changes from https://github.com/ayumifuji/ADC-WW3-NWM-NEMS/
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…rtium#400) The ICE_MACHINE_COMPILER variable is incorrectly set to "conda" instead of "linux" in env.conda_linux. Fix that to reflect the documentation.
On Ubuntu and its derivatives, the csh shell at /bin/csh, which is used in the shebangs of the CICE scripts, is not compatible with conda. Mention that in the documentation and explain how to install tcsh as an alternative, and configure the system such that /bin/csh points to /bin/tcsh.
CICE-Consortium#395) * update suite.submit script and add new controls and cice.setup options, update documentation * update cice.setup new --setup options * update documentation * update documentation
…oner (CICE-Consortium#406) * add cice.setup --case and cice.setup --test script tests to the travis yml file * fix cice.setup script
…for minor release, update icepack (CICE-Consortium#409)
…-Consortium#404) * Made the following basalstress parameters namelist items in dynamics_nml: k2, alphab, threshold_bw. * Updated documentation for updated basalstress parameters * Correct typo in user_guide/ug_case)settings.rst * Modified ice_read_write.F90:ice_open. Added nbytes variable to allow for large grids that can cause integer overflow * Modified ice_read_write.F90:ice_open. Added nbytes variable to allow for large grids that can cause integer overflow * Revert "Correct typo in user_guide/ug_case)settings.rst" Reverting to make new branch to commit code changes, instead of working off of master. This reverts commit 06c614a. * Correct typo in ug_case_settings.rst * Reverting to version prior to updating ice_open * retrigger checks
CICE-Consortium#408) * Added JRA55 forcing for gx3 grid; modified ice-forcing.F90 to now handle both the gx1 and gx3 grid. JRA55 forcing files named were changed to include gx1 and gx3 * Updated set_nml.jra55* files to reflect correct ICE_MACHINE_INPUTDATA path, reverted to previous cice.batch.csh script; will use --queue option in seting up test suites. * corrected typo in set_nml.jra55_2008 file * Modified ice_forcing.F90 to revert to using original naming convention for JRA55 forcing files for gx1 grid * Updated icepack to version 1.2.1 * update icepack to current version in consortium master * updated user_guide to account for JRA55 options for both the gx1 and gx3 grid * Revert changes to get_wave_spec in ice_forcing.F90 * revert icepack to 2fa887f
* Made the following basalstress parameters namelist items in dynamics_nml: k2, alphab, threshold_bw. * Updated documentation for updated basalstress parameters * Correct typo in user_guide/ug_case)settings.rst * Modified ice_read_write.F90:ice_open. Added nbytes variable to allow for large grids that can cause integer overflow * Modified ice_read_write.F90:ice_open. Added nbytes variable to allow for large grids that can cause integer overflow * Revert "Correct typo in user_guide/ug_case)settings.rst" Reverting to make new branch to commit code changes, instead of working off of master. This reverts commit 06c614a. * Correct typo in ug_case_settings.rst * Reverting to version prior to updating ice_open * retrigger checks * In ice_open and ice_open_ext, made grid variables 8 byte integers. This is to allow for large grids (Like GOFS) that have integer overflow with 4 byte integers * Implement nbytes to determine record lengts for ice_open. This helps with large grids thta might cause integer overflow when using nbits * Minor comment update in ice_read_write.F90 * Moved bits_per_byte to module level parameters
…um#418) On Linux, compiling CICE in serial mode under the conda environment currently fails as the linker does not find the NetCDF libraries. Compiling in parallel mode does work as the MPI compilation wrappers seem to pass the necessary flag to the linker under the hood. Explicitely tell the linker the location of the libraries using the `SLIBS` variable in the Macros file. To be on the safe side, also do it on macOS.
