| b25e37f | Jon Wolfe | 18 October 2023, 19:04:38 UTC | Merge branch 'xylar/machinefiles/update-chicoma-cpu' (PR #5986) Update modules for chicoma-cpu Several modules are no longer available after a recent machine upgrade. [BFB] | 18 October 2023, 19:04:38 UTC |
| f703513 | Jon Wolfe | 18 October 2023, 18:59:30 UTC | Merge branch 'darincomeau/ice/add-cice-qc-testing' (PR #5969) Add CICE-QC testing script Adds a script to perform "CICE-QC" test, which determines if non-BFB changes in the sea ice model are climate-changing. This has been adapted from the CICE implementation for MPAS-Seaice. Documentation on usage is provided in a README.md alongside test script. [BFB] | 18 October 2023, 18:59:30 UTC |
| 1cab48c | Wuyin Lin | 18 October 2023, 16:41:35 UTC | Fixed SSP585 surfdata filename | 18 October 2023, 16:41:35 UTC |
| 9ed66d9 | Wuyin Lin | 17 October 2023, 22:01:17 UTC | Update lnd surfdata to use TOP for ne30pg2 and r05 with workaround for wcprod tests | 17 October 2023, 22:01:17 UTC |
| cb073b9 | noel | 17 October 2023, 20:36:19 UTC | For NERSC machines only, update to latest AMD compiler Add some modules to remove before loading what we want. | 17 October 2023, 20:36:19 UTC |
| 9a5d441 | James Foucar | 17 October 2023, 17:00:00 UTC | Add jenkins save timing to cime update | 17 October 2023, 17:00:00 UTC |
| f963238 | noel | 17 October 2023, 16:11:09 UTC | Merge branch E3SM-Project/ndk/machinefiles/pm-cpu-remove-pelayout-workaround (PR #5971) For pm-cpu/alvarez, adjust pelayouts to remove performance work-around with CPL_PSTRID after maintenance | 17 October 2023, 16:11:09 UTC |
| 8e84f5a | Walter Hannah | 16 October 2023, 19:54:44 UTC | allow SCM cases to use default ncdata | 16 October 2023, 19:54:44 UTC |
| 94822ce | James Foucar | 16 October 2023, 19:45:54 UTC | Try setting hdf5 path explicitly | 16 October 2023, 19:45:54 UTC |
| 6b75a3a | James Foucar | 16 October 2023, 19:28:48 UTC | Fix cmake_opts mistake | 16 October 2023, 19:28:48 UTC |
| 2236937 | Azamat Mametjanov | 16 October 2023, 19:04:55 UTC | Merge branch 'azamat/sunspot/update-oneapi-20230515007' (PR #5881) Update Sunspot's OneAPI compiler to 2023.05.15.007 . Also, - add netcdf libs to LD_LIBRARY_PATH after recent CMake updates - rearrange modules by loading defaults after module purge - clean up cmake Fixes E3SM-Project/E3SM#5707 [BFB] | 16 October 2023, 19:04:55 UTC |
| 78b2fe8 | Bryce Harrop | 16 October 2023, 17:20:33 UTC | Added in ifdefs to avoid errors related to MACv2 when not running MMF | 16 October 2023, 17:27:51 UTC |
| 24276fc | Bryce Harrop | 23 May 2023, 21:02:38 UTC | Cleaned up the code and fixed an indexing issue | 16 October 2023, 17:27:51 UTC |
| 8cca060 | Bryce Harrop | 19 May 2023, 21:29:31 UTC | MACv2 implementation working for direct radiative effect. Still needs code cleanup and indirect effect will need to be added in the future for P3 microphysics | 16 October 2023, 17:27:51 UTC |
| 728504a | Bryce Harrop | 10 May 2023, 23:35:25 UTC | Stapled in macv2 changes. Need to edit radiation to make functional still | 16 October 2023, 17:27:51 UTC |
| b22c83b | James Foucar | 16 October 2023, 17:06:28 UTC | Update CIME submodule ... to 88255d5a5a1b160ec523a95fd26d6be079c54935 Changes: 1) Copy only necessary cmake macros to case 2) Update ESMCI docker, no impact to E3SM 3) update instructions for building cprnc with cmake 4) Updates how performance baselines are created and compared! Fixes: 1) Fixes workflow job dependencies 2) Fixes ww3 archiving [BFB] | 16 October 2023, 17:06:28 UTC |
| f85ea21 | donghuix | 16 October 2023, 17:04:31 UTC | address comments | 16 October 2023, 17:04:31 UTC |
| d9c80c3 | James Foucar | 16 October 2023, 16:56:52 UTC | Fix circleCI to refer to correct PIO build name | 16 October 2023, 16:56:52 UTC |
