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bc4a498 Luca Bertagna 29 June 2020, 17:54:01 UTC HOMME: added possibility of building library instead of execs This helps if Homme is part of another cmake project. In this case, it is helpful if homme builds a library (and no execs), so the outher project can simply 'link' to it. 29 June 2020, 19:33:43 UTC
788db80 Jon Wolfe 26 June 2020, 18:53:18 UTC Merge branch 'mark-petersen/mpas/makefile_PIO2' (PR #3649) Update mpas-source: fix E3SM Makefile This PR brings in a new mpas-source submodule, with changes only to the E3SM Makefile. Specifically, it adds -DUSE_PIO2 to override flags in E3SM Makefile. Fixes #3646 [BFB] 26 June 2020, 18:53:18 UTC
4acf213 Wuyin Lin 26 June 2020, 17:25:37 UTC Merge v2alpha-clubbv2-062020 (PR #3660) Reinstate clubbv2 This is to reinstate clubbv2 by reverting the previous revert of clubbv2 to clubbv1 (PR #3518). The PR also adds clubb_c_k10h as a namelist variable to control c_K10h value at runtime. [non-BFB] [NML] clubb_c_K10h added to all atm use_case files 26 June 2020, 17:25:37 UTC
86408de Oksana Guba 25 June 2020, 20:15:37 UTC Merge 'AMB/ambrad/eam/mass-conservation-test' into master (PR #3614) Set up a theta-sl-pg2 ne4pg2 test with -co2_cycle. Use POSTRUN_SCRIPT to run a python-2/3-compatible script to read "qv( 42)" and "dry M" output from Homme's prim_state_mod. Tracer 42 is CO2_FFF in this test. Check mass conservation for tracer 42 and dry air in the script. If they are fine, exit with 0; if bad, 1. A non-0 exit in a POSTRUN_SCRIPT makes the RUN phase fail. The new test is SMS_Ld9.ne4pg2_ne4pg2.FC5AV1C-04P2.cam-thetahy_sl_pg2_mass Addresses verification part of #3588 [non-BFB] BFB for all existing tests, but adds one new test 25 June 2020, 20:15:37 UTC
7a43474 Jon Wolfe 25 June 2020, 14:49:02 UTC Merge branch 'mark-petersen/ocean/update_mpas_AM_hmix' (PR #3636) Update mpas-source: Add mixed layer AM, add del2 ref. cell width This PR brings in a new mpas-source submodule with changes only to the ocean core. It includes the following updates: * Adds Mixed layer heat and salinity budgets (MPAS-Dev/MPAS-Model#568) * Add reference cell width to del2 and del4 scaling (MPAS-Dev/MPAS-Model#599) * Moves constrain_Haney_number namelist (init mode only) to init mode Registry file. [BFB] [NML] 25 June 2020, 14:49:02 UTC
8d79770 Wuyin Lin 25 June 2020, 13:41:17 UTC Merge brhillman/mmf/fix-undefined-rrtmgp-bands (PR #3639) Fix setting of swband/lwband for history files Fix setting of swband and lwband coordinate variables for history files. Since add_hist_coord simply sets up pointers to the arrays that are passed in, the data needs to persist. Thus, we make these arrays module-scope variables in radiation.F90. Also a little bit of clean-up in radiation.F90 and radconstants.F90. In particular, we now use nswbands and nlwbands from radconstants.F90, rather than defining new versions of these in radiation.F90. Since these values are set at compile time and should never change, we should be using these in radiation.F90 anyways, and it does not make sense to make new versions of these that could inadvertently get changed from what we expect in radconstants.F90. So instead of setting new values for these based on the absorption coefficient data, we simply verify that the number of bands in the input files matches what we expect in the code (14 for, shortwave, 16 for longwave). These fixes are BFB in regards to the simulation, but EAM history files will be non-BFB due to the fix in the swband and lwband coordinate variables. This will only affect simulations that are long enough to generate history files, i.e., either long (month-plus) runs, or high temporal output frequency runs (like the crmout test). [non-BFB] for tests with RRTMGP on band-by-band output fields. 25 June 2020, 13:41:17 UTC
b963978 Benjamin Hillman 24 June 2020, 22:27:08 UTC Fix uninitialized LW optical depths 24 June 2020, 22:27:08 UTC
6383db6 Andrew M. Bradley 24 June 2020, 19:01:29 UTC EAM: Move mass-conservation test to e3sm_atm_integration. Previously, it was in a share tests.py block, and the 44 constituents conflicted with the 40 in the other tests in that block. 24 June 2020, 19:01:29 UTC