… CFLAGS_HOST (CICE-Consortium#424) * update conda macos Macros file to address older versions of sdk in setting CFLAGS_HOST * update travis data download to zenodo
* initial changes to cice driver for isotopes * add isotope fluxes * forcing and restarts for isotopes * interim commit for isotopes * more isotopes code including ice_step * diagnostics and history for isotopes * update both RunMods * isotope testing option * fix diags and ice_in; add isotope tests * changing badger acct * fix isotope indexing * initialize trcrn(isotopes) * fix isotope restarts * Add isotope documentation * updating copyright to 2020 * update icepack version * update non standalone drivers for isotope changes Co-authored-by: apcraig <[email protected]> Co-authored-by: David Bailey <[email protected]>
* add codecov.yml * update for codecov * update code coverage implementation * update documentation * update documentation * update error message in cice.setup * update travis testing to eliminate error by adding sleep between icepack.setup calls
* update code coverage documentation * remove cice_test_codecov script * update code coverage documentation * Update configuration/scripts/tests/cice_test_codecov.csh Co-Authored-By: Philippe Blain <[email protected]> * update codecov script and documentation Co-authored-by: Philippe Blain <[email protected]>
* machines: rename brooks to daley brooks has been decommissioned, daley replaces it. * machines: port to daley (ECCC) * machines: port to banting (ECCC) * machines: add GNU port for banting and daley * machines: disable HDF5 locking for ECCC machines * machines: eccc: use sice500 account for input data
) * update to include a 'high_Sierra' machine with gnu compilers, only marginally modified from the travisCI env and Macros. * Syncing theia and upstream/master branch * theia execution * intel compiler version tests -- 15.0.0 or greater * working on variations for round robin test * syncing to main * sync * testing * end test * successful on phase2 for all regression tests * start on phase3 execution * add phase3 system * syncing and phase3 modules * update configs manually from master * env edit * builds on phase3 now * test * trying to pull/merge cice master * theia * successful theia build * garbage * update theia intel env * mods for running in NOAA * start towards hera * tmp * theia passes with most recent of all modules * moving to hera * clean regression run on hera * cleanup * phase3 work * minor manual move towards master copy * re-fix phase3 script * nearing full phase3 * update path for data * actual final version of phase3 * from master * cicecore updating from master * from consortium/master * more from master * retry sync * manual add/subtrace * script perms and large diff files * retrieve hera * docs and cicecore sync to master * machine syncing * couple more * some more * finally the right template * finally correct template * typography in master * restore working batch.csh * towards matching consortium master * last? add for syncing * Revert icepack to 1.1.2 Co-authored-by: Tony Craig <[email protected]>
* Add history_precision option for history files. * Update to work with pio2 * Precision updates * Fix missing value precision * Add documentation * revert the Macros and env * revert cice.build * Move abort statement for history_precision
…efault value (CICE-Consortium#586) * Update gx1 ic - update set_nml.gx1prod to match current production system - add apr 1 test case for gx1 - update landice tests, use gx1 - fix hmix default CICE-Consortium#585 - delete old code in ice_forcing.F90 (should have been done in earlier PR) * update gx1coreii initial condition * update icepack * add gx1 debug test, expected to fail * Update version number to 6.2.0 * Update gx3 and gx1 input filenames Update CI wget implementation CICE-Consortium#588 Create variable in ice_forcing.F90 called mixed_layer_depth_default and use it instead of c20 Fix bug in hourly output, created in time manager update CICE-Consortium#589 Set start year for all runs to 2005 and turn leap years on by default Update documentation in history output section to add information about hist_avg namelist, noted in CICE-Consortium#566 * update ic filenames, tests, and documentation * update color links in test results wiki * update hmix initialization
Fix error in gx1coreii initial condition filename Update conda macos Macros Add documentation about updating the conda environment
…ing (CICE-Consortium#597) * Remove hc_jday. Not used anymore after introducing of new ice_calendar * Calculate "hc_jday" inline using compute_days_between and _init fields from ice_calendar * Correct hcdate using "compute_days_between" * Remove unused variables from ice_calendar
Allow setting the ice surface roughness at the atmosphere interface, 'iceruf', in the CICE namelist. This makes it easier to modify this value.