| 15b7889 | Walter Hannah | 16 October 2023, 15:32:01 UTC | Merge remote-tracking branch 'origin/master' into whannah/atm/add-L80-support | 16 October 2023, 15:32:01 UTC |
| 89e8388 | Andrew Roberts | 16 October 2023, 14:19:53 UTC | Tidying up branch to also include update to ice coupling documentation | 16 October 2023, 14:19:53 UTC |
| db2cac0 | Azamat Mametjanov | 14 October 2023, 01:38:46 UTC | Update Depends file Update Depends file - don't need `-fc=ifort` any more, newer ifx can build 50K+ line sources - move OpenMP-offload to GPU-enabled CIME compiler | 14 October 2023, 01:38:46 UTC |
| d61fb8e | dqwu | 11 October 2023, 22:27:20 UTC | Update and remove ADIOS2_ROOT for some E3SM machines To facilitate testing of the ADIOS IO type, ADIOS2_ROOT is now configured on the following machines: Perlmutter, Frontier, Summit, and ANL GCE workstations. Additionally, the ADIOS2 library has been upgraded from version 2.8.3 to 2.9.1 on these machines. Existing ADIOS2_ROOT configurations have been removed on specific machines, including Chrysalis, Anvil, Bebop, and Compy. | 14 October 2023, 00:07:00 UTC |
| 0fd8844 | jayeshkrishna | 13 October 2023, 23:15:45 UTC | Merge branch 'jayeshkrishna/externals/scorpio_1_4_2' (PR #5991) Upgrading SCORPIO from 1.4.1 to 1.4.2 SCORPIO v1.4.2 release includes the following fixes over v1.4.1, * Performance tuning (file striping settings) for Frontier * ADIOS performance improvements and fixes [BFB] | 13 October 2023, 23:15:45 UTC |
| f6f7b13 | Azamat Mametjanov | 13 October 2023, 23:07:04 UTC | Merge branch 'azamat/machines/add-gnu-invalid-check' (PR #5808) Add check for invalid fp-ops for GNU in debug mode. Also, fix ncol/pcol indexes in 2 eam-chemistry subroutines (flagged by `-ffpe-trap=invalid`). [non-BFB] - in fully-coupled tests | 13 October 2023, 23:07:04 UTC |
| cff4226 | James Foucar | 13 October 2023, 22:36:47 UTC | Merge branch 'jgfouca/pm_cpu_gnu_lapack_blas' into master (PR #5998) pm-cpu/gnu use Generic blas/lapack Not the 'implicitly linked' ones. This fixes DIFFs. | 13 October 2023, 22:36:47 UTC |
| 396bcb4 | James Foucar | 13 October 2023, 22:34:47 UTC | pm-cpu/gnu use Generic blas/lapack Not the 'implicitly linked' ones. This fixes DIFFs. | 13 October 2023, 22:34:47 UTC |
| 95a13d9 | James Foucar | 13 October 2023, 22:07:11 UTC | Merge branch 'jgfouca/ascent_summit_blas' into master (PR #5995) Fix blas/lapack on ascent/summit Tell cmake to use Generic so it doesn't think ESSL is sufficient. [BFB] | 13 October 2023, 22:07:11 UTC |
| 67e2180 | James Foucar | 13 October 2023, 22:04:07 UTC | PIO: Remove dependence on CIME/Tools/Makefile We need to remove all dependencies on CIME/Tools/Makefile so we can change our macros to use cmake-style names for things. PIO/Scorpio was the first thing I picked. The situation with spio was strange. It was using CIME/Tools/Makefile to call CMake. It translated the Makefile-style settings to Cmake using a lot of extra code in the Makefile to set up CMAKE_OPTS. We change the python wrapper build script, buildlib.spio, to instead just set up the cmake options in python, allowing us to skip the CIME/Tools/Makefile. On top of removing the dependency, I think this makes the overall spio build a lot easier to understand, although it was a bit tedious pulling things out of the macros. Once the macros are in proper cmake-stype, I think we could just pass them directly to scorpio's CMake build via -C and things will be even simpler. [BFB] | 13 October 2023, 22:04:07 UTC |
| 91b23a3 | Walter Hannah | 13 October 2023, 21:18:43 UTC | remove compsets with unused chemsitry options | 13 October 2023, 21:18:43 UTC |
| 9e6d115 | James Foucar | 13 October 2023, 21:16:17 UTC | Fix blas/lapack on ascent/summit Tell cmake to use Generic so it doesn't think ESSL is sufficient. [BFB] | 13 October 2023, 21:16:17 UTC |
| 5568147 | Walter Hannah | 13 October 2023, 21:03:52 UTC | remove "-P3" compsets | 13 October 2023, 21:03:52 UTC |
