) ... to b10d452d1073d1d06d10a6b3269e9f35a872bb50 Changes 1. support wildcard for machine and compiler name in testname syntax 2. Add new 'perf' test property: This will be used to mark suites as performance test suites. 3. PFS tests should always save timing Fixes 1. env_batch: Fix flag/val separator. Fixes submit commands on some platforms 2. Moves check_input_data to SystemTestsCommon when running a test. Should fix missing data files when pe-layout changes for tests. 3. ERIO fix: Removes .* between hist_file_extension and suffix in get_all_hist_files. [BFB] * jgfouca/cime_update_2023_09_21: CIME submodule update | 25 September 2023, 18:48:30 UTC |
| f1fe818 | Jon Wolfe | 25 September 2023, 17:33:57 UTC | Merge branch 'scalandr/fix_submeso_standalone' (PR #5892) Fix for submesoscale parametrization in standalone At the moment, the submesoscale parametrization does not work properly in MPAS-O standalone, that is even if config_submesoscale_enable = .true. the parametrization is not active. To solve this issue, the subroutine ocn_submesoscale_compute_velocity() has to called in src/mode_forward/mpas_ocn_forward_mode.F. [BFB] | 25 September 2023, 17:33:57 UTC |
| a746149 | Jon Wolfe | 22 September 2023, 16:00:33 UTC | Merge branch 'jonbob/seaice/fix-ir-zero-check' (PR #5252) Fix floating-point exception in MPASSI incremental remap code High-res (ne120pg2_r0125_oRRS18to6v3.WCYCL1950) B-case tests on summit using gnu have been failing with a floating-point exception that points to a line in the seaice incremental remap code: if (abs(massTracerProd) > 0.0_RKIND) then @whannah1 reported the issue and has found that the error occurs when massTracerProd is extremely small, so its inverse ends up being extremely large. He also found that it can be avoided by replacing the 0.0 with a tiny number. However, after discussion this PR fixes the issue by removing the reciprocal calculation and dividing by the mean0 (and massTracerProd) quantities instead -- @ambrad thank you for the suggestion. Fixes #5463 [non-BFB] | 22 September 2023, 16:00:33 UTC |
| 4311d16 | Robert Jacob | 22 September 2023, 03:47:48 UTC | Merge branch 'rljacob/docs/addgh-pages' (PR #5942) Add infrastructure to build markdown-based documentation located in each components "docs" directory into a single web-page of documentation. Makes use of mkdocs-monorepo-plugin. Also add a skeleton of documentation subdirs and markdown files for EAM, ELM and MOSART. Also add a github action to build and deploy the documentation on e3sm-project.github.io/e3sm whenever master is updated. And an action to build the docs on every PR. [BFB] | 22 September 2023, 03:47:48 UTC |
| ba16f5b | Azamat Mametjanov | 22 September 2023, 02:47:26 UTC | Avoid uninitialized array references in v3atm | 22 September 2023, 02:47:26 UTC |
| 7e3658e | Robert Jacob | 22 September 2023, 01:08:16 UTC | Don't specify repo/branch to check out Don't specify which repo/branch to check out. Action will do the right thing. Co-authored-by: Naser Mahfouz <naser.mahfouz@pnnl.gov> | 22 September 2023, 01:08:16 UTC |
| a1e0c08 | Robert Jacob | 21 September 2023, 23:20:41 UTC | Remove submodule checkout in pages workflow Remove submodule checkout in pages workflow. Will be faster. | 21 September 2023, 23:20:41 UTC |
| 97092c8 | Robert Jacob | 21 September 2023, 23:19:32 UTC | Rename gh-pages workflow file Rename gh-pages workflow file to e3sm-gh-pages.yml | 21 September 2023, 23:19:32 UTC |
| 19e571e | Robert Jacob | 21 September 2023, 23:15:44 UTC | Apply suggestions from code review Modify workflow to operate on both PR creation and pushes to master. Update version of checkout action. Co-authored-by: Naser Mahfouz <naser.mahfouz@pnnl.gov> | 21 September 2023, 23:15:44 UTC |