…E-Consortium#602) * Update test coverage - add alt06 test, ncat=7, kcatbound=3, nslyr=3 - add bigdiag test with lots of diagnostic output, debug_model=true, debug_blocks=true, etc - add spiralcenter decomp test - add gx1 weightfile decomp test - add gbox180 with spacecurve decomp test to trigger Peano and Cinco decompositions - rename boxdyn to boxnodyn - modify boxslotcyl, turn off tr_lvl and tr_pond_lvl, changes answers - clarify boxadv, boxnodyn, boxrestore, explicitly set shortwave=ccsm3, albedo_type=constant - cleanup spacecurve implementation including debug flagging, recode print to write, module private, add printcurve for gridsize of 30, remove qsort and partition subroutines. - remove CICE_RunMod.F90_debug and migrate high level debug checks to CICE_RunMod.F90 with new debug_model namelist. Also add debug_model_step to specify at what timestep to start writing debug_model output. debug_model writes data for the first point specified by lonpnt, latpnt. - move debug_ice routine into ice_diagnostics.F90 and out of CICE.F90 - remove writeout_finished_file from CICE_Finalize in several drivers - deprecate print_points_state via an ifdef - rename l_stop in ice_transport_driver.F90 to ckflag. This looked like l_stop logic because of the naming but it isn't. - fix issue of size of fcontopn_d and fsurfn_d when ncat greater than 6 in init_coupler_flux. Would go out of bounds, now initializes fcontopn and fsurfn to 6th value for any category greater than 6. - rename dbug variable name in ice_forcing.F90 to forcing_diag and change namelist variable name. - update ice_distributionGet output and implementation to support more general arguments - add ice_distributionGet test in init_domain_distribution when debug_blocks is true. - fix bug in create_distrb_rake for 1d rake. add a test that triggers the 1d rake. - update debug flag in ice_distribution.F90 leverage debug_blocks. - update documentation. * - Deprecate IsLoadBalanced in ice_spacecurve - Update calchk to check 100,000 years - Update sectrobin decomp test to check land block elimination * update complog part of baseline script to report missing data as MISS instead of FAIL
…ines (CICE-Consortium#604) * Update the coverage implementation. The gcov/lcov tool occasionally generates false negatives or incorrect statistics with respect to coverage for Fortran 90 continuation lines (using "&"). In some cases, within a single continuation block, some lines have hits which are correctly counted while other lines have misses which are incorrect and also counted. This seems to be partly associate with the lcov -a feature that we use to aggregate multiple tests, but it also probably is ultimately created by gcov because it doesn't seem to handle skipped vs missed lines entirely consistently. With this modification, --coverage creates a temporary sandbox where the tests are run. Prior to running the tests, lcov_modify_source.sh is invoked. " ! LCOV_EXCL_LINE" (a special defined string in lcov) is added to the end of some source code lines to request that gcov exclude them. The lines excluded are Fortran 90 continuation lines. In all cases the first and last line of a continuation block and lines that continue after an "if" are never excluded. This seems to improve the accuracy of the coverage output overall. Several other attempts were made to modify the lcov and geninfo perl scripts to handle the Fortran90 continuation line filtering there without success, so this solution was implemented. * update documentation
* icepack: update to support staggered atmospheric levels In the following commit, we will add support for staggered atmoshperic levels, i.e. receiving the momentum and scalar atmospheric variables at different vertical levels. Icepack already supports this through optional arguments, so start by updating the icepack submodule. * cicecore: add support for staggered atmoshperic levels In order to support atmospheric input data given at different levels for winds and scalars, introduce a new array 'zlvs' in module ice_flux, and pass it down to 'icepack_atmo_boundary'. Initialize 'zlvs' to the same value as 'zlvl' (10 metres) so as not to change the standalone model answers.
