| 0f13c8b | noel | 30 May 2022, 21:32:33 UTC | For cori use 4 nodes as the default for land-only tests (as it was before) Change the machine name perlmutter to now be: pm-gpu and/or pm-cpu Fixes #4959 Fixes #4981 [bfb] | 30 May 2022, 21:32:33 UTC |
| fa1d32e | Min Xu | 27 May 2022, 19:23:39 UTC | Merge branch 'sarats/machinefiles/summit-queues-envvars' (PR #4978) This resolves the following issues: * Unable to select debug queue * Environment variables are set multiple times with the last invocation doing the right option. * Avoided by changing the CPU env vars conditional on compilers. [BFB] | 27 May 2022, 19:23:39 UTC |
| 9281eda | Jon Wolfe | 27 May 2022, 15:45:07 UTC | Merge branch 'brobey/mpas-ocean/openacc-topofsplit' (PR #4939) Adding OpenACC directives to top of split time integration routine Adding OpenACC to top of split time integration routine. This is mostly adding directives and should not impact anything else. [BFB] | 27 May 2022, 15:45:07 UTC |
| 7fc418e | James Foucar | 26 May 2022, 17:46:03 UTC | Merge pull request #4947 from mt5555/dtime-updates update dtime for high res meshes Set correct ATM_NCPL (which controls the atmosphere timestep, dtime) for ne256, ne512 and ne1024 meshes. No impact on E3SM. Needed for SCREAM. [BFB] | 26 May 2022, 17:46:03 UTC |
| bec5a6f | Andrew M. Bradley | 26 May 2022, 17:04:08 UTC | Merge branch 'ambrad/homme/compose-cmake-for-eamxx' (PR #4967) Homme: Rework HOMME_ENABLE_COMPOSE symbol machinery for use in EAMxx Modify how HOMME_ENABLE_COMPOSE is defined in HOMME's cmake system, affecting standalone HOMME and EAMxx. This enables running SL transport in EAMxx v1. Fix a vectorization-related issue in trajectory calculation. Passes e3sm_developer and homme_integration on Chrysalis. Passes compose_ut and *GB-sl*cxx_vs_f90 tests on weaver GPU. [BFB] | 26 May 2022, 17:04:08 UTC |
| ba16635 | Jon Wolfe | 25 May 2022, 17:56:06 UTC | Merge branch 'darincomeau/ocn/gm-horizontal-resolution-function' (PR #4864) Add horizontal tapering function to mesoscale eddy parameterizations This PR adds a new 'RossbyRadius' option to the horizontal tapering of GM and Redi, which is based on Hallberg (2013) - https://doi.org/10.1016/j.ocemod.2013.08.007, which turns the parameterization on if the Rossby Radius is resolved by at least two cells. These flags are: * config_Redi_horizontal_taper = 'ramp' (def), 'none', 'RossbyRadius' * config_GM_horizontal_taper = 'ramp' (def), 'none', 'RossbyRadius' This PR replaces the variable `gmResolutionTaper`, which was used for both GM and Redi, to the separate variables `RediHorizontalTaper` and `gmHorizontalTaper` so that Redi and GM tapering can be chosen separately, and it is clear in the code. Logic was added to the GM and Redi schemes so that the there is a base value in the arrays for Redi Kappa and GM Kappa. The base value is then multiplied by the taper array, which has a value between 0 and 1. Arrays that are static in time are computed on init. Under the following conditions, the arrays are recomputed at every time step: * config_Redi_horizontal_taper = 'RossbyRadius' (recompute RediHorizontalTaper and RediKappa) * config_GM_horizontal_taper = 'RossbyRadius' (recompute gmHorizontalTaper) [NML] adds MPAS-Ocean namelist options [BFB] | 25 May 2022, 17:56:06 UTC |
| 9a7ba1b | Sarat Sreepathi | 25 May 2022, 03:46:40 UTC | Summit: add killable queue and change wallltimemax Evidently, walltime max is used as default wall time by CIME (which is weird). Anyway, setting that to 2 hours. Add killable queue. | 25 May 2022, 03:46:40 UTC |
| 1d97dfc | Andrew M. Bradley | 25 May 2022, 02:03:23 UTC | Homme/SL: Fix a pack-size-related bug. If packsize % nlev != 0, eta_dot_dpdn's bottom boundary value of 0 was being overwritten by NaN. Re-zero it in this case. | 25 May 2022, 02:29:27 UTC |
| 3e29568 | Jon Wolfe | 24 May 2022, 16:29:23 UTC | Update testmods to new variable names | 24 May 2022, 16:29:23 UTC |
| 184002d | Sarat Sreepathi | 24 May 2022, 00:01:06 UTC | Summit batch: add additional queues and attributes On Summit, add debug and other queues along with limits. | 24 May 2022, 00:01:06 UTC |
| 88dfd2b | Sarat Sreepathi | 23 May 2022, 23:59:57 UTC | Summit:change env vars to compiler specific This avoids confusion from duplicate settings where the last invocation does the right setting for GPU compilers. | 23 May 2022, 23:59:57 UTC |
