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06 April 2024, 03:10:57 UTC
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Revision Author Date Message Commit Date
3b7f6d0 Iulian Grindeanu 04 December 2023, 20:51:37 UTC fix restart!!!! two major issues: 1) atm import moab had to comment a line, it was commented in mct import after we did moab import 2) factoring during atm second init call that was always missing 04 December 2023, 20:51:37 UTC
2e983e8 Iulian Grindeanu 02 December 2023, 16:31:19 UTC big error in not reading accumulation counter for lnd to rof l2racc_lm_cnt should have been read from file 02 December 2023, 16:31:19 UTC
8f64651 Iulian Grindeanu 02 December 2023, 16:30:28 UTC more debug in prep rof averages also, replace MOABCOMP with MOABDEBUG in seq_map_map 02 December 2023, 16:30:28 UTC
370f8b2 Iulian Grindeanu 30 November 2023, 21:28:23 UTC more debugging during flux albedo calc 30 November 2023, 21:28:23 UTC
be0f6f0 Iulian Grindeanu 29 November 2023, 05:13:34 UTC export uses the component clock step number easier to track restart this way 29 November 2023, 05:13:34 UTC
bf3e23a Iulian Grindeanu 28 November 2023, 16:06:03 UTC write atm comp moab instance before creating the surface restart for debugging only, to be sure that we are writing/reading the same data 28 November 2023, 16:06:03 UTC
55c4a00 Iulian Grindeanu 22 November 2023, 13:46:57 UTC write moab state before importing use the local clock 22 November 2023, 13:46:57 UTC
f159df1 Iulian Grindeanu 22 November 2023, 06:14:02 UTC write moab state after surface restart and before atm import also, retrieve step number from driver clock and atmosphere clock compare to our counter (num_moab_exports) 22 November 2023, 06:14:02 UTC
1ae8338 Iulian Grindeanu 15 November 2023, 05:58:03 UTC mark the After and Before files with step counter 15 November 2023, 05:58:03 UTC
a0d1b67 iulian07 22 May 2023, 15:29:49 UTC ne30 bilin new map replace map_ne30pg2_to_EC30to60E2r2_bilin.201005.nc with map_ne30pg2_to_EC30to60E2r2_bilin.tr.230522.nc 07 November 2023, 03:27:47 UTC
9ef740a iulian07 20 May 2023, 04:23:15 UTC bilinear maps generated with tr replace with map_ne4pg2_to_oQU480_bilin.tr.230519.nc this is for atm to ocn/ice map 07 November 2023, 02:56:36 UTC
cb2f6d1 Iulian Grindeanu 02 November 2023, 20:44:57 UTC write to the moab restart file the moab counter it is used only in debugging, for numbering h5m output files makes easier to compare when restart happens 02 November 2023, 20:44:57 UTC
593f56d Iulian Grindeanu 01 November 2023, 16:33:37 UTC mixup in send/receive also, rlimit gave some errors 01 November 2023, 16:33:37 UTC
09c347c Iulian Grindeanu 31 October 2023, 21:52:10 UTC add surface atm restart file for moab 31 October 2023, 21:52:10 UTC
059bddb Robert Jacob 30 October 2023, 20:58:50 UTC Remove debugging prints from cmake Remove debugging prints from build_model.cmake 30 October 2023, 20:58:50 UTC
48808a4 Iulian Grindeanu 28 October 2023, 03:01:43 UTC atm moab import needed during restart big oversight 28 October 2023, 03:01:43 UTC
7528057 Iulian Grindeanu 26 October 2023, 21:10:28 UTC define stack rlimit for anlgce machine also, need to have MOAB_PATH defined too both MOAB_ROOT and MOAB_PATH are needed the build should work with only one of them defined 26 October 2023, 21:10:28 UTC
f878e78 Iulian Grindeanu 23 October 2023, 05:05:02 UTC fix compile error when MOABCOMP defined 23 October 2023, 05:05:02 UTC