42e08b7 Oksana Guba 24 June 2020, 18:56:12 UTC Merge 'AMB/ambrad/homme/fast-dirk-f90' into master (PR# 3612) Backport the fast DIRK solver from Hommexx (C++) to Homme (F90). First, since the Jacobian is strictly diagonally dominant, pivoting is not needed for stability. Second, since pivoting isn't needed, it's natural to batch the solves in the GLL direction. This leads to perfect vectorization of the tridiagonal system solve. Third, since the solves are batched along the GLL direction, everything in the driver loop can be done in Homme's usual fast layout. [non-BFB] for 4 nonhydrostatic standalone Homme tests and 5 nonhydrostatic e3sm_atm_integration tests 24 June 2020, 18:56:12 UTC
19e20a3 Benjamin Hillman 24 June 2020, 18:20:06 UTC Fix initialization of opoptics 24 June 2020, 18:20:06 UTC
1291e64 Jon Wolfe 24 June 2020, 16:49:22 UTC Merge branch 'darincomeau/cime/fix_cryo_runoff_time_interpolation' (PR #3495) Changing modified CORE runoff files time interpolation to be consistent with standard CORE runoff This PR adds entries for time interpolation for the modified CORE runoff files used by cryosphere compsets to be 'upper' (from the default 'linear'), to be consistent with the default CORE runoff file. [NML] for Cryosphere compsets only (G-cases using the 'ISMF' or 'DIB' tags). [non-BFB] for Cryosphere compsets only (G-cases using the 'ISMF' or 'DIB' tags). 24 June 2020, 16:49:22 UTC
86f18ad Aaron Donahue 24 June 2020, 15:51:43 UTC Merge branch 'azamat/comps/rm-warnings' (PR #3656) Cleanup compiler warnings Fixes #3624, #2250 Addresses #2247 [BFB] 24 June 2020, 15:51:43 UTC
e2793f5 mark-petersen 23 June 2020, 21:33:33 UTC mpas-source:Update flags in Makefile.in.E3SM MPAS#603 23 June 2020, 21:33:33 UTC
4b6f807 Wuyin Lin 23 June 2020, 21:28:09 UTC Add clubb_c_K10h to all atm use case files that set clubb_c_K10 23 June 2020, 21:28:09 UTC
1bbbdb6 Benjamin Hillman 23 June 2020, 16:18:10 UTC Minor clarification in comments 23 June 2020, 16:18:10 UTC
b9e68ce Wuyin Lin 23 June 2020, 04:31:33 UTC Merge wlin/lnd/F2010SC5-r05-fsurdat (PR #3655) Add default fsurdat for r05 and sim_year 2010 fsurdat specifications for F2010SC5-CMIP6 are moved from lnd use_case file 2010_CMIP6_control.xml to namelist_defaults_clm4_5.xml. This is to add the default fsurdat for r05 grid. [BFB] 23 June 2020, 04:31:33 UTC
ef1d4de Wuyin Lin 23 June 2020, 04:21:20 UTC Merge origin/tangq/atm/antarcticarrm (PR #3449) Add Antarctica RRM support for F2010SC5-CMIP6 compset This PR adds Antarctica RRM grid and supporting files and enables the grid for the F2010SC5-CMIP6 compset. [BFB] 23 June 2020, 04:21:20 UTC
336bcb5 Robert Jacob 23 June 2020, 00:32:00 UTC Merge branch 'naromero77/IntelGPU_ifx_support' (PR #3654) Initial support for the Intel GPU compiler on the JLSE iris nodes. 23 June 2020, 00:32:00 UTC
a0301dd Robert Jacob 23 June 2020, 00:06:59 UTC Merge branch `oksanaguba/homme/cmake-bfb2` (PR #3595) Adding a homme bfb cmake file for anvil to enable hommexx testing. 23 June 2020, 00:06:59 UTC
589ddb5 Benjamin Hillman 22 June 2020, 23:38:19 UTC Fix limiter calls for MMF Fix calls to the `clip_values` routines for MMF. These were recently changed to functions instead of subroutines (#3630) so that we can decide at the calling level whether to handle error messages as fatal errors or warnings, and somehow the PR that changed the behavior missed updating the MMF radiation interface. Also adds the limiters on temperature and optical properties that were added in PR #3630. 22 June 2020, 23:38:19 UTC
94d345c mark-petersen 22 June 2020, 22:01:51 UTC Update mpas-source for maxMeshDensity correction 22 June 2020, 22:01:51 UTC
1259711 Benjamin Hillman 15 June 2020, 23:11:42 UTC Fix setting of swband/lwband for history files Fix setting of swband and lwband coordinate variables for history files. Since add_hist_coord simply sets up pointers to the arrays that are passed in, the data needs to persist. Thus, we make these arrays module-scope variables in radiation.F90. Also a little bit of clean-up in radiation.F90 and radconstants.F90. In particular, we now use nswbands and nlwbands from radconstants.F90, rather than defining new versions of these in radiation.F90. Since these values are set at compile time and should never change, we should be using these in radiation.F90 anyways, and it does not make sense to make new versions of these that could inadvertently get changed from what we expect in radconstants.F90. So instead of setting new values for these based on the absorption coefficient data, we simply verify that the number of bands in the input files matches what we expect in the code (14 for, shortwave, 16 for longwave). These fixes are BFB in regards to the simulation, but EAM history files will be non-BFB due to the fix in the swband and lwband coordinate variables. This will only affect simulations that are long enough to generate history files, i.e., either long (month-plus) runs, or high temporal output frequency runs (like the crmout test). 22 June 2020, 19:02:29 UTC
