| 6175cb7 | Jon Wolfe | 20 March 2019, 14:46:42 UTC | Merge branch 'xylar/mpaso/fix_jigsaw_in_compass' (PR #2797) Update MPAS source for fixes to V2 mesh generation in MPAS-O (COMPASS) This pull request fixes two issues with generating E3SM V2 meshes in MPAS's COMPASS testing suite: * The meshes are now reproducible because we use the same random seed each time * Cells are no longer culled based on a bathymetry needed only for coastal test case. [BFB] | 20 March 2019, 14:46:42 UTC |
| 446913f | Gautam Bisht | 20 March 2019, 14:05:35 UTC | Merge branch 'rgknox/lnd/fates-api-7' (PR #2754) This updates the interface with FATES to match is most recent api release. Major API changes were needed to accommodate hydraulics in dynamic plants. [non-BFB] | 20 March 2019, 14:05:35 UTC |
| 4db256d | James Foucar | 19 March 2019, 15:59:12 UTC | Merge branch 'jgfouca/cime/fix_input_issues' into master (PR #2808) Fix some issues with downloading input files We (e3sm) don't have chksum files set up yet. Also, remove old input data server from XML. [BFB] * jgfouca/cime/fix_input_issues: Remove dupe Fix some issues with downloading input files Update CIME to ESMCI cime5.8.0 (#2799) | 19 March 2019, 16:00:42 UTC |
| d11ddfc | James Foucar | 19 March 2019, 15:53:09 UTC | Remove dupe | 19 March 2019, 15:53:09 UTC |
| 162b323 | James Foucar | 19 March 2019, 15:39:34 UTC | Fix some issues with downloading input files We (e3sm) don't have chksum files set up yet. Also, remove old input data server from XML. [BFB] | 19 March 2019, 15:39:34 UTC |
| 3eebd7f | James Foucar | 19 March 2019, 14:26:21 UTC | Update CIME to ESMCI cime5.8.0 (#2799) Update CIME to ESMCI cime5.8.0 Squash merge of jgfouca/branch-for-to-acme-2019-03-12 Features: * Better handling of file permissions when copying files * Minor JRA & CORE2 DATM forcing changes * Modifications to allow for E3SM developer tests for the SE SCM * Report missing variables in cprnc * Merge to latest pio2 version * update NYF CORE2 DROF data stream file. (non-BFB) * Refactor communication between build.py and Makefile: use cmd-line args instead of environment vars. * Implement share field for e3sm test suites * Implement support for checksums when download input data Bug fixes: * Fixes #2800 [non-BFB] | 19 March 2019, 14:26:21 UTC |
| 4c4aeff | jayeshkrishna | 18 March 2019, 21:09:08 UTC | Merge pull request #2772 from E3SM-Project/jayeshkrishna/pio2_clm_mosart_fixes This PR includes some fixes in CLM and Mosart required for PIO2. Although these fixes are not specific to PIO2, they showed up during testing with PIO2. Fixes #2778 [BFB] | 18 March 2019, 21:09:08 UTC |
| 97fe01a | James Foucar | 15 March 2019, 20:02:19 UTC | Merge branch 'jgfouca/cime/sandiatoss3_multiqueue' into master (PR #2804) Support multiqueueing for sandiatoss3 Any job that could run on our 'short' queue could also run on our 'batch' queue. If the short queue is full and the batch one isn't, it would make sense to run the job in the batch queue. [BFB] * jgfouca/cime/sandiatoss3_multiqueue: Support multiqueueing for sandiatoss3 | 15 March 2019, 20:03:06 UTC |
| 0ed3cc1 | James Foucar | 15 March 2019, 19:53:32 UTC | Support multiqueueing for sandiatoss3 Any job that could run on our 'short' queue could also run on our 'batch' queue. If the short queue is full and the batch one isn't, it would make sense to run the job in the batch queue. [BFB] | 15 March 2019, 19:53:32 UTC |
| 1fa556a | Wuyin Lin | 14 March 2019, 22:01:53 UTC | Merge singhbalwinder/atm/v2compset (PR #2789) Implements remaining changes for gustiness feature for EAMv2 This PR completes the gustiness feature in EAM by implementing all the right namelist settings for gustiness. A new use case file 2000_cam5_av1c-04p2_gust.xml has all the namelist values for invoking this feature using FC5AV1C-L compset. Several new namelist variables required for this feature will now appear in the namelist (atm_in). A test mod directory is also created to add a test for this feature in the nightly testing. [BFB] [NML] | 14 March 2019, 22:01:53 UTC |
| ed919b2 | Xylar Asay-Davis | 12 March 2019, 17:24:51 UTC | Update mpas-source Add changes to COMPASS to fix serveral issues with JIGSAW. These include lack of reproducibility and culling of incorrect land cells from the wrong bathymetry file. | 14 March 2019, 16:20:01 UTC |