| 3b6253d | Azamat Mametjanov | 24 July 2023, 23:30:02 UTC | Add more array-init in cam_diagnostics.F90 | 21 September 2023, 20:00:51 UTC |
| c3b3451 | Azamat Mametjanov | 12 July 2023, 00:32:07 UTC | Init uninitialized arrays in ELM | 21 September 2023, 20:00:50 UTC |
| bb43968 | Azamat Mametjanov | 12 July 2023, 00:28:17 UTC | Additional initializations of un-init arrays in EAM | 21 September 2023, 20:00:50 UTC |
| 31040bf | Azamat Mametjanov | 11 July 2023, 03:11:08 UTC | Init uninitialized arrays in HOMME | 21 September 2023, 20:00:50 UTC |
| 8003975 | Azamat Mametjanov | 11 July 2023, 03:08:02 UTC | Init uninitialized arrays in EAM | 21 September 2023, 20:00:50 UTC |
| 0fd0583 | Azamat Mametjanov | 11 July 2023, 03:01:10 UTC | Initialize arrays and scalars to signaling NaNs for intel in debug mode | 21 September 2023, 20:00:50 UTC |
| d6b098d | noel | 21 September 2023, 18:12:24 UTC | Merge branch E3SM-Project/ndk/machinefiles/perlmutter-pelayout-cleanup (PR #5934) Cleanup pelayouts for NERSC machines | 21 September 2023, 18:12:24 UTC |
| c3f7cb3 | noel | 21 September 2023, 18:11:38 UTC | Merge branch E3SM-Project/ndk/machinefiles/perlmutter-update-cprnc (PR #5933) For NERSC machines, built a new cprnc with GNU and updated the cprnc path | 21 September 2023, 18:11:38 UTC |
| e61ff92 | Gautam Bisht | 21 September 2023, 18:06:11 UTC | Merge branch 'peterdschwartz/lnd/remove-nan-from-v2-restart' (PR #5811) Replaced the NaN values for TWS_MONTH_BEGIN with a fill value of `1.e+36` in the elm restart file. Fixes #5665 | 21 September 2023, 18:06:11 UTC |
| f352596 | James Foucar | 21 September 2023, 18:00:00 UTC | CIME submodule update ... to b10d452d1073d1d06d10a6b3269e9f35a872bb50 Changes 1) gpu_enabled needs to be true only when gpu is used 2) support wildcard for machine and compiler name 3) Add new 'perf' test property: This will be used to mark suites as performance test suites. 4) PFS tests should always save timing Fixes 1) env_batch: Fix flag/val separator. Fixes submit commands on some platforms 2) Moves check_input_data to SystemTestsCommon when running a test. Should fix missing data files when pe-layout changes for tests. 3) ERIO fix: Removes .* between hist_file_extension and suffix in get_all_hist_files. [BFB] | 21 September 2023, 18:00:00 UTC |
| 2271d8a | Robert Jacob | 20 September 2023, 19:48:05 UTC | Add more installs to workflow. Need to add more python modules to the pip install command | 20 September 2023, 19:48:05 UTC |
| 1a37666 | Robert Jacob | 20 September 2023, 19:18:39 UTC | Update repo in gh-pages Update repo in gh-pages from fork to main repo | 20 September 2023, 19:18:39 UTC |
| 716ebbe | Robert Jacob | 20 September 2023, 19:05:18 UTC | Change Intro to Introduction Change Intro to Introduction in ELM, EAM and main | 20 September 2023, 19:05:18 UTC |
| 24bdb5e | Robert Jacob | 20 September 2023, 18:27:53 UTC | Add docs skeleton for MOSART Add docs skeleton for MOSART and include it in the main docs | 20 September 2023, 18:27:53 UTC |
| 433c4f3 | Robert Jacob | 20 September 2023, 05:13:04 UTC | Add themes and extensions Add a theme to start with and some useful mkdocs extensions | 20 September 2023, 05:13:04 UTC |
| 5c23495 | Robert Jacob | 20 September 2023, 05:12:17 UTC | Add EAM documentation skeleton Add EAM documentation skeleton. subdirs, index.md and mkdocs.yml | 20 September 2023, 05:12:17 UTC |
| 65c6976 | Robert Jacob | 20 September 2023, 04:53:15 UTC | Remove out-of-date eam/doc dir Remove out-of-date eam/doc dir which only had old ChangeLog and ReleaseNotes (no actual docs) | 20 September 2023, 04:53:15 UTC |
