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f82b954 James Foucar 14 June 2019, 20:02:36 UTC Upgrades to bld_diff for cpp handling 14 June 2019, 20:02:36 UTC
66e2025 James Foucar 13 June 2019, 20:07:45 UTC Make MPAS seaice build using CMake! [BFB] 13 June 2019, 20:07:45 UTC
1ef9791 James Foucar 10 June 2019, 18:12:42 UTC Updates to bld_diff to accomodate MPAS 10 June 2019, 18:12:42 UTC
5897537 James Foucar 07 June 2019, 21:16:18 UTC Make mpas-ocean build using CMake! [BFB] 07 June 2019, 21:18:18 UTC
f2089ed James Foucar 07 June 2019, 19:56:19 UTC Merge branch 'jgfouca/mosart/cmakify' (PR #2978) Make mosart build using CMake! [BFB] * jgfouca/mosart/cmakify: Switch mosart buildlib to python and cmake 07 June 2019, 19:56:19 UTC
69ee772 James Foucar 07 June 2019, 19:45:29 UTC Merge branch 'jgfouca/cice/workaround_cmake_bug' into master (PR #2981) Workaround bug in cmake f90 dependency scanner Cmake continues to struggle to find the correct .mod dependencies for some cice files. These seems to happen when the file has certain preprocessor directives and the use statements are within a subroutine. [BFB] * jgfouca/cice/workaround_cmake_bug: Workaround bug in cmake f90 dependency scanner 07 June 2019, 19:45:29 UTC
f07d740 James Foucar 07 June 2019, 19:05:41 UTC Workaround bug in cmake f90 dependency scanner Cmake continues to struggle to find the correct .mod dependencies for some cice files. These seems to happen when the file has certain preprocessor directives and the use statements are within a subroutine. [BFB] 07 June 2019, 19:05:41 UTC
b15089f James Foucar 04 June 2019, 17:20:04 UTC Switch mosart buildlib to python and cmake 06 June 2019, 17:53:39 UTC
fb71bd3 James Foucar 06 June 2019, 17:51:53 UTC Merge branch 'jgfouca/cice/cmakify' (PR #2968) Make cice build using CMake! [BFB] * origin/jgfouca/cice/cmakify: Fix mysterious dep issue Progress 06 June 2019, 17:51:53 UTC
96ca2b2 James Foucar 06 June 2019, 17:06:00 UTC Merge branch 'jgfouca/cime/update_anvil_cmake' into master (PR #2977) Update anvils cmake version [BFB] * jgfouca/cime/update_anvil_cmake: Update anvils cmake version 06 June 2019, 17:06:00 UTC
8860076 James Foucar 06 June 2019, 17:04:00 UTC Update anvils cmake version [BFB] 06 June 2019, 17:04:00 UTC
ccea096 James Foucar 06 June 2019, 16:55:22 UTC Update CIME to ESMCI cime5.8.2-3 (PR #2967) Update CIME to ESMCI cime5.8.2-3 Squash merge of jgfouca/branch-for-to-acme-2019-06-03 Features: * Provide default for the number of create_test parallel jobs * Nuopc cmeps removed (moved to separate repository) * RCP cmip5 scenarios - these have been removed and replaced in datm with the SSP scenarios of cmip6 Bug fix: * Use truncated division operator in SEQ SystemTest for py2+3 compatibility [BFB] 06 June 2019, 16:55:22 UTC
34083d2 James Foucar 05 June 2019, 23:06:54 UTC Merge branch 'bishtgautam/lnd/sbetr-cmake-fix' (PR #2969) Updates SBeTR module to simplify cmake for ELM In SBeTR submodule, all use bshr_assert_mod, only <> statements are removed from bshr_assert.h and explicitly added them in all files that have #include "bshr_assert.h". This simplifies E3SM Cmake for ELM. [BFB] * origin/bishtgautam/lnd/sbetr-cmake-fix: Updates SBeTR module to simplify cmake for ELM 05 June 2019, 23:06:54 UTC
07e202a Oksana Guba 04 June 2019, 19:11:03 UTC Merge remote-tracking branch 'AMB/ambrad/homme/gpu-reduction-fix' into master PR#2898 Fixes definition of HOMMEXX_GPU_BFB_WITH_CPU. At some point HOMMEXX_GPU_BFB_WITH_CPU became a cmakedefine01, but we still used it as a cmakedefine. This then forced team reductions to serialize on GPU. This in turn masked a bug in one of the reductions. This commit fixes both issues. This PR is BFB w.r.t. the usual testing but fixes a GPU issue in the performance build. (It gives a little more performance but now is truly non-BFB w.r.t, say, Fortran on P9.) [BFB] 04 June 2019, 19:11:03 UTC