7679680 Robert Jacob 20 October 2023, 20:25:27 UTC Remove CPL_BYPASS from moab import. Use moab latv,lonv Remove CPL_BYPASS from moab import because its to much code duplication. Also use the new moab versions of latv and lonv 20 October 2023, 20:25:27 UTC
6a8d6fb Robert Jacob 20 October 2023, 20:24:14 UTC Introduce new variables for moab latv,lonv Introduce new variables for moab latv,lonv coordinates. Were using ones for pflotran which only worked because use_pflotran is false in all our cases. 20 October 2023, 20:24:14 UTC
258d4f7 Iulian Grindeanu 19 October 2023, 19:39:55 UTC Merge branch 'iulian787/array_references' into rljacob/driver-moab/add-mb-intf 19 October 2023, 19:39:55 UTC
cb83021 Iulian Grindeanu 19 October 2023, 15:36:21 UTC replace array references instaead of tmparray(1) it is enough to pass tmparray 19 October 2023, 15:36:21 UTC
ce9b5cc Iulian Grindeanu 17 October 2023, 23:33:59 UTC remove serwal cmake files 17 October 2023, 23:33:59 UTC
8622d5d Robert Jacob 17 October 2023, 18:51:40 UTC Set Sa_uovern in moab export routine Set Sa_uovern in moab export routine. Make sure it always has a value. 17 October 2023, 18:51:40 UTC
68bf4ff Robert Jacob 17 October 2023, 18:39:31 UTC Remove Sa_topo from MOAB coupler Remove Sa_topo from field list in moab coupler. Was not initialized by EAM or used by ELM. init=snan debugging caught this. 17 October 2023, 18:39:31 UTC
a62b553 Robert Jacob 14 October 2023, 20:22:21 UTC Update MOAB locations on chrysalis Update MOAB locations on chrysalis for gnu and intel. 14 October 2023, 20:22:21 UTC
26139d1 Iulian Grindeanu 12 October 2023, 18:04:53 UTC add MOAB_ROOT on anlgce machine 12 October 2023, 18:04:53 UTC
1fcc42d Iulian Grindeanu 11 October 2023, 23:57:14 UTC Merge branch 'iulian787/moab-driver/compare_restart' into rljacob/driver-moab/add-mb-intf 11 October 2023, 23:57:14 UTC
84fde90 iulian07 11 October 2023, 05:48:43 UTC cherry-pick branch compare_restart_states commit d7a00bb4412238964564530b3c481764050e3549 moab arrays need moab local sizes commit 387a5aafab84a4296b72cffacb4cb92b7666d03b allocate accumulated x2o during init the matrix has to be allocated for restart to work correctly commit 7cf98dd58cb6018f94e84d7df6d206c555e09979 size of the arrays can be 0 gnu does not like 0 sized arrays intel is more forgiving also, maybe we need to redistribute lnd domain, to not allow empty partitions commit 10df494851b9836dee076c56b69c4d95dcafd74b commit b6dd082ad82e8ac3 write before and after states for debugging 11 October 2023, 05:48:43 UTC
a048199 Robert Jacob 11 October 2023, 04:53:02 UTC Change vect_map default to none in moab driver Change vect_map default to none in moab driver since it doesn't yet support cart3d. 11 October 2023, 04:53:02 UTC
717a22c Robert Jacob 10 October 2023, 21:27:40 UTC Add fields to export moab Add ssh and avgOceanSurfaceDOCSemiLabile to moab export routine. Catching up to development in the mct coupler. 10 October 2023, 21:27:40 UTC
7280a6b Robert Jacob 10 October 2023, 18:39:43 UTC increase tagname size increase tagname size in the moab export routine. 10 October 2023, 18:39:43 UTC
2caaa6e Robert Jacob 10 October 2023, 18:37:57 UTC Add nlmaps_verbosity to moab infodata Add nlmaps_verbosity namelist var to the moab version of seq_infodata. Will get a namelist read error otherwise. 10 October 2023, 18:37:57 UTC