| 31b474f | Jon Wolfe | 23 May 2022, 18:39:25 UTC | Merge branch 'philipwjones/mpas-framework/fix-config-dup' (PR #4907) Remove duplicate config variables in ocean Removes the auto-generation of duplicate config scalars (varinp_name) that were introduced in a previous commit for safety when adding the get_config_scalar routine. [BFB] | 23 May 2022, 18:39:25 UTC |
| 97a5112 | Bob Robey | 20 May 2022, 18:40:01 UTC | Fixing sshNew equals sshCur loop for Summit and cleanup of OpenACC directives | 20 May 2022, 18:40:01 UTC |
| 4b21b54 | Andrew M. Bradley | 19 May 2022, 19:18:42 UTC | Merge branch 'ambrad/homme/pg-rm-reshape' (PR #4786) Homme, physgrid: Remove reshape use in low-level code. Noel noticed on PM that the AMD compilers have trouble with optimizing reshape. Remove the use of reshape. On chrysalis: * e3sm_developer (which includes e3sm_atm_developer) and e3sm_atm_integration pass. * In homme_integration, the HOMMEBFB suite passes, while in the HOMME suite, the test thetah-sl-dcmip16_test1pg2 diffs by a reasonable amount. It is known that thetah-sl-dcmip16_test1pg2 is sensitive in the opt build (HOMME rather than HOMMEBFB). [BFB] except thetah-sl-dcmip16_test1pg2 in the HOMME suite of homme_integration | 19 May 2022, 19:18:42 UTC |
| 11b48ab | Mark Petersen | 18 May 2022, 21:35:33 UTC | Change back order of operations for BFB | 19 May 2022, 02:18:02 UTC |
| 63768fc | Milena Veneziani | 18 May 2022, 23:41:23 UTC | Update name of Rossby_ramp_min/max config options | 18 May 2022, 23:41:23 UTC |
| 7d24582 | Milena Veneziani | 18 May 2022, 23:17:33 UTC | Fix Rossby Radius taper for small c_mode1 values | 18 May 2022, 23:17:33 UTC |
| 574082a | Phil Jones | 18 May 2022, 22:21:13 UTC | removed duplicate declarations left from prior commit | 18 May 2022, 22:21:13 UTC |
| 7991455 | Andrew M. Bradley | 17 May 2022, 00:49:24 UTC | Homme: Rework HOMME_ENABLE_COMPOSE symbol machinery for use in EAMxx. | 18 May 2022, 21:19:15 UTC |
| 1bf3a6d | noel | 18 May 2022, 15:16:34 UTC | Merge branch E3SM-Project/ndk/machinefiles/add-pm-cpu-pm-gpu (PR #4951) Add new machine for CPU-only nodes of perlmutter (and other perlmutter changes) | 18 May 2022, 15:16:34 UTC |
| 175eec6 | Oksana Guba | 17 May 2022, 20:04:34 UTC | Merge remote-tracking branch 'OG/og/cleanup' (PR #4753) Removing allocates for cpair and rair variables, since they are always set to dry constants, in parts that are related to energy calculations. Removing repeated code in check_energy wrt TE and total water. Removing calls to strings comparisons in physpkg and in check_energy. Removing some if-statements related to waccm (mostly regarding energy routines). There are such calls (waccm and string comparison) in other places, esp. in parametrizations, leaving them for now. [bfb] | 17 May 2022, 20:04:34 UTC |
| 1c7673a | noel | 16 May 2022, 18:04:46 UTC | Fix typo in last commit | 16 May 2022, 18:04:46 UTC |
| 160cc23 | noel | 16 May 2022, 17:58:50 UTC | Add pm-cpu as a new machine -- CPU-only nodes of perlmutter Move the machine "perlmutter" to pm-gpu. Increase version of gnu and mpich. Adjust default perlmutter machine/compilers. Add in AMD compiler for pm-cpu. Adjust pelayouts for the default 1-node cases (just for testing) Add conditional for nersc slurm settings for GPU (only affects kokkos) | 16 May 2022, 17:58:50 UTC |
| 04c0376 | Azamat Mametjanov | 14 May 2022, 00:02:30 UTC | Merge branch 'azamat/anvil/trigrid-bgc-pes' (PR #4950) Add tri-grid EAM+DOCN BGC PEs on Anvil [BFB] | 14 May 2022, 00:02:30 UTC |
| 102bbbc | Azamat Mametjanov | 13 May 2022, 23:55:21 UTC | Rm tri-grid eam+docn BGC PEs from allactive PEs | 13 May 2022, 23:55:21 UTC |
| 9b14d67 | Azamat Mametjanov | 13 May 2022, 23:22:32 UTC | Add tri-grid EAM+DOCN BGC PEs | 13 May 2022, 23:22:32 UTC |
