| 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 |
| 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 |
| 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 |
| b0d51bf | Peter Thornton | 12 February 2019, 18:46:12 UTC | Example implementation of subroutine calling interface, v2 data Uses the subroutines in CNCStateUpdate1Mod.F90 as an example of how we could implement the subroutine interfaces across the whole model. Tested against full land developer test suite. [BFB] | 13 February 2019, 20:55:47 UTC |
| 816ca41 | Peter Thornton | 12 February 2019, 06:23:46 UTC | Completes phosphorus flux data migration for v2 data architecture All gridcell, column, and vegetation-level phosphorus flux variables are migrated to new data structures. Tested against full land developer test suite. [BFB] | 13 February 2019, 20:53:36 UTC |
| 640b4e0 | Peter Thornton | 12 February 2019, 04:54:18 UTC | Adds infrastructure for phosphorus flux variables in v2 data structs Intermediate commit prior to bulk substitution. Not evaluated against any developer tests. | 13 February 2019, 20:52:46 UTC |
| 7297b6a | Peter Thornton | 11 February 2019, 17:50:56 UTC | Add all phosphorus state variables to v2 data architecture Introduces gridcell, column, and vegetation-level infrastructure for phosphorus state types, and migrates all variables to subgrid data structures. Tested against full land developer test suite. [BFB] | 13 February 2019, 20:52:42 UTC |
| f2296df | Peter Thornton | 11 February 2019, 00:50:32 UTC | Add all nitrogen flux variables to v2 data architecture All gridcell, column, and vegetation-level nitrogen flux variables are added to v2 data structures. Tested against full land developer test suite. [BFB] | 13 February 2019, 20:51:56 UTC |
| f84b2fb | Peter Thornton | 10 February 2019, 22:07:46 UTC | Add infrastructure for nitrogen flux variables in v2 data architecture Intermediate commit in advance of automated search-and-replace. Not evaluated against any tests. | 13 February 2019, 20:50:38 UTC |
| d2235a9 | Peter Thornton | 10 February 2019, 06:27:05 UTC | Adds all column and vegetation-level N state variables to v2 data Creates new data data types and migrates all nitrogen state variables from vegetation, column, and gridcell to v2 data architecture. Passes full land developer test suite. [BFB] | 13 February 2019, 20:50:35 UTC |
| fe0fb83 | Peter Thornton | 05 February 2019, 14:44:35 UTC | Completes the migration of carbon flux variables into v2 data types All column-level and vegetation-level carbon fluxes are migrated, with their initialization, history, and restart support. Includes C13 and C14 flux instances. Also includes a few variables at the gridcell level. Tested against full land developer suite. [BFB] | 13 February 2019, 20:49:19 UTC |
| 0c63a0f | Peter Thornton | 04 February 2019, 22:06:46 UTC | Adds the column-level carbon flux structures to v2 data architecture Intermediate commit, in advance of automated revision of all column carbon flux variables. | 13 February 2019, 20:47:25 UTC |
| c16aa6b | Peter Thornton | 04 February 2019, 06:14:58 UTC | Add vegetation-level carbon fluxes to v2 data architecture An intermediate commit, capturing the migration of all but three veg carbon flux variables, and the infrastructure changes in state update and isoflux code to receive the new data. Still need to migrate a subset of the column-level carbon fluxes before this will compile and run. | 13 February 2019, 20:46:45 UTC |
| 416bde3 | Peter Thornton | 03 February 2019, 17:22:32 UTC | Complete migration of carbon state variables to v2 data architecture Adds all remaining gridcell, column, and vegetation-level carbon state variables to the v2 data architecture. Includes handling for dynamic subgrid. Some dynamic subgrid methods are moved from the carbon state variable structures into the dyn_subgrid subdir as a new module. Tested against full land developer test suite. [BFB] | 13 February 2019, 20:29:10 UTC |
| 526e14c | Peter Thornton | 03 February 2019, 06:06:45 UTC | Add additional vegetation-level carbon state variables to v2 data types An intermediate commit, while finalizing remaining column-level carbon state variables. | 13 February 2019, 20:24:12 UTC |