| d945092 | Robert Jacob | 20 September 2023, 04:11:03 UTC | Add tech and dev to ELM index Add tech and dev guide skeleton to ELM index | 20 September 2023, 04:11:03 UTC |
| f2aa4ea | Robert Jacob | 20 September 2023, 04:01:28 UTC | Add more basic structure for ELM docs Add more basic structure for ELM docs including tech and dev guid subdirs change users-guide to user-guide | 20 September 2023, 04:01:28 UTC |
| 2278000 | jayeshkrishna | 19 September 2023, 20:07:55 UTC | Merge branch 'jayeshkrishna/share/support4spio_legacy' (PR #5919) The Fortran interface implementation in SCORPIO was recently refactored but users still have the option to use the legacy/old Fortran interface implementation. Adding support in CIME for the SCORPIO legacy Fortran interface [BFB] | 19 September 2023, 20:07:55 UTC |
| 28426b9 | James Foucar | 19 September 2023, 15:16:32 UTC | Merge branch 'jgfouca/cmake_fix_sourcemods_rebuild' into master (PR #5928) CMake build system: Fix SourceMods rebuild detection Prior to this change, if you went to an already-built case and made a SourceMod change, then went to the build dir and re-ran 'make', the SourceMod would not be picked up. On some systems, even re-running case.build would not pick up the change. Fixes #5924 [BFB] * jgfouca/cmake_fix_sourcemods_rebuild: CMake build system: Fix SourceMods rebuild detection | 19 September 2023, 15:16:32 UTC |
| feb8b3c | noel | 19 September 2023, 03:46:32 UTC | Remove several pelayout entries for cori-knl and cori-haswell. Correct a mistake for one pm-cpu pelayout where CPL_PSTRID was 1 instead of 8. | 19 September 2023, 03:46:32 UTC |
| efda26c | noel | 19 September 2023, 01:47:45 UTC | For NERSC machines, built a new cprnc with GNU and updated the cprnc path. [bfb] | 19 September 2023, 01:47:45 UTC |
| 1bfc7fc | James Foucar | 18 September 2023, 17:34:58 UTC | Merge branch 'jgfouca/mpas_common_lib_fix' into master (PR #5923) MPAS: Change common lib from OBJECT to STATIC Fixes GPU multiple def errors. Fixes #4903 [BFB] | 18 September 2023, 17:34:58 UTC |
| 3f56099 | James Foucar | 15 September 2023, 20:27:53 UTC | CMake build system: Fix SourceMods rebuild detection Prior to this change, if you went to an already-built case and made a SourceMod change, then went to the build dir and re-ran 'make', the SourceMod would not be picked up. On some systems, even re-running case.build would not pick up the change. [BFB] | 15 September 2023, 20:27:53 UTC |
| 84e5056 | Wuyin Lin | 14 September 2023, 12:22:06 UTC | Merge branch 'wlin/atm/fix_1pctco2_linozfile' (PR #5926) Fix linoz data file for 1pctCO2 use_case PR #5860 updated linoz data files for use cases. But the PR did not involve the use_case file for WCYCL1850-1pctCO2 as it was introduced at a later time. This fixes WCYCL1850-1pctCO2 tests, though some machines were able to run with the old file. [non-BFB] only for compy and anvil prod tests that were able to run with the old file | 14 September 2023, 12:22:06 UTC |
| a021604 | Robert Jacob | 14 September 2023, 02:20:36 UTC | Merge branch 'mkstratos/tests/change-tsc-compset' (PR #5873) Revert TSC non-b4b test to use the F2010 compset With the fix in MPAS-SI: "Corrects thin ice/snow treatment of enthalpy and other tracers" (#5630) the TSC test can now generate a baseline with dtime=1 using MPAS-SI [non-BFB] only for TSC test | 14 September 2023, 02:20:36 UTC |
| 8f412c6 | Wuyin Lin | 13 September 2023, 23:27:48 UTC | Fix linoz data file for 1pctCO2 use_case | 13 September 2023, 23:27:48 UTC |