| 8b12fc5 | Benjamin R. Hillman | 13 May 2022, 17:34:26 UTC | Merge branch 'whannah/mmf/rename-compsets' (#4837) This reorganizes the MMF compsets to have a single "supported" MMF configuration type with 1-moment microphysics (i.e. MMF1). This also introduces a new naming convention for the MMF compsets as follows: - F2010-MMF1 - F20TR-MMF1 - FAQP-MMF1 - FRCE-MMF1 - FSCM-RICO-MMF1 - FSCM-ARM97-MMF1 Currently, these new compsets point to the C++ CRM code, but the idea is that this can be updated with new options or a new CRM without having to add new compset names. We intend to add corresponding "MMF2" compsets after the P3 microphysics is integrated. The other MMF configuration options are still available, but it is up to the user to know how to use these configurations either with a testmod or manually appending the appropriate flags to CAM_CONFIG_OPTS. I also took this opportunity to do a major clean up of components/eam/cime_config/config_component.xml, including renaming the AQP/RCE/SCM compsets for EAM to make everything more consistent. I delete the AQP<N> compsets in favor of "AQP" being equivalent to the old "AQP1" option. No one makes use of these other compsets and they are still available if we need them, so I think it's a good change to simplify full range of F compsets. I also tried to identify and delete several older compsets that are no longer in use and don't follow the current naming conventions. I probably missed some that could be deleted, but the file is still much cleaner and readable than before. | 13 May 2022, 17:34:26 UTC |
| ed696b5 | Jon Wolfe | 13 May 2022, 16:18:38 UTC | Merge branch 'maltrud/ocean/fix-BGC-diags' (PR #4944) Fix diagnostic bugs in ocean BGC This PR fixes a number of diagnostic fields in ocean BGC that were ok for E3SMv1 but are no longer consistent with definitions require by MarBL in E3SMv2. Fixes #4925 [BFB] | 13 May 2022, 16:18:38 UTC |
| e07709c | Phil Jones | 13 May 2022, 15:19:40 UTC | replace deprecated mesh, config Pool retrievals in self-attract and loading removed/replaced meshPool and configPool retrievals since info available through module use statements removed a block loop since multiple blocks no longer supported | 13 May 2022, 15:19:40 UTC |
| 81730f9 | Phil Jones | 18 April 2022, 22:30:04 UTC | remove duplicate config variables removes the duplicate config scalars (varinp_name) that were introduced in a previous commit for safety when adding the get_config_scalar routine | 12 May 2022, 23:08:40 UTC |
| c377707 | Mark Taylor | 12 May 2022, 22:57:50 UTC | update dtime for high res meshes | 12 May 2022, 22:57:50 UTC |
| 013fe19 | Jon Wolfe | 12 May 2022, 17:06:47 UTC | Merge branch 'jonbob/coupler/fix-bgcbudget-restart' (PR #4934) Fix coupler BGC carbon budget restarts Make the BGC carbon budget output BFB after restarting by moving lnd and ocn BGC budget calls to cime_run_calc_budgets2, where the atm BGC call is. Previously the BGC budget calls were located with the physics budget calls but this resulted in the "direct" lnd2atm and ocn2atm terms being missed in the lnd and ocn budget calculations but included in the atm. Fixes #4920 [BFB] | 12 May 2022, 17:06:47 UTC |
| 023fb93 | Jon Wolfe | 11 May 2022, 21:59:52 UTC | Reorder logic with do_bgc_budgets as outer check | 11 May 2022, 21:59:52 UTC |
| 24859cf | Xylar Asay-Davis | 11 May 2022, 18:38:30 UTC | Update E3SM namelist options | 11 May 2022, 18:58:35 UTC |
| 872c037 | Jon Wolfe | 11 May 2022, 17:45:17 UTC | Merge branch 'matthewhoffman/mpas/stream_read_input_only' (PR #4929) Differentiate input and input/output streams in MPAS stream manager This PR improves the MPAS Stream Manager by introducing an optional argument to differentiate between streams of direction INPUT and direction INPUT_OUTPUT. Previously, the mpas_stream_mgr_read() routine ignored the difference between streams of direction INPUT and direction INPUT_OUTPUT (i.e. restart streams). However, there are situation where it would be desirable to read only truly direction INPUT streams. One example is at the initial time of a coldstart run - one would typically want to read any input streams without reading the restart stream (which does not exist yet). This PR adds an optional argument to force mpas_stream_mgr_read to ignore INPUT_OUTPUT streams and only read truly INPUT streams. Its default value maintains the previous behavior. A second commit modifies the MALI driver to make use of this new capability to improve and simplify the input stream handling at the initial time of a MALI simulation. [BFB] | 11 May 2022, 17:45:17 UTC |