| 85c7d36 | Peter Thornton | 02 February 2019, 20:25:38 UTC | Add and initialize vegetation-level carbon state data structures This is an intermediate commit for the v2 data architecture migration. Not evaluated with land test suite. | 13 February 2019, 20:23:29 UTC |
| 9e8410d | Peter Thornton | 01 February 2019, 03:55:01 UTC | Add column-level carbon state structures to v2 data architecture Adds the c12, c13, and c14 versions of column-level carbon states, and includes a number of temporary data structures required to make incremental tests on state and flux variable migration. Adds the vertically-resolved column-level variables as a first increment. Tested against full land developer test suite. Includes a few additional water flux structures at gridcell and landunit level. [BFB] | 13 February 2019, 20:14:41 UTC |
| 855e728 | Peter Thornton | 30 January 2019, 13:36:23 UTC | Moves vegetation-level water flux variables into v2 data architecture Tested against full land developer test suite [BFB] | 13 February 2019, 20:03:49 UTC |
| 2eb42ec | Peter Thornton | 30 January 2019, 03:10:18 UTC | Add column-level water flux variables to v2 data architecture Tested against full land developer test suite. [BFB] | 13 February 2019, 20:00:15 UTC |
| 4f5b406 | Peter Thornton | 29 January 2019, 18:47:42 UTC | Add gridcell, landunit, and vegetation-level water state vars v2 data Adds all water state variables at the gridcell, landunit, and vegetation levels to V2 data structures. Tested against full land developer test suite. [BFB] | 13 February 2019, 19:53:46 UTC |
| ebfcbc0 | Peter Thornton | 29 January 2019, 13:38:10 UTC | Add remaining column water state variables to v2 data architecture [BFB] | 13 February 2019, 19:44:09 UTC |
| 70f4499 | Peter Thornton | 29 January 2019, 05:07:05 UTC | Add column water state component of v2 data architecture Create new data structure for column-level water state variables, and begin migrating variables into it. Also a little clean-up on gridcell level energy flux variables. Tested successfully against the full land developer test suite. [BFB] | 13 February 2019, 19:33:10 UTC |
| d065951 | Peter Thornton | 25 January 2019, 19:55:46 UTC | Add landunit and gridcell-level energy flux variables to v2 data types Add and initialize a few remaining energy flux variables. [BFB] | 13 February 2019, 19:33:08 UTC |
| f508f5c | Peter Thornton | 25 January 2019, 18:56:20 UTC | Migrate all veg-level energy flux variables to v2 data architecture All vegetation-level energy flux variables are migrated, although a few variables previously defined in the energy flux type at the patch level will be moved later to the water flux structures (e.g. btran). [BFB] | 13 February 2019, 19:33:07 UTC |
| a744c4f | Peter Thornton | 25 January 2019, 13:38:42 UTC | Add a few additional energy variables to v2 data architecture Add new variables to column-level energy flux data structure, and remove calls to the initialization, history, and restart subroutines for the obsolete TemperatureType data structure. [BFB] | 13 February 2019, 19:33:06 UTC |
| 1370b0e | Peter Thornton | 25 January 2019, 04:53:03 UTC | Add column-level energy flux variables to v2 data architecture Added new data structure for column energy fluxes, and migrated all existing column-level variables. [BFB] | 13 February 2019, 19:33:05 UTC |
| a1b0b0a | Peter Thornton | 24 January 2019, 20:50:06 UTC | Add landunit-level temperature variables to v2 data architecture Building temperature and urban canopy temperature added to landunit-level data structure. [BFB] | 13 February 2019, 19:33:03 UTC |
| 64b8148 | Peter Thornton | 24 January 2019, 16:27:50 UTC | Added history fields for atmospheric flux variables to v2 data structs Completed the addition of new history variables for the v2 data architecture at the topounit level. All previous history field names and other metadata are maintained in the new code, so this change is BFB with master. At a later date, ELM team may want to add additional history outputs, or remove some that are duplicates with different names as part of the code cleanup process. [BFB] | 13 February 2019, 19:33:02 UTC |