7c34501 Oksana Guba 04 June 2019, 19:10:17 UTC Merge branch bartgol:homme_remap_bugfix_kokkos into master (PR#2875) Fixes hommexx remap bug: Propagates a fix in vertical remap (already present in the Fortran code) to the C++/Kokkos code. Also: suppressing some compiler warnings (unused/shadowing variables). Fixes #2711 . [BFB] 04 June 2019, 19:10:17 UTC
4a6ccb2 James Foucar 04 June 2019, 18:59:02 UTC Merge branch 'bartgol/Fix-2964' (PR #2965) Homme: changes in Kokkos.cmake related to internal kokkos build. This fixes issue #2964 . See that issue for details. [BFB] * bartgol/Fix-2964: Fixes #2964 04 June 2019, 18:59:02 UTC
d7b1637 James Foucar 04 June 2019, 18:55:52 UTC Merge branch 'oksanaguba/homme/patch-restart-thetal' (PR #2934) Fixing restart for theta-l, round 2 Fixes 1 memory bug and 1 unnecessary EOS check up that were preventing restart runs for theta H and NH. Should be BFB because we don't have restart tests yet. [BFB] * origin/oksanaguba/homme/patch-restart-thetal: removing a comment fix memory bug for restart, wrap eos state check for h/nh. 04 June 2019, 18:55:52 UTC
0f6ec76 Gautam Bisht 04 June 2019, 17:35:04 UTC Updates SBeTR module to simplify cmake for ELM In SBeTR submodule, all `use bshr_assert_mod, only <>` statements are removed from `bshr_assert.h` and explicitly added them in all files that have `#include "bshr_assert.h"`. This simplifies E3SM Cmake for ELM. 04 June 2019, 17:35:04 UTC
44943f2 James Foucar 31 May 2019, 23:24:25 UTC Fix mysterious dep issue 04 June 2019, 17:23:42 UTC
24325dc James Foucar 31 May 2019, 20:28:11 UTC Progress 04 June 2019, 17:23:42 UTC
aae9dfa James Foucar 04 June 2019, 17:22:37 UTC Merge branch 'jgfouca/clm/cmakify' (PR #2954) Make lnd build using CMake! Includes some minor fixes and cleanups for atm. [BFB] * jgfouca/clm/cmakify: Sandiatoss3 needs newer cmake Run_sub_or_cmd is not thread safe Progress, building on melvin Progress 04 June 2019, 17:22:37 UTC
d66481c Luca Bertagna 03 June 2019, 18:12:14 UTC Fixes #2964 Also, change names of some cmake variables and folders involved in the in-house kokkos build, since in that case, kokkos is only built, not installed. 03 June 2019, 22:54:08 UTC
3fd4034 James Foucar 03 June 2019, 19:14:45 UTC Sandiatoss3 needs newer cmake 03 June 2019, 19:14:45 UTC
4122eb4 James Foucar 31 May 2019, 22:27:42 UTC Run_sub_or_cmd is not thread safe Need to use run_cmd. 31 May 2019, 22:27:42 UTC
da4601b James Foucar 30 May 2019, 23:55:41 UTC Merge branch 'jgfouca/cime/create_test_share_upgrade' into master (PR #2961) Implement a more-advanced way of sharing builds within test suites Implements a concept of build groups within test_scheduler. [BFB] * origin/jgfouca/cime/create_test_share_upgrade: Swtich build group output to debug Implement a more-advanced way of sharing builds within test suites 30 May 2019, 23:56:24 UTC
c72f5c8 James Foucar 30 May 2019, 23:35:21 UTC Swtich build group output to debug 30 May 2019, 23:35:21 UTC
789e060 James Foucar 30 May 2019, 22:07:31 UTC Implement a more-advanced way of sharing builds within test suites Implements a concept of build groups within test_scheduler. [BFB] 30 May 2019, 23:29:39 UTC
2e712dd James Foucar 30 May 2019, 21:11:59 UTC Merge branch 'jgfouca/cime/fix_cmake_anlworkstation' into master (PR #2960) Fix cmake building of atm on anlworkstation Fixes #2956 [BFB] * jgfouca/cime/fix_cmake_anlworkstation: Fix cmake building of atm on anlworkstation 30 May 2019, 21:13:33 UTC
028d6b8 James Foucar 30 May 2019, 21:08:49 UTC Fix cmake building of atm on anlworkstation [BFB] 30 May 2019, 21:08:49 UTC
9b9cfe4 Bibi Mathew 30 May 2019, 17:42:14 UTC Merge branch 'worleyph/cime/compy_perf_arch' Add support for performance archiving on Compy #2943 Added logic for compy to provenance.py, specified the location of the performance archive in the compy entry in config_machines.xml (enabled for all projects) and added the job progress monitoring script syslog.compy. Also removed performance archiving support for edison, now that it has been decommissioned. [BFB] - Bit-For-Bit 30 May 2019, 17:42:25 UTC