| d665e95 | Jon Wolfe | 11 May 2022, 16:16:26 UTC | Make streams field list consistent with BGC changes | 11 May 2022, 16:16:26 UTC |
| 18310ce | Mathew Maltrud | 10 May 2022, 20:40:28 UTC | fix ocn BGC diags that are no longer compatible with v2 (MarBL) | 10 May 2022, 20:40:28 UTC |
| b808d07 | Wuyin Lin | 10 May 2022, 18:32:54 UTC | Merge branch 'beharrop/atm/fix-co2-diags-restarts' (PR #4941) Fix restart issue for CO2 diagnostics in EAM Prevent failure in the CO2 diagnostics checker in EAM when using restart files produced on time steps not equal to the last time step in EAM. The fix is accomplished by removing the logical flag controlling when co2_diags_store_fields is called. Fixes #4935 [BFB] | 10 May 2022, 18:32:54 UTC |
| 1080383 | Min Xu | 10 May 2022, 18:05:20 UTC | Merge branch 'ykim/crusher/craypr' (PR #4914) adds '-O1 -hfp0' flags for crayclang to reduce NaN-related errors This change updates only "crayclang_crusher.cmake" | 10 May 2022, 18:05:20 UTC |
| f315409 | Walter Hannah | 09 May 2022, 19:44:10 UTC | Merge master into whannah/mmf/rename-compsets | 09 May 2022, 19:44:10 UTC |
| 37f1f48 | Xylar Asay-Davis | 09 May 2022, 19:01:34 UTC | Switch RossbyRadius GM taper to use a ramp This merge adds 2 namelist options: config_GM_Rossby_ramp_min config_GM_Rossby_ramp_max that control a ramp used to taper the GM Kappa coefficient based on the ratio of the cell size (dcEdge) to the Rossby Radius. The default minimum ratio was chosen so that GM turns off when the Rossby radius is resolved by 2 grid cells (the previous threhsold). The maximum ratio was chosen so that GM is fully on when a grid cell is 3 Rossby radii in size, corresponding to ~30 km in the Southern Ocean, or a little higher resolution than the EC30to60 mesh. This upper limit needs exploration! | 09 May 2022, 19:22:57 UTC |
| a6090eb | Xylar Asay-Davis | 09 May 2022, 19:07:10 UTC | Remove trailing whitespace | 09 May 2022, 19:07:10 UTC |
| 25ea3db | James Foucar | 09 May 2022, 18:42:23 UTC | Merge branch 'azamat/pes/split-config-pesall' (PR #4928) PE-layouts are picked based on active component of a case or based on the prior config_pesall for all-active compsets. This PR also comes with a CIME update: To a3c94512e105ff1f21adf500fd317ac56961635e Changes: 1) Add RUNDIR as an accessible setting in the cmake build system 2) First step in the direction of implementing async IO in CESM 3) Add numeric time-stamp to jenkins archiving 4) Update grid schema 5) Set component-specific config_pes in E3SM 6) Allow any case env to be used as a directives selector in config_batch.xml Fixes #4834 [BFB] * azamat/pes/split-config-pesall: Homme genf90 fix Add back custom mpaso and elm PEs for Mappy Add minor CIME fix for configure tool CIME update Add cime update to set component-specific PES_SPEC_FILE Split config_pesall into component-specific config_pes | 09 May 2022, 18:42:42 UTC |
| 5322849 | Jon Wolfe | 09 May 2022, 17:32:48 UTC | Merge branch 'hkang/ocean/si_bfbsum' (PR #4898) Change a reproducible sum algorithm in SI solver Change a reproducible sum algorithm in the ocean split-implicit barotropic mode solver. The changed algorithm uses a global reproducible summation module in components/mpas-framework/src/framework/mpas_global_sum_mod.F. This option is off by default. [BFB] | 09 May 2022, 17:32:48 UTC |
| 50a5fbd | Bryce E Harrop | 06 May 2022, 23:31:34 UTC | Add a fix for restarts generated before the final time step | 06 May 2022, 23:31:34 UTC |
| 996c7e7 | James Foucar | 06 May 2022, 21:19:50 UTC | Merge branch 'jasonb5-fix_cime_templates' into master (PR #4940) Fixes CIME import paths in template files Fixes CIME imports for template.case.run.sh and template.case.st_archive. Also fixes imports for template.case.run and template.case.test, not sure if these are needed as they're only called by CIME, which fixes up the import paths when executing the scripts. [BFB] * jasonb5-fix_cime_templates: Fixes CIME import paths in template files | 06 May 2022, 21:19:50 UTC |
| ba02fd0 | Wuyin Lin | 06 May 2022, 20:26:45 UTC | Merge branch 'wlin/lnd/fsurdat_2010_ne120np4' (PR #4932) Added fsurdat for simyr2010 on ne120np4 This is to enable simulations with ne120_ne120 grid. [BFB] | 06 May 2022, 20:26:45 UTC |