| f29a2e2 | Peter Thornton | 23 January 2019, 21:06:03 UTC | Update all references to atmospheric state and flux structures. Created a new data structure for the state and flux variables that are defined at topounit level. Revised all references to these data structures in "use" statements. [BFB] | 13 February 2019, 19:32:58 UTC |
| 1900262 | Peter Thornton | 23 January 2019, 20:06:00 UTC | Add history file handling for topounit-level variables Add topounit-to-gridcell scaling factor, and ability to accept history file variables defined at the topounit level. [BFB] | 13 February 2019, 19:31:44 UTC |
| 5447e9d | Peter Thornton | 22 January 2019, 19:51:43 UTC | Added gridcell-level energy state variables to V2 data architecture [BFB] | 13 February 2019, 19:31:43 UTC |
| 9e585f1 | Peter Thornton | 17 January 2019, 21:03:35 UTC | Adds vegetation energy state data structure, ELM V2 data architecture Complete migration of all vegetation (pft) level energy state variables from the vegetation_vars structure in veg_es structure. Requires a change to the BeTR submodule for data passing to use new data structures. With that change, all land developer test suite tests pass BFB. [BFB] | 13 February 2019, 19:31:42 UTC |
| d61434b | Peter Thornton | 16 January 2019, 18:36:51 UTC | Add vegetation-level energy state structure and begin populating Added initialization, history, and restart capability for vegetation energy state structure. Also introduced a new module for vegetation data structures. Tested against land developer test suite [BFB] | 13 February 2019, 19:31:36 UTC |
| 48b2da7 | Peter Thornton | 15 January 2019, 17:04:26 UTC | Complete migration of column energy state variables to v2 data types Add remaining temperature-related variables to new data type, and update the use of these variables throughout the code. Unused variables removed (e.g. dt_grnd_col) or treated as constant (e.g. beta_col). Also modified the instantiation of urbanparams_type, moving this out of clm_instMod.F90, and into UrbanParamsType.F90. This fixes some issues with circular use referencing. [BFB] | 13 February 2019, 19:30:24 UTC |
| 68cbb39 | Peter Thornton | 05 December 2018, 18:33:33 UTC | Add rural and urban ground temperature to new data structures Continued migration of column-level temperature variables. [BFB] | 13 February 2019, 19:30:23 UTC |
| 1226f34 | Peter Thornton | 27 November 2018, 02:32:47 UTC | Add t_grnd, t_lake, and a few derived temperature variables to col_es Continued migration of column-level energy state variables, with history, cold start, and restart. [BFB] | 13 February 2019, 19:30:22 UTC |
| 9786cfc | Peter Thornton | 26 November 2018, 02:11:09 UTC | Add soil and snow temperature variables to the column energy state type Includes migration of history initialization and restart for soil and snow temperatures. [BFB] | 13 February 2019, 19:30:15 UTC |
| 1a7cdd5 | Peter Thornton | 25 November 2018, 22:03:03 UTC | Add a few more column-level temperature variables to new data type An incremental commit in preparation for major update associated with tsoisno variable. [BFB] | 13 February 2019, 19:26:49 UTC |
| ef783cc | Peter Thornton | 25 November 2018, 19:39:59 UTC | Reorganize column data types to avoid circular references Created a new module for the state and flux variables at the column level (ColumnDataType). Needed because col_pp is referenced inside HistFileMod, and initialization of the history fields for state and flux variables references HistFileMod. Implementation will be extended later to other sub-grid levels. [BFB] | 13 February 2019, 19:26:48 UTC |
| eff6be9 | Peter Thornton | 21 November 2018, 19:37:49 UTC | Preliminary test for migrating one variable to col_es | 13 February 2019, 19:26:46 UTC |
| d1a592b | Peter Thornton | 15 November 2018, 18:39:40 UTC | Update column, vegetation, and landunit levels with new data types Adds subroutines to initialize and clean all the new column and vegetation level data structures. also renames a few physical_properties types to improve data structure naming consistency [BFB] | 13 February 2019, 19:26:44 UTC |
| 6d8e7ab | Peter Thornton | 14 November 2018, 20:55:00 UTC | Introduce state and flux variable sub-types at veg level | 13 February 2019, 19:26:38 UTC |
| 1346113 | Peter Thornton | 14 November 2018, 19:43:58 UTC | introduce column sub-types for state and flux variables | 13 February 2019, 19:24:43 UTC |