| 043a5aa | Walter Hannah | 13 October 2023, 21:02:56 UTC | update v3 intergration tests | 13 October 2023, 21:02:56 UTC |
| 97e527f | Azamat Mametjanov | 13 October 2023, 20:50:36 UTC | Merge branch 'azamat/anvil/update-e3sm-prod-PEs' (PR #5987) Update Anvil config to fix OOM and link errors - Fix csm_share link errors - Update Anvil cmake 3.20.3->3.26.3 - Update Anvil e3sm_prod PEs to avoid OOM errors [BFB] | 13 October 2023, 20:50:36 UTC |
| 235a851 | Wuyin Lin | 13 October 2023, 20:44:54 UTC | Merge branch 'yunpengshan2014/E3SM/P3SedimenttaionFluxChange' (PR #5891) Fix the calculations of p3 sedimentation fluxes Original calculation in the P3 code: the precipitation (rain and snow) flux (sflx for snow ) is summed over the flux at each sub-timestep during one microphysics timestep: sflx=flux_qit_1+ flux_qit_2+ flux_qit_3+… flux_qit_n, where the flux_qit_i (i=1,2,3,…n) represents the snow flux at each sub-timestep for sedimentation. This should not be correct. The correct flux should be the mean value for each microphysics timestep. Changed calculation in the current version: In E3SM-P3, since the sub-timestep is not a fixed value, the mean flux over the microphysics timestep should be calculated with: sflx=(flux_qit_1dt1+ flux_qit_2dt2+ flux_qit_3dt3+… flux_qit_ndtn)/( dt1+ dt2+ dt3+… dtn), where dti represents sub-timestep length. This is similar to the equation used to calculate the surface precipitation rate. This PR does not effect the model simulation results, but only change the diagnostic precipitation flux output. [BFB] for simulation results, COSP output affected. | 13 October 2023, 20:44:54 UTC |
| d98c4fc | Wuyin Lin | 13 October 2023, 20:42:58 UTC | Merge branch 'wlin/atm/ssp_tentativefix' (PR #5965) Implemented a tentative fix for SSP tests Future scenario forcing files for new species introduced by v3atm are not ready. The cime SSP tests using default v3 configuration therefore failed to be created. The tentative fix uses config that mixes v3 physics with v2 chemistry. Also fixed a couple misuses of eqv operator in linoz-related code that do not properly consider the precedence relative to AND/OR operators. The misuses have no impact on default v3 configuration, but would cause fatal runtime error when using the hybrid configuration as implemented here. [BFB] for existing tests. | 13 October 2023, 20:42:58 UTC |
| 6be429d | Andrew Roberts | 13 October 2023, 20:30:38 UTC | Replace pbot with pslv as atmospheric pressure coupling field for the ocean | 13 October 2023, 20:30:38 UTC |
| 495ba1d | James Foucar | 13 October 2023, 18:22:39 UTC | Merge branch 'jgfouca/fix_pm_intel_blas' into master (PR #5993) Fix MKL linking on pm-cpu_intel Need to tell cmake to use Intel vendor for blas. [BFB] | 13 October 2023, 18:22:39 UTC |
| a6a9d6f | Walter Hannah | 13 October 2023, 17:35:13 UTC | add L80 ncdata defaults for ne4 and ne30 | 13 October 2023, 17:35:13 UTC |
| 3494eec | Walter Hannah | 13 October 2023, 17:34:41 UTC | add L80 default for v3 and clean up config_components | 13 October 2023, 17:34:41 UTC |
| dc5947c | Elizabeth Hunke | 13 October 2023, 16:25:20 UTC | Merge pull request #43 from eclare108213/move_submodule updating icepack to hash 8fad768 on main | 13 October 2023, 16:25:20 UTC |
| a063972 | James Foucar | 13 October 2023, 16:17:38 UTC | Fix MKL linking on pm-cpu_intel Need to tell cmake to use Intel vendor for blas. [BFB] | 13 October 2023, 16:19:59 UTC |
| 79cc95c | Elizabeth Hunke | 13 October 2023, 15:27:47 UTC | updating icepack to hash 8fad768 on main | 13 October 2023, 15:27:47 UTC |
| 3f78dfa | Azamat Mametjanov | 13 October 2023, 00:31:18 UTC | Add netcdf libs to LD_LIBRARY_PATH after recent CMake updates Also rearrange modules by loading defaults after module purge and clean up cmake. | 13 October 2023, 00:31:18 UTC |