cf077ea noel 22 June 2020, 17:46:06 UTC Merge branch E3SM-Project/ndk/machinefiles/cori-intel19 (PR #3645) For cori-knl, update the version of default intel compiler to be version 19 22 June 2020, 17:46:06 UTC
9af0012 Wuyin Lin 30 April 2020, 15:16:15 UTC Add clubb_c_K10h as nml variable to control c_K10h at runtime [BFB] 21 June 2020, 04:20:13 UTC
7ef0f27 Wuyin Lin 21 June 2020, 04:17:57 UTC Revert "Merge wlin/v2alpha_clubbv1 (PR #3518)" This reverts commit 300f564133c6a9c8bceb21b486e1fbda28975d3c, reversing changes made to ba4e824c6ff2c28d81486808d717dd1a52ae9dd8. This is to reinstate clubbv2 for v2alpha [non-BFB] 21 June 2020, 04:17:57 UTC
f4d8e4d Wuyin Lin 20 June 2020, 01:42:32 UTC Update default fsurdat file with the one for simyear 2010 20 June 2020, 01:42:32 UTC
7c04964 Azamat Mametjanov 19 June 2020, 22:19:03 UTC Cleanup GNU compiler warnings 19 June 2020, 22:19:03 UTC
e723c32 naromero77 19 June 2020, 20:05:37 UTC Global replace of intelGPU to intelgpu in CIME machine files. 19 June 2020, 20:05:37 UTC
0610b11 Azamat Mametjanov 19 June 2020, 19:42:04 UTC Cleanup IBM compiler warnings 19 June 2020, 19:42:04 UTC
f877fde Wuyin Lin 19 June 2020, 17:55:33 UTC Add default fsurdat for r05 and sim_year 2010 fsurdat specifications for F2010SC5-CMIP6 are moved from lnd use_case file 2010_CMIP6_control.xml to namelist_defaults_clm4_5.xml. This is to add the default fsurdat for r05 grid. 19 June 2020, 17:55:33 UTC
bcdb7b8 naromero77 19 June 2020, 16:43:13 UTC Intel oneAPI SDK compiler flags confuses configure. Strip out -loopopt=0 compiler flag in configure. 19 June 2020, 16:43:13 UTC
e9c22e5 Min Xu 19 June 2020, 16:25:19 UTC Merge branch 'azamat/summit/add-ibm-gpu-flags' (PR #3621) Add ibmgpu compiler for XL+OpenMP_offload runs on Summit [BFB] 19 June 2020, 16:25:19 UTC
1117812 Azamat Mametjanov 05 June 2020, 21:17:53 UTC Add ibmgpu compiler for XL+OpenMP_offload runs on Summit 19 June 2020, 05:09:49 UTC
b8fc926 naromero77 19 June 2020, 04:42:08 UTC Support for JLSE iris nodes and the Intel GPU 19 June 2020, 04:42:08 UTC
ea06360 Min Xu 19 June 2020, 02:10:21 UTC Merge branch 'whannah/mmf/fix-summit-mmf' (PR #3616) This fixes the ability to run the MMF on Summit using both CPU and GPU configurationsbuilt with the PGI compiler. The "summit-cpu" machine is removed because new CIME functionality allows us to set the max tasks per node according to the compiler option. In this case "pgi" is meant for running on the CPU and "pgigpu" is used for running the MMF with the CRM on the GPU. A caveat is that the MMF ERP and ERS tests are still broken when using PGI on Summit and Compy, but SMS tests pass, so that appears to be a separate issue. The "-Mvect=nosimd" for GNU compiler is removed and the gcc version is updated from 6.4.0 to 8.1.1 on Summit 19 June 2020, 02:10:21 UTC
bdd6cc3 Azamat Mametjanov 19 June 2020, 01:57:01 UTC Remove Intel compiler warnings 19 June 2020, 01:57:01 UTC
6ea131d Walter Hannah 18 June 2020, 21:45:15 UTC Add cuda/10.1.243 for pgigpu and -O for GNU modified: cime/config/e3sm/machines/config_compilers.xml modified: cime/config/e3sm/machines/config_machines.xml 18 June 2020, 21:45:15 UTC
14a575d Jon Wolfe 18 June 2020, 19:19:53 UTC Merge branch 'jonbob/scripts/add-ARRM60to10-trigrid' (PR #3617) Add oARRM60to10 tri-grid support This PR adds support for ne30pg2_r05_oARRM60to10 and ne30pg2_r05_oARRM60to10_ICG configurations. The oARRM60to10 mesh was previously supported only for C- and G-compsets, so this adds fully-coupled capability. All new necessary files have been staged to the inputdata repo. [BFB] 18 June 2020, 19:19:53 UTC