e783325 Balwinder Singh 30 May 2019, 16:28:36 UTC Merge branch 'singhbalwinder/machines/compy-cmake3'(PR #2957) Adds cmake 3.11.4 module to Compy's machine files Compy default cmake was 2.8.12.2, which doesn't work with the new Cmake build for EAM. This updates cmake to 3.11.4. SMS test built fine on Compy with this new cmake version. [BFB] - Bit-For-Bit * singhbalwinder/machines/compy-cmake3: Adds cmake 3.11.4 module to Compy's machine files 30 May 2019, 16:28:36 UTC
d98ffb9 Balwinder Singh 30 May 2019, 16:05:17 UTC Adds cmake 3.11.4 module to Compy's machine files [BFB] - Bit-For-Bit 30 May 2019, 16:05:17 UTC
fc918ee Jon Wolfe 30 May 2019, 14:34:18 UTC Merge branch 'mark-petersen/mpas/threading_update' (PR #2852) MPAS-Ocean threading and GPU update This PR updates OpenMP and OpenACC calls in MPAS-Ocean, including: * GPU optimization in EOS: MPAS-Dev/MPAS-Model#69 and MPAS-Dev/MPAS-Model#170 * Update ocean BGC threading: MPAS-Dev/MPAS-Model#152 * Reduce threading barriers: MPAS-Dev/MPAS-Model#194 It is not bfb due to change in order of operations. It should not be climate changing. Fixes #2860 [non-BFB] 30 May 2019, 14:34:18 UTC
527d42a James Foucar 29 May 2019, 22:06:30 UTC Progress, building on melvin 29 May 2019, 22:50:16 UTC
61b937c James Foucar 28 May 2019, 16:18:09 UTC Progress 29 May 2019, 22:50:16 UTC
b932309 James Foucar 29 May 2019, 22:48:28 UTC Merge branch 'jgfouca/cam/cmakify' (PR #2922) Make atm build using CMake! Switch atm component over to using CMake. I tried to mimic the original behavior as closely as possible. I wrote a tool to compare bld logs and this PR appears to be flag-for-flag identical to old system, with a couple minor exceptions. Change list: * Change FFLAGS_NOPT to be an append to the normal set of flags. This reduces duplication with FFLAGS * Remove Depends files for obsolete/unsupported platforms * Make CMake versions of remaining Depends files * New bld_diff tool for comparing bld logs, necessary to validate this work * Add ability to ask for CMake args (get_standard_cmake_args) * CMake macros should NOT be looking at environment, just CMake vars * Homme test needs to use GMAKE_J and do a verbose build * build_model_thread can now use run_sub_or_cmd * case_setup will make both macro types (Make and CMake) * Import a FindPetsc CMake module * components/CMakeLists.txt will be the CMake file to configure builds of our components. It currently is only doing so for cam. * Remove obsolete bld files from cam * Convert cam buildlib to python * Someone appears to have added their genf90'd files to cam a long time ago, remove them. * Convert cosp to Cmake. Cosp files are now just part of libatm, not their own library. This means CMake can handle the circular dependencies. User impact: * Since this is just the initial phase, user impacts are minimal * Build times look roughly the same, CMake is slightly faster * cosp integration with atm is different, it will need to be managed through cosp/Cosp.cmake. * When adding Depends files for machine/compiler-specific flag changes, both a Make and CMake version will be needed until all components are switched over. * It is no-longer enough to have NETCDF settings in the environment, they need to be explicit in the Macros (config_compilers.xml). * Putting up for an early review due to the high-impact of this PR. [BFB] 29 May 2019, 22:48:28 UTC
7773f86 James Foucar 29 May 2019, 18:19:44 UTC Merge branch 'oksanaguba/eam/fc-test-thetasl' into master (PR #2942) Adding an FC test with theta SL Adding a short test for coupled run with theta-l and SL. [BFB] * oksanaguba/eam/fc-test-thetasl: addign the test 29 May 2019, 18:21:25 UTC
abda40a mark-petersen 27 May 2019, 13:55:36 UTC Update mpas-source: threading, EOS GPU, missing deallocates 29 May 2019, 15:46:21 UTC