| a94a6fb | Jon Wolfe | 13 February 2019, 15:36:24 UTC | Merge branch 'milena/scripts/update-IC-machines' (PR #2641) Update machine files for LANL IC This PR updates machine files for LANL IC machines: * removes wolf, which has been deactivated * updates grizzly * introduces badger, which is not fully supported yet [BFB] | 13 February 2019, 15:36:24 UTC |
| f567a62 | Junqi Yin | 12 February 2019, 14:43:11 UTC | Merge branch 'bishtgautam/lnd/fix-WaterBudgetMod' (PR #2688) Minor fixes to WaterBudgetMod Incorporates minor fixes to WaterBudgetMod for IBM compiler as identified by Min Xu. Fixes #2687 [BFB] | 12 February 2019, 14:43:11 UTC |
| 65ccd97 | Jon Wolfe | 07 February 2019, 17:57:55 UTC | Merge branch 'jonbob/scripts/add-jra-forcing' (PR #2712) Initial scripts changes to add JRA support to mpas-ocean This PR brings in the scripts changes to support JRA forcing in mpas-ocean, including new compsets and grids. These new configurations will need to be tested and validated before they can be considered scientifically supported. Tested with: * SMS.TL319_oEC60to30v3.GMPAS-JRA.anvil_intel * SMS.T62_oEC60to30v3.GMPAS-IAF.anvil_intel [BFB] | 07 February 2019, 17:57:55 UTC |
| b1ac533 | James Foucar | 31 January 2019, 18:07:21 UTC | Merge branch 'worleyph/cime/startstop_fix' into master (PR #2696) modify behavior of t_startstop_valsf The perf_mod command t_startstop_valsf (GPTL command GPTLstartstop_vals) is used to create a timer or add time to an existing timer when t_startf/t_stopf cannot be used to time the corresponding event. The motivating example is measuring the time spent in MPI_Init (before the timing library has been initialized). When the "call count" parameter callcount is set to 1, the max and min for the event are updated as expected. However, when callcount is 0 (adding time without incrementing the call count) or greater than 1 (adding time associated with multiple calls that are not recorded individually), max and min cannot be updated in the usual way. The current implementation is insufficient even given this basic ambiguity, and this PR modifies the min/max update logic to improve upon this. [BFB] * origin/worleyph/cime/startstop_fix: modify behavior of t_startstop_valsf | 06 February 2019, 20:15:20 UTC |
| 4e4f213 | Junqi Yin | 06 February 2019, 18:05:35 UTC | Merge branch 'bishtgautam/lnd/add-finidat-for-ne30' (PR #2681) Adds new land initial conditions at ne30np4 Land initial conditions at ne30np4 are added for 1850 and 2000. The new initial conditions are for satellite phenology mode (i.e. non-BGC) and were created by remapping the following files: * For 1850, clmi.I1850CRUCLM45SP.0521-01-01.0.9x1.25_g1v6_simyr1850_c140111.nc. * For 2000, clmi.ICRUCLM45SP.2000-01-01.0.9x1.25_g1v6_simyr2000_c140111.nc. Fixes #2523 [non-BFB] | 06 February 2019, 18:05:35 UTC |
| 71f4e19 | Mark Taylor | 02 February 2019, 22:38:21 UTC | Merge branch 'oksanaguba/homme/bench-nl-theta' (PR #2693) NEw namelists are created for theta-l hydro and nonhydro versions for NGGPS and V1 benchmarks for both Euler and SL transport. There will also be namelists for ne1024 (3km). Note that all new namelists will use lim9. namelists only, skipping integration testing [BFB] | 02 February 2019, 22:38:21 UTC |
| 5fc2505 | Mark Taylor | 02 February 2019, 22:37:32 UTC | Merge branch 'mt5555/nggps-nh' into next (PR #2708) namelists only, skipping integration testing [BFB] | 02 February 2019, 22:37:32 UTC |
| b72f231 | Mark Taylor | 01 February 2019, 23:44:38 UTC | nu_q should be 0 for SL transport | 02 February 2019, 22:28:21 UTC |
| 65cbbc5 | Mark Taylor | 01 February 2019, 22:21:12 UTC | updates to hydrostatic SL namelist so it will work with theta | 02 February 2019, 22:28:21 UTC |
| f568312 | Mark Taylor | 01 February 2019, 16:04:43 UTC | hopefully final tweaks to NGGPS NH namelists | 02 February 2019, 22:28:21 UTC |
| 60f9341 | Mark Taylor | 25 January 2019, 22:37:31 UTC | tweaks to NE1024 namelist | 02 February 2019, 22:28:21 UTC |
| 55afe79 | Mark Taylor | 25 January 2019, 13:24:14 UTC | adding cori run script for NH benchmark | 02 February 2019, 22:28:21 UTC |
| c85cf28 | Mark Taylor | 25 January 2019, 02:16:55 UTC | scripts and namelists for NH version of NGGPS benchmark | 02 February 2019, 22:28:21 UTC |