71dc334 Jon Wolfe 17 June 2020, 16:44:39 UTC Merge branch 'jonbob/scripts/update-lanlIC-200615' (PR #3637) Update LANL IC machine files to fix small issues This PR fixes two small issues on the LANL IC machines badger and grizzly. Specifically, it: * removes -lmpi_cxx from c++ libraries for the gnu compiler on both machines * removes -lmpi_cxx from c++ libraries for the intel compiler on badger * reorders the options for compiler on badger, so intel is default * reorders the options for mpi on both machines, so openmpi is default No tests are run on either of these platforms, so there should be no impact on E3SM tested configurations. [BFB] 17 June 2020, 16:44:39 UTC
566d7e8 Qi Tang 16 June 2020, 23:58:25 UTC uncomment ATM2ROF maps 16 June 2020, 23:58:25 UTC
e2a2104 Jon Wolfe 16 June 2020, 22:26:14 UTC Change output_interval to "none" for the new analysis member 16 June 2020, 22:26:14 UTC
9a2be1b Jon Wolfe 16 June 2020, 19:07:04 UTC Change defaults so new mixedLayerHeatBudget AM is on 16 June 2020, 19:07:04 UTC
23426d8 Jon Wolfe 16 June 2020, 18:53:53 UTC Add the new analysis member to the streams file generation script 16 June 2020, 18:53:53 UTC
4d18c8d noel 16 June 2020, 18:29:00 UTC Add C++ flags to both cori-knl and cori-haswell that changes the default to use fp-model consistent. This is just to be "consistent" with the fp-model used in the fortran compiler on these machines. We intend to re-investigate the compiler flags after this PR. 16 June 2020, 18:29:00 UTC
c9873d4 Jon Wolfe 16 June 2020, 17:56:47 UTC Update bld scripts to match changes to ocean Registry 16 June 2020, 17:56:47 UTC
cff12d2 Jon Wolfe 16 June 2020, 16:35:48 UTC Merge branch 'mark-petersen/ocean/update_mpas_200611' (PR #3634) Update mpas-source: three ocean bug fixes This PR brings in a new mpas-source submodule with changes only to the ocean core. It fixes three small bugs that do not impact any current E3SM test configurations: * fixes bad array sizes in local ocean arrays (MPAS-Dev/MPAS-Model#598) * removes RediKappa from gm package (MPAS-Dev/MPAS-Model#602) * fixes bugs in tracer_advection_std (MPAS-Dev/MPAS-Model#587) [BFB] 16 June 2020, 16:35:48 UTC
ff6f08f Wuyin Lin 16 June 2020, 16:08:59 UTC Merge brhillman/atm/add-rrtmgp-optics-limiters (PR #3630) Add limiters on RRTMGP cloud and aerosol optics Add limiters on RRTMGP cloud and aerosol optical properties. This prevents the internal RRTMGP sanity checks from aborting the run with these quantities go slightly outside the expected range. The behavior is now to always clip these values, but to throw an error and abort when they fall outside the expected range plus/minus an accepted tolerance. This fixes an error that arose in some coupled runs where single scattering albedo would go slightly above 1.0, possibly due to floating point precision issues. [BFB] 16 June 2020, 16:08:59 UTC
e35033e Aaron Donahue 16 June 2020, 14:11:59 UTC Merge branch 'thetal-intialcondition' (PR #3608) Dont neglect moisture when initializing theta-l dycore's virtural potential temperature variable. Also added a T/theta conversion consistency check of the initial condition. theta-l ne4 was accidently picking up the preqx value of nu_div=2.5*nu. theta-l should be using nu_div=nu. tested by running for 1 year using the F2010SC5-CMIP6 compset on ne4np4_ne4np4 and ne4pg2_ne4pg2 grids with theta-l dycore in hydrostatic mode and nonhydrostatic mode (all 4 combinations run for 1 year). Running ne4pg2_ne4pg2 required PR #3606 and uses CLM cold start. [non-BFB] but only for theta-l tests. 16 June 2020, 14:11:59 UTC
6a7fb89 noel 16 June 2020, 02:26:18 UTC Update default compiler for cori-knl to be intel version 19. Remove the "intel19" compiler option for cori-knl. 16 June 2020, 02:26:18 UTC
cc6ebec Jon Wolfe 15 June 2020, 21:40:02 UTC Remove -lmpi_cxx from badger settings for gnu 15 June 2020, 21:40:02 UTC
c7cf6d0 noel 15 June 2020, 20:32:37 UTC Merge branch E3SM-Project/ndk/machinefiles/cori-craype262 (PR #3633) For Cori, update module version of the craype module and force static linking 15 June 2020, 20:32:37 UTC
d18824a Jon Wolfe 15 June 2020, 20:08:53 UTC Reorder compiler/mpi options for IC machines grizzly and badger 15 June 2020, 20:08:53 UTC
5fcc612 Jon Wolfe 15 June 2020, 20:07:36 UTC Remove "-lmpi_cxx" from IC machines grizzly and badger for the gnu compiler 15 June 2020, 20:07:36 UTC
0f004f5 Gautam Bisht 15 June 2020, 15:58:04 UTC Merge branch 'hongyili/mosart/mosart-heat-v3' (PR #3611) The latent heat formula for water vaporization from Wu et al. (2012) has been replaced by that from Dingman (2009). Also adjusted a couple of parameters to be more reasonable. BFB] 15 June 2020, 15:58:04 UTC