a4fa625 Robert Jacob 10 October 2023, 18:36:17 UTC Add MOAB include dirs to coupler target For the cpl target, add the MOAB include dirs if USE_MOAB is defined. 10 October 2023, 18:36:17 UTC
23d0efc Robert Jacob 09 October 2023, 22:40:33 UTC Update module name in moab subroutines Update module name from clm to elm in moab subroutines. 09 October 2023, 22:40:33 UTC
12dd046 James Foucar 05 October 2023, 21:25:27 UTC Fixes for moab 05 October 2023, 21:25:27 UTC
d755958 Robert Jacob 05 October 2023, 18:37:55 UTC Merge remote-tracking branch 'upstream/master' into rljacob/driver-moab/add-mb-intf Merge master into this branch in order to get the latest build system updates. 05 October 2023, 18:37:55 UTC
2ff3742 James Foucar 05 October 2023, 17:46:26 UTC Merge branch 'jgfouca/cmake_mct_csm_share' into master (PR #5964) CMake: Improve dependency management for mct and csm_share Neither of these packages are cmake packages, so we have to roll our own Find$package.cmake modules. These can be pretty simple for e3sm since we build them ourselves (no worries about version or not found etc). Also, remove a lot of unused for special handling of clm and stuff for pio building. [BFB] 05 October 2023, 17:46:26 UTC
4b8c026 Robert Jacob 05 October 2023, 16:07:46 UTC Change MOAB_PATH for chrysalis Change MOAB_PATH for chrysalis to one built with latest compilers 05 October 2023, 16:07:46 UTC
612f02e Robert Jacob 05 October 2023, 16:06:15 UTC Add find_package for MOAB and cpp Add find_package call for MOAB and the CPP def needed 05 October 2023, 16:06:15 UTC
e9191e8 Robert Jacob 05 October 2023, 16:04:37 UTC Add MOAB_ROOT for chrysalis Add setting of MOAB_ROOT for chrysalis. 05 October 2023, 16:04:37 UTC
573137b noel 04 October 2023, 19:50:10 UTC Merge branch E3SM-Project/ndk/machinefiles/alvarez-update (PR #5966) For alvarez (internal test machine for pm-cpu), update machine file settings 04 October 2023, 19:50:10 UTC
653b97b James Foucar 04 October 2023, 18:51:50 UTC Fixes frontier netcdf handling 04 October 2023, 18:51:50 UTC
50b3694 James Foucar 04 October 2023, 16:38:15 UTC For now, make rrtmgp depend on spio instead of netcdf This will ensure correct link order 04 October 2023, 16:38:15 UTC
4366d53 Robert Jacob 03 October 2023, 22:22:23 UTC Add more rof_sed and dust mods to driver-moab Add new shr_dust_mod.F90 and changes for dust and rof_sed in seq_flds_mod.F90 from MCT driver. 03 October 2023, 22:22:23 UTC
b7a78cb James Foucar 03 October 2023, 18:47:33 UTC Progress on refactored netcdf handling 03 October 2023, 18:47:33 UTC
eddad77 James Foucar 03 October 2023, 16:59:02 UTC Attempting to improve netcdf situation 03 October 2023, 16:59:02 UTC
0ded494 Robert Jacob 03 October 2023, 04:18:27 UTC Update driver-moab with cime_config developments Add the nonlinear maps definitions and also definitions for rof_sed, dust_scheme and eps values for high-res grids 03 October 2023, 04:18:27 UTC
8129b1b Robert Jacob 03 October 2023, 04:14:34 UTC Merge branch 'sarich/moab/update-moab-driver' into rljacob/driver-moab/add-mb-intf Merge driver-moab development to a branch off of recent E3SM master and resolve conflicts. Verified that driver-mct fully coupled cases build. 03 October 2023, 04:14:34 UTC
a1a2f94 Robert Jacob 02 October 2023, 21:21:17 UTC Remove some commented out code Remove some commented out code and unused code from component model MOAB interfaces. 02 October 2023, 21:21:17 UTC
fe64ea0 James Foucar 02 October 2023, 20:44:21 UTC Workaround adios2 find cmake problem 02 October 2023, 20:44:36 UTC