| 44d5be1 | Mark Taylor | 02 February 2019, 22:26:31 UTC | Merge branch 'ambrad/homme/vertical-remap-fix' (PR #2709) This commit focuses on the line kk = k ! Keep from an order n^2 search operation by assuming the old cell ! index is close. in remap_Q_ppm. It is not always the case that this value of kk gives pio(kk) <= pin(k+1). Then the subsequent search cannot succeed. To fix this, if pio(kk) > pin(k+1) perform a binary search to find the correct kk. [CC] This fixes a rarely triggered bug and may be BFB w.r.t. to our existing tests, but is potentially [CC] | 02 February 2019, 22:26:31 UTC |
| b3e0d39 | Oksana Guba | 02 February 2019, 04:56:31 UTC | minor | 02 February 2019, 04:56:31 UTC |
| b90f056 | Oksana Guba | 02 February 2019, 04:39:09 UTC | deleting theta h namelists, fixing hydro sl list | 02 February 2019, 04:39:09 UTC |
| 53f1834 | Jon Wolfe | 31 January 2019, 21:31:44 UTC | Merge branch 'jonbob/seaice/fix-oRRS30to10v3wLI-IC' (PR #2718) Fix seaice initial conditions for oRRS30to10v3wLI grid This PR changes the latitudes north and south that define the initial seaice disks as default initial conditions for the oRRS30to10v3wLI grid. The current initial conditions result in failures in the ocean model when the ice sheet melt fluxes are off, due to a negative layer thickness. Initializing with reduced seaice initial disks seems to allow the models to spinup together without issue. Tested with several one year runs on theta, with ice shelf melt fluxes on and off Fixes #2606 Fixes #2654 [non-BFB] only for G-compsets using this medium-res grid [NML] only for configurations using this medium-res grid | 31 January 2019, 21:31:44 UTC |
| 395b818 | Jon Wolfe | 31 January 2019, 20:10:16 UTC | Fix seaice initial conditions for oRRS30to10v3wLI grid | 31 January 2019, 20:10:16 UTC |
| fa9300f | James Foucar | 31 January 2019, 18:45:14 UTC | Merge branch 'oksanaguba/homme/thetal-sha' into master (PR #2715) add sha to theta-l [BFB] * origin/oksanaguba/homme/thetal-sha: add sha to theta-l | 31 January 2019, 18:45:57 UTC |
| 18077e3 | Min Xu | 31 January 2019, 03:17:59 UTC | Merge pull request #2701 from E3SM-Project/machines/summit/update-modules Update modules and paths on Summit | 31 January 2019, 03:17:59 UTC |
| ddac584 | Min Xu | 31 January 2019, 02:36:23 UTC | Update the software env and path on Summit - Update the software env for PGI and GNU compilers - Set E3SM pathes (run, bld, case, short-term archive directories) under project directory - Set E3SM input, baseline and tool directories under cli115 world shared directory | 31 January 2019, 02:36:23 UTC |
| 2aa6b9c | Jon Wolfe | 30 January 2019, 20:50:59 UTC | Combine COREFORCED and JRAFORCED flags into DATMFORCED | 30 January 2019, 20:50:59 UTC |
| 932f14c | Balwinder Singh | 30 January 2019, 17:50:38 UTC | Merge branch 'polunma/atm/eamv2' (PR #2679) Gustiness, tpert, wsubmin for EAMv2 This includes subgrid wind gustiness (ocean and land; ZM and clubb), subgrid temperature (tpert), lower wsubmin for activation, and theta-v formula fix. These code mods are controlled by namelist. EAMv1 is BFB. [BFB] [NML] | 30 January 2019, 17:50:38 UTC |
| 95ede2a | Jon Wolfe | 30 January 2019, 15:39:02 UTC | Merge branch 'jonbob/ocean/fix-salinity-restoring' (PR #2707) Changes to mpas-ocean and its driver to fix issues with salinity restoring This PR brings in a new mpas_source submodule which includes a fix to the salinity restoring forcing time interval (see MPAS PR #138). It also includes a reordering of the mpas-ocean driver so that the salinity restoring forcing passes ERS testing. Tested with: * ERS.T62_oEC60to30v3.GMPAS-IAF.anvil_intel * ERS.ne30_oECv3.BGCEXP_BCRC_CNPRDCTC_1850.anvil_intel [non-BFB] (only for G-cases) | 30 January 2019, 15:39:02 UTC |