| 294cada | Jason Boutte | 06 May 2022, 18:50:34 UTC | Fixes CIME import paths in template files | 06 May 2022, 18:50:34 UTC |
| f689be6 | Jon Wolfe | 06 May 2022, 18:11:00 UTC | Merge branch 'njeffery/seaice/update_ice_bgc_namelist' (PR #4918) Updates seaice BGC namelist defaults to match Registry defaults Update E3SM default BGC parameter values have been tested in ocean-ice bgc sensitivity simulations for 200+ years. Also turns on kill simulation if carbon conservation in sea ice fails bounds (only if BGC is active). [NML] [non-BFB] only when marine BGC is active | 06 May 2022, 18:11:00 UTC |
| 9ad8f20 | James Foucar | 06 May 2022, 16:10:19 UTC | Homme genf90 fix | 06 May 2022, 16:10:24 UTC |
| 7170a47 | Azamat Mametjanov | 05 May 2022, 22:18:31 UTC | Add back custom mpaso and elm PEs for Mappy | 05 May 2022, 22:18:31 UTC |
| 03e3252 | James Foucar | 05 May 2022, 18:09:01 UTC | Add minor CIME fix for configure tool | 05 May 2022, 18:09:01 UTC |
| 866cca7 | James Foucar | 04 May 2022, 21:31:59 UTC | Merge remote-tracking branch 'origin/master' into azamat/pes/split-config-pesall * origin/master: run_e3sm.sh: Make it explicit for users to change case name run_e3sm: case_group argument activated for create_newcase when valid run_e3sm script: Replace default case name and case group placeholders Add support for northamericax4v1pg2_EC30to60E2r2 resolution Corrected possible division by zero in ice bgc MPAS Standalone: Add OpenMP support to gnu-nersc Add MPI process stride for tasks exclusively owned by a component | 04 May 2022, 21:31:59 UTC |
| 157f1fc | James Foucar | 04 May 2022, 21:24:14 UTC | CIME update To a3c94512e105ff1f21adf500fd317ac56961635e Changes: 1) Add RUNDIR as an accessible setting in the cmake build system 2) First step in the direction of implementing async IO in CESM 3) Add numeric time-stamp to jenkins archiving 4) Update grid schema 5) Set component-specific config_pes in E3SM 6) Allow any case env to be used as a directives selector in config_batch.xml Fixes: [BFB] | 04 May 2022, 21:24:14 UTC |
| 00e5c34 | Azamat Mametjanov | 04 May 2022, 19:33:55 UTC | Merge branch 'azamat/driver/add-exclusive-process-stride' (PR #4859) Add MPI process stride for tasks exclusively owned by a component This lets a component run exclusively on an MPI task: e.g. ATM on 6 MPI tasks for 6 GPUs on a Summit node. [NML] - due to new excl_stride namelist variables | 04 May 2022, 19:33:55 UTC |
| b797163 | Jon Wolfe | 04 May 2022, 17:59:06 UTC | Move lnd and ocn BGC budget calls to cime_run_calc_budgets2 | 04 May 2022, 17:59:06 UTC |
| d57fb31 | Jon Wolfe | 04 May 2022, 14:54:48 UTC | Merge branch 'origin/njeffery/seaice/correct_ice_bgc_nan' (PR #4916) Correct possible division by zero in ice bgc Sets BGC vertical diffusion to zero when ice thickness is small Also removes trailing spaces in ice_brine.F90 Fixes #4913 [BFB] | 04 May 2022, 14:54:48 UTC |
| e7a5ea1 | Wuyin Lin | 04 May 2022, 12:03:05 UTC | Added fsurdat for simyr2010 on ne120np4 | 04 May 2022, 12:03:05 UTC |
| 34c112a | Jon Wolfe | 03 May 2022, 17:44:34 UTC | Merge branch 'xylar/mpas-framework/add-openmp-to-gnu-nersc' (PR #4910) MPAS Standalone: Add OpenMP support to gnu-nersc For some reason this was omitted when OpenMP support was added 8 years ago. This has become a problem in compass because we switched to building with OpenMP on by default: MPAS-Dev/compass#364 Does not impact E3SM builds. [BFB] | 03 May 2022, 17:44:34 UTC |
| 3a6b4ed | Jon Wolfe | 03 May 2022, 17:23:42 UTC | Merge branch 'jonbob/scripts/add-northamericax4v1pg2-ec30to60e2r2' (PR #4919) Add support for northamericax4v1pg2_EC30to60E2r2 resolution Brings in the grid definition for the northamericax4v1pg2_EC30to60E2r2 resolution as well as all necessary files. It uses r05 for the runoff resolution, so make comparisons with low-res atm/high-res ocn (ne30pg2_WC14) more consistent. All new files have been staged on the inputdata repo. [BFB] | 03 May 2022, 17:23:42 UTC |
| d45a620 | Azamat Mametjanov | 02 May 2022, 22:28:26 UTC | Add cime update to set component-specific PES_SPEC_FILE | 02 May 2022, 22:28:26 UTC |