| b7149dd | Jon Wolfe | 14 March 2019, 15:32:03 UTC | Merge branch 'xylar/add_standalone_mpaso_wind_pressure_forcing' (PR #2788) Update MPAS source for standalone time-varying forcing This pull request ibrings in a new mpas-source submodule, which adds capability for stand-alone MPAS-Ocean to include time varying wind and pressure forcing. The added code is not called during E3SM simulations and should not impact any tested configurations. It also includes associated COMPASS files for testing. [BFB] | 14 March 2019, 15:32:03 UTC |
| 751d2f5 | Balwinder Singh | 13 March 2019, 23:23:23 UTC | Applies a simpler solution using added parentheses to fix nbfb issue [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 13 March 2019, 23:23:23 UTC |
| dfedcd2 | Balwinder Singh | 13 March 2019, 21:40:10 UTC | Fixes cam_export subroutine such that this PR stays BFB [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 13 March 2019, 21:40:10 UTC |
| 4e1f399 | jayeshkrishna | 13 March 2019, 15:35:08 UTC | Merge pull request #2773 from E3SM-Project/jayeshkrishna/pio2_cice_fixes This PR includes a minor fix in CICE required for PIO2. Although this fix is not specific to PIO2, it showed up during testing with PIO2. [BFB] | 13 March 2019, 15:35:08 UTC |
| 79087fe | jayeshkrishna | 13 March 2019, 15:34:30 UTC | Merge pull request #2771 from E3SM-Project/jayeshkrishna/pio2_cam_fixes This PR includes some fixes in CAM required for PIO2 and adds the build script required to build HOMME on anlworkstation. Although these fixes are not specific to PIO2, they showed up during testing with PIO2. [BFB] | 13 March 2019, 15:34:30 UTC |
| 9a68348 | Min Xu | 12 March 2019, 21:05:46 UTC | Merge branch 'minxu74/machines/summit/add_netcdff_4MPAS' (PR #2796) Add the NETCDFF environment for MPAS on Summit | 12 March 2019, 21:05:46 UTC |
| 7c705c2 | Wuyin Lin | 12 March 2019, 20:45:10 UTC | Merge wlin/atm/cosp-modis-tau-fix (PR #2770) Bug fix for optical thickness calculation in COSP-MODIS Addition of optical thickness due to stratiform snow incorrectly used the values from convective cloud. Fixes #2782 [BFB] except for cosp modis diagnostics output | 12 March 2019, 20:45:10 UTC |
| 1bf22e3 | Junqi Yin | 12 March 2019, 17:17:36 UTC | Merge branch 'thorntonpe/lnd/archv2_cols' (PR #2742) Implement ELM v2 data architecture for mass and energy state and flux variables Migrates mass and energy state and flux variables from CLM4.5 data structures, which mixed variables at multiple subgrid levels, to ELM v2 data structures, which separate the variables according to subgrid level. For example, carbon state variables are moved from a single type into three distinct types, one for gridcell-level, one for column-level, and one for vegetation (patch)-level variables. Methods acting on these types are also defined independently for each subgrid level. Migrates all energy, water, carbon, nitrogen, and phosphorus state and flux variables and data-type methods. Leaves open the issue of how to structure subroutine calling interfaces. The original code uses a variety of methods. Here, an example is provided for the module biogeochem/CNCStateUpdate1Mod.F90 and all its upstream calls, based on explicit references to data type instances at the clm_driver() level, and passed references at all lower levels. Branch tests bit-for-bit against the E3SM land developer test suite. [BFB] | 12 March 2019, 17:17:36 UTC |
| b61be29 | Xylar Asay-Davis | 08 March 2019, 21:23:21 UTC | update mpas-source This pull request adds capability for stand-alone MPAS-Ocean to include time varying wind and pressure forcing. The added code is not called during E3SM simulations. Also adds associated COMPASS files for testing. bfb | 12 March 2019, 03:43:11 UTC |
| 33ccf67 | Junqi Yin | 11 March 2019, 16:23:57 UTC | Initialize qflx_lateral to 0.0 | 11 March 2019, 19:57:38 UTC |
| 9cea565 | Junqi Yin | 07 March 2019, 20:48:36 UTC | Minor fix for build error with dynSubgridAdjustmentsMod.F90 | 11 March 2019, 19:56:10 UTC |
| 5f48dca | Min Xu | 11 March 2019, 18:04:33 UTC | Add the NETCDFF environment for MPAS on Summit As suggested by Phil, the NETCDFF environment was added into the Summit machine file for MPAS. [BFB] - Bit-For-Bit | 11 March 2019, 18:04:33 UTC |
