https://github.com/E3SM-Project/E3SM

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Revision Author Date Message Commit Date
885cbdc Remove unnecessary tag comments 06 January 2023, 18:21:56 UTC
1a979e5 Code changes ensuring MCSP will not be on when coefficients are set to 0 by default 06 January 2023, 18:21:56 UTC
75928db Add zmconv_tpert_fix as a default namelist parameter 06 January 2023, 18:21:56 UTC
ebeda93 Fixes to ZM micro for BFB behavior 06 January 2023, 18:21:31 UTC
4b930ae Remove comments where redundant 06 January 2023, 18:21:05 UTC
7671dc4 Code clean up and turn tpert fix into namelist switch 06 January 2023, 18:21:04 UTC
a8a9d25 Fix where physconst pi is defined in zm_conv_intr 06 January 2023, 18:21:04 UTC
2b031ab Add MCSP capability in ZM convection and add namelist options *********1*********2*********3*********4*********5*********6*********7** This commit adds Multiscale Coherent Structure Parameterization developed by Chih-Chieh Chen (Jack Chen) into the ZM deep convection scheme. [CC] - Climate Changing 06 January 2023, 18:21:04 UTC
40338e8 Merge crterai/atm/add_zmmp_namelists to add namelist parameters in ZMMP 06 January 2023, 18:21:04 UTC
aaf4ad3 Add dynamic adjustment to CAPE closure 06 January 2023, 18:21:03 UTC
d0da5b1 add missing zm_microp flag 06 January 2023, 18:19:49 UTC
9b45255 Add default value of zmconv_microp parameter 06 January 2023, 18:19:48 UTC
1730e70 Ported over ZMmicro code 06 January 2023, 18:19:47 UTC
f636ffc Merge branch E3SM-Project/ndk/machinefiles/pm-cpu-add-hi-res-layouts (PR #5374) For pm-cpu, add PE layouts to allow e3sm_hi_res suite to run 05 January 2023, 18:58:00 UTC
03f7d6d Merge branch 'erinethomas/ww3/spectra-update' (PR #5368) Update ww3 spectra Update to WW3 to allow flexible options for spectral resolution of waves (N Freq x N Dir). Default is set to 36x36. Alternative options of high resolution (50x36) and low resolution (25x36). Defining case with 'alias' that includes "WW3" component will use default spectral resolution. Alternative options require use of "long name" to define components. [NML] [BFB] 05 January 2023, 17:33:23 UTC
c498794 Merge branch E3SM-Project/ndk/machinefiles/pm-modup-dec22 (PR #5373) Update module versions for pm-cpu and pm-gpu after machine maintenance 26 December 2022, 17:54:14 UTC
3705ce9 Add PE layouts for pm-cpu to allow e3sm_hi_res suite to run efficiently 24 December 2022, 16:50:05 UTC
5228f1c Update module versions for pm-cpu and pm-gpu after machine maintenance 23 December 2022, 20:36:04 UTC
bce4e06 remove chrysalis pe config (not yet tested) 19 December 2022, 19:44:21 UTC
f595d92 Merge branch 'bishtgautam/lnd/20TR-GSWP' (PR #5340) The alias for the 20TR BGC compset for BGC is corrected. [BFB] 16 December 2022, 19:57:03 UTC
4b872d5 Merge branch 'akturner/mpas-seaice/refactor-velocity-init' (PR #5290) Refactor of MPAS-Seaice velocity solver Refactor of MPAS sea ice velocity solver to allow easier testing of new options and methods, including: * Move domain reference to within subroutines avoiding messy passing of variables * Move wachspress basis routines to separate module * Move triangular quadrature rules to new module * Move some mesh related routines to the mesh module * Rename block variable to blockPtr * Rename all pool types to end in Pool Fixes #5289 [BFB] 15 December 2022, 18:00:41 UTC
83d265b Merge remote-tracking branch 'glemieux/fates-satphen-call-fix' (PR #5345) Move the fates-specific `satellitephenology` call out of an area that is unreachable when `fates` is active. Fixes https://github.com/NGEET/fates/issues/953. [Non-B4B] 15 December 2022, 17:56:03 UTC
a4520d5 Merge branch 'azamat/crusher/update-project-name' (PR #5363) Update project name on Crusher. [BFB] 15 December 2022, 16:49:18 UTC
eb7a8cc Merge branch 'azamat/anvil/bgc-pes-fix-OOM' (PR #5362) Increase ELM PEs in BGC runs on Anvil to avoid OOM issues. [BFB] 15 December 2022, 16:44:06 UTC
56a7e57 Update project name on Crusher 15 December 2022, 01:12:43 UTC