34f2eec James Foucar 02 October 2023, 19:58:50 UTC Fix a couple more adios things 02 October 2023, 19:59:55 UTC
4392296 Robert Jacob 02 October 2023, 19:46:10 UTC Remove whitespace only Remove whitespace only changes that were the only diffs in these files. 02 October 2023, 19:46:10 UTC
db34761 James Foucar 02 October 2023, 17:41:34 UTC Another syntax fix 02 October 2023, 17:41:34 UTC
a514f98 James Foucar 02 October 2023, 17:36:29 UTC Fix paren 02 October 2023, 17:36:29 UTC
c92837c James Foucar 02 October 2023, 17:30:26 UTC Only find adios if ADIOS2_ROOT is set 02 October 2023, 17:30:26 UTC
a5177a0 James Foucar 02 October 2023, 17:28:18 UTC Fix adios stuff in FindPIO 02 October 2023, 17:28:18 UTC
7075e9a James Foucar 02 October 2023, 16:55:23 UTC Better handling of adios2 02 October 2023, 16:55:23 UTC
1f42fb8 noel 30 September 2023, 17:30:46 UTC machine file changes for alvarez (internal test system for pm-cpu) 30 September 2023, 17:30:46 UTC
8ab1f1d James Foucar 29 September 2023, 17:23:49 UTC Make mpas depend on spio instead of just netcdf This ensures correct link order 29 September 2023, 17:23:49 UTC
293a797 James Foucar 29 September 2023, 16:16:04 UTC Better way of handling the spio->netcdf dependency 29 September 2023, 16:16:04 UTC
3fcd94e James Foucar 28 September 2023, 22:06:58 UTC Guard all Find modules from repetition so users don't have to Fix mpas netcdf dep, should be public 28 September 2023, 22:06:58 UTC
1de6606 James Foucar 28 September 2023, 20:45:01 UTC Remove pnetcdf cppdef 28 September 2023, 20:45:01 UTC
89f28a0 James Foucar 28 September 2023, 20:39:07 UTC More netcdf fixes. Mpas was using old approach 28 September 2023, 20:39:07 UTC
ab75f35 James Foucar 28 September 2023, 20:28:33 UTC Fix for rrtmgp netcdf dep 28 September 2023, 20:28:33 UTC
3a78f4d James Foucar 28 September 2023, 19:40:43 UTC Ensure netcdf dep is in the right order 28 September 2023, 19:40:43 UTC
360bf8a James Foucar 28 September 2023, 16:33:31 UTC Remove unused MCT_INTERFACE cppdef 28 September 2023, 16:33:31 UTC
ac40a2c James Foucar 28 September 2023, 16:24:26 UTC Some minor fixes. Add find MCT to find module for csm_share 28 September 2023, 16:24:26 UTC
fbdfc20 James Foucar 27 September 2023, 22:31:10 UTC Fixes 27 September 2023, 22:31:10 UTC
f2786de James Foucar 27 September 2023, 21:46:13 UTC Add modules 27 September 2023, 21:46:13 UTC
cf3c1a8 James Foucar 27 September 2023, 21:40:32 UTC CMake: improve dep on mct and csm_share 27 September 2023, 21:40:32 UTC
894b5b2 Jon Wolfe 27 September 2023, 17:55:59 UTC Merge branch 'xylar/mpas-ocean/fix-parabolic-bowl-registry' (PR #5930) Fix parabolic bowl registry for MPAS-Ocean init mode There were a few syntax issues with the MPAS-Ocean registry for the parabolic bowl test case that prevent it from being parsed correctly in Polaris. They are fixed here. Not used in E3SM. [BFB] 27 September 2023, 17:55:59 UTC
614d911 James Foucar 27 September 2023, 15:40:57 UTC Merge branch 'jgfouca/cmake_petsc' into master (PR #5959) Cleanup petsc cmake stuff Also remove a lot of unused stuff. [BFB] * jgfouca/cmake_petsc: Cleanup petsc cmake stuff 27 September 2023, 15:40:57 UTC
67b20d1 James Foucar 25 September 2023, 21:15:50 UTC Cleanup petsc cmake stuff [BFB] 26 September 2023, 21:15:48 UTC