| 4f0fb8a | Balwinder Singh | 11 March 2019, 17:58:31 UTC | Adds missed changes to cam_export in camsrfexch.F90 | 11 March 2019, 17:58:31 UTC |
| 4ecc855 | Balwinder Singh | 11 March 2019, 17:34:31 UTC | initializes vmag_gust to 0. in physpkg.F90 | 11 March 2019, 17:34:31 UTC |
| 2aa9cde | Balwinder Singh | 10 March 2019, 01:00:46 UTC | Adds a test for gustiness feature in integration testing | 10 March 2019, 01:00:46 UTC |
| 8a8eefb | Wuyin Lin | 09 March 2019, 19:58:23 UTC | Merge bogensch/atm/SE_SCM_test (PR #2710) Modifications to allow for E3SM developer tests for the SE SCM This PR includes modifications to allow for E3SM developer tests for the Spectral Element (SE) version of the Single Column Model (SCM), which will be the default version of the SCM for E3SMv2. Modifications to the ARM97 compset test case are made to make the case flexible whether the test case is run for the Eulerian or SE core. In addition, the restrictive message in the configure file that forces the user to compile SCAM with a serial build is removed as this is no longer a requirement for SCM no matter what dycore is used. This PR also includes a bug fix for the SE SCM pertaining to the definition of a CAM grid attribute, that was often causing error messages when this value was written to the output file in SCM mode. Note that the actual SE SCM test itself is added in a companion CIME PR. All e3sm_developer tests (including the Eulerian SCM test, which is still supported for the time being) pass. [BFB] | 09 March 2019, 19:58:23 UTC |
| f601228 | Junqi Yin | 09 March 2019, 03:25:51 UTC | Merge branch 'dmricciuto/machinefile/cades20190308' (PR #2790) Update modules in CADES machine file Updates the paths for cmake/3.6.1 and nco/4.6.4 after system defaults were changed. Set the MAX_MPITASKS_PER_NODE to 32. [BFB] | 09 March 2019, 03:25:51 UTC |
| 91ab3de | Daniel Ricciuto | 08 March 2019, 22:52:21 UTC | Update cmake and nco modules on CADES system | 08 March 2019, 22:52:21 UTC |
| f1a4ead | Balwinder Singh | 08 March 2019, 21:53:57 UTC | Removes av2c compset and renames av2c use case file [BFB] - Bit-For-Bit | 08 March 2019, 21:53:57 UTC |
| 72ee6ae | Balwinder Singh | 08 March 2019, 19:52:33 UTC | Adds a testmod directory for gustiness | 08 March 2019, 19:52:33 UTC |
| f9a6059 | Balwinder Singh | 08 March 2019, 19:45:29 UTC | Fixes bug where tp_fac was not broadcasted [BFB] - Bit-For-Bit | 08 March 2019, 19:45:29 UTC |
| 08c23ee | Balwinder Singh | 08 March 2019, 00:01:06 UTC | Merge branch 'brhillman/atm/update-topo-tool'(PR #2706) Add argument parsing and update documentation for topography tool Add a command line interface to the topography interpolation tool used to generate new topography inputdata for atmosphere simulations. Generating topography involves multiple steps: Interpolate high resolution topography on cubed-sphere to target grid Apply dycore-specific smoothing to interpolated topography so that atmosphere can run stably Recompute subgrid surface roughness This tool performs steps 1 and 3, while the smoothing needs to be handled by the dycore. However, using the tool in these two different modes required manual changes to the source code and recompiling for the two different use cases. Adding a command line interface to this tool allows a single executable to perform both of these tasks depending on the input arguments. This also enables more flexibility in the input filenames, which previously needed to have very specific names. The new usage is documented in the README (which has also been rewritten), as well as in a help message that can be displayed by running the code with no arguments or by passing the --help flag on the command line. [BFB] * brhillman/atm/update-topo-tool: Add notes about SGH30 Delete old README Add some more info to README Update usage text Update README Fix argument passing for write routines. Update Makefile. Pass filenames by command line argument | 08 March 2019, 00:10:50 UTC |