0273cfa Merge branch 'hongyili/mosart/mosart_heat_v3' (PR #5343) The use of uninitialized variables (i.e., `Qsur` and `Qsub`) in the computation of the change of energy due to heat exchange with the environment and advection is fixed. Currently, it is assumed that those changes in energy are zero. Fixes #5332 [BFB] 14 December 2022, 20:00:40 UTC
db896b2 Merge branch 'darincomeau/ice/add-DMPAS-JRA1p5' (PR #5357) Add DMPAS-JRA1p5 compset Adds DMPAS-JRA1p5 compset: D-case with active sea ice only. Also adds PE layouts for any D-case on Chrysalis and Anvil, S layouts on 20 nodes, with ~47 and 23 SYPD, respectively. [BFB] 14 December 2022, 19:42:02 UTC
0614e7b Merge branch 'mark-petersen/ocn/fix-intel-opt-decomp' (PR #5356) Move bottomDepthEdge calculation to single loop over all edges After #5195 was merged, the MPAS-Ocean standalone test ocean/baroclinic_channel/10km/decomp_test failed to match between 4 and 8 partitions, but only for intel optimized. All compass nightly suite tests passed for gnu debug, gnu optimized, intel debug. This PR solves the problem by merging the computation of bottomDepthEdge into a single edge loop. Previously it was split into two loops, 1:nEdgesOwned (with many other calculations) and another from nEdgesOwned+1:nEdgesArray(4). The intel optimized compiler must have changed order-of-operations in these two loops for different partitions. Fixes #5219 [BFB] 14 December 2022, 19:31:22 UTC
b6d9e0c Increase ELM PEs in BGC runs on Anvil To avoid OOM issues. 14 December 2022, 02:48:16 UTC
8d4376f bug fix 13 December 2022, 23:00:14 UTC
a9ca88a removed non-supported mesh option from WW3 configuation 13 December 2022, 21:26:51 UTC
c0123a2 removed placeholder PE configurations for WW3 (PE configs will be added later after testing) 13 December 2022, 21:25:46 UTC
19a550e Merge branch 'darincomeau/data_comps/add-JRA-1p5-cryo' (PR #5355) Add GMPAS-JRA1p5-DIB-ISMF compset Adds a new GMPAS-JRA1p5-DIB-ISMF compset, an updated version of the existing GMPAS-JRA1p4-DIB-ISMF compset that uses JRA v1.5. This compset is for use with ocean meshes with ice-shelf cavities, and uses prognostic ice-shelf basal melting, and prescribed iceberg forcing. To compensate for this Antarctic runoff, the rofi and rofl fields have been zeroed out below 60S in the modified runoff forcing files. New modified runoff files (with the no_rofi_no_rofl tag are on the public inputdata server and world readable. [BFB] 13 December 2022, 18:47:23 UTC
8dac39f Merge branch 'xylar/mpas-framework/rename-nersc-build-targets-to-cray' (PR #5281) Clean up "*-nersc" build targets in MPAS standlone build system Remove pgi-nersc and cray-nersc, which are not used or supported. Rename intel-nersc and gnu-nersc to intel-cray and gnu-cray, espectively, as they should work on other cray machines as well such as Chicoma. [BFB] 13 December 2022, 18:43:37 UTC
9aa622e Merge branch 'trhille/mali/develop-221115' (PR #5309) Update MALI version This merge includes numerous updates to MALI. The major updates include: • A glacier retreat parameterization based on change in ocean thermal forcing and subglacial runoff • Coupling to a 1-D global sea level model • A CFL-like limit on time step length based on calving velocity • A new definition of the grounding line that depends on the flotation condition, which no longer includes the grounded marine margin if that is above the flotation thickness. This is necessary for mass budget calculations Minor changes include: • The ability to use rate-based and damage threshold-based calving parameterizations simultaneously • Spatially variable calving stress thresholds for the von Mises stress calving parameterization • An option to prevent positive surface mass balance in ice-free regions • An optional clean-up for rate-based iceberg calving routines • New fields containing the basal mass balance that was actually applied in a time step • Logic that prevents the original input basal mass balance field from ever being modified in case of an instability in the thermal solver • Clean up for compiling with Intel, including memory bug fix in Sea Level Model • Bug fixes necessary for regional statistics output • A step to remove isolated regions of dynamic floating ice connected to the rest of the ice shelf by non-dynamic ice. These were causing the velocity solver to fail in simulations with evolving calving • Additional new calving metrics and minor bug fixes • A new field that defined the flux across the grounding line on cell centers • Use indexToCellID(iCell) instead of iCell in log messages • Write out additional fields to ascii files to import into Albany • Bug fixes in MALI–Sea Level Model coupling: initialize variables [NML] [non-BFB] for configurations with MALI 13 December 2022, 18:34:34 UTC
b3f20e1 Replace some where/elsewhere/elsewhere coding to make pgi happy 12 December 2022, 18:55:39 UTC
7c078d7 Merge branch 'mkstratos/mpas/mpas-multi-instance' (PR #5123) Add instance string to MPAS output filenames Creates a stream file for multiple instances of MPAS Ocean and Sea Ice. Adds the instance string to streams.ocean_* and streams.seaice_* output and restart filenames Fixes #5122 [BFB] 12 December 2022, 17:20:36 UTC
bd9e2ac Merge branch E3SM-Project/ndk/machinefiles/alvarez-module-update (PR #5347) For alvarez at NERSC, update modules to defaults. 10 December 2022, 23:32:09 UTC
8950d28 Merge branch E3SM-Project/ndk/machinefiles/gcp-MEMLEAK-allowance (PR #5350) On GCP only, add larger allowance for MEMLEAK detection in tests 09 December 2022, 23:36:35 UTC
824850e Change nEdgesArray to nEdgesHalo 08 December 2022, 21:04:25 UTC
39c37fc Move setting of branch/hybrid init files inside of inst loop 08 December 2022, 16:15:26 UTC
be4f238 Adding DMPAS-JRA1p5 compset and PE layouts for LCRC 07 December 2022, 23:17:38 UTC
a4be221 Add support for a GMPAS-JRA1p5-DIB-ISMF compset for cryo 07 December 2022, 20:35:49 UTC
34d2fc9 Merge branch 'jayeshkrishna/externals/scorpio_1_4_1' (PR #5348) Updating the version of SCORPIO submodules to 1.4.1 This release includes the following changes, * Fix for a performance bug where the NetCDF header was reallocated multiple times, slowing down runs that create large output files * Support for ADIOS BP5 file format * Preliminary support (disabled by default) for HDF5 * Improved performance by reducing some collectives * Support for Perlmutter/Crusher * Minor bug fixes [BFB] 07 December 2022, 19:50:50 UTC
95a4541 adding a mosart-heat test directly into the e3sm_mosart_developer suite 07 December 2022, 18:45:43 UTC
582899e Move bottomDepthEdge calculation to single loop over all edges 07 December 2022, 14:20:31 UTC
e0b5c9f minor clean up for PE layout 06 December 2022, 20:48:19 UTC
b5e9eb9 Default WW3 spectral resolution updated to 36x36 06 December 2022, 20:43:46 UTC
90fb60d Merge branch E3SM-Project/ndk/machinefiles/pm-cpu-layouts-e3sm-prod (PR #5338) For pm-cpu (and alvarez), adjust/add PE layouts. 06 December 2022, 20:35:40 UTC
5994e45 On GCP only, add larger allowance for MEMLEAK detection in tests and add a slightly smaller allowance for TPUT. This fixes a fail for one test in e3sm_extra_coverage ERP_Lm3.ne4_oQU240.F2010.gcp_gnu 06 December 2022, 20:27:08 UTC
d5b864c Merge branch 'ambrad/elm/fix-scream-2057' (PR #5334) ELM: Use intent(inout) to preserve values in early exit. In PhotosynthesisMod.F90, early exits from brent and brent_PHS do not assign gs_mol outputs values. The desired behavior in those cases is for the input values to be retained. Thus, this commit changes intent(out) to intent(inout) for these variables. The original code usually works because Fortran normally doesn't overwrite these inputs at the start of the routine. But if an option like crayftn's -hzero is provided, intent(out) stack variables are 0-init'ed, causing a bug. Fixes SCREAM issue 2057. e3sm.log was being filled with messages like this: 7: Ball-Berry error check - stomatal conductance error: 7: 0., 52577.053632404488 The 0 in the second line is important: it implies that gs_mol was being set to 0 unintentionally. e3sm_developer passes on Chrysalis. [BFB] 06 December 2022, 18:42:01 UTC
