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316610c James Foucar 28 February 2019, 20:55:19 UTC jenkins_generic_job: Update archiving capilities Add archive-only option. Remove empty dirs. [BFB] 28 February 2019, 20:55:19 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
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
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
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
19c962d mark-petersen 15 February 2019, 23:26:57 UTC Add active tracer fluxes to analysis terms 21 February 2019, 15:28:58 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
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
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
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
777fbcb Min Xu 14 February 2019, 04:17:41 UTC Merge branch 'minxu74/machines/summit/add_netcdf_path_env' (PR #2723) Add the NETCDF_PATH env for Summit. The MPAS components use the NETCDF_PATH env to find the NetCDF package and the env has not been defined in the machine and compiler xml files. [BFB] - Bit-For-Bit 14 February 2019, 04:17:41 UTC
6ecdeda Min Xu 14 February 2019, 04:02:45 UTC Merge branch 'worleyph/cime/project_updates_2019' (PR #2738) Add performance archiving support for cli133 at OLCF 14 February 2019, 04:02:45 UTC
65ab567 mark-petersen 13 February 2019, 22:12:04 UTC Update mpas-source 13 February 2019, 22:12:04 UTC
f292cba James Foucar 13 February 2019, 21:04:18 UTC Merge branch 'jgfouca/cime/create_test_single_exe' into master (PR #2694) create_test: Add new single-exe option Allows for all cases to share a single build. [BFB] * jgfouca/cime/create_test_single_exe: create_test: Add new single-exe option 13 February 2019, 21:08:32 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
0400d9a asteyer 12 February 2019, 23:10:24 UTC added the imkg252a method as tstep_type = 8 12 February 2019, 23:10:24 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
ec95980 Patrick Worley 10 February 2019, 19:21:43 UTC Add performance archiving support for cli133 at OLCF Support for a new project (cli133) needs to be added for Titan/Eos. [BFB] 10 February 2019, 19:21:43 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
73651d6 Min Xu 05 February 2019, 04:06:22 UTC Add the NETCDF_PATH env for Summit *********1*********2*********3*********4*********5*********6*********7** The MPAS components use the NETCDF_PATH env to find the NetCDF package and the env has not been defined in the machine and compiler xml files. [BFB] - Bit-For-Bit 05 February 2019, 04:06:22 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
450bb5e Andrew M. Bradley 16 January 2019, 20:13:59 UTC Homme: Change means of 0-initing IEner_wet. Instead of using ifndef, move model-specifc, prim_state_mod- specific 0-initing to prim_printstate_init. 16 January 2019, 20:13:59 UTC
a023d65 Andrew M. Bradley 16 January 2019, 20:13:39 UTC Homme: Fix a warning. Fix ``` prim_advance_mod.F90:1200:79: elem(ie)%state%w_i(:,:,k2,nt)*stens(:,:,k2,3,ie))/2 ) / +& 1 Warning: Extension: Unary operator following arithmetic operator (use parentheses) at (1) ``` 16 January 2019, 20:13:39 UTC
544221a Gautam Bisht 16 January 2019, 20:06:30 UTC Adds support back for Lawrencium LR2/LR3 16 January 2019, 20:06:30 UTC
f4a6d08 James Foucar 15 January 2019, 18:07:23 UTC Update CIME to ESMCI cime5.7.6 (PR #2689) Squash merge of jgfouca/branch-for-to-acme-2019-01-14 into master Features: * Improve error/exception handling throughout CIME * Update pio1 * Update pio2 * Improve errors messages coming from generic_xml * Remove support for CLM4.0 * bring in latest nuopc developments Bug fixes: * docn: make sure optional arg exists before using * improve the logic of the continue run check * case.cmpgen_namelists needs to be able to write to the case * Fix Case context manager enforcement [BFB] 16 January 2019, 18:21:34 UTC
7a5e14a Oksana Guba 16 January 2019, 17:01:51 UTC minor change, no repeated defs are found for *.nl in this folder 16 January 2019, 17:01:51 UTC
94f9600 Oksana Guba 16 January 2019, 05:32:44 UTC now it also finds multiple declarations 16 January 2019, 05:32:44 UTC
d47742c Oksana Guba 16 January 2019, 02:06:35 UTC line that compares 2 namelists indep. of order 16 January 2019, 02:06:35 UTC
d1fccb3 Oksana Guba 15 January 2019, 22:45:52 UTC removing extra def of nu_q. however we\d better have a utility of some sort for doubles like this 15 January 2019, 22:45:52 UTC
cddc305 James Foucar 15 January 2019, 22:10:20 UTC create_test: Add new single-exe option Allows for all cases to share a single build. [BFB] 15 January 2019, 22:10:20 UTC
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