| 74b9768 | Jon Wolfe | 07 March 2019, 17:15:51 UTC | Merge branch 'mark-petersen/mpas/update_mpas-source_compass_only' (PR #2779) Update mpas-source, COMPASS only, no code changes This PR brings in a new mpas-source submodule that only has changes to COMPASS. COMPASS is a python-based initial condition generation tool that is included the MPAS-Model. We have made changes to be able to reproduce E3SM V1 initial conditions, and improvements for E3SM V2 simulation meshes. None of this affects the source code used by E3SM, so it will have no effect on simulations. [BFB] | 07 March 2019, 17:15:51 UTC |
| 02ab543 | Robert Jacob | 06 March 2019, 23:47:48 UTC | Merge branch 'brhillman/cime/fix-domain-tool' (PR #2633) Remove dependence on "mask" variables in the mapping files that are input to the gen_domain tool. The gen_domain tool is used to construct "domain files", which indicate the fractional coverage of component grids. This tool previously expected "mask" variables for both the target and source grids, which indicated whether or not component values would be valid at each point in the grid. This concept applied to FV grids, where a global mesh was established but various components may or may not be active at each point in that mesh. For example, the ocean would not be active over land points, so the mask should be zero for those points. This concept does not necessarily apply to newer unstructured grids, which can be designed to simply not include points where the component would not be active. Thus, a mask variable is unnecessary for these grids. Add options to set the ocean mask to 1 if its not present. Program will still die if mask is not present and --set-omask is not given. Also make the fminval and fmaxval optional input paramaters. | 06 March 2019, 23:47:48 UTC |
| 09061d0 | Jayesh Krishna | 23 March 2018, 21:10:56 UTC | Fixing starts/counts for pio puts The starts/counts for puts where the vars (1d/2d/3d) had no time dimensions were wrong, i.e., always had an extra start/count corresponding to the time dimension. Now we have the starts/counts for time dimension only when the var is supposed to have multiple timesteps | 06 March 2019, 16:25:56 UTC |
| f3c6880 | mark-petersen | 06 March 2019, 14:44:52 UTC | Update mpas-source, COMPASS only, no code changes | 06 March 2019, 14:44:52 UTC |
| 92a0d41 | Wuyin Lin | 06 March 2019, 05:19:38 UTC | Merge worleyph/cam/create_chunks_fix (PR #2736) Fix bug in create_chunks n the routine create_chunks in the file components/cam/src/physics/cam/phys_grd.F90 is logic to determine the number of columns assigned to each virtual SMP during the dynamics. As part of this a mapping from each column to the owner SMP is computed using the physics (lon-lat) ordering of the columns. To count the number of columns per SMP, this mapping array is then accessed as if the entries had been assigned using the native dynamics ordering of the columns. This error however does not prevent the correct calculation of the number of columns per SMP, and the column-to-SMP mapping array is then deleted, so the inconsistency is not repeated and does not introduce an error. However, when enhancing the load balancing logic to use data on the computational cost of columns, this column-to-smp mapping is needed. To introduce clarity in the current logic and in support of this future enhancement, the ordering used is changed to that of the natural dynamics ordering of the columns (not necessarily lon-lat), and used consistently throughout create_chunks. Fixes #2735 [BFB] | 06 March 2019, 05:19:38 UTC |
| 7d8ac05 | Junqi Yin | 05 March 2019, 19:58:35 UTC | Merge branch 'bishtgautam/lnd/updated-ic-at-ne30-and-ne120' (PR #2741) Updates multiple land initial conditions Land IC files are updated at following resolution/compset: 1. ne11_oQU240/ICLM45BC 2. ne120_g16/ICLM45BC 3. ne30_oECv3_ICG/A_WCYCL1950S_CMIP6_LRtunedHR 4. ne120_oRRS18v3_ICG/A_WCYCL2000_H01AS Fixes #2692 [non-BFB] | 05 March 2019, 19:58:35 UTC |
| 62044d6 | James Foucar | 04 March 2019, 19:56:16 UTC | Merge branch 'jgfouca/update_kokkos' into master (PR #2776) Update kokkos submodule There were debug build errors in the previous version. [BFB] * jgfouca/update_kokkos: Update kokkos submodule | 04 March 2019, 19:57:03 UTC |
| 2247133 | James Foucar | 04 March 2019, 19:54:17 UTC | Update kokkos submodule There were debug build errors in the previous version. [BFB] | 04 March 2019, 19:54:39 UTC |