45fe3d7 Jon Wolfe 29 May 2019, 14:28:48 UTC Merge branch 'jonbob/ocean/fix-ismf' (PR #2948) Fix the setting of ocn_c2_glcshelf based on value of land_ice_flux_mode This PR fixes the value of ocn_c2_glcshelf that is passed from mpas-o to the coupler and used to determine whether or not the coupler computes ice sheet melt fluxes. It is now based on all possible values of land_ice_flux_mode and fixes issues with ocean ISMF compsets. Fixes #2947 [BFB] 29 May 2019, 14:28:48 UTC
9250341 James Foucar 28 May 2019, 21:43:25 UTC Better handling of kokkos 28 May 2019, 21:43:25 UTC
59ce0c8 James Foucar 28 May 2019, 19:08:12 UTC Merge branch 'jgfouca/cime/fix_hist_bless' into master (PR #2950) Fix bug in generating baselines Need to use the base case id when parsing test opts. [BFB] * jgfouca/cime/fix_hist_bless: Fix bug in generating baselines 28 May 2019, 19:09:19 UTC
3a50066 James Foucar 28 May 2019, 19:06:38 UTC Fix bug in generating baselines Need to use the base case id when parsing test opts. [BFB] 28 May 2019, 19:06:41 UTC
1a84342 James Foucar 28 May 2019, 18:47:56 UTC Merge branch 'jgfouca/cime/fix_pet_timestamp_bug' into master (PR #2949) Fix bug in PET timestamp Need to use build as a library, not a subprocess. [BFB] * jgfouca/cime/fix_pet_timestamp_bug: Fix bug in PET timestamp 28 May 2019, 18:48:39 UTC
879c32d James Foucar 28 May 2019, 18:39:39 UTC Fix bug in PET timestamp Need to use build as a library, not a subprocess. [BFB] 28 May 2019, 18:39:39 UTC
9438ebb Jon Wolfe 28 May 2019, 17:59:51 UTC Fix the setting of ocn_c2_glcshelf based on value of land_ice_flux_mode 28 May 2019, 17:59:51 UTC
1a6d114 James Foucar 24 May 2019, 19:53:56 UTC Sync up with latest Makefile 24 May 2019, 19:53:56 UTC
9d608ad James Foucar 24 May 2019, 19:43:41 UTC Merge remote-tracking branch 'origin/master' into jgfouca/cam/cmakify * origin/master: (159 commits) Update CIME to ESMCI cime5.8.2-3 (PR #2938) Update namelist scripts to reflect changes in mpas-ocean Registry files Update mpas source. bless_test_results: Be able to handle build-only tests Fix machine file entry for C++ compiler on melvin. Add x2g_*_from_lnd lists for use in prep_glc LND routines Update config_machines.xml Fix optics allocation Cleanup formatting in compute_melt_fluxes() Remove no longer-used cime_model variable Fix unallocated cloud optics Fix unallocated band midpoints COMPOSE: Fix the scope of the share_kokkos_ut standalone unit tests. Update CIME to ESMCI cime5.8.2-2 (#2908) Minor cleanup to previous commit Add default to PIO_CLOBBER if mode unset Test with changing logic for ocn-glc coupling Fix formatting and whitespace Remove `mode_in` in calls to `cam_pio_createfile` Add subroutine call to get PIO format ... 24 May 2019, 19:43:41 UTC
b14f3d3 James Foucar 24 May 2019, 18:38:32 UTC Another try for pnetcdf 24 May 2019, 18:38:32 UTC
7eb00eb James Foucar 24 May 2019, 18:27:58 UTC Fix PNETCDF for some platforms 24 May 2019, 18:27:58 UTC
c38f3ad James Foucar 24 May 2019, 18:07:05 UTC Fix configure to work with cmake Depends files 24 May 2019, 18:07:19 UTC
bec2df0 Patrick Worley 24 May 2019, 14:10:07 UTC Add support for performance archiving on Compy Added logic for compy to provenance.py, specified the location of the performance archive in the compy entry in config_machines.xml (enabled for all projects) and added the job progress monitoring script syslog.compy. Also removed performance archiving support for edison, now that it has been decommissioned. [BFB] - Bit-For-Bit 24 May 2019, 14:10:07 UTC
57859cb Oksana Guba 24 May 2019, 05:43:23 UTC addign the test 24 May 2019, 05:43:23 UTC
383a082 James Foucar 23 May 2019, 21:48:27 UTC Fix for bebop 23 May 2019, 21:48:27 UTC
d4092ad James Foucar 23 May 2019, 19:38:02 UTC Update theta cmake 23 May 2019, 19:38:02 UTC
e3d7f9b James Foucar 23 May 2019, 18:47:48 UTC Fixes for anvil 23 May 2019, 18:47:48 UTC
bd84d8c James Foucar 23 May 2019, 17:47:14 UTC Reduce cmake requirement to 3.9 23 May 2019, 17:47:21 UTC