8025078 Merge branch 'jonbob/mpas-framework/fix-missing-threadnum' (PR #5337) Add missing code to set threadNum before its use Fixes an issue where a variable threadNum was used before it was set Fixes #5333 [BFB] 05 December 2022, 20:37:31 UTC
627683e Merge branch 'cbegeman/ocn/mask-time-series-stats-vars' (PR #5325) Mask ocean time series stats variables This PR applies fill value masking to non-restart time series stats streams in the ocean component. It also specifies the masking array for a subset of variables in the Registry. Fixes #5253 [BFB] 05 December 2022, 20:34:11 UTC
146732c Merge branch 'brhillman/eam/update-rrtmgp-20221117' (#5336) Update YAKL and RRTMGP. MMF tests will DIFF due to new FFT libraries in YAKL backend, but everything else should be BFB. [non-BFB] 05 December 2022, 20:19:16 UTC
f687930 Merge branch 'peterdschwartz/lnd/add-endwb-restart' (PR #5311) Required for runs that restart at the beginning of a month as TWS_MONTH_BEGIN is calculated at beginning of each timestep. [BFB] Fixes #5079 05 December 2022, 20:15:00 UTC
be81aed Merge branch 'mark-petersen/mpas/shallow-water-comments' (PR #5303) Add comments to mpas shallow water code These are comments only, to explain the RK4 algorithm and coefficients. There is an identical PR for MPAS-Dev at MPAS-Dev/MPAS-Model#667. We still use the shallow water core for teaching and testing purposes, so better documentation is useful. [BFB] 05 December 2022, 19:35:37 UTC
9f91b69 Updating to SCORPIO 1.4.1 Updating the version of SCORPIO submodule to 1.4.1 This release includes the following changes, * Fix for a performance bug where the NetCDF header was reallocated multiple times, slowing down runs that create large output files * Support for ADIOS BP5 file format * Preliminary support (disabled by default) for HDF5 * Improved performance by reducing some collectives * Support for Perlmutter/Crusher * Minor bug fixes 05 December 2022, 18:32:38 UTC
a7e823d Merge branch 'azamat/chrysalis/add-oneapi' (PR #5240) Add Intel OneAPI compiler on Chrysalis. [BFB] 05 December 2022, 17:41:25 UTC
ff3f377 adding a new test for mosart-heat 04 December 2022, 18:34:39 UTC
46a0794 For alvarez at NERSC, update modules to defaults. Including using GNU 12.1 03 December 2022, 00:24:50 UTC
ba073dd cleaning up minor stuff 02 December 2022, 23:34:01 UTC
666595e Merge branch E3SM-Project/ndk/machinefiles/cori-hires-test-pe-layout (PR #5344) For cori-knl, add PE layout for a new test in e3sm_hi_res suite. 02 December 2022, 20:25:57 UTC
04b0bc5 add compy perlmutter configurations (may need to be altered for optimization) to cime_config/allactive/config_pesall.xml 02 December 2022, 17:35:14 UTC
e6853b9 added mach PE Layout options for Cori to cime_config/allactive/config_pesall.xml 02 December 2022, 17:27:35 UTC
04dd4df Minor edits to comments 02 December 2022, 16:35:37 UTC
6df7197 Merge branch 'jgfouca/cmake_cxx_standard' into master (PR #5339) CMake: Set E3SM CXX standard globally Not in macros. [BFB] 02 December 2022, 16:30:13 UTC
9f9ec11 ww3/cime_config/buildnml is throwing an error when it check that the ww3 grid and spectral combination is supported. This is commented out for now. needs to be fixed in future. 02 December 2022, 01:08:00 UTC
63574fe minor bug fix 02 December 2022, 00:45:55 UTC
9bb8a35 bug fix in buildnml 02 December 2022, 00:42:51 UTC
bc2b299 minor clean up for ww3/cime_config/config_component.xml 02 December 2022, 00:32:44 UTC
e70b7ef set spectral option for WW3 to be set as part of the COMPONENT i.e. the component long lame = WW3%sp50x36, WW3%sp36x36,WW3%sp25x36. if you use WWW3 with a short alias, the default at the moment is 50x36. This will be updated to a default spectral resolution of 36x36 in the near future. 02 December 2022, 00:21:57 UTC
81a2c3c Update JLSE to currently default oneapi module Prior oneapi/eng-compiler/2022.01.30.008 is now broken/deprecated 01 December 2022, 23:27:40 UTC
63810b8 remove doalb check for fates satphen call 01 December 2022, 22:53:37 UTC
1945b41 For cori-knl, add PE layout for a new test in e3sm_hi_res suite. SMS.T62_SOwISC12to60E2r4.GMPAS-IAF.cori-knl_intel 01 December 2022, 21:50:48 UTC