| 897984c | Jon Wolfe | 04 March 2019, 19:05:07 UTC | Merge branch 'gennaro/ARRM_SSSrestoring' (PR #2751) Add SSS restoring files for E3SM-ARRM to buildnml This PR modifies the scripots to include the surface salinity restoring files for the two E3SM-ARRM configurations we currently have (ARRM60to10 and ARRM60to6). It also updates the mapping files to correct names for TL319_to_oARRM60to6 (the JRA grid to higher resolution ARRM grid). [BFB] | 04 March 2019, 19:05:07 UTC |
| a984449 | “Gennaro” | 15 February 2019, 21:11:33 UTC | Added SSS restoring files for E3SM-ARRM | 01 March 2019, 05:29:15 UTC |
| d21dea3 | James Foucar | 27 February 2019, 23:00:56 UTC | Merge branch 'jgfouca/cime/add_kokkos' into master (PR #2756) Add kokkos submodule to e3sm Add kokkos submodule to e3sm. Also, integrate it into the CIME build system. Also, add a cam-homme testmod to set CAM_TARGET to preqx_kokkos. [BFB] * jgfouca/cime/add_kokkos: Filter -arch argument, fortran can't handle it Getting close Remove hardcoding of USE_KOKKOS_KERNELS pylint fixes Fixes Builds on melvin | 28 February 2019, 22:18:04 UTC |
| 1921512 | Jon Wolfe | 28 February 2019, 19:17:57 UTC | Merge branch 'jonbob/ocean/index-flux-analysis' (PR #2769) Update mpas-source submodule to pick up indexing fix This PR brings in a new mpas-source submodule that fixes an indexing issue on an array that was causing debug tests to fail in the online time-averaging mpas analysis. Vertical index k=1 on activeTracerVerticalAdvectionTopFlux is the ocean surface, so is always zero. It was using some uninitialized values when using k=1, so start loop at k=2. See [MPAS-Model PR #165](MPAS-Dev/MPAS-Model#165) Fixes #2768 [BFB] | 28 February 2019, 19:17:57 UTC |
| 6d6ba88 | James Foucar | 28 February 2019, 17:40:43 UTC | Rename homexx testmod | 28 February 2019, 17:40:43 UTC |
| 0513d56 | Wuyin Lin | 28 February 2019, 15:55:10 UTC | Bug fix for optical thickness calculation in COSP-MODIS Addition of optical thickness due to stratiform snow incorrectly used the values from convective cloud. [BFB] except for cosp modis diagnostics output | 28 February 2019, 15:55:10 UTC |
| fdcf046 | noel | 28 February 2019, 00:29:30 UTC | Merge branch E3SM-Project/ndk/machinefiles/cori-intel19b (PR #2682) For cori-knl only, add intel19 compiler as an option and remove gnu7 option. Will have no effect on default build/runs. [bfb] | 28 February 2019, 00:29:30 UTC |
| d88dcf8 | James Foucar | 27 February 2019, 22:21:38 UTC | Filter -arch argument, fortran can't handle it | 27 February 2019, 22:21:38 UTC |
| 1cca628 | James Foucar | 27 February 2019, 21:41:57 UTC | Getting close | 27 February 2019, 21:41:57 UTC |
| 68e337d | Jon Wolfe | 26 February 2019, 22:02:26 UTC | Update mpas-source submodule to pick up indexing fix | 27 February 2019, 03:57:34 UTC |
| 85789d6 | Balwinder Singh | 25 February 2019, 22:41:21 UTC | Adds zmconv_tp_fac value for av2c use case [BFB] - Bit-For-Bit [FCC] - Flag Climate Changing [Non-BFB] - Non Bit-For-Bit [CC] - Climate Changing [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 25 February 2019, 22:41:21 UTC |
| 7a3e32d | Jon Wolfe | 25 February 2019, 15:20:13 UTC | Merge branch 'mark-petersen/ocn/captureEdgeTracerFluxes' (PR #2760) Add ocean active tracer fluxes to analysis terms This PR adds variables within tracer_advection_mono to capture the edge based fluxes of temperature and salinity to fully close the heat and salinity budgets regionally. It requires a new mpas-source submodule as well as corresponding changes in E3SM. [BFB] | 25 February 2019, 15:20:13 UTC |
| c587cce | James Foucar | 22 February 2019, 22:33:59 UTC | Merge branch 'oksanaguba/homme/xx-dndebug-fix' into master (PR #2762) Adding -DNDEBUG to performance builds of hommexx This flag corresponds to 'no assertions' in xx version, assertions are 10% of a run. The flag got lost somewhere in previous integration work. [BFB] * origin/oksanaguba/homme/xx-dndebug-fix: waterman cmake file adding dndebug | 22 February 2019, 22:35:40 UTC |
| 8ed3388 | James Foucar | 20 February 2019, 18:41:33 UTC | Merge branch 'jgfouca/cime/refactor_test_specs' into master (PR #2753) Refactor e3sm test suite definition format The use of tuples is not scalable as we increase the configurability of test suites. Fixes #2409 [BFB] * jgfouca/cime/refactor_test_specs: Add commas after all entries, even last one Refactor e3sm test suite definition format | 22 February 2019, 22:29:08 UTC |