| 38cb8e0 | Wuyin Lin | 13 September 2023, 22:38:14 UTC | Merge branch 'oksanaguba/clubb-shflx' (PR #5009) Fix surface heat flux conversion and use more accurate theta_l formulation in CLUBB Two fixes in this PR: 1. change how SHFLX is used in clubb to make it consistent with clubb thermodynamic variable. 2. Redefine thetal to not to use an approximation https://glossary.ametsoc.org/wiki/Liquid_water_potential_temperature A series of runs was performed first with fix 1 and then with both 1 and 2. Using clubb energy fixer as a measure, fix 1 and fixes 1+2 reduce the fixer. Also, 1+2 is the best option among the two. [non-BFB] for any active atmosphere with clubb | 13 September 2023, 22:38:14 UTC |
| 887b6ff | Wuyin Lin | 13 September 2023, 22:35:49 UTC | Merge branch 'mingxuanwupnnl/atm/prsd_oxid_for_VBS_MAM5' (PR #5887) Use prescirbed oxidants of corresponding time period for VBS SOA and MAM5 Current v3alpha02 uses prescribed oxidants (O3, OH, NO3) of 1995 for VBS SOA and MAM5 for all historical/amip, F2010, and PiControl runs. This PR improves this by using the file of corresponding time period. The file proposed to use is from v1 and v2 default setting. [CC] [NML] | 13 September 2023, 22:35:49 UTC |
| 6d8f872 | Wuyin Lin | 13 September 2023, 22:32:57 UTC | Merge branch 'wlin/atm/revert_revert_lightningNoxFix' (PR #5867) Revert the revert of lightning NOx bug fix and rename chem package This is to reactivate the bug fix. It was merged but then reverted to maintain v3alpha02 code base. The campp autogenerated files associated with the updated mechanism are also committed to let the bug fix take effect. The chem package superfast_mam5_resus_mom_soag is renamed as chemuci_linozv3_mam5_vbs, along with other changes in the codes and build scripts accordingly. [CC] [NML] | 13 September 2023, 22:32:57 UTC |
| 6e74648 | Wuyin Lin | 13 September 2023, 22:28:11 UTC | Merge branch 'jinboxie/rebase_master/eam/master_MAM5_wetaero_chemdyg_add_linoz_new' (PR #5860) Implementation of the UCI vertical interpolation and forcing for Linoz Implement the UCI vertical interpolation and forcing to Linoz. The rationale behind it is that the linoz in e3sm currently use the linear interpolation that does not conserve mass. The UCI interpolation is implemented to remedy this problem and the associated forcing is also implemented. [CC] [NML] | 13 September 2023, 22:28:11 UTC |
| 243f3fd | Wuyin Lin | 13 September 2023, 22:25:13 UTC | Merge branch 'mahf708:dms-emis-scale' (PR #5918) Add dms emis scale factor Add a DMS emission scaling factor as a namelist parameter [BFB] [NML] | 13 September 2023, 22:25:13 UTC |
| d0e588f | Wuyin Lin | 13 September 2023, 22:21:39 UTC | Merge branch 'mahf708:eam/Mass_at_diags' (PR #5862) Add select Mass_at_pressure 2D fields for 7 aerosol species Adds output fields for 2D Mass_at_pressure fields for 7 aerosol species in lieu of their 3D counterparts. Since the move to get rid of 3D Mass_aerosol fields from the standard output in the upcoming simulations, aerosol developers and domain scientists wanted the 2D equivalent at select pressure levels. Previously, we added the column-integrated quantities as replacement, now we add vertical slices as well. None so far is added to the default output. I elected to add only five levels for now, but it should be relatively easy to expand this or change the levels. We could also expand this to non-aerosol species, e.g., gaseous precursors if needed. [BFB] | 13 September 2023, 22:21:39 UTC |
| acfcf76 | Wuyin Lin | 13 September 2023, 14:16:21 UTC | Fix line continuation that fails nvidia tests | 13 September 2023, 14:16:21 UTC |
| 51dd660 | Wuyin Lin | 12 September 2023, 17:50:10 UTC | Fix reference to unallocated array wrksrf | 12 September 2023, 17:50:10 UTC |