a8d2a3a Addressing a few minor formatting issues 01 December 2022, 21:39:24 UTC
a8c0733 deal with uninitialized variables in MOSART_heat_mod.F90 01 December 2022, 17:02:30 UTC
19711c3 Merge branch 'sbrus89/wav/fix_mpaso_streams' (PR #5302) Fix logic for wave output in mpaso streams The file generation for mpas ocean contained an incorrect logic comparison which caused wave output to be written for cases without waves. Fixes #5300 [BFB] 01 December 2022, 16:09:21 UTC
fc85899 update YAKL submodule to fix FFT cleanup issue 30 November 2022, 23:43:23 UTC
26a0f28 add YAKL fence before FFT cleanup 30 November 2022, 23:43:05 UTC
7d2b71d Fixes the definition of 20TR GSWP BGC compset The alias for the 20TR BGC compset for BGC is corrected. 30 November 2022, 21:51:09 UTC
057532c CMake: Set E3SM CXX standard globally Not in macros. [BFB] 30 November 2022, 19:27:17 UTC
bad4451 For pm-cpu (and alvarez), adjust/add PE layouts. Add PE layout for RRM test in e3sm_prod. Minor adjustment to PE layout for compset A_WCYCL* with res ne30pg2_oECv3 on 7 nodes. Add a large (L) layout for compset A_WCYCL* res ne30pg2_oECv3 on 58 nodes. Add alvarez to same to match pm-cpu. [bfb] 30 November 2022, 18:21:08 UTC
05a8c91 Update bld files with output from scripts to match Registry changes 30 November 2022, 17:59:08 UTC
f560da9 Merge branch 'dev_WW3Spectra' of github.com:erinethomas/E3SM into dev_WW3Spectra 30 November 2022, 17:45:35 UTC
f172b3f another FFT fix 30 November 2022, 14:42:05 UTC
70fc3e5 move fates satellitephenology call out of unreachable area 30 November 2022, 03:55:39 UTC
b2dad5f move fft objects to vars.h 30 November 2022, 00:27:00 UTC
06ab25b new fix for FFT init problem 30 November 2022, 00:21:44 UTC
71e281e Multiple Spectral options for wQU225EC30to60E2r2 grid for WW3. 30 November 2022, 00:03:30 UTC
82c8bd4 fix FFT initialization 29 November 2022, 23:46:33 UTC
0656967 Update YAKL to fix ArrayIR bug 29 November 2022, 21:46:46 UTC
37328b6 Add missing code to set threadNum before its use 29 November 2022, 20:01:41 UTC
4f448c4 bug fix for ESMT fft 29 November 2022, 18:00:35 UTC
21ffb4d Merge branch 'ambrad/hommexx/fix-scream-2058' (PR #5323) Hommexx: Limit HIP team size in debug builds. Also clean up the team_num_threads_vectors routine to consolidate the rules. Fixes SCREAM issue 2058. In SCREAM: Verified no change in team policy on Ascent. Verified _D tests now build on Crusher. e3sm_developer and homme_integration pass on Chrysalis. [BFB] 29 November 2022, 17:11:50 UTC
0b6c1ba Merge 'CONRAD/add_pgrad_correction_to_theta-l_kokkos' (PR #5299) Add pgrad_correction to theta-l_kokkos. A few changes: -- Change test using thetahs1.nl namelist to use pgrad_correction and test BFB -- Add cxx_log() callable from F90 to compute log on device for BFB -- Moved some computations around in CaarFunctorImpl to match F90 ordering (some needed for BFB now that pgrad_correction exists) [nonBFB] for HOMMEBFB only due to new test option for theta-fhs1. 29 November 2022, 16:49:35 UTC
69adea6 misc YAKL FFT updates 29 November 2022, 16:48:56 UTC
bd3f2f7 update YAKL submodule 29 November 2022, 16:15:17 UTC
d4c69e6 update FFT for vriance transport 29 November 2022, 15:31:24 UTC
1c9ea8b ELM: Use intent(inout) to preserve values in early exit. In PhotosynthesisMod.F90, early exits from brent and brent_PHS do not assign gs_mol* outputs values. The desired behavior in those cases is for the input values to be retained. Thus, this commit changes intent(out) to intent(inout) for these variables. The original code usually works because Fortran normally doesn't overwrite these inputs. But if an option like crayftn's -hzero is provided, intent(out) stack variables are 0-init'ed, causing a bug. 29 November 2022, 02:35:51 UTC
7c95fc7 Hommexx: Limit HIP team size in debug builds. Also clean up the team_num_threads_vectors routine to consolidate the rules. Fixes SCREAM issue 2058. [BFB] 28 November 2022, 18:34:39 UTC
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