| a9e0878 | Robert Jacob | 02 May 2022, 21:42:20 UTC | Merge 'sarats/scripts/run-e3sm-case-group' (PR #4922) Replace default case name and case group placeholders. This is required to avoid unwarranted usage of case_group that interferes with aggregation of various production simulation campaigns. [BFB] Testing: I was able to run ./create_newcase with --case-group "" as defined. | 02 May 2022, 21:42:20 UTC |
| 1da6aad | Bob Robey | 02 May 2022, 21:30:08 UTC | Adding OpenACC deeper from top of split time integration routine | 02 May 2022, 21:30:08 UTC |
| 9bd5730 | Bob Robey | 02 May 2022, 21:20:03 UTC | Adding OpenACC at top of split time integration routine | 02 May 2022, 21:20:03 UTC |
| 1ceddf7 | Matthew Hoffman | 29 April 2022, 20:04:33 UTC | Simplify & generalize MALI stream read behavior at initial time This commit removes the restriction that the initial condition stream have the name 'input' and now allows any streams of direction input that have input_interval='initial_only' to be read at the initial time. This allows an initial condition to be spread across multiple files. It also prevents an obscure error that was causing streams of input_interval='initial_only' to be read on the initial time of a restart. With this change, 'initial_only' truly means the initial time of a simulation, regardless of restarting it or not. This commit also adds some missing timer calls. | 02 May 2022, 17:18:51 UTC |
| a2fc6b9 | Matthew Hoffman | 29 April 2022, 20:00:36 UTC | Allow mpas_stream_mgr_read() to read only strictly INPUT direction streams Previously, the mpas_stream_mgr_read() routine ignored the difference between streams of direction INPUT and direction INPUT_OUTPUT (i.e. restart streams). However, there are situation where it would be desirable to read only truly direction INPUT streams. One example is at the initial time of a coldstart run - one wants to read any input streams without reading the restart stream (which does not exist yet). This commit adds an optional argument to force mpas_stream_mgr_read to ignore INPUT_OUTPUT streams and only read truly INPUT streams. Its default value maintains the previous behavior. | 02 May 2022, 17:18:08 UTC |
| 54858fb | Azamat Mametjanov | 30 April 2022, 02:32:01 UTC | Split config_pesall into component-specific config_pes | 30 April 2022, 02:32:01 UTC |
| 87cb5bb | Jon Wolfe | 29 April 2022, 19:07:24 UTC | Merge branch 'jonbob/cpl/add-bgc-budget2' (PR #4885) Initial implementation of BGC carbon budget in the coupler Brings in a new coupler carbon budget which is implemented similarly to the current heat and water budgets, but in a separate source file. The output is intermingled with that from the other budgets, so that the monthly budget tables are all output before the annual ones, for example. The BGC budget is controlled overall by the BUDGETS flag found in env_run.xml but also has its own "do_bgc_budgets" flag that is included in the driver seq_infodata_inparm namelist and can be set by user_nl_cpl. By default it is off unless the compset includes BGC fluxes, in which case it is set to true. [NML] [BFB] | 29 April 2022, 19:07:24 UTC |
| 3044461 | Sarat Sreepathi | 29 April 2022, 17:04:48 UTC | run_e3sm.sh: Make it explicit for users to change case name [BFB] | 29 April 2022, 17:04:48 UTC |
| 8543cba | Sarat Sreepathi | 29 April 2022, 00:43:33 UTC | run_e3sm: case_group argument activated for create_newcase when valid | 29 April 2022, 00:43:33 UTC |
| e1e2c84 | Sarat Sreepathi | 29 April 2022, 00:22:45 UTC | run_e3sm script: Replace default case name and case group placeholders This is required to avoid unwarranted usage of case_group that interferes with aggregation of various production simulation campaigns. [BFB] | 29 April 2022, 00:22:45 UTC |
| fa9fef0 | Jon Wolfe | 28 April 2022, 19:35:29 UTC | Add support for northamericax4v1pg2_EC30to60E2r2 resolution | 28 April 2022, 19:35:29 UTC |
| 2778814 | Min Xu | 28 April 2022, 18:09:24 UTC | Merge branch 'sarats/machinefiles/summit-perf-archive2' (PR #4917) Set performance archive location to cli115 for everyone [BFB] | 28 April 2022, 18:09:24 UTC |
| b4b1bef | Nicole Jeffery | 28 April 2022, 16:14:29 UTC | Updates seaice BGC namelist defaults to match Registry defaults. 1.BGC parameter values have been tested in ocean-ice bgc sensitivity simulations for 200+ years. 2. Also turns on kill simulation if carbon conservation in sea ice fails bounds (only if BGC is active). Ran to completion in a 5 year GCASE with BGC active. Passed for restartability. non-BFB when BGC is active. BFB otherwise. | 28 April 2022, 16:14:29 UTC |