| 1ca4f00 | Naser Mahfouz | 12 September 2023, 02:29:25 UTC | fix namelist-build for select tests As suggested by wlin7 | 12 September 2023, 02:29:25 UTC |
| 21aa5d3 | James Foucar | 11 September 2023, 17:28:42 UTC | MPAS: Change common lib from OBJECT to STATIC Fixes GPU multiple def errors. [BFB] | 11 September 2023, 17:28:42 UTC |
| 230ddeb | Oksana Guba | 11 September 2023, 17:15:55 UTC | Merge branch 'origin/oksanaguba/eam/rr-diagnostics' (PR #4599) Improving energy diagnostics: The idea is to compare dTE (difference of energy before phys step and energy after phys step) versus fluxes at each physics time step using globally integrated quantities. We do not have such diagnostics in EAM, and it was shown that because of that packages can introduce undetected leaks into the model. In the same way in this PR we compare differences of total mass of water, using variables dWater_step (dW for phys time step) and dWater_flux (water fluxes). Enable testing with print_additional_diagn (a new namelist var) for new global diagnostics. The variable controls additional calculations, including new gmean call. Use post processing python the same way it is done for mass conservation by AMB. About water mass: the current state of the model has leaks that are much bigger than roundoff. One source of leaks is qneg4 that acts on cflx. Another significant known leak is in clubb. Clubb leak is fixed by mass_borrower (when active, controlled by use_mass_borrower). With use_mass_borrower and ignoring qneg4 on cflx, (dWater_step - dWater_flux)/TotWaterMass = 1e-16 [kg/m2 / kg/m2] for some short ne4 run. I decided to turn on this new diagnostics in a way that qneg4 influence on cflx is ignored, but with use_mass_borrower=.false. . The reason is that we know about qneg4, and qneg4 on cflx leads to significant and very variable leaks (which makes analysing statistics hard), but turning on use_mass_borrower will potentially mask not only clubb issue, but other leaks (since mass borrower, when active, is active for all packages at the same time). Other known issues in the model -- infrequent mass leaks from MG2 and ZM, where ZM leaks not only at the column level, it also triggers a hard clipping limiter in cam_export(). I decided to not to use column checks in this PR. Currently we are not running with column mass/energy checks in any tests. Turning them on would require another python postprocessing script. This new global diagnostics accounts for column leaks anyway. [bfb] but a new SMS test (no new build) | 11 September 2023, 17:15:55 UTC |
| 643afd1 | Oksana Guba | 08 September 2023, 18:54:08 UTC | lower tolerances | 08 September 2023, 18:54:08 UTC |
| 97b1ed3 | mahf708 | 07 September 2023, 19:10:03 UTC | add dms_emis_scale to namelist | 07 September 2023, 21:45:38 UTC |
| 4771ef4 | Oksana Guba | 07 September 2023, 21:40:55 UTC | remove a new var from each nl | 07 September 2023, 21:40:55 UTC |
| 39b5b36 | Aaron Donahue | 07 September 2023, 21:07:51 UTC | Merge branch 'aarondonahue/update_livermore_computing_machine_files' (PR #5769) Updates the livermore computing machine config entries to match the current 2023-09-07 configuration of the machines. [BFB] | 07 September 2023, 21:07:51 UTC |
| fef4483 | Aaron Donahue | 07 September 2023, 20:49:25 UTC | Update the Livermore Computing machine entries Updates the livermore computing machine config entries to match the current 2023-09-07 configuration of the machines. | 07 September 2023, 20:49:25 UTC |