ba49c36 Aaron Donahue 23 May 2019, 17:43:19 UTC Add 'buildlibc' to gitignore, which shows up during an LC build. [BFB] - Bit-For-Bit See confluence for a more detailed description about these tags. 23 May 2019, 17:43:19 UTC
4bc4a69 Aaron Donahue 23 May 2019, 17:42:11 UTC Update Livermore Computing configs [BFB] - Bit-For-Bit See confluence for a more detailed description about these tags. 23 May 2019, 17:42:11 UTC
bb7f550 James Foucar 23 May 2019, 16:53:15 UTC Update anvil cmake 23 May 2019, 17:16:39 UTC
fe07217 Jon Wolfe 23 May 2019, 16:40:27 UTC Merge branch 'mark-petersen/update_mpas_bfb' (PR #2918) Update mpas source This PR update the mpas-source git submodule but only includes changes that will not impact E3SM. These changes include: * LIGHT update (MPAS-Ocean Lagrangian particles): MPAS-Dev/MPAS-Model#56 * clean up ice shelf melt flag: MPAS-Dev/MPAS-Model#164 * merge coastal branch: MPAS-Dev/MPAS-Model#54 * CONUS mesh update: MPAS-Dev/MPAS-Model#201 * Major COMPASS upgrade to python 3: MPAS-Dev/MPAS-Model#229 * Eliminate outdated -DUNDERSCORE flag: MPAS-Dev/MPAS-Model#156 * PIO Version Compatibility Check - PGI Compiler Bug Fix: MPAS-Dev/MPAS-Model#212 These changes do not alter E3SM standard cases or tested configurations. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests. [NML] [BFB] 23 May 2019, 16:40:27 UTC
d115201 James Foucar 23 May 2019, 16:34:45 UTC Update CIME to ESMCI cime5.8.2-3 (PR #2938) Update CIME to ESMCI cime5.8.2-3 Squash merge of jgfouca/branch-for-to-acme-2019-05-21 Features: * Allow custom run_exe and run_misc_suffix * send run two TestStatus.log to case1 log for 2-case tests Bugs: * Fix ConfigParser fails with some saved submit_options [BFB] 23 May 2019, 16:34:45 UTC
fd97485 Jon Wolfe 22 May 2019, 20:14:48 UTC Update namelist scripts to reflect changes in mpas-ocean Registry files 22 May 2019, 20:14:48 UTC
6003c19 James Foucar 22 May 2019, 19:29:50 UTC Update cori's cmake version 22 May 2019, 19:29:50 UTC
36763e1 mark-petersen 20 May 2019, 18:58:08 UTC Update mpas source. Includes: 1. LIGHT update (MPAS-Ocean Lagrangian particles): MPAS-Dev/MPAS-Model#56 2. clean up ice shelf melt flag: MPAS-Dev/MPAS-Model#164 3. merge coastal branch: MPAS-Dev/MPAS-Model#54 4. CONUS mesh update: MPAS-Dev/MPAS-Model#201 5. Major COMPASS upgrade to python 3: MPAS-Dev/MPAS-Model#229 6. Eliminate outdated -DUNDERSCORE flag: MPAS-Dev/MPAS-Model#156 7. PIO Version Compatibility Check - PGI Compiler Bug Fix: MPAS-Dev/MPAS-Model#212 These changes do not alter E3SM standard cases or testing on next. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests. 22 May 2019, 13:36:07 UTC
577f07f James Foucar 21 May 2019, 21:53:47 UTC Merge branch 'jgfouca/cime/bless_test_results_with_B' into master (PR #2937) bless_test_results: Be able to handle build-only tests [BFB] * jgfouca/cime/bless_test_results_with_B: bless_test_results: Be able to handle build-only tests 21 May 2019, 21:54:28 UTC
b17aed1 James Foucar 21 May 2019, 21:52:10 UTC bless_test_results: Be able to handle build-only tests [BFB] 21 May 2019, 21:52:10 UTC
40013ee James Foucar 21 May 2019, 21:10:04 UTC Merge branch 'worleyph/cime/init_profiling' into master (PR #2882) Add checkpoint of timing data immediately after initialization Currently a timing checkpoint is saved at the end of the first simulation day, capturing both initialization cost and possibily anomalous first simulation day performance. However, when evaluating performance of initialization for high resolution cases, this may not be sufficiently fine grain, especially if the evaluation job runs out of time before completing the first simulation day. Here an additional timing checkpoint is output immediately before the beginning of the run loop, with a name consistent with the other checkpoint timing files, i.e. including the simulation timestamp in the suffix. Existing timer names associated with the writing out of performance data are modified slightly, to better attribute time associated with the new performance data write. Also, missing documentation for the TPROF_TOTAL env_run.xml variable is added to config_component_e3sm.xml. [BFB] - Bit-For-Bit * origin/worleyph/cime/init_profiling: Change optional checkpoint of initialization to mandatory Enable optional checkpointing of timing data during initialization 21 May 2019, 21:10:04 UTC