| 2a93b58 | Azamat Mametjanov | 15 August 2023, 00:12:52 UTC | Update Sunspot's OneAPI compiler to 2023.05.15.007 | 12 October 2023, 22:28:04 UTC |
| 0dfc07f | Azamat Mametjanov | 12 October 2023, 21:40:59 UTC | Update Anvil e3sm_prod PEs for in test-PEs Also remove `-mkl` from link line after CMake BLAS updates | 12 October 2023, 21:40:59 UTC |
| 26e5834 | Gautam Bisht | 12 October 2023, 18:23:10 UTC | Second attempt at fixing bmatrix equation | 12 October 2023, 18:41:08 UTC |
| 81e7ff4 | Gautam Bisht | 12 October 2023, 18:12:01 UTC | Fixes one more equation | 12 October 2023, 18:41:08 UTC |
| dbee7a8 | Gautam Bisht | 12 October 2023, 18:09:11 UTC | Fixes eqnarray for Github | 12 October 2023, 18:41:08 UTC |
| 97f4117 | Gautam Bisht | 12 October 2023, 18:01:09 UTC | Changes how equations are defined | 12 October 2023, 18:41:07 UTC |
| 91de0a4 | Gautam Bisht | 11 October 2023, 03:15:27 UTC | Updates references | 12 October 2023, 18:41:07 UTC |
| 77e8477 | Gautam Bisht | 11 October 2023, 02:02:57 UTC | Adds labels to equations and cross-references | 12 October 2023, 18:41:07 UTC |
| 5cbabd7 | Gautam Bisht | 11 October 2023, 00:07:56 UTC | Adds mathjax.js for equation numbering | 12 October 2023, 18:41:07 UTC |
| 198a31d | Naser Mahfouz | 10 October 2023, 18:41:22 UTC | add mkdocs-bibtex to pip install | 12 October 2023, 18:41:07 UTC |
| d5c4bd3 | Gautam Bisht | 10 October 2023, 18:18:38 UTC | Initial commit of TOP parameterization documentation | 12 October 2023, 18:41:07 UTC |
| c03531a | Gautam Bisht | 12 October 2023, 18:40:46 UTC | adds syntax highlighting | 12 October 2023, 18:40:46 UTC |
| ed32fda | jayeshkrishna | 12 October 2023, 18:33:47 UTC | Upgrading SCORPIO to 1.4.2 Upgrading SCORPIO from 1.4.1 to 1.4.2 SCORPIO v1.4.2 release includes the following fixes over v1.4.1, * Performance tuning (file striping settings) for Frontier * ADIOS performance improvements and fixes | 12 October 2023, 18:33:47 UTC |
| 6223567 | James Foucar | 12 October 2023, 17:34:49 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/more_cmake_cleanup * origin/master: (325 commits) Set mappy to use generic blas blas/lapack settings should not depend on mpilib Refactor blas and lapack stuff a bit more revert fix for gravity wave convective heating Add back in kokkos options Revert to master version of gnugpu_pm-gpu.cmake add Kokkos_ENABLE_OPENMP=Off for gnugpu on pm-gpu add Kokkos_ENABLE_OPENMP=Off for gnugpu on Frontier add Kokkos_ENABLE_OPENMP=Off for Summit remove configure support for MMF m2005 microphysics configure clean up and remove samomp support add new lines re-enable CRM variance and momentum transport for MMF1 add new line at end of pam_debug update default PAM time step update PAM submodule disable kokkos finalize in PAM driver add hyperdiffusion to PAM and refactor PAM driver update pam_statistics refactor pam_output ... | 12 October 2023, 17:34:49 UTC |
| 14d8fa1 | James Foucar | 12 October 2023, 17:13:48 UTC | Merge branch 'jgfouca/cmake_blas_lapack' into master (PR #5972) Convert blas/lapack/mkl to new cmake style This was a more challenging task than I thought it would. FindBLAS / FindLAPACK are built in to cmake and can also handle MKL stuff via the BLA_VENDOR setting (if you set it to Intel... you get various flavors of MKL). The find_package for blas/lapack is pretty smart and should do the right thing most of the time. Machine POCs should refine the settings on their machines using https://cmake.org/cmake/help/latest/module/FindBLAS.html#blas-lapack-vendors as as guide. I suspect many of these cache files were copy/pasted without a ton of consideration. As an example, pm-cpu_nvidia is one platform where you will get DIFFs if you don't use the right blas/lapack. To set this up, I added the following to the environment block for that