| 82c581e | Jon Wolfe | 07 September 2023, 18:09:40 UTC | Merge branch 'trhille/mali/develop-230808' (PR #5857) Update MALI version This merge includes numerous updates to MALI. The major updates include: * Allow mask calving and physically based calving laws to be used simultaneously. * Prevent basal melting in subglacial lakes. * Use 3D thermal forcing field to drive grounded marine terminus melt parameterization. Minor changes include: * Updated Albany input file * Allow restore_calving_front to be applied after a calving law is applied * Add an option for restore_calving_front to allow retreat * Add totalFaceMeltingFlux to global and regional stats * Limit velocity to user-defined maximum instead of calving fast-flowing ice when there is an instability. * Fix treatment of von Mises stress on extended cells. * Mask out floating ice for coupling to sea level model. * Check that flow rate parameter is not constant when using von Mises calving. * Fix grounded marine melting routine in order to pass decomposition tests. * Calculate ismip6 retreat parameterization rate on initial time solve to be consistent with other calving routines. * Calculate cellMask on initial solve for coupling with sea level model. * Halo update during von Mises calving routine to pass decomposition tests. * Change stride used in velocity solver interface. * Bug fix involving invalid cell IDs in velocity solver interface. [NML] [non-BFB] for cases with MALI | 07 September 2023, 18:09:40 UTC |
| 99d0d69 | jayeshkrishna | 07 September 2023, 18:04:25 UTC | Add support for SPIO legacy interface Adding support for SCORPIO Fortran legacy interface | 07 September 2023, 18:04:25 UTC |
| 679c64f | James Foucar | 07 September 2023, 18:01:21 UTC | Merge branch 'jgfouca/change_ocean_petsc_libs' into master (PR #5824) * jgfouca/change_ocean_petsc_libs: Add MPASO_USE_PETSC to mpaso config_component.xml | 07 September 2023, 18:01:21 UTC |
| e2245dd | Naser Mahfouz | 07 September 2023, 17:11:45 UTC | add dms emis scale factor | 07 September 2023, 17:11:45 UTC |
| eb0f0c9 | Benjamin Hillman | 06 September 2023, 21:57:51 UTC | Merge remote-tracking branch 'tcclevenger/valgrind_fix_for_eamxx' (#5915) In EAMxx, COSP is called without allocating cospOUT%isccp_meantb. Every instance in EAM's cosp.F90 we ask associated(cospOUT%isccp_meantb) before accessing the array, except here where we ask for it's size, leading to a valgrind error. Solution is just to ask associated(cospOUT%isccp_meantb) before asking for the array size. [BFB] | 06 September 2023, 21:57:51 UTC |
| 6ede88d | tcclevenger | 05 September 2023, 21:04:28 UTC | Verify array is allocated before accessing size attribute | 05 September 2023, 21:04:28 UTC |
| f183a7c | Naser Mahfouz | 02 September 2023, 03:11:54 UTC | move aerosol_idx inside routines move aerosol_idx inside routines to avoid threading safety issues and race conditions uncovered during integration tests (h/t to Wuyin for suggesting this fix right away) | 02 September 2023, 03:11:54 UTC |
| 86f7e8b | Jon Wolfe | 01 September 2023, 16:04:39 UTC | Merge branch 'sbrus89/ocn/parabolic_bowl' (PR #5889) Add parabolic bowl test case This is an init mode only PR that creates the initial conditions for a parabolic bowl test case used to test wetting and drying. Used only by mpas-ocean standalone. [BFB] | 01 September 2023, 16:04:39 UTC |
| 908f55d | Jon Wolfe | 31 August 2023, 18:24:24 UTC | Merge branch 'cbegeman/ocn/new-se-upwind-feature' (PR #5829) New upwinded advection feature for split-explicit time integrator This PR adds the option to use upwinded advection with the split-explicit time integrator. Formerly, upwinded advection was only available with the RK4 time integrator. For the barotropic subcycle's SSH predictor and corrector steps, the barotropic velocity is first computed on edges, then used to determine the water column thickness on edges (either centered or upwinded), then both barotropic velocity and water column thickness on edges is used to compute the SSH tendency on cells. We also compute the normal velocity correction factor using layerThickEdgeFlux, which is updated if upwinded advection is used. Upwinding of the water column thickness is done with a new diagnostic subroutine, ocn_diagnostic_solve_wctEdge, which is modeled after ocn_diagnostic_solve_layerThicknessEdge. [BFB] stealth | 31 August 2023, 18:24:24 UTC |