| ff5633a | Jon Wolfe | 28 April 2022, 15:18:23 UTC | Merge branch 'jonbob/data-models/solar-zenith-angle-correction' (PR #4589) Corrects the calculation of solar zenith angle, which was off by a timestep The solar zenith angle calculation used by the data models was off by one timestep. This issue was first reported by CESM in ESMCI Issue #3380 and subsequently fixed in ESCOMP PR #123. This PR implements that solution in E3SM. Fixes #4575 [non-BFB] for some configurations with data models | 28 April 2022, 15:18:23 UTC |
| 5d6c7b8 | Sarat Sreepathi | 27 April 2022, 22:16:50 UTC | Summit perf archive: set location to cli115 for all [BFB] | 27 April 2022, 22:16:50 UTC |
| e8c94b9 | Nicole Jeffery | 27 April 2022, 19:10:12 UTC | Corrected possible division by zero in ice bgc Fixes issue #4913 1. Sets BGC vertical diffusion to zero when ice thickness is small 2. Also removes trailing spaces in ice_brine.F90 BFB in 10 day test with BGC active. | 27 April 2022, 19:10:12 UTC |
| e25d6a7 | Min Xu | 27 April 2022, 03:09:39 UTC | Merge branch 'sarats/machinefiles/summit-perf-archive' (PR #4915) Previously only enabled for cli115, cli127. Performance archival for Walter's ALCC project (cli145) was not enabled. Included a wildcard entry to match any project. [BFB] | 27 April 2022, 03:09:39 UTC |
| ee6c7a4 | Sarat Sreepathi | 27 April 2022, 00:38:47 UTC | Enable performance archiving for all projects on Summit Previously only enabled for cli115, cli127. [BFB] | 27 April 2022, 00:38:47 UTC |
| 0b23c2f | Youngsung Kim | 26 April 2022, 19:28:49 UTC | added '-O1 -hfp0' flags for crayclang to reduce NaN-related errors | 26 April 2022, 19:28:49 UTC |
| d4f7c0b | Xylar Asay-Davis | 24 April 2022, 08:45:47 UTC | MPAS Standalone: Add OpenMP support to gnu-nersc For some reason this was omitted when OpenMP support was added 8 years ago. | 26 April 2022, 12:43:48 UTC |
| 1833a0d | Mark Petersen | 25 April 2022, 21:36:04 UTC | Add 1e-11 in denominator in Visbeck This is needed to prevent a divide by zero error when using Visbeck with certain meshes, like the QUwISC240. | 25 April 2022, 21:38:02 UTC |
| d36c7bc | Jon Wolfe | 25 April 2022, 19:35:42 UTC | Merge branch 'sbrus89/ocn/add-self-attraction-loading' (PR #4472) Add in-line self attraction and loading for global tidal simulation Self attraction and loading (SAL) forcing involves a spherical harmonic transform (SHT) of the SSH (Ray, 1998). The spherical harmonic coefficients are scaled by the load Love numbers, then an inverse transformation is performed to compute the SAL field. The SAL forcing is incorporated in the pressure gradient term along with the tidal potential. Two different approaches are implemented for performing the SHT: 1. SSH is gathered onto a single MPI rank and interpolated to a Gaussian mesh. A very fast library, SHTns, is used to compute the forward/inverse SHT. The SAL field is then interpolated back to the unstructured mesh and scattered back to the other MPI ranks. This work was done by @knbarton. 2. The SHT integration is performed on each subdomain and the SH coefficients are globally summed with an all-reduce. Approach 1 ) performs better at low core-counts, but 2) scales better for larger runs. This PR includes an init mode option for verification testing of the forward/inverse SHT. This work was done as a part of the tides task of the ICoM project. [NML] [BFB] for all standard E3SM tests | 25 April 2022, 19:35:42 UTC |
| cebe3f9 | James Foucar | 25 April 2022, 19:25:02 UTC | Merge branch 'jgfouca/cime_ninja_update' into master (PR #4911) Update CIME by one commit Needed to fix get_case_env [BFB] | 25 April 2022, 19:25:02 UTC |
| f92dd7e | James Foucar | 25 April 2022, 19:22:38 UTC | Update CIME by one commit Needed to fix get_case_env [BFB] | 25 April 2022, 19:22:38 UTC |
| 7492b8e | Mark Petersen | 25 April 2022, 17:36:39 UTC | Clarify Kappa variables in description | 25 April 2022, 17:36:39 UTC |
| bc29799 | Mark Petersen | 25 April 2022, 17:11:02 UTC | remove additional equalGM line | 25 April 2022, 17:11:02 UTC |