| 288ee8c | Balwinder Singh | 29 January 2019, 17:53:03 UTC | Fixes a GNU compile time error The error was due to gust_fac being declared as an array and used as a scalar: /global/cscratch1/sd/bsingh/delete/tmp/gnu_compile/E3SM/components/cam /src/physics/cam/clubb_intr.F90:1253:30: real(r8) :: gust_fac(pcols) 1 Error: Argument 'gust_fac' of statement function at (1) must be scalar /global/cscratch1/sd/bsingh/delete/tmp/gnu_compile/E3SM/components/cam /src/physics/cam/clubb_intr.F90:1248:20: real(r8) :: ugust ! function: gustiness as a function of convective rainfall 1 Error: Incompatible ranks 0 and 1 in assignment at (1) /global/cscratch1/sd/bsingh/acme_scratch/cori-knl/SMS_Ln1.ne4_ne4. FC5AV1C-L.cori-knl_gnu.gnu_tst_del/Tools/Makefile:934: recipe for target 'clubb_intr.o' failed gmake: *** [clubb_intr.o] Error 1 [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 29 January 2019, 17:56:54 UTC |
| fcbd574 | Mark Taylor | 29 January 2019, 14:30:22 UTC | Merge branch 'azamat/homme/add-kind-parameter' (PR #2700) Add kind parameter to centroids in mesh_mod. [BFB] except for 1 HOMME subtest | 29 January 2019, 14:30:22 UTC |
| 96bd7f6 | Robert Jacob | 28 January 2019, 18:51:00 UTC | Merge branch 'worleyph/components/taskmap_control2' (PR #2672) A recent commit added the env_run.xml parameter INFO_TASKMAP_COMP and the associated cime_pes namelist parameter info_taskmap_comp to enable (> 0) or disable (<= 0) the output of the task-to-node mapping for the component models. If enabled, it further specifies whether to use a compact (== 1) or a more verbose (> 1) output format. Here the necessary control logic is added to CAM, CLM, Mosart, mpas-albany-landice, mpas-ocean, and mpas-seaice. At the moment, the default for INFO_TASKMAP_COMP is 0, so this removes all component-specific task-to-node mapping information from the log files but allows us to experiment with this and supports writing out all task-to-node mapping information in the new more compact representation simply by changing the default for INFO_TASKMAP_COMP to 1 (or 2). [BFB] | 28 January 2019, 18:51:00 UTC |
| 6fb9b56 | Oksana Guba | 28 January 2019, 15:43:35 UTC | add sha to theta-l | 28 January 2019, 15:43:35 UTC |
| c9f0178 | Mark Taylor | 26 January 2019, 16:57:26 UTC | Merge branch 'HStopo3' (PR #2699) Support of ultra high resolutions in standalone HOMME Add support for 'netcdf4p' and 'pnetcdf64' formats change "compdof" array to integer*8 (including intermediate calclulations) use -D_NO_MPI_RSEND for PIO builds, following E3SM practices. This prevents hangs during the PIO1 box rearraanger on KNL Non scalable temporary arrays in SetElemOffset() function: reduced from 3 arrays to 2 arrays. This will have to be fixed in the future if we want to run NE>=4096 for nodes with ~1GB per MPI task. bug fix (unitialized variable) in surfarea() added missing edgebuf deallocate Also has updates and tweaks to many of the scripts used to test and debug the above ( ultra-high resolution DCMIP 2016 test1 and SCRIP template generation tool). Fixes #2697 [BFB] | 26 January 2019, 16:57:26 UTC |
| 1cb8a84 | Balwinder Singh | 25 January 2019, 22:49:24 UTC | Adds some cosmetic changes and removes code which is not required [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 25 January 2019, 22:49:24 UTC |
| a3aaada | Mark Taylor | 25 January 2019, 16:48:30 UTC | use -D_NO_MPI_RSEND for PIO builds, to prevent flow control hangs | 25 January 2019, 16:48:30 UTC |
| c5555f0 | Mark Taylor | 25 January 2019, 02:12:54 UTC | tweaks to template run script | 25 January 2019, 02:12:54 UTC |
| c896819 | Mark Taylor | 25 January 2019, 02:09:49 UTC | reduce non-scalable init memory | 25 January 2019, 02:09:49 UTC |
| 210fd00 | Mark Taylor | 24 January 2019, 21:32:54 UTC | adding makegrid-cori run script | 24 January 2019, 21:32:54 UTC |
| 4249f8e | Mark Taylor | 24 January 2019, 20:14:38 UTC | reorg run script for anvil | 24 January 2019, 20:14:38 UTC |
| f2c8b0f | Jon Wolfe | 24 January 2019, 19:59:39 UTC | Changes to mpas-ocean and its driver to fix issues with salinity restoring | 24 January 2019, 19:59:39 UTC |
| bc96cd2 | James Foucar | 18 January 2019, 20:02:45 UTC | Merge branch 'homme/preqx_kokkos-summit-mods1' into master (PR #2695) Homme/preqx kokkos summit mods1 This PR does the following: * Fix a compile error in the code meant to handle the case that MPI does not handle on-device pointers. * Work around a Cuda 9.1.* parse error in this same section of code. * Fix some deprecated Kokkos usage. * Fix a bug in Homme in which accum%IEner_wet was not being 0-initialized, leading to NaNs in repro sum in preqx_kokkos. [BFB] * ambrad/homme/preqx_kokkos-summit-mods1: Homme: Change means of 0-initing IEner_wet. Homme: Fix a warning. Homme: IEner_wet does not exist in all models, so safeguard it. Hommexx: Update a Kokkos call to the new name. Homme: Fix a bug in 0-initialization of energy diagnostic arrays. Work around Cuda 9.1.85 parse error. Fix syntax error. | 24 January 2019, 19:10:06 UTC |