6bd8fc4 Mark Taylor 13 June 2020, 23:04:05 UTC set HOMME's internal moisture variables in prim_init1, not prim_init2 use_moisture needs to be set correctly *before* EAM reads in the initial condition 13 June 2020, 23:29:02 UTC
2b7e264 Andrew M. Bradley 12 June 2020, 21:13:21 UTC Homme: Use tracer name instead of hard-coded index. 12 June 2020, 21:13:21 UTC
27a5712 Andrew M. Bradley 12 June 2020, 01:02:37 UTC Homme: Relax tridiag solver test a bit. 12 June 2020, 01:02:37 UTC
d93a46b Andrew M. Bradley 12 June 2020, 00:49:05 UTC Homme: Fix index order in test_imex_jacobian. 12 June 2020, 00:49:05 UTC
c920494 mark-petersen 11 June 2020, 22:24:34 UTC Update mpas-source 11 June 2020, 22:24:34 UTC
0c668f0 Oksana Guba 11 June 2020, 21:41:18 UTC set launcher for skybridge too 11 June 2020, 21:41:18 UTC
7280437 Matt Norman 11 June 2020, 20:32:45 UTC Fixing GNU 11 June 2020, 20:32:45 UTC
8edb7cd Balwinder Singh 11 June 2020, 18:22:28 UTC Merge branch 'yfeng/eam/dust2updatesRRTMGP' (PR #3610) Update dust shortwave optics for RRTMGP and retuned emis factor for V2 Update dust shortwave optics file for RRTMGP Update dust emission factor retuned for V2 for all compsets (from 0.95 to 1.38) [Non-BFB] - Non Bit-For-Bit [NML] - Namelist Changing * yfeng/eam/dust2updatesRRTMGP: Update dust shortwave optics for RRTMGP and retuned emis factor for V2 11 June 2020, 18:22:28 UTC
a24770c mark-petersen 11 June 2020, 17:11:46 UTC Update mpas-source: three bug fixes fixed bad array sizes in local ocean arrays https://github.com/MPAS-Dev/MPAS-Model/pull/598 Remove RediKappa from gm package https://github.com/MPAS-Dev/MPAS-Model/pull/602 Fixes bugs in tracer_advection_std https://github.com/MPAS-Dev/MPAS-Model/pull/587 11 June 2020, 17:11:46 UTC
bb2b27a Jon Wolfe 11 June 2020, 16:34:42 UTC Merge branch 'mark-petersen/ocean/update_mpas_200610' (PR #3631) mpas-source: Move daysSinceStartOfSim calculation to master when threaded This PR brings in a new mpas-source submodule, with changes only to the ocean core. It moves the calculation of daysSinceStartOfSim, which is done in three places, to inside a loop with "omp master" pragmas around it. Previously, one was inside an "omp single" pragma, but that did not guarantee that the master thread would get the correct result. While this does not impact the results at all, it was causing random problems in testing using threaded configurations where cprnc output from globalStats files would find an error, just in the daysSinceStartOfSim field. With thanks to @amametjanov See MPAS-Dev/MPAS-Model#601 [BFB] 11 June 2020, 16:34:42 UTC
7dcd0ad noel 11 June 2020, 03:31:25 UTC For Cori, update module version of the craype module and force static linking. With this newer version of craype, the new default is to use dynamic linking. E3SM still works with dynamic linking, but the performance was degraded. Forcing static linking seems to resolve this (by setting an environment variable CRAYPE_LINK_TYPE to static). [bfb] 11 June 2020, 03:31:25 UTC
e568748 Benjamin Hillman 10 June 2020, 22:34:33 UTC Fixes for consistency with SCREAM 10 June 2020, 22:34:33 UTC
320720a Wuyin Lin 10 June 2020, 20:54:29 UTC Merge tangq/atm/O3_hole_diags (PR #3625) Add total column ozone output for diagnosing ozone hole Ozone hole diagnostics require daily output. This commit adds the inline calculation for total column ozone and the corresponding output field "TOZ" and thus reduces the cost of saving daily 3D "O3" to 2D "TOZ". Additionally, the inline calculation is more accurate, because it uses instantaneous values instead of the averages, which is potentially important for ozone hole areas where large variances may occur. [BFB] - Bit-For-Bit 10 June 2020, 20:54:29 UTC
b46bac3 Benjamin Hillman 10 June 2020, 20:05:36 UTC Make temperature limiting the default too 10 June 2020, 20:05:36 UTC
678123a mark-petersen 10 June 2020, 19:54:23 UTC mpas-source: Move daysSinceStartOfSim calculation to master when threaded 10 June 2020, 19:54:23 UTC
85c6db0 noel 10 June 2020, 18:40:24 UTC Merge branch E3SM-Project/ndk/machinefiles/gnu-remove-Og (PR #3629) Remove the -Og flag from all DEBUG GNU builds and add C++ flags for GNU 10 June 2020, 18:40:24 UTC
0f7c2ea Benjamin Hillman 10 June 2020, 18:25:07 UTC Handle errors in radiation_tend 10 June 2020, 18:25:07 UTC