80d2acf James Foucar 21 May 2019, 20:44:37 UTC The best way to deal with the circular deps between cosp and cam is to just put all the sources into cam 21 May 2019, 20:44:37 UTC
9f45860 Jon Wolfe 21 May 2019, 18:25:27 UTC Merge branch 'matthewhoffman/coupler/iceshelf_ocean_coupling_Fyke2_cleaned' (PR #2726) Add first stage of ocean/ice shelf coupling This merge introduces coupler changes to allow coupling between the ocean model and ice shelves within the GLC model. As part of model coupling necessary for Antarctic simulations, ice shelf melt fluxes due to (primarily) ocean temperatures must be calculated. These melt fluxes correspond to oceanic heat and moisture fluxes at the upper ocean surface, and ice sheet heat and ice column thickness changes. Coupling is characterized by 1) calculations carried out by "subroutine compute_melt_fluxes" on the GLC grid, but 2) on the OCN coupling timestep (<GLC coupling timestep). This is why these fluxes cannot be calculated in either component and are done here in the coupler itself. These factors result in 1) frequent OCN2GLC remapping that is not associated with a GLC run step and 2) accumulation of GLC-bound "subroutine compute_melt_fluxes" output fields, but no equivalent accumulation of OCN-bound outputs. Inputs to the flux calculations (all mapped to GLC grid): From OCN: * oceanTemperature(:) -> o2x_gx%rAttr(index_o2x_So_blt,:) * oceanSalinity(:) -> o2x_gx(1)%rAttr(index_o2x_So_bls,:) * oceanHeatTransferVelocity(:) -> o2x_gx(1)%rAttr(index_o2x_So_htv,:) * oceanSaltTransferVelocity(:) -> o2x_gx(1)%rAttr(index_o2x_So_hsv,:) From GLC: * interfacePressure(:) -> o2x_gx(1)%rAttr(index_o2x_So_phieff,:) * iceTemperature(:) -> g2x_gx%rAttr(index_g2x_Sg_tbot,:) * iceTemperatureDistance(:) -> g2x_gx%rAttr(index_g2x_Sg_dztbot,:) * iceFloatingMask(:) -> g2x_gx%rAttr(index_g2x_Sg_icemask_floating,:) Outputs from flux calculations (all calculated natively on GLC grid): To OCN: * g2x_gx%rAttr(index_g2x_Sg_blis,:) -> outInterfaceSalinity(:) * g2x_gx%rAttr(index_g2x_Sg_blit,:) -> outInterfaceTemperature(:) * g2x_gx%rAttr(index_g2x_Fogx_qiceho,:) -> outOceanHeatFlux(:) * g2x_gx%rAttr(index_g2x_Fogx_qicelo,:) -> outFreshwaterFlux(:) TO GLC: * x2g_gx%rAttr(index_x2g_Fogx_qicehi,:) -> outIceHeatFlux(:) * x2g_gx%rAttr(index_x2g_Fogx_qiceli,:) -> -1*outFreshwaterFlux(:) These changes also include necessary driver and build script changes and a new compset "GMPAS-MALI-DIB-IAF-ISMF" that includes active MPAS-Ocean and MPAS-Albany-Land-Ice (as well as active MPAS-Sea-Ice). In this compset, MPAS-Albany-Land-Ice is configured in a "static" mode where ice sheet geometry and temperature do not evolve. [NML] [BFB] for all previously existing compsets 21 May 2019, 18:25:27 UTC
5c123fb James Foucar 21 May 2019, 16:35:33 UTC bld_diff should not fail so easily 21 May 2019, 16:35:38 UTC
ef9e1b9 Balwinder Singh 20 May 2019, 18:41:29 UTC Merge branch 'brhillman/atm/fix-cam-pioformat'(PR #2911) Allow EAM to respect PIO_NETCDF_FORMAT Allow EAM to respect the value of the XML variable PIO_NETCDF_FORMAT that is set in env_run.xml. Previously, setting this variable had no effect on the actual format used to write EAM output files (restart, history, initial conditions), due to calls to cam_pio_createfile explicitly passing in a mode argument hard-coded to PIO_CLOBBER. Note that there are some whitespace changes in components/cam/src/ dynamics/se/dyn_comp.F90 just because I found some inconsistent indenting when opening that file to remove the hard-coded mode argument in the call to cam_pio_createfile. Fixes #2903 [BFB] * brhillman/atm/fix-cam-pioformat: Add default to PIO_CLOBBER if mode unset Fix formatting and whitespace Remove `mode_in` in calls to `cam_pio_createfile` Add subroutine call to get PIO format 20 May 2019, 18:41:29 UTC