| 2eede72 | Balwinder Singh | 22 February 2019, 18:40:16 UTC | Merge branch 'singhbalwinder/scripts/tsc-forced-pend-st' (PR #2764) Modifies baseline compare status to PEND for TSC test Baseline comparison is not complete yet for TSC test. This PR changes the status to PEND so that test shows 'Not Run' on the dashboard instead of FAIL [BFB] - Bit-For-Bit | 22 February 2019, 18:40:16 UTC |
| 82215f1 | Balwinder Singh | 22 February 2019, 17:36:42 UTC | Modifies baseline compare status to PEND for TSC test Baseline comparison is not complete yet for TSC test. This PR changes the status to PEND so that test shows 'Not Run' on the dashboard instead of FAIL [BFB] - Bit-For-Bit | 22 February 2019, 17:36:42 UTC |
| 458c2fa | jason sarich | 22 February 2019, 16:53:44 UTC | Merge branch 'azamat/machines/update-project-name' (PR #2656) Update project paths on Theta [BFB] | 22 February 2019, 16:53:44 UTC |
| 2c4ab1e | Oksana Guba | 21 February 2019, 22:30:12 UTC | waterman cmake file | 21 February 2019, 22:30:12 UTC |
| 9231fa9 | Oksana Guba | 21 February 2019, 22:16:31 UTC | adding dndebug | 21 February 2019, 22:16:31 UTC |
| e451e58 | James Foucar | 21 February 2019, 19:41:44 UTC | Make pylint happy | 21 February 2019, 19:41:44 UTC |
| cce31aa | James Foucar | 21 February 2019, 19:39:50 UTC | Fix doc | 21 February 2019, 19:39:50 UTC |
| 2a35f24 | James Foucar | 21 February 2019, 19:36:08 UTC | Loads of fixes 1) Fix cmakemacroswriter doctests to work for both py2 and py3 2) Fix case_st_archive doctests missing import 3) Tests are now an optional field (can inherit from multiple suites instead) 4) Improve get_tests inheritance doctest 5) Fix bug in retrieving inherit data for suite 6) scripts_regression_tests was missing lots of modules' doctests | 21 February 2019, 19:36:08 UTC |
| bb7d5f1 | Gautam Bisht | 21 February 2019, 19:02:26 UTC | Merge branch 'brhillman/clm/fix-mksurfdatamap-build' (PR #2757) Fix build environment for the `mksurfdata_map` tool, which is used to build new land surface datasets. This only requires a simple change to the Makefile to not assume a path for `nf-config` relative to `LIB_NETCDF`. This was causing a problem because different machines would have a different location for `nf-config` relative to `LIB_NETCDF`. So calling `nf-config` without specifying a path (and assuming that `nf-config` exists in the `PATH` environment variable) seems to make the build more portable and not require hand editing the Makefile. [BFB] | 21 February 2019, 19:02:26 UTC |
| 9f0c5b2 | jayeshkrishna | 07 June 2018, 21:12:22 UTC | Adding cmake build script for anlworkstation Adding the HOMME cmake build script for anlworkstation. | 21 February 2019, 17:42:40 UTC |
| 7916637 | dqwu | 24 March 2018, 03:02:10 UTC | Using interface shr_pio_getrearranger to set pio_rearranger In components/cam/src/utils/cam_pio_utils.F90, pio_rearranger is hard-coded to pio_rearr_subset. We should use interface shr_pio_getrearranger to read user settings from env_run.xml. Fixes #2168 | 21 February 2019, 17:41:47 UTC |
| 6f4e75d | dqwu | 24 March 2018, 01:02:47 UTC | Fixing a Fortran runtime error in subroutine cam_pio_get_var_3d_r8_perm Without this fix, strt and cnt are passed to pio_get_var with a hard-coded length of 3, even when ndims is 4. Also making assignment statements for strt and cnt consistent across all module procedures of interface cam_pio_get_var. | 21 February 2019, 17:40:19 UTC |
| b502241 | dqwu | 24 March 2018, 00:45:29 UTC | Updating some calls to interface shr_scam_getCloseLatLon With this fix, module procedure shr_scam_getCloseLatLonPIO is called instead of shr_scam_getCloseLatLonNC. For PIO2, the ncid returned to the user is not the actual ncid returned by the underlying netcdf/pnetcdf library. This opaque pio_ncid is unusable from outside PIO2, such as nf90_inquire calls in shr_scam_getCloseLatLonNC. | 21 February 2019, 17:39:55 UTC |
| d5377ef | Jayesh Krishna | 24 March 2018, 00:26:38 UTC | Fixing CICE restart fail - freeing iodesc Closing the File handle after we free the associated io descriptors. Without the change when freeing io descriptors PIO tries to perform a syncfile on the File handle (that is no longer valid because it was closed) resulting in an abort (PIO sync fails since it cannot find the file handle). | 21 February 2019, 17:38:22 UTC |