| 7f97076 | xie7 | 31 August 2023, 06:41:42 UTC | Edit minor bug in tracer_data.F90 | 31 August 2023, 06:41:42 UTC |
| 6ec8582 | xie7 | 31 August 2023, 06:32:49 UTC | Edit the tracer to have wrk_in for ch4_avg_srf input | 31 August 2023, 06:32:49 UTC |
| 02ca256 | xie7 | 31 August 2023, 00:01:07 UTC | Edit the comments for padding and minor issue of cnt. | 31 August 2023, 00:01:07 UTC |
| b6cc931 | xie7 | 30 August 2023, 22:53:09 UTC | Edit the code to add the ch4_avg_srf that is missing in the previous code. BFB change. | 30 August 2023, 22:53:09 UTC |
| aa5535b | Wuyin Lin | 30 August 2023, 14:00:04 UTC | Add explicit if-condition on referening pint used only by linoz | 30 August 2023, 14:00:04 UTC |
| 3516f7d | Wuyin Lin | 30 August 2023, 12:25:10 UTC | Fix reading and interpolation bugs of zonal mean surface tracers that fail debug and PET/PEM tests | 30 August 2023, 12:25:10 UTC |
| ff9157c | Jon Wolfe | 29 August 2023, 22:59:46 UTC | Add new stealth test and corresponding testdef | 29 August 2023, 22:59:46 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 |
| e974b5c | Robert Jacob | 28 August 2023, 03:17:16 UTC | Add skeleton for ELM Add docs skeleton for ELM and verify it renders. | 28 August 2023, 03:17:16 UTC |
| 0213140 | Robert Jacob | 27 August 2023, 05:30:49 UTC | Add gh-pages build and publish workflow | 27 August 2023, 05:30:49 UTC |
| 63edd77 | Robert Jacob | 27 August 2023, 05:19:13 UTC | Tell .gitignore to ignore the site dir | 27 August 2023, 05:19:13 UTC |
| 73cef25 | Robert Jacob | 27 August 2023, 05:18:55 UTC | Add basic mkdocs.yaml file | 27 August 2023, 05:18:55 UTC |
| 5f22a71 | Robert Jacob | 27 August 2023, 05:15:12 UTC | Add an index.md file | 27 August 2023, 05:15:12 UTC |
| b2fbe42 | Qi Tang | 26 August 2023, 07:47:36 UTC | Minor fixes for loop ordering and typos [BFB] | 26 August 2023, 07:47:36 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 |
| ae3b0c9 | Wuyin Lin | 25 August 2023, 13:05:43 UTC | Rename chem package as chemuci_linozv3_mam5_vbs plus related changes | 25 August 2023, 13:05:43 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 |
| 7c9c10d | Naser Mahfouz | 09 August 2023, 03:09:18 UTC | add Mass_at_pressure 2D fields for Mass_aerosol 3D fields | 24 August 2023, 01:40:49 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 |
| d9ee8f5 | Sara Calandrini | 23 August 2023, 02:12:23 UTC | added call for submeso parametrization in standalone | 23 August 2023, 02:12:23 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 |
| a33b38a | Carolyn Begeman | 17 August 2023, 17:36:07 UTC | Fixup diag routine for upwinded wctEdge | 20 August 2023, 17:39:05 UTC |
| 2c3e8c1 | Carolyn Begeman | 15 August 2023, 14:48:43 UTC | Exclude boundaries from centered wctEdge | 20 August 2023, 17:39:05 UTC |
| e3607d4 | Carolyn Begeman | 11 May 2023, 23:56:51 UTC | Add upwinded ssh to SE and routine to diagnostics | 20 August 2023, 17:38:55 UTC |
| ff27c9d | Carolyn Begeman | 13 August 2023, 17:08:15 UTC | Use diag routine for wctEdge | 20 August 2023, 17:38:28 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 |
| 785d6fd | Steven Brus | 24 August 2022, 20:11:11 UTC | Add parabolic bowl test case | 18 August 2023, 16:12:18 UTC |