958d7bf Balwinder Singh 10 June 2020, 16:38:07 UTC Merge branch 'mingxuanwupnnl/atm/trop_strat_mam' (PR #3541) Fix bugs for running E3SM with trop_strat_mam3/mam7 Current model can't run with MOZART chemistry (trop_strat_mam3/mam7) as well as MAM3/MAM7 (trop_mam3/trop_mam7). These modifications don't change the results for default configurations (linoz_mam4_resus_mom_soag). To run E3SM with trop_strat_mam7, one also needs to modify namelist setting for now. linoz_data_file = '' linoz_data_path = '' demott_ice_nuc = .false. gas_wetdep_method = 'NEU' For running trop_strat_mam3, one also needs to either modify chem_mech.in or resetting CAM_CONFIG_OPTS (remove resus). Fixes #3542 [BFB] * mingxuanwupnnl/atm/trop_strat_mam: Fix bugs for running E3SM with trop_strat_mam3/mam7 10 June 2020, 16:38:07 UTC
ee648f0 Jon Wolfe 10 June 2020, 15:41:52 UTC Merge branch 'mark-petersen/ocn/update_mpas_200608' (PR #3627) Update mpas-source: cvmix driver area weighted average bug This PR brings in a new mpas-source submodule with changes only in the ocean core. Specifically, it fixes a bug in the area weighted averaging for 3 CVMix quantities. See MPAS-Dev/MPAS-Model#556 [non-BFB] 10 June 2020, 15:41:52 UTC
af3d238 Aaron Donahue 10 June 2020, 15:28:08 UTC Merge branch 'jayeshkrishna/scorpio_support_homme_standalone' (PR #3615) Adding support for standalone HOMME builds with Scorpio. The HOMME standalone builds can now use E3SM Scorpio by turning on the HOMME_USE_SCORPIO cmake option. By default the standalone builds were using the PIO library available with CIME. Now by default the HOMME standalone builds use the E3SM Scorpio classic library. This PR also updates the Scorpio submodule to bring in some fixes required for standalone HOMME builds [BFB] 10 June 2020, 15:28:08 UTC
9d30365 Benjamin Hillman 10 June 2020, 14:52:34 UTC Always limit optics 10 June 2020, 14:52:34 UTC
8ca93d8 Oksana Guba 10 June 2020, 01:21:42 UTC set launcher to match whats in cmake file 10 June 2020, 01:21:42 UTC
e45232c noel 10 June 2020, 00:39:44 UTC Merge branch E3SM-Project/ndk/machinefiles/cori-update-mpich-netcdf (PR #3626) Update Cori modules for mpich and netcdf/hdf 10 June 2020, 00:39:44 UTC
343a277 Hong-Yi Li 09 June 2020, 23:25:09 UTC a few minor fixes on format, wording etc 09 June 2020, 23:25:09 UTC
bbdb8c7 Benjamin Hillman 09 June 2020, 21:23:42 UTC Fix typo in comment 09 June 2020, 21:23:42 UTC
5bc6a94 Benjamin Hillman 09 June 2020, 21:15:41 UTC Add tolerance argument to clipping routines Add a tolerance argument to clipping routines. This determines the tolerance for issuing warnings; if values exceed the specified range plus/minus the tolerance, a warning is issued when clipping. Otherwise, values outside the specified range are clipped *without warning*. 09 June 2020, 21:15:41 UTC
581e2e3 Benjamin Hillman 09 June 2020, 19:11:09 UTC Add limiters for RRTMGP optics Add code to support turning on limiters on RRTMGP optical properties. These are enabled by setting `rrtmgp_clip_optics = .true.` in the atmosphere namelist (i.e., `user_nl_cam` in a case directory). When enabled, the `clip_values` function is called to make sure optics going into RRTMGP are within the range expected by the RRTMGP codes (`0 <= tau < huge(tau)`, `0 <= ssa <= 1`, `-1 <= asm <= 1`). Note that turning this flag on clips values and issues a warning, but allows the simulation to continue. This is to work around the case where values are *slightly* outside the expected range (due to, e.g., floating point precision issues), but not that turning this feature on will prevent the radiation code from catching the much larger errors. Since a warning is spit out to the log files in this case though, once can simply check the log to see if optical properties fell well outside of the expected range. 09 June 2020, 19:11:09 UTC