| 09ab663 | Jon Wolfe | 24 January 2019, 18:12:55 UTC | Merge branch 'darincomeau/seaice/dib_ers_bugfix' (PR #2705) Bug fix so that compsets with data icebergs (DIB) pass E3SM ERS tests This PR fixes a bug where data icebergs were not being properly read in on restarts in E3SM. This PR only impacts cryosphere science campaign compsets with data icebergs (DIB). Tested with: * ERS.ne30_oECv3wLI.A_WCYCL1850-DIB_CMIP6.edison_intel [BFB] | 24 January 2019, 18:12:55 UTC |
| d2dbbe5 | Junqi Yin | 24 January 2019, 15:51:10 UTC | Merge branch 'bishtgautam/lnd/add-2010-to-mksurfdata' (PR #2678) Extends supported years in mksurfdata Adds 2010 as a supported year [BFB] | 24 January 2019, 15:51:10 UTC |
| fbe8704 | Darin Comeau | 23 January 2019, 19:18:25 UTC | Bug fix so that compsets with data icebergs (DIB) pass E3SM ERS tests. | 23 January 2019, 19:18:25 UTC |
| d430595 | Mark Taylor | 23 January 2019, 16:32:09 UTC | bugfix to allow utilities to run with nmax=0 (no timesteps) | 23 January 2019, 16:32:09 UTC |
| 6add7f8 | Mark Taylor | 23 January 2019, 15:01:46 UTC | simplified makegrid.job script, namelist | 23 January 2019, 15:01:46 UTC |
| b4fbc32 | Mark Taylor | 23 January 2019, 01:52:36 UTC | bugfix in area calculation - uninitialized variable | 23 January 2019, 01:52:36 UTC |
| 91747d3 | Gautam Bisht | 22 January 2019, 18:57:41 UTC | Merge branch 'bishtgautam/script/updates-for-lawrencium' (PR #2686) Updates machine files for lawrencium-lr2 and lawrencium-lr3, while new support for lawrencium-lr6 is added. Additionally, support for GNU compiler for lawrencium-lr6 is added. [BFB] | 22 January 2019, 18:57:41 UTC |
| 8352dd4 | James Foucar | 22 January 2019, 18:01:36 UTC | Merge branch 'jgfouca/cime/improve_bless_robustness' into master (PR #2703) Improve bless_test_results robustness Using xmlquery to get case values opens the possibility of permissions errors if the source repo is not visible to the current user. Instead, open a Case object which was already needed in some code paths anyway. [BFB] * jgfouca/cime/improve_bless_robustness: Improve bless_test_results robustness Update CIME to ESMCI cime5.7.6 (PR #2689) | 22 January 2019, 18:02:27 UTC |
| 9ae072a | James Foucar | 22 January 2019, 18:00:20 UTC | Improve bless_test_results robustness Using xmlquery to get case values opens the possibility of permissions errors if the source repo is not visible to the current user. Instead, open a Case object which was already needed in some code paths anyway. | 22 January 2019, 18:00:20 UTC |
| 6a6fcb6 | Azamat Mametjanov | 22 January 2019, 01:08:06 UTC | Update modules and paths on Summit | 22 January 2019, 01:08:06 UTC |
| a82b935 | Mark Taylor | 21 January 2019, 23:22:22 UTC | fix integer overflow in compdof fixes #2697 compdof() in HOMME changed to integer*8 All calculaitons of compdof() values done with integer*8 precision with this change, was able to run HOMME with NE=2048,20L and produce output | 21 January 2019, 23:22:22 UTC |
| 49b5a03 | Balwinder Singh | 21 January 2019, 18:09:43 UTC | Merge branch 'brhillman/atm/update-rrtmgp-inputdata'(PR #2675) Update RRTMGP inputdata data and fix read issue Update RRTMGP inputdata with new absorption coefficient data from the main RRTMGP repo, and convert to proper format to be read on OLCF and NERSC machines. Fixes #2565. Should be BFB for all tests other than the RRTMGP test, which will produce a namelist compare error and a baseline compare error due to the differing absorption coefficients, but this is expected. [NML] [NBFB] * brhillman/atm/update-rrtmgp-inputdata: Add PGI flag for F2003-style allocate Reset fluxes and heating rates when no day columns Remove old copy of mo_load_coefficients.F90 Make sure all dimension names have same length Replace "merge" with if statement Handle case where no sunlit points in chunk Remove old version of mo_load_coefficients Pull in read routine from rte-rrtmgp source Update RRTMGP coefficients files Remove old version of mo_load_coefficients Pull in read routine from rte-rrtmgp source Update RRTMGP coefficients files | 21 January 2019, 18:13:09 UTC |