machine/compiler combo: <environment_variables compiler="nvidia"> <env name="BLAS_ROOT">$SHELL{if [ -z "$BLAS_ROOT" ]; then echo /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers; else echo "$BLAS_ROOT"; fi}</env> <env name="LAPACK_ROOT">$SHELL{if [ -z "$LAPACK_ROOT" ]; then echo /opt/nvidia/hpc_sdk/Linux_x86_64/22.7/compilers; else echo "$LAPACK_ROOT"; fi}</env> <env name="BLA_VENDOR">NVHPC</env> </environment_variables> The documentation indicates that the find modules for blas may be smart enough to auto detect the bla_vendor: BLA_VENDOR Set to one of the [BLAS/LAPACK Vendors] to search for BLAS only from the specified vendor. If not set, all vendors are considered. Once again, I am impressed at how much clutter is removed when we do things t "right" (using find_package instead of packing stuff into SLIBS) way. [BFB] | 12 October 2023, 17:13:48 UTC |
| bcd8798 | James Foucar | 12 October 2023, 17:04:16 UTC | Set mappy to use generic blas | 12 October 2023, 17:04:16 UTC |
| c64b721 | Gautam Bisht | 12 October 2023, 04:18:54 UTC | Updates ELM surface datasets for few resolutions Surface datasets dataset for following resolutions have been updated to include new fields needed for TOP parameterization in ELM: - ne4_oQU240 - ne4pg2_oQU480 - northamericax4v1pg2_WC14to60E2r3 | 12 October 2023, 04:18:54 UTC |
| d9e1400 | Wuyin Lin | 11 October 2023, 22:29:34 UTC | Revert "Revert "Merge branch 'jonbob/seaice/fix-ir-zero-check' (PR #5252)"" This reverts commit 40a7f522369aaf4c8d3d643d0f90d9219b71a633. | 11 October 2023, 22:29:34 UTC |
| 26170af | James Foucar | 11 October 2023, 21:35:43 UTC | blas/lapack settings should not depend on mpilib | 11 October 2023, 21:35:43 UTC |
| 23e9e30 | James Foucar | 11 October 2023, 21:30:20 UTC | Refactor blas and lapack stuff a bit more Get rid of all the BLA_VENDOR stuff in the macros. It had no impact because deps are loading before macros are processed. We should prefer using the environment to set this stuff like we are doing for the other libs. pm-cpu_nvidia seems to be the one platform sensitive to lapack/blas so can be used as an example of how to specify these libraries. | 11 October 2023, 21:30:20 UTC |
| 613312c | Azamat Mametjanov | 11 October 2023, 20:52:14 UTC | Update Anvil e3sm_prod PEs to avoid OOM errors. | 11 October 2023, 20:52:14 UTC |
| 048078f | Azamat Mametjanov | 11 October 2023, 20:46:46 UTC | Update Anvil cmake 3.20.3->3.26.3 Also disable test archiving on Bebop and Anvil. | 11 October 2023, 20:46:46 UTC |
| 9525073 | Azamat Mametjanov | 11 October 2023, 20:36:07 UTC | Fix csm_share link errors Link to MKL single dynamic library with `-mkl` to avoid undefined references to Intel's vector math routines vdsqrt, vdexp and others in csm_share. | 11 October 2023, 20:36:07 UTC |
| a8b5b59 | Elizabeth Hunke | 11 October 2023, 20:01:19 UTC | Merge pull request #42 from eclare108213/icepack_default Set Icepack as the default column physics package in MPAS-SI | 11 October 2023, 20:01:19 UTC |
| 99a3acc | Xylar Asay-Davis | 31 August 2023, 10:47:13 UTC | Update intel cmake macros for chicoma | 11 October 2023, 18:09:29 UTC |
| a36c7d6 | Walter Hannah | 15 August 2023, 21:24:32 UTC | bug fix | 11 October 2023, 18:03:42 UTC |
| 6eb65d9 | Walter Hannah | 07 August 2023, 22:48:29 UTC | add hdepth_scaling_factor namelist parameter | 11 October 2023, 18:03:42 UTC |
| c18e11b | Xylar Asay-Davis | 30 August 2023, 10:10:56 UTC | Update modules for chicoma-cpu | 11 October 2023, 18:01:35 UTC |
| 8a14ed5 | Xylar Asay-Davis | 30 August 2023, 10:03:26 UTC | Fix trailing whitespace | 11 October 2023, 18:01:35 UTC |
| f090e7d | Walter Hannah | 11 October 2023, 14:37:37 UTC | update conv GW input heating to remove radiation | 11 October 2023, 14:37:37 UTC |