| 3bead91 | Azamat Mametjanov | 23 April 2022, 02:38:09 UTC | Merge branch 'azamat/chrys/throttle-bld-par' (PR #4909) Reduce parallel build jobs on Chrysalis down to 4 to reduce intel license errors. [BFB] | 23 April 2022, 02:38:09 UTC |
| f7950c8 | Azamat Mametjanov | 23 April 2022, 02:21:47 UTC | Reduce parallel build jobs on Chrysalis down to 4 | 23 April 2022, 02:21:47 UTC |
| 0996cfa | Mark Petersen | 21 April 2022, 19:33:24 UTC | Fix Redi resolution taper | 21 April 2022, 20:16:57 UTC |
| 284527b | Jon Wolfe | 21 April 2022, 17:56:32 UTC | Remove extraneous character | 21 April 2022, 17:56:32 UTC |
| abfdea1 | Jon Wolfe | 21 April 2022, 17:30:08 UTC | Add updates missed in mpas-ocean build-namelist file | 21 April 2022, 17:30:08 UTC |
| 88fd9c0 | Mark Petersen | 20 April 2022, 23:34:28 UTC | Remove config_Redi_closure='equalGM' | 20 April 2022, 23:34:28 UTC |
| a376631 | Oksana Guba | 20 April 2022, 22:16:44 UTC | Merge 'bartgol/homme/prevent-full-rebuild-due-to-sha-change' into next (PR #4889) Currently, in homme standalone mode, the GIT sha of the repo is stored in the config.h files. This means that if one adds a commit, and/or rewrites history, the sha changes. Since these files are included (directly or indirectly) by _a lot_ of other files in Homme, this cause basically a full rebuild of Homme. This PR allows to do changes that affect the git sha (such as amending a commit) without triggering a full rebuild of all execs/libs. I verified that the only files to be rebuilt are all the copies of namelist_mod, which is the only place that uses the GIT sha (printing it to screen for debug purposes). Side mod: when the var CPRNC_DIR is not set, Homme set it to the internal path to CIME's cprnc. However, recent changes in CIME changed the location of cprnc, so this path had to be adjusted. This only affects builds where the CPRNC_DIR var is _not_ set. If a mach file already stores CPRNC_DIR, nothing changes with this PR. [bfb] | 20 April 2022, 22:16:44 UTC |
| 1972b36 | Jon Wolfe | 20 April 2022, 17:19:34 UTC | Merge branch 'njeffery/seaice/update_carbon_analysis_member' (PR #4826) Update carbon conservation analysis member Brings in an updated seaice carbon conservation am that: * tracks individual ocean-ice carbon fluxes * computes accumulated error, relative errors, error bounds over the run * adds flag option to end the run if carbon errors exceed bounds * includes three additional diagnostics * adds molecular weight of carbon as a shared constant for all carbon conservation calculations * includes a non-BFB correction in merge-fluxes-bgc which uses the initial ice area to merge BGC fluxes rather than the ice area after step therm 1. Passes all tests in the sea ice testing suite. [NML] [non-BFB] only for runs with active sea ice BGC | 20 April 2022, 17:19:34 UTC |
| 083ccd2 | jayeshkrishna | 19 April 2022, 21:02:06 UTC | Merge branch 'dqwu/anlgce/update-modules' (PR #4873) Most GCE nodes have been upgraded from Ubuntu 18.04 to 20.04 and we need to update some modules and software libs accordingly to run E3SM on these nodes. A new machine name anlgce-ub18 is created to support two legacy GCE nodes (compute-01.cels.anl.gov and compute-02.cels.anl.gov) that still use Ubuntu 18.04. Open MPI support is also added for ANL GCE nodes in this PR. [BFB] | 19 April 2022, 21:02:06 UTC |
| 48e9195 | Peter Schwartz | 19 April 2022, 17:33:45 UTC | Merge branch 'jayeshkrishna/mosart_mean_mnth_flow_shrt_ckt_fix' (PR #4861) Since the Fortran standard does not support short circuit evaluation, avoiding indexing the array when the index can be <= 0. Fixes #4727 [BFB] | 19 April 2022, 17:33:45 UTC |
| bfcfece | Hyun-Gyu Kang | 19 April 2022, 15:18:14 UTC | Change a reproducible sum algorithm in SI solver Change a reproducible sum algorithm in the ocean split-implicit solver. The changed algorithm uses a global reproducible summation module in components/mpas-framework/src/framework/mpas_global_sum_mod.F | 19 April 2022, 15:18:14 UTC |
| e3098ee | Jason Sarich | 19 April 2022, 15:14:40 UTC | Merge branch 'azamat/chrys/update-openmpi-4.1.3' (PR #4890) Update Chrysalis to OpenMPI-4.1.3 Addresses #4819 [BFB] | 19 April 2022, 15:14:40 UTC |
| 72ac093 | Mark Petersen | 16 April 2022, 04:02:11 UTC | Add more comments | 16 April 2022, 04:02:11 UTC |