…-Consortium#605) * drivers/hadgem3: add missing 'subname' and use existing 'subname's * drivers/hadgem3/CICE_InitMod: update 'init_lvl' call Add the required 'iblk' argument. * drivers/hadgem3/CICE_RunMod: remove uneeded 'dt' arguments The subroutines 'prep_radiation', 'zsal_diags', 'bgc_diags' and 'hbrine_diags' do not take a 'dt' argument anymore, so remove it. * drivers/hadgem3/CICE_RunMod: get 'Lsub' from Icepack * drivers/hadgem3/CICE_RunMod: remove 'da_state_update' subroutine This subroutine is inside an 'ICE_DA' CPP, which is not used in any configuration. Remove it. * drivers/hadgem3/CICE_RunMod: remove stray '+' This '+' sign was copy-pasted there in error in 29b99b6 (CICE: Floe size distribution (CICE-Consortium#382), 2019-12-07). Remove it. * drivers/hadgem3: remove obsolete 'check_finished_file' subroutine Remove the call to 'check_finished_file' as well as the definition of the subroutine, as the 'hadgem3' driver is not used on machine 'bering' and it's unclear if machine 'bering' still exists. * drivers/hadgem3: fix cice_init so it calls 'count_tracers' This was forgotten back in 8b0ae03 (Refactor tracer initialization (CICE-Consortium#235), 2018-11-16) * drivers/hadgem3/CICE_RunMod: add call to 'save_init' The hadgem3 driver was not updated when 'save_init' was added in 83686a3 (Implement box model test from 2001 JCP paper (CICE-Consortium#151), 2018-10-22). As this subroutine is necessary to ensure proper initialization of the model, add it now. * drivers/hadgem3/CICE_RunMod: tweak loop indices in 'coupling_prep' Other drivers use 'ilo,ihi' and 'jlo,jhi' here. Do the same. * drivers/hagdem3: update driver to new time manager * drivers/hadgem3: pass 'mpi_comm_opa' explicitely to init_communicate In 066070e (Fix minor issues in documentation, key_ CPPs, bfbcomp return codes (CICE-Consortium#532), 2020-11-23), the 'ice_communicate' module was updated to remove CPP macros relating to the OASIS coupler (key_oasis*) and to the NEMO ocean model (key_iomput). These CPPs were used to make the correct MPI communicator accessible to the 'init_communicate' subroutine. However, that subroutine already accepts an optional MPI communicator as argument and it was deemed cleaner to require the driver layer to explicitely pass the communicator instead of making it accessible through 'use' statements. Update the 'hadgem3' driver, used for coupling with NEMO, to explicitely pass the NEMO MPI communicator 'mpi_comm_opa' to 'init_communicate'. * drivers: add 'nemo_concepts' driver Historically the 'hadgem3' driver has been used when compiling a single NEMO-CICE executable at ECCC. Going forward, all driver-level adjustements will be done in our own driver, 'nemo_concepts', 'CONCEPTS' being the name of the multi-departmental collaboration around using the NEMO ocean model. Copy CICE_InitMod, CICE_RunMod and CICE_FinalMod from the 'hadgem3' directory to a new 'nemo_concepts' directory under 'drivers/direct'. The following commits will clean up this new driver and port over some in-house adjustments. * drivers/nemo_concepts: remove unused 'writeout_finished_file' subroutine This subroutine was only called on machine 'bering', which is not an ECCC machine and probably does not exist anymore anyway. Remove it. * drivers/nemo_concepts: call 'scale_fluxes' with 'aice_init' Since 'merge_fluxes' is called with aice_init, it is more consistent to also call 'scale_fluxes', in 'coupling_prep' with 'aice_init' instead of 'aice'. Copy this in-house change to the new 'nemo_concepts' driver.