| 7f86c16 | Sean Patrick Santos | 01 August 2023, 00:24:58 UTC | Prevent ELM from adding extra gustiness when EAM supplies gustiness. When EAM is running, it provides a gustiness value that includes the effects of boundary layer turbulence. This is redundant with the calculation of convective gustiness `wc` that is performed by ELM. See #5837. This commit turns off the calculation of `wc` when the `atm_gustiness` namelist variable is set, signifying that EAM is providing the gustiness value. This commit also adds the `force_land_gustiness` option to ELM. This option forces the old behavior, where ELM adds gustiness regardless of what the atmosphere model does. [CC] for cases where EAM is running, should be bit-for-bit otherwise. Expected effect is to increase wind speeds over land, and likely reduce surface fluxes a bit when wind speed is low. [NML] | 10 October 2023, 23:05:43 UTC |
| 5813d41 | Sean Patrick Santos | 31 July 2023, 23:16:07 UTC | Remove gustiness from U10 and add U10WITHGUSTS. The E3SM wind at the 10 meter reference level (an output from the atmosphere, land, and sea ice components) has previously included the effects of gustiness, but this is not correct for comparison to most other data sets. This commit therefore removes the effect of gustiness from these outputs. See #5836. Note that MPAS-Ocean does not output such a wind itself, only the mean-squared wind, which is used solely to determine flux of tracers and should in fact include gustiness. Therefore, MPAS-Ocean has not been changed. This change applies to both atmosphere-calculated gustiness, and the land-calculated gustiness used in cases where ELM is active but EAM is not. (E.g. in ELM, both `ugust` from the atmosphere and `wc` from ELM are removed from ELM's u10 calculation.) The removal of the gustiness is accomplished by changes that effectively multply u10 by a factor of `ubot / sqrt(ubot^2 + ugust^2 + wc^2)` where `ubot` is the resolved wind speed in the atmosphere's lowest level. Similar expressions (without the `wc` term) are used in the ocean coupling code. Since the gustiness parameterization is not currently used by MPAS-Seaice, the 10 meter reference wind speed output by the sea ice is not changed by this commit. For those cases where a gustiness-enhanced output may be useful, for instance where it is desirable to know which wind was used to calculate surface energy fluxes, or for comparison to previous model versions. This commit therefore adds the diagnostic output U10WITHGUSTS to EAM. This is defined identically to to the old definition of U10. [non-BFB], but only the U10 outputs of EAM and ELM should be affected, and only in cases where EAM or ELM are used. | 10 October 2023, 23:00:28 UTC |
| ff839a7 | Sean Patrick Santos | 31 July 2023, 22:27:30 UTC | Fix incorrect wind "addition" in gustiness calculations. As described in Ma et. al. (2022), the correct equation for combining two sources of gustiness with the resolved wind speed is U^2 = U0^2 + a UZM^2 + b UCLUBB^2 where U is the desired gustiness-enhanced wind, and * U0 is resolved wind. * UZM is deep convective gustiness. * UCLUBB is turbulent/boundary-layer gustiness. * a and b are tuning parameters. The prior implementation did not follow this formula (see #5835), by failing to properly account for the squaring of each wind speed in the formula (or in the case of UCLUBB, accounting for it incorrectly). This commit fixes that bug. Note that the parameters "a" and "b" also no longer multiply the diagnostic outputs 'VMAGDP' and 'VMAGCL'. This results in output that is more consistent with the literature, though less consistent with previous model versions. Multiplying by sqrt(a) and sqrt(b) can easily be done in post-production, however. This commit also allows atm_gustiness to be used with downscaling in ELM; previously, these features were not allowed to be combined, but that restriction appears to have been unnecessary. Ma et. al. (2002): https://doi.org/10.5194/gmd-15-2881-2022 Reported-by: @mabrunke [CC] for all configurations with EAM, but should be bit-for-bit for all other configurations. Expected effect is a reduction in the effect of gustiness, resulting in larger resolved wind speeds but smaller surface fluxes where the resolved wind speed is still low. | 10 October 2023, 22:50:22 UTC |