| 679a1c8 | dqwu | 23 March 2018, 20:37:14 UTC | Commenting out LND_PIO_REARRANGER entry in config_pio.xml for E3SM This setting causes LND to use a hard-coded value of 1 for I case and F case. | 21 February 2019, 17:31:01 UTC |
| 19c962d | mark-petersen | 15 February 2019, 23:26:57 UTC | Add active tracer fluxes to analysis terms | 21 February 2019, 15:28:58 UTC |
| 4f7ef9f | Balwinder Singh | 21 February 2019, 00:04:36 UTC | defines missing variable for pbuf id for vmag_gust [BFB] - Bit-For-Bit | 21 February 2019, 00:04:36 UTC |
| 3382111 | Balwinder Singh | 20 February 2019, 23:41:54 UTC | Adds vmag_gust to infld calls in physpkg.F90 [BFB] - Bit-For-Bit | 20 February 2019, 23:41:54 UTC |
| e12590f | James Foucar | 20 February 2019, 23:38:55 UTC | Remove hardcoding of USE_KOKKOS_KERNELS | 20 February 2019, 23:38:55 UTC |
| 34e9cee | Benjamin Hillman | 20 February 2019, 23:17:29 UTC | Do not assume relative path for nf-config Do not assume a path for `nf-config` relative to `LIB_NETCDF`. This was causing a problem because different machines would have a different location for `nf-config` relative to `LIB_NETCDF`. So calling `nf-config` without specifying a path (and assuming that `nf-config` exists in the `PATH` environment variable) seems to make the build more portable and not require hand editing the Makefile. | 20 February 2019, 23:17:29 UTC |
| e370557 | James Foucar | 20 February 2019, 23:11:37 UTC | pylint fixes | 20 February 2019, 23:11:37 UTC |
| 7b217bd | James Foucar | 20 February 2019, 23:05:31 UTC | Fixes | 20 February 2019, 23:05:31 UTC |
| 7644829 | James Foucar | 20 February 2019, 22:36:33 UTC | Builds on melvin | 20 February 2019, 22:36:33 UTC |
| cb4858a | James Foucar | 20 February 2019, 18:40:36 UTC | Merge remote-tracking branch 'origin/master' into jgfouca/cime/refactor_test_specs * origin/master: bless_test_results: when multiple sets of tests match test-id, use newest Add oceanice extra coverage tests including PEM and ERS low-res tests | 20 February 2019, 18:40:36 UTC |
| 721ce2d | Jon Wolfe | 20 February 2019, 15:24:00 UTC | Merge branch 'jonbob/scripts/add-ocnice-extra-tests' (PR #2749) Add oceanice extra coverage tests including PEM and ERS low-res tests This PR adds e3sm_ocnice_extra_coverage definition to the tests.py file and includes them in the e3sm_extra_coverage suite. It also adds the first two tests to this sub-suite: * ERS_P480_Ld5.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF * PEM_P480_Ld5.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF to provide testing of the new data iceberg (DIB) and ice-sheet melt flux (ISMF) capabilities in the ocnice components. [BFB] | 20 February 2019, 15:24:00 UTC |
| bb0fd8c | James Foucar | 19 February 2019, 23:05:26 UTC | Merge branch 'jgfouca/btr_auto_testid' into master (PR #2755) bless_test_results: when multiple sets of tests match test-id, use newest [BFB] * jgfouca/btr_auto_testid: bless_test_results: when multiple sets of tests match test-id, use newest | 19 February 2019, 23:06:02 UTC |
| 1ff0f3e | James Foucar | 19 February 2019, 22:51:51 UTC | bless_test_results: when multiple sets of tests match test-id, use newest | 19 February 2019, 22:51:51 UTC |
| 556a623 | Ryan Knox | 19 February 2019, 20:01:12 UTC | Update to fates api 7.10, matches tag sci.1.23.0_api.7.1.0 | 19 February 2019, 20:01:12 UTC |
| 1fa6ee0 | James Foucar | 19 February 2019, 17:41:44 UTC | Add commas after all entries, even last one It's harmless and prevents missing commas when things are added to the end. | 19 February 2019, 17:41:44 UTC |
| 4325f76 | James Foucar | 19 February 2019, 01:04:44 UTC | Refactor e3sm test suite definition format The use of tuples is not scalable as we increase the configurability of test suites. [BFB] | 19 February 2019, 01:04:44 UTC |
| 4531c4f | Mark Taylor | 15 February 2019, 23:36:03 UTC | Merge remote-tracking branch 'origin/imkg252a' (PR #2746) Added the imkg252a method (5 stages, 2 implicit solves). [BFB] | 15 February 2019, 23:36:03 UTC |