b16eae1 Balwinder Singh 09 June 2020, 18:19:21 UTC Merge branch 'worleyph/cam/runtime_pcols_part1' (PR #3620) Implement pcols as a runtime option in EAM In the earlier 2000's, empirical experiments indicated that setting the first dimension of the chunk data structure (pcols) at compile-time allowed the compiler to generate more performance-efficient code, and this motivated this design choice in CAM. However, CAM/EAM has evolved significantly since then, and, for example, physics_types now uses psetcols to define this first dimension, and the compiler never sees a compile-time parameter. So the compile-time setting of pcols may no longer serve a useful purpose. Extensive experiments indicate that there is still a small performance advantage from setting pcols at compile-time, but also that being able to set pcols at runtime greatly simplifies the process of optimizing over the pcols parameter. Here pcols is implemented as a runtime option, currently specified via the user_nl_cam namelist variable phys_chnk_fdim. phys_chnk_fdim must be at least as large as 1, but there is no specified upper bound. The current compile-time value of the CPP variable PCOLS is used to define the default value for phys_chunk_fdim (and pcols). PCOLS is now represented in EAM as the parameter ppcols, but is only referenced in defining the default for phys_chunk_fdim. To restore the compile-time setting of pcols, and also to specify a pcols value of PCOLS, add -pcols to CAM_CONFIG_OPTS in env_build.xml . For example, to specify 32 as the compile-time value of pcols, add '-pcols 32' . This allows the recovery of any lost performance from the runtime-specification of pcols. Note that this is the first part of a two-part introduction of runtime pcols. This PR sets the runtime pcols during the call to read_namelist. To calculate a better default than the compile-time PCOLS CPP variable requires that it be calculated in phys_grid_init, and this requires changing the order of certain steps in the initialization of EAM. The current PR, however, stands on its own, and is acceptable even if the second part PR is never submitted. [BFB] This addresses some aspects of Issue #3538 , but not all. The issue will be resolved by a second runtime pcols PR. If we decide not to submit this follow-on PR, the issue will also be closed. * worleyph/cam/runtime_pcols_part1: Back out change in diag_surf Modify variables names Enable compile-time setting of pcols via CAM_CONFIG_OPTS Eliminate compile-time dependence on pcols in crm_physics.F90 Implement pcols as a runtime option in EAM Eliminate compile-time dependence on pcols in diag_surf Eliminate compile-time dependence on pcols in zm_conv Eliminate compile-time dependence on pcols in phys_grid.F90 Eliminate compile-time dependence on pcols in unicon_cam Eliminate compile-time dependence on pcols in check_tracers logic Eliminate compile-time dependence on pcols in camsrfexch.F90 Eliminate compile-time dependence on pcols in chemistry 09 June 2020, 18:19:21 UTC
e9a4ccc Jason Sarich 09 June 2020, 17:54:34 UTC Merge branch 'ndk/run_e3sm/adjust-order-submodule-init' (PR #3530) Update the run_e3sm template to do the submodule command after checking out any branches. Update the github location to refer to git@github.com:E3SM-Project/E3SM.git Also remove reference to retired edison machine. For the example "customknl" layout, switch to using the correct variable: MAX_MPITASKS_PER_NODE [bfb] 09 June 2020, 17:54:34 UTC
a69b2b2 Jon Wolfe 09 June 2020, 17:09:36 UTC Merge branch 'mark-petersen/ocn/update_mpas_200605' (PR #3623) Update mpas-source, compass only. Add WC14 This PR brings in a new mpas-source submodule, with changes only to the ocean model. Specifically, this modifies COMPASS initial conditions only by adding the Water Cycle 14 km case. [BFB] 09 June 2020, 17:09:36 UTC
cde90b1 noel 09 June 2020, 16:12:20 UTC Add boilerplate CXXFLAGS for GNU compiler. [bfb] 09 June 2020, 16:12:20 UTC
ca9476f Patrick Worley 08 June 2020, 23:04:56 UTC Back out change in diag_surf After re-examination with the total package of the changes, the line call outfld('QFLX', cam_in%cflx(1,1), pcols, lchnk) in subroutine diag_surf in physics/cam/cam_diagnostics.F90 no longer fails to compile when pcols is not a parameter. As clfx is a 2D array (pcols,pcnst), the original form of the call to outfld is more self-documenting, and also matches the style of other calls to outfld accessing slices of multidimensional arrays. Here, the original code is restored. [BFB] 08 June 2020, 23:04:56 UTC
b676b30 noel 08 June 2020, 22:56:32 UTC Removing the -Og flag from all DEBUG GNU builds. The -g flag remains in place, of course. This allows us to run on Cori with GNU DEBUG. I also removed the "gnu7" compiler definition as it's no longer used. [bfb] 08 June 2020, 22:56:32 UTC
9634acf Walter Hannah 08 June 2020, 18:42:45 UTC Fix CXX_LINKER option for pgigpu 08 June 2020, 18:42:45 UTC
2fb73b0 Oksana Guba 08 June 2020, 18:18:43 UTC another fix: making unit texts that dont need mpi run with mpiexec -n 1 08 June 2020, 18:18:43 UTC