| b73b77f | Sean Patrick Santos | 31 July 2023, 06:14:28 UTC | Make ATM_SUPPLIES_GUSTINESS=TRUE the default/only option for EAM. The ATM_SUPPLIES_GUSTINESS XML variable governs whether the atmosphere model exports a "gustiness" wind speed to the other components. It is now always set to TRUE for EAM runs, except for SCREAM runs. (SCREAM has not implemented its own gustiness parameterization yet.) The ATM_SUPPLIES_GUSTINESS=TRUE setting is required for EAM, rather than simply the default, because the old behavior where ATM_SUPPLIES_GUSTINESS=FALSE was considered buggy. Specifically, it caused surface components to return a "scalar" averaged stress rather than a vector stress to the atmosphere, potentially resulting in unphysical discontinuities in the returned stress vector. See #5834, which documented this scalar/vector mixup. This bug did not affect SCREAM or any compset where EAM is disabled (e.g. with data atmosphere), and those configurations should be unaffected (bit-for-bit). [CC] for EAM cases. This change is expected to cause an increase in average near-surface wind speeds, and hence also an increase in surface fluxes. [NML] | 10 October 2023, 22:34:36 UTC |
| a093fa2 | James Foucar | 10 October 2023, 20:29:20 UTC | Clean up remaining cmake deps | 10 October 2023, 20:29:20 UTC |
| 94dadc0 | Elizabeth Hunke | 10 October 2023, 20:11:09 UTC | Merge branch 'eclare108213/seaice/icepack-integration' of github.com:eclare108213/E3SM into icepack_default | 10 October 2023, 20:11:09 UTC |
| b5a16aa | Elizabeth Hunke | 10 October 2023, 20:08:24 UTC | make Icepack the default column physics package | 10 October 2023, 20:08:24 UTC |
| 732e699 | Benjamin Hillman | 10 October 2023, 20:00:05 UTC | Merge branch 'whannah/mmf/pam-impl' (#5906) ntegration of new CRM for MMF, referred to as the "portable atmosphere model" or PAM, that uses the P3 and SHOC physics implementation from SCREAM/EAMxx. The new CRM is used by the compsets with "MMF2" in their name. While the PAM code is isolated to a submodule, several large changes outside were required to facilitate this integration. The PAM interface code is a substantial part of this, but there was also new conflicts created by EAMv3 integration efforts which led to the creation of various "dummy" modules to avoid building the conflicting modules, which are unnecessary for MMF. A new integration is added to test the new CRM => SMS_Ln3.ne4pg2_ne4pg2.F2010-MMF2 A few things to note about the current MMF2 implementation - When running with PAM on the GPU the use of openMP threads is problematic for reasons that are unclear. This seems fixable, but more work is needed to look into this. For now, running on GPUs without OMP threads is sufficient, and CPU cases are not affected by this problem - Although some offline PAM tests have used longer time steps, when running within the MMF configuration at ne30 the PAM time step needs to be 4 seconds for stability. A lot of performance can be gained by increasing this time step, but more work is needed to understand the source of the instability. - PAM performance also seems highly machine dependent. For example, using 22 nodes on Perlmutter runs 6x faster than 64 nodes on Summit for the same case. [BFB] | 10 October 2023, 20:00:05 UTC |
| 9b40b2d | James Foucar | 10 October 2023, 16:48:35 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cmake_blas_lapack * origin/master: Fix nvidia_pm-cpu diffs for some tests Fix PIO dep on mpi-serial add ghp preview | 10 October 2023, 16:48:35 UTC |