4fe4d26 James Foucar 20 May 2019, 17:16:49 UTC Homme needs to use GMAKE_J and should do a VERBOSE build 20 May 2019, 17:16:49 UTC
741cae2 James Foucar 20 May 2019, 16:42:09 UTC bld_diff can run with any python 20 May 2019, 16:42:09 UTC
dca3685 Oksana Guba 20 May 2019, 15:06:21 UTC removing a comment 20 May 2019, 15:06:21 UTC
490c0a2 Oksana Guba 19 May 2019, 23:42:33 UTC fix memory bug for restart, wrap eos state check for h/nh. 19 May 2019, 23:42:33 UTC
96f2772 James Foucar 17 May 2019, 22:34:30 UTC Get cosp integration working 17 May 2019, 22:34:30 UTC
ebcce63 Balwinder Singh 17 May 2019, 16:48:35 UTC Merge branch 'brhillman/atm/fix-rrtmgp-debug' (PR #2927) Fix allocations errors in RRTMGP for DEBUG mode Fix allocation errors in RRTMGP interface code to enable running with DEBUG=True. These fixes do not seem to affect runs configured with DEBUG=False (RRTMGP tests are BFB), but without these fixes runs configured with DEBUG=True will fail. [BFB] * brhillman/atm/fix-rrtmgp-debug: Fix optics allocation Fix unallocated cloud optics Fix unallocated band midpoints 17 May 2019, 16:48:35 UTC
55db1a6 James Foucar 16 May 2019, 23:01:08 UTC Get CMake to load Depends files 16 May 2019, 23:01:08 UTC
0767538 James Foucar 16 May 2019, 22:42:42 UTC Port Depends to cmake 16 May 2019, 22:42:42 UTC
ec985f9 James Foucar 16 May 2019, 21:19:44 UTC Remove Depends files for unsupported platforms 16 May 2019, 21:19:44 UTC
5230fd5 James Foucar 16 May 2019, 20:29:31 UTC Progress changing cam/buildib to python 16 May 2019, 20:29:31 UTC
531b647 James Foucar 16 May 2019, 20:18:15 UTC Merge branch 'ambrad/homme/fix-melvin-build' into master (PR #2930) Fix machine file entry for C++ compiler on melvin. Previously, it was set to mpicc, which meant that -lmpi_cxx -lstdc++ was missing in link.txt. This caused a build failure in test HOMME_P24.f19_g16_rx1.A.melvin_gnu in e3sm_developer_master_gnu on melvin. [BFB] * ambrad/ambrad/homme/fix-melvin-build: Fix machine file entry for C++ compiler on melvin. 16 May 2019, 20:19:05 UTC
407775a Andrew M. Bradley 16 May 2019, 20:02:09 UTC Fix machine file entry for C++ compiler on melvin. Previously, it was set to mpicc, which meant that -lmpi_cxx -lstdc++ was missing in link.txt. This caused a build failure in test HOMME_P24.f19_g16_rx1.A.melvin_gnu in e3sm_developer_master_gnu on melvin. 16 May 2019, 20:02:09 UTC
3f4fd4c Matthew Hoffman 16 May 2019, 19:23:47 UTC Add x2g_*_from_lnd lists for use in prep_glc LND routines In prep_glc_mod, there are two routines (prep_glc_calc_l2x_gx and prep_glc_merge_lnd_forcing) handling coupling from LND to GLC that operate on lists of coupling fields. Currently they operate on the lists seq_flds_x2g_states and seq_flds_x2g_fluxes. However, now with the addition of the OCN-GLC coupling, those lists include coupling fields that are not coming from LND, and therefore operating over the full lists leads to errors, inappropriate calculations, or unnecessary calculations. This commit introduces two new lists that can be used instead: seq_flds_x2g_states_from_lnd, seq_flds_x2g_fluxes_from_lnd These are restricted to the coupling fields only coming from LND and therefore maintain the existing behavior for these LND->GLC prep routines. One check was removed, because it was no longer meaningful: mct_aVect_nRattr(x2g_g) will no longer be equal num_flux_fields + num_state_fields when num_flux_fields and num_state_fields are restricted to fields from LND. 16 May 2019, 19:23:47 UTC
c37b94a James Foucar 15 May 2019, 22:41:02 UTC Fixes for generated files 15 May 2019, 22:41:02 UTC
886dab9 James Foucar 15 May 2019, 22:40:47 UTC Someone appears to have checked-in generated fortran files Remove them. 15 May 2019, 22:40:47 UTC