f2dc02e Jon Wolfe 26 September 2023, 18:52:27 UTC Merge branch 'xylar/mpas-ocean/accumulate-data-land-ice-fluxes' (PR #5910) Accumulate data land-ice mass fluxes Before this merge, we were only accumulating this flux in prognostic flux mode. With this merge, we accumulate the mass flux in data mode as well, as this term is needed in the total mass budget of the model. To facilitate this and reduce issues related to initialization vs. forward time stepping, this accumulation step has been broken into its own subroutine, ocn_surface_land_ice_fluxes_accumulate_fluxes(). This subroutine is called when time-stepping the model but not at initialization (since we do not want to accumulate any fluxes at that time). Fixes #5911 [BFB] 26 September 2023, 18:52:27 UTC
ffc0e2b James Foucar 26 September 2023, 16:22:45 UTC Merge branch 'jgfouca/cmake_albany' into next (PR #5950) CMake: Improve handling of Albany and related packages Specifically: * Albany * Trilinos * Kokkos This PR establishes the new paradigm of setting ${Package}_ROOT to find the packages we need. So far, I am very happy with how this is going. You can see how much cleaner it is to do things the CMake-3 so you don't have to micro-manage flags. In order to be consistent, changes kokkos override env var from KOKKOS_PATH to Kokkos_ROOT. Fixes #5786 [BFB] * jgfouca/cmake_albany: Remove obsolete references to ALBANY_PATH in cmake macros Improve Kokkos handling CMake: Improve handling of Albany and related packages 26 September 2023, 16:22:45 UTC
13c5352 James Foucar 26 September 2023, 16:20:57 UTC Merge branch 'jgfouca/cmake_minor_cleanups' into master (PR #5948) CMake: Some minor cleanups Remove OS concept from cmake macros. We can maybe remove it entirely from config_machines but that will be trickier. Remove some unneeded or repeated things from CMakeLists.txt. Remove FMS dependency support. [BFB] * jgfouca/cmake_minor_cleanups: Remove FMS support CMake: Some minor cleanups 26 September 2023, 16:20:57 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
c5ad9f9 James Foucar 25 September 2023, 20:11:41 UTC Remove obsolete references to ALBANY_PATH in cmake macros 25 September 2023, 20:11:41 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
9fa94e0 Iulian Grindeanu 25 June 2023, 19:32:42 UTC import moab last so moab import now takes precedence over 22 September 2023, 23:36:46 UTC
c4ecf63 James Foucar 22 September 2023, 21:12:01 UTC Improve Kokkos handling 22 September 2023, 21:12:01 UTC
ecb3576 James Foucar 22 September 2023, 21:01:19 UTC CMake: Improve handling of Albany and related packages 22 September 2023, 21:03:50 UTC
8b08bc5 iulian 22 September 2023, 20:25:03 UTC initialize moab atm meshes always also, do not create vertices if nelemd == 0 22 September 2023, 20:25:03 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
9113e86 Xylar Asay-Davis 22 September 2023, 15:09:08 UTC Update possible values Co-authored-by: Steven Brus <steven.r.brus@gmail.com> 22 September 2023, 15:09:08 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
29a6ea5 James Foucar 21 September 2023, 22:23:48 UTC Remove FMS support 21 September 2023, 22:23:48 UTC
7c3c8a9 iulian 21 September 2023, 22:16:32 UTC add pm-cpu on gnu compiler 21 September 2023, 22:16:32 UTC
6e7e585 James Foucar 21 September 2023, 22:12:33 UTC CMake: Some minor cleanups Remove OS concept from cmake macros. We can maybe remove it entirely from config_machines but that will be trickier. [BFB] 21 September 2023, 22:12:33 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
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