| 0c5a53e | Peter Thornton | 15 February 2019, 20:22:10 UTC | Remove the CNDV dynamic biogeography code and data structures Following up on decision within Land/Energy NGD, removes the CNDV files and all references to CNDV data structures and vegetation parameters. Tested against the full land developer test suite. [BFB] | 15 February 2019, 20:22:10 UTC |
| e67fe99 | Ryan Knox | 15 February 2019, 01:04:51 UTC | changed soilstate boundary type to inout to accomodate fates call | 15 February 2019, 01:04:51 UTC |
| cd338b9 | Balwinder Singh | 15 February 2019, 01:01:28 UTC | Adds clubb_use_sgv to use case for av2c | 15 February 2019, 01:01:28 UTC |
| f5fc360 | Balwinder Singh | 06 February 2019, 22:19:29 UTC | Modifies use case for v2 compset to match po-lin's case [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 15 February 2019, 00:56:40 UTC |
| 2ab4e74 | Balwinder Singh | 03 January 2019, 03:57:14 UTC | Updates V2 compset with new coefficient, V1 is BFB [BFB] - Bit-For-Bit | 15 February 2019, 00:56:40 UTC |
| 0b9b338 | Balwinder Singh | 31 December 2018, 23:30:21 UTC | Temp Commit- adds some vars to use case of new compset [BFB] - Bit-For-Bit | 15 February 2019, 00:56:40 UTC |
| 6141747 | Balwinder Singh | 27 December 2018, 23:38:40 UTC | Adds compset FC5AV2C so that it is BFB with FC5AV1C-L [BFB] - Bit-For-Bit | 15 February 2019, 00:56:40 UTC |
| 2c41493 | Balwinder Singh | 25 December 2018, 07:29:37 UTC | Added clubb_c1b definition to namelist_definition.xml clubb_c1b was in usecases but not in the namelist_definitions.xml file. It has to be defined in namelist_definitions.xml for it to appear in atm_in file. [BFB] - Bit-For-Bit | 15 February 2019, 00:56:39 UTC |
| 185bace | Balwinder Singh | 24 December 2018, 21:07:04 UTC | Adds clubb_c1b in all files which had clubb_c1 Adds clubb_c1b=clubb_c1 in all files which had clubb_c1 [BFB] - Bit-For-Bit | 15 February 2019, 00:56:39 UTC |
| 6e4b55e | Balwinder Singh | 21 December 2018, 22:37:54 UTC | Adds clubb's c1b and c1c to be read from namelist [BFB] - Bit-For-Bit | 15 February 2019, 00:56:39 UTC |
| 965430e | Peter Thornton | 14 February 2019, 18:34:51 UTC | Resolve some merge conflicts resulting from rebase of branch on master Introduction of new water balance variables, and migration of filename and subroutine names needed to be reconciled with the branch changes. New baselines were generated for master (at commit 4f22ec), and the branch was tested successfully against those baselines for the full land developer test suite. [BFB] | 14 February 2019, 22:16:29 UTC |
| d9fa06d | Benjamin Hillman | 14 February 2019, 17:47:10 UTC | Require command line flag to infer masks Require a command line flag (set-omask) to enable inferring ocean mask when it is not present in the input mapping file. By default, if mask_a is not present in the input mapping file, the code will throw and error and exit. However, if --set-omask is passed, then in the absence of mask_a, it will be inferred by setting the mask to a vector of 1s, which are then remapped onto the land grid. This option is only appropriate for unstructured grids which cover only the area in which the ocean is active. I.e., this is NOT an appropriate thing to do for regular lat-lon grids, but should be fine for MPAS-O grids. Tested with a mapping file from oRRS30to10 to ne30np4 and confirmed these two modes of operation (using provided mask, and omitting the mask and passing --set-omask to calculate it) give the same answers. | 14 February 2019, 17:47:10 UTC |
| ee3338b | Jon Wolfe | 14 February 2019, 16:20:03 UTC | Add oceanice extra coverage tests including PEM and ERS low-res tests | 14 February 2019, 16:20:03 UTC |
| 4f22ec7 | Jon Wolfe | 14 February 2019, 15:46:05 UTC | Merge branch 'mark-petersen/ocean/fix_ERS_PEM_with_ISMF' (PR #2747) Fixes for bfb restart and partitions tests in E3SM This PR brings in a new mpas-source submodule with three changes: 1. Widen halo computation ring for kinetic energy. 2. Widen halo computation ring for melt fluxes. 3. Add halo exchange for surfaceFrictionVelocity When running E3SM with melt fluxes on (compsets with ISMF), the first is needed for bfb restarts and all three for bfb partition tests (#2739). Fixes #2702 Fixes #2739 [BFB] for all non-ISMF configurations | 14 February 2019, 15:46:05 UTC |