194b973 wadeburgess 15 May 2019, 22:31:38 UTC Merge pull request #2929 from E3SM-Project/wadeburgess-patch-1 Update config_machines.xml 15 May 2019, 22:31:38 UTC
2c36809 wadeburgess 15 May 2019, 22:26:59 UTC Update config_machines.xml update melvin to load cmake 3.10.3 instead of 2.8.12.2 15 May 2019, 22:26:59 UTC
83ad80d Oksana Guba 15 May 2019, 14:45:18 UTC Merge branch 'ambrad/ambrad/homme/compose-theta-l' into master (PR #2896) Bring COMPOSE semi-Lagrangian tracer transport code into HOMME and E3SM. [non-BFB] for HOMME suite for 1 test, baroCamMoistSL and [NML] in the same test. Includes the following: Changes to E3SM model build system to permit SL in theta-l (only). Nontrivial changes to the HOMME standalone build system to use E3SM Kokkos submodule automatically. A cosmetic issue was changing things to move away from associating Kokkos specifically with the HOMMEXX work. If HOMME_ENABLE_COMPOSE=OFF and BUILD_HOMME_PREQX_KOKKOS=OFF, then all the Kokkos-related code is skipped. A trivial new target for testing. Will eventually expand to make a convergence test in the standalone test suite. removal of old sl_advection.F90 Add the new libcompose target. It builds COMPOSE C++ code, which is expensive relative to Fortran, just once. Then any target that wants SL links against this library. If HOMME_ENABLE_COMPOSE=OFF, this is not built. Since this is a separate lib, the files are in share/compose rather than just share. Add Fortran interfaces to libcompose. These files must be included in the list of sources for a target and so are in the share directory. They are fast to compile, like all short Fortran files. If HOMME_ENABLE_COMPOSE=OFF, code is appropriately ifdefed out, so it is innocuous to include these in the target's file list. Add a hook for a nice COMPOSE testing capability and one test. Miscellaneous changes: Remove some old code for the previous version of SL transport. Little things to support the new SL code. dcmip16_mu_s -> dcmip16_mu_s for scalars in the dynamics and dcmip16_mu_q. This is an orthogonal change we discussed a while ago. It permits SL not to do dissipation on tracers in a dcmip test as an option. Namelist and control changes for SL. [BFB] for E3SM [BFB] for all HOMME standalone tests except [non-BFB] baroCamMoistSL. 15 May 2019, 14:45:18 UTC
cca92fc Benjamin Hillman 09 May 2019, 20:24:04 UTC Fix optics allocation 14 May 2019, 21:02:58 UTC
120491f James Foucar 14 May 2019, 19:38:16 UTC Change FFLAGS_NOOPT to be an append 14 May 2019, 19:38:16 UTC
16fbd26 James Foucar 14 May 2019, 16:24:57 UTC Warn users if files are being skipped due to repeated basename 14 May 2019, 16:24:57 UTC
f3ed491 Matthew Hoffman 14 May 2019, 02:09:09 UTC Cleanup formatting in compute_melt_fluxes() Whitespace has been adjusted in this routine to better match the rest of the module. Also, changed variable names nCells->gsize and iCell->n to be consistent with other loops in the module. 14 May 2019, 02:09:09 UTC
4a265bf Matthew Hoffman 14 May 2019, 02:07:42 UTC Remove no longer-used cime_model variable It was added earlier in this branch but the usage of it was subsequently removed. 14 May 2019, 02:07:42 UTC
79631ef James Foucar 13 May 2019, 23:42:18 UTC Fix optimization remove for certain files 13 May 2019, 23:42:18 UTC
9392755 James Foucar 13 May 2019, 23:42:08 UTC Tool for validating transition to CMake 13 May 2019, 23:42:08 UTC
09a6137 James Foucar 13 May 2019, 18:54:27 UTC Fix library path, now melvin works for a full build of SMS_Ln9.ne4_ne4.FC5AV1C-L 13 May 2019, 18:54:27 UTC
75f15ed James Foucar 13 May 2019, 18:14:09 UTC Build at full speed 13 May 2019, 18:14:09 UTC
7d43d90 James Foucar 13 May 2019, 18:11:49 UTC Melvin working 13 May 2019, 18:11:49 UTC
d623473 James Foucar 10 May 2019, 22:59:40 UTC More progress 10 May 2019, 22:59:40 UTC
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