65db573 mark-petersen 08 June 2020, 16:54:30 UTC Update mpas-source: cvmix driver area weighted average bug 08 June 2020, 16:54:30 UTC
a3ef027 Wuyin Lin 08 June 2020, 16:15:53 UTC Merge tangq/atm/PSC_Temp (PR #3618) Make PSC T threshold a namelist variable This PR makes the hard-coded T threshold of PSC ozone loss a namelist variable to facilitate model tuning. The default T threshold is set to 193 K, the same as the hard-coded value, so it won't change the model results by default. [BFB] 08 June 2020, 16:15:53 UTC
f023cf0 Qi Tang 06 June 2020, 05:00:10 UTC Add total column ozone output for diagnosing ozone hole Ozone hole diagnostics require daily output. This commit adds the inline calculation for total column ozone and the corresponding output field "TOZ" and thus reduces the cost of saving daily 3D "O3" to 2D "TOZ". Additionally, the inline calculation is more accurate, because it uses instantaneous values instead of the averages, which is potentially important for ozone hole areas where large variances may occur. [BFB] - Bit-For-Bit 06 June 2020, 05:00:10 UTC
0b84efa Walter Hannah 06 June 2020, 02:34:56 UTC Fixes for summit w/ pgigpu modified: cime/config/e3sm/machines/config_compilers.xml modified: cime/config/e3sm/machines/config_machines.xml 06 June 2020, 02:34:56 UTC
865793e mark-petersen 05 June 2020, 23:13:43 UTC Update mpas-source, compass only. Add WC14 05 June 2020, 23:13:43 UTC
864fc21 Walter Hannah 05 June 2020, 22:36:28 UTC Remove pgiacc modified: cime/config/e3sm/machines/config_batch.xml modified: cime/config/e3sm/machines/config_compilers.xml modified: cime/config/e3sm/machines/config_machines.xml 05 June 2020, 22:36:28 UTC
a205707 Walter Hannah 05 June 2020, 22:24:15 UTC Remove obsolete batch_system entries modified: cime/config/e3sm/machines/config_batch.xml 05 June 2020, 22:24:15 UTC
847d92c Walter Hannah 05 June 2020, 22:22:47 UTC Remove summitdev and titan machines 05 June 2020, 22:22:47 UTC
5363c7b noel 05 June 2020, 17:28:23 UTC Update Cori (cori-knl and cori-haswell) modules to be current defaults for the following: cray-mpich/7.7.6 -> cray-mpich/7.7.10 cray-netcdf-hdf5parallel/4.6.1.3 -> cray-netcdf-hdf5parallel/4.6.3.2 cray-hdf5-parallel/1.10.2.0 -> cray-hdf5-parallel/1.10.5.2 cray-parallel-netcdf/1.8.1.4 -> cray-parallel-netcdf/1.11.1.1 gcc/8.2.0 -> gcc/8.3.0 cray-libsci/19.02.1 -> cray-libsci/19.06.1 impi/2019.up3 -> impi/2020 And only affecting builds with intel19 compiler, use the latest version of intel19 which is intel/19.1.1.217. Not updating craype or the default intel compiler (still intel18). Those will be in another PR. [bfb] 05 June 2020, 17:28:23 UTC
a206b22 AaronDonahue 05 June 2020, 16:53:58 UTC Merge branch 'ambrad/eam/v2-perf-and-mass' PR #3594) Improve vectorization and threading in SL transport, physgrid remap, and theta-l. Fix a mass conservation error due to finite precision effects. These code mods would cause no answer change in exact arithmetic but are non-BFB in finite precision. Summary: Physgrid remap: Switch indexing from (:nf,:nf) to (:nf2) to improve vectorization. SL transport: Speed up global CAAS by locally reducing what can be reduced decomp-BFB. Improve own_q, rmt_q thread load balance. Flip level, q indexing to improve memory locality. After a performance regression to calc_q a few months ago to work around a compiler bug, address the performance issue in a different way. I avoid using pragma ivdep but get the performance that annotation provides by explicitly blocking. The result is effective vectorization of a key computation in SL transport. Fix dp_fv so it agrees numerically with the pdel calculation in dp_coupling.F90: derived_physics. Add a C++ block to the cori-knl/intel19 block in config_compilers.xml. Work around an Intel 17 -O3 bug to fix a standalone-Homme test on Anvil. Fixes #3588. [non-BFB] 4 EAM tests and 3 standalone Homme tests 05 June 2020, 16:53:58 UTC
f898f39 Junqi Yin 04 June 2020, 23:59:47 UTC Merge branch 'bishtgautam/lnd/ne120np4' (PR #3484) Adds support for F20TRC5-CMIP6 compset at ne120 resolution The definition of ne120np4 is modified to use 0.125deg river grid instead of 0.5deg river grid. The missing landuse timeseries for ne120 resolution is added for F20TRC5-CMIP6 [non-BFB] 04 June 2020, 23:59:47 UTC
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