| 7816bdc | Mark Taylor | 21 January 2019, 17:40:21 UTC | netcdf4p support for making ne>512 SCRIP files | 21 January 2019, 17:40:21 UTC |
| 4a12f75 | Mark Taylor | 20 January 2019, 19:42:22 UTC | tweaks to HStopo NCL diagnostics | 20 January 2019, 19:42:22 UTC |
| 77bc343 | Azamat Mametjanov | 19 January 2019, 01:26:02 UTC | Add kind parameter to centroids in mesh_mod | 19 January 2019, 01:26:02 UTC |
| 3ac5c8e | James Foucar | 14 January 2019, 22:51:06 UTC | Merge branch 'homme/preqx_kokkos_build_fix' into master (PR #2665) HOMME: fixing some issues with the preqx_kokkos target #2665 One issue this PR fix is #2648 . The other issue it fixes (which was not opened on github) is the duplication of files between preqx and preqx_kokkos targets. In particular, the files in the folder preqx/share were copied verbatim in the folder preqx_kokkos. This causes maintenance issues, and led to a build error when some changes were made in the files in preqx/share but not in the corresponding files in preqx_kokkos. Instead, we now simply include the preqx/share folder content in the list of files to be compiled for the preqx_kokkos target. Note: there are a few files in preqx that are copied verbatim in preqx_kokkos. It would be tempting to also remove those files in preqx_kokkos, and simply use the files in preqx. This would work in a cmake standalone homme build, but it would be problematic with cime. The reason is that not all files in the preqx folder are copied in preqx_kokkos; for instance, prim_driver_mod.F90 is different. In cmake, we can manually specify the files we want to compile, but in cime, we can only specify the folders where the files are, and cime will glob all source files in those folders. For now, we are ok with the removal of some duplicate files. We will think about how to remove the other duplicates later. [BFB] * bartgol/homme/preqx_kokkos_build_fix: i need this file under version control and i cannot use master with preqx_kokkos, so, placing it here HOMME: Fixing preqx/preqx_kokkos duplication issue Fix #2648 | 18 January 2019, 20:00:38 UTC |
| c164447 | rgknox | 17 January 2019, 19:07:05 UTC | typo fix on the lawrencium partition batch files | 17 January 2019, 19:07:05 UTC |
| 5947727 | Patrick Worley | 16 January 2019, 23:49:33 UTC | modify behavior of t_startstop_valsf The perf_mod command t_startstop_valsf (GPTL command GPTLstartstop_vals) is used to create a timer or add time to an existing timer when t_startf/t_stopf cannot be used to time the corresponding event. The motivating example is measuring the time spent in MPI_Init (before the timing library has been initialized). When the "call count" parameter callcount is set to 1, the max and min for the event are updated as expected. However, when callcount is 0 (adding time without incrementing the call count) or greater than 1 (adding time associated with multiple calls that are not recorded individually), max and min cannot be updated in the usual way. The current implementation is insufficient even given this basic ambiguity, and this PR modifies the min/max update logic to improve upon this. [BFB] | 16 January 2019, 23:49:33 UTC |
| 743d9d5 | Wuyin Lin | 16 January 2019, 23:39:24 UTC | Merge bogensch/atm/SCM_omegafix (PR #2690) Large scale vertical velocity bug fix in Eulerian SCM Bug fix to allow prescribed omega to propagate to state variable. The prescribed omega (wfld) is used directly by the dynamics and this implementation has always been correct. However, CLUBB (physics parameterization) uses the large scale vertical velocity as well. Thus, since wlfd was not being passed to state correctly CLUBB was never seeing the updated wfld, only the wfld at the first time step. CLUBB is not very sensitive to changes in wfld, so the SCM solutions are not very sensitive, but not bit for bit. In addition, after this fix, the outfld conditional call for OMEGA in cam_diagnostics.F90 is not necessary and has been removed. [BFB] except for SCM mode. | 16 January 2019, 23:39:24 UTC |
| 7f733eb | Po-Lun Ma | 16 January 2019, 21:04:22 UTC | Rename flag to use_sgv | 16 January 2019, 21:04:22 UTC |