| e195c80 | James Foucar | 10 October 2023, 16:43:27 UTC | Merge branch 'jgfouca/fix_nvidia_pm_cpu_diffs' into master (PR #5976) Fix nvidia_pm-cpu diffs for some tests Be explicit about which hdf5 and blas/lapack libraries to link so that later -L options don't mess things up. Also, make some minor enhancements to the compare-flags tool in order to get more useful output when comparing unordered flags. [BFB] | 10 October 2023, 16:43:27 UTC |
| 85addcc | James Foucar | 10 October 2023, 16:40:57 UTC | Merge branch 'jgfouca/fix_mpi_serial_link' into master (PR #5975) Fix PIO dep on mpi-serial PIO needs to depend on mpi-serial in order for the link order to be correct. [BFB] | 10 October 2023, 16:40:57 UTC |
| 40b1347 | Gautam Bisht | 10 October 2023, 14:06:51 UTC | Minor updates | 10 October 2023, 14:06:51 UTC |
| 003959d | Gautam Bisht | 10 October 2023, 03:50:46 UTC | Adds notes on running e3sm land developer testsuite | 10 October 2023, 03:50:46 UTC |
| ddf0c37 | Walter Hannah | 09 October 2023, 22:12:30 UTC | revert fix for gravity wave convective heating | 09 October 2023, 22:12:30 UTC |
| c4e81db | James Foucar | 09 October 2023, 21:20:18 UTC | Fix nvidia_pm-cpu diffs for some tests Be explicit about which hdf5 and blas/lapack libraries to link so that later -L options don't mess things up. Also, make some minor enhancements to the compare-flags tool in order to get more useful output when comparing unordered flags. [BFB] | 09 October 2023, 21:20:18 UTC |
| 05cbb2e | James Foucar | 09 October 2023, 21:13:54 UTC | Fix PIO dep on mpi-serial PIO needs to depend on mpi-serial in order for the link order to be correct. [BFB] | 09 October 2023, 21:13:54 UTC |
| 2f2639c | Benjamin Hillman | 09 October 2023, 18:50:54 UTC | Add back in kokkos options | 09 October 2023, 18:50:54 UTC |
| b39578d | Benjamin Hillman | 09 October 2023, 18:49:53 UTC | Revert to master version of gnugpu_pm-gpu.cmake | 09 October 2023, 18:49:53 UTC |
| 4d82d99 | James Foucar | 09 October 2023, 18:31:40 UTC | Update minimum cmake | 09 October 2023, 18:31:40 UTC |
| 589f08c | Robert Jacob | 09 October 2023, 18:07:34 UTC | Merge branch 'mahf708/docs/improve-gh-pages-docs' (PR #5951) Adds docs preview to PR page. Preview appears in a comment. This workflow will update the same comment if there are changes (it won't pollute the PR page with more comments). Additionally, I spaced out the GitHub action so that it is easier to read and maintain (and shortened the names) [BFB] | 09 October 2023, 18:07:34 UTC |
| 8057ebc | donghuix | 09 October 2023, 15:45:25 UTC | add tests in elm for surface water dynamics with calibrated parameters for NLDAS domain | 09 October 2023, 15:45:25 UTC |
| 6fe63a4 | donghuix | 09 October 2023, 14:54:22 UTC | debug fover, need to remove _r8 to keep it consistent with master | 09 October 2023, 14:54:22 UTC |
| b4fbcd7 | Elizabeth Hunke | 09 October 2023, 14:03:16 UTC | Merge pull request #41 from eclare108213/config_colpkg_physics Replace config_use_column_package with config_use_column_physics | 09 October 2023, 14:03:16 UTC |
| eecfaf4 | Elizabeth Hunke | 09 October 2023, 14:01:30 UTC | Merge pull request #40 from eclare108213/mpas_namelist Adds and amends critical parameters to MPAS - ice-ocean drag, snow conductivity | 09 October 2023, 14:01:30 UTC |
| d936aee | Naser Mahfouz | 08 October 2023, 21:51:58 UTC | use updated container with singularity | 08 October 2023, 23:17:48 UTC |
| 0b2fcd2 | Andrew Roberts | 08 October 2023, 22:19:48 UTC | Replace config_use_column_package with config_use_column_physics to avoid confusion with Icepack | 08 October 2023, 22:19:48 UTC |
| 01d79a5 | Andrew Roberts | 08 October 2023, 16:06:16 UTC | Bug fix - removal of line continuation | 08 October 2023, 16:06:16 UTC |
