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Initialize thermalCellMask in li_advection_thickness_tracers. The previous commit neglected to initialize and deallocate this array, and thus it was not being applied properly.
Add internalMeltRate directly to basalMassBal instead of adding it to groundedBasalMasBal and then repartitioning between grounded and floating. Also define internalMeltRate in Registry.xml.
The name internalMeltRate was misleading because there is a component that is not accounted for in this variable, which is the the amount needed to fill the maximum water fraction.
Fix runoff configuration in the BGC land-atm compsets
…5178) Add script support for ARRM10to60E2r1 ocn/ice grid Brings in support for the ARRM10to60E2r1 ocn/ice mesh. MPAS-Dev/compass#414 has details on the mesh generation, which is an updated version of the oARRM60to10 mesh. This PR includes all necessary mapping, runoff, and domain files for the following configurations: * ne30pg2_ARRM10to60E2r1 * arcticx4v1pg2_ARRM10to60E2r1 * TL319_ARRM10to60E2r1 (JRA-forced) * T62_ARRM10to60E2r1 (CORE-forced) [BFB] for all currently tested configurations
Add scm_zero_non_iop_tracers option For single-column runs, this sets all tracers in the atmospheric constituent list to qmin (typically zero) after the initial condition file (ncdata) is read in, but before the IOP file values are applied. As a result, non-IOP tracers are initialized to qmin rather than taking their values from the initial condition file, while IOP-defined tracers are unaffected. This option defaults to .false., and hence does not change answers for existing cases. However, it may be considered safer in the future to change the default to .true. (at least for non-replay runs), to avoid inconsistencies between the initial condition file state and the IOP file state that exacerbate transient spin-up behavior and potentially bias free-running model results. Like most single column model options, this option has no effect in global runs. This PR addresses E3SM-Project#5177, at least in part. Actually changing default behavior for existing SCM cases would require the option to be enabled in scmlib. [BFB] No impact on existing tests
… of an un-allocated o2r_rx is passed as an argument.
…-Project#5195) Fix barotropic thickness on edge in split explicit subcycling Barotropic thickness at the edge must match the sum of baroclinic thicknesses at that edge. This PR corrects a long-standing problem of noise in the vertVelocityTop variable, which is the Eulerian (fixed-frame) velocity for momentum. The vertTransportVelocityTop variable for tracer and thickness transport was smooth, both before and after this change. Currently in the code, the thickness at an edge used for volume (SSH) transport in the barotropic subcycling is thicknessSum = sshEdge + min(bottomDepth(cell1), bottomDepth(cell2)) That is, the thickness at an edge is taken as the shallower of the two neighboring cells. This was inconsistent with the baroclinic mode, which takes the average thickness of the two neighboring cells. [CC]
Fix threading issues in submesoscale code Adds some missing variables to the omp pragmas in the new submesoscale model code, to fix some issues with a test not being reproducible with threading and debug on. Fixes E3SM-Project#5215 [non-BFB] only with threading on
…ect#5209) Corrects sea ice snicar_ad error Fixes interpolation of shortwave parameters for the 5-band scheme. This error was introduced in the Snicar_ad feature implementation. Fixes E3SM-Project#5206 [non-BFB]
Previously, the unstructured SL-internal communication rounds were done using device pointers regardless of the value of HOMMEXX_MPI_ON_DEVICE. Now they are done on host if HOMMEXX_MPI_ON_DEVICE is true.
Add CF-compliant Time coordinate This variable has CF-compliant units and calendar. To accommodate the CF-compliant units, a new config option has been added to supply the reference time, 0001-01-01 by default. This merge also adds a Time_bnds variable. For output from a single point in time, the values in Time_bnds are the same as Time. For time-averaged (or min or max) output, Time_bnds contains the start and end times of the interval covered by the output. [BFB]
…ject#5189) Change defunct Fortran line labels to end do Update from numerical line labels to closing end do. Fixes E3SM-Project#5188 [BFB]
…#5223) Hommexx/SL: Implement HOMMEXX_MPI_ON_DEVICE=Off in SL transport. Previously, the unstructured SL-internal communication rounds were done using device pointers regardless of the value of HOMMEXX_MPI_ON_DEVICE. Now they are done on host if HOMMEXX_MPI_ON_DEVICE is true. Chrysalis e3sm_developer and homme_integration pass. Performance tested in SCREAM on Summit. [BFB]
Removed "nu_com = 'RD'" check since it isn't use in lnd_in but is the default setting in ELM source code.
HIP can't handle the reference, but we still need it for the F90 dycore with HORIZ_OPENMP enabled, since in that code path we enter all of our routines within a threaded region and so cannot create new Kokkos::Serial views during time stepping. (Recall Kokkos::Serial is necessary b/c Homme's threading is not compatible with Kokkos::OpenMP.) Thus, if COMPOSE_PORT is not defined, take a reference.
- Add uost files to input file list - Add cesm_namelist as -infile to build-namelist call so user_nl_ww3 modifications are considered
Many changes for HIP. Adding a new macro, HOMMEXX_ENABLE_GPU, redoing templates to generalize CUDA/HIP code. Arch-dependent code (very few lines) still uses kokkos macros. Regarding HIP -- standalone homme with output builds and runs, but no eye ball norm tests wrt output were performed. Also, not performed: bfb tests, unit tests (not tried to run), investigating bfb flags. This is for future PRs. Fixes E3SM-Project#5069 for team sizes too large with asserts and nans in reprosums for cxx execs with diagnostics macro ENERGY_DIAGNOSTICS. [bfb] for nightlies and v100.
Updates the settings for JRA data Removes the hard-coded start and end year for JRA from 1958/2016 to be the start/end values specified by DATM_CLMNCEP_YR_START/ DATM_CLMNCEP_YR_END. [BFB]
(PR E3SM-Project#5224) Shorten test-job-id with --jenkins-id Jenkins script option for amdclang on Crusher. [BFB]
…oject#5194) Replace device_resident and other OpenACC fixes for ocean The OpenACC declare device resident was not universally supported so replaced these with the more standard create/delete pairs. Also fixed some other missing private declarations that were possibly resulting in race conditions and bad results. Cleaned up some long lines, removed meshPool and other things along the way. Fixes E3SM-Project#5006 Fixes E3SM-Project#5176 [BFB]
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
E3SM-Project#5338) For pm-cpu (and alvarez), adjust/add PE layouts.
…#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]
…3SM-Project#5350) On GCP only, add larger allowance for MEMLEAK detection in tests
…3SM-Project#5347) For alvarez at NERSC, update modules to defaults.
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 E3SM-Project#5122 [BFB]
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
…' (PR E3SM-Project#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]
…ct#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]
To avoid OOM issues.
…t#5356) Move bottomDepthEdge calculation to single loop over all edges After E3SM-Project#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 E3SM-Project#5219 [BFB]
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]
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 E3SM-Project#5332 [BFB]
Increase ELM PEs in BGC runs on Anvil to avoid OOM issues. [BFB]
Update project name on Crusher. [BFB]
…SM-Project#5345) Move the fates-specific `satellitephenology` call out of an area that is unreachable when `fates` is active. Fixes NGEET/fates#953. [Non-B4B]
…roject#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 E3SM-Project#5289 [BFB]
The alias for the 20TR BGC compset for BGC is corrected. [BFB]
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