…um#606) * Update testing - Set default debug_model_step=0 (was 99999999) - Add debug_model_[i,j,iblk,task] to define the debug_model diagnostic point in local grid index space. If this point is not set and debug_model is turned on, it will use lonpnt(1),latpnt(1). - Rename forcing_diag namelist/variable to debug_forcing to be more consistent with other "debug_" namelist variables - Rename the local variable forcing_debug in ice_forcing.F90 to local_debug to avoid confusion with global varaible debug_forcing. - Add namelist variable optics_file. Was hardwired in ice_forcing_bgc.F90 - Update optics file variable name to read, still hardwired in model. - Update setting of nbtrcr_sw and allocation of trcrn_sw. nbtrcr_sw was not set in icepack after it was computed and trcrn_sw was allocated before nbtrcr_sw was computed. This impacts the dedd_algae implementation which still isn't working. - move default distribution_wgt_file for gx1 to set_nml.gx1 - update test suite, add testing of debug_model_[i,j,iblk,task], add addtional testing of maskhalo - update documentation * add sumchk unit test to test global reduction methods * - add bcstchk unit test - update ice_broadcast to sync up serial and mpi versions - add get_rank to ice_communicate.F90 - add global_[min/max]val_scalar_int_nodist method to ice_global_reductions.F90 - add tripole output in ice_blocks.F90 with debug_blocks - update set_nml.tx1 to set ns_boundary_type to 'tripole', was 'open' * update lsum16 to revert to double precision if NO_R16 is set * sync up serial ice_global_reductions.F90 * - add optics_file_fieldname namelist - add grid_type and ns_boundary_type tripole check - update sumchk unit test to check both Nface and center points. these are treated differently for tripole grids. - update documentation of unit tests
Update NUOPC/CMEPS driver Update hera port
* updated orbital calculations needed for cesm * fixed problems in updated orbital calculations needed for cesm * update CICE6 to support coupling with UFS * put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied * update icepack submodule * Revert "update icepack submodule" This reverts commit e70d1ab. * update comp_ice.backend with temporary ice_timers fix * Fix threading problem in init_bgc * Fix additional OMP problems * changes for coldstart running * Move the forapps directory * remove cesmcoupled ifdefs * Fix logging issues for NUOPC * removal of many cpp-ifdefs * fix compile errors * fixes to get cesm working * fixed white space issue * Add restart_coszen namelist option * Update NUOPC cap to work with latest CICE6 master * nuopc,cmeps or s2s build updates * fixes for dbug_flag * Update nuopc2 to latest CICE master * Fix some merge problems * Fix dbug variable * Manual merge of UFS changes * fixes to get CESM B1850 compset working * refactored ice_prescribed_mod.F90 to work with cdeps rather than the mct data models * Fix use_restart_time * changes for creating masks at runtime * added ice_mesh_mod * implemented area correction factors as option * more cleanup * Fix dragio * Fix mushy bug * updates to nuopc cap to resolve inconsistency between driver inputs and cice namelists * changed error message * added icepack_warnings_flush * updates to get ice categories working * updates to have F compset almost working with cice6 - still problems in polar regions - need to resolve 253K/cice6 versus 273K/cice5 differences * changed tolerance of mesh/grid comparison * added issues raised in PR * Update CESM-CICE sync with new time manager * Add back in latlongrid Co-authored-by: Mariana Vertenstein <[email protected]> Co-authored-by: apcraig <[email protected]> Co-authored-by: Denise Worthen <[email protected]>
…CICE-Consortium#612) * icepack: optionally compute 'dragio' using under-ice roughness length In CICE-Consortium/Icepack@a80472b (icepack_parameters: optionally compute 'dragio' from under-ice roughness (CICE-Consortium/Icepack#366), 2021-06-22), Icepack was updated to optionally compute the ice-ocean drag coefficicent 'dragio' using an under-ice roughness length and the thickness of the first ocean level. Leverage this new feature in CICE by adding 'calc_dragio' and 'iceruf_ocn' to the CICE namelist. Add the new variables to the index in the documentation and add a test with the new feature (using default values for 'iceruf_ocn' and 'thickness_ocn_layer1'). As this new feature will mostly be useful in a coupled context, we do not add 'thickness_ocn_layer1' to the namelist as it is expected that the ocean model will pass this information to CICE. * ice_grid: set 'thickness_ocn_layer1' if using 'calc_dragio' In the previous commit we updated Icepack to allow computing the ice-ocean drag coefficient 'dragio' using an under-ice roughness length and the thickness of the first ocean layer, 'thickness_ocean_layer1', a new Icepack parameter. In some situations, we have access in CICE to the thicknesses of the ocean levels, either hard-coded (use_bathymetry = false, bathymetry_format = default), read from a file (use_bathymetry = true, bathymetry_format = pop), or generated from the kmt_file (use_bathymetry = false, bathymetry_format = pop). In these situations, for consistency set 'thickness_ocean_layer1' in Icepack to the thickness of the first ocean level, 'thick(1)' if 'calc_dragio' is active.
…ortium#610) * Fix history/restart frequency bugs and update scripts - Fix bugs in history/restart frequency associated with new calendar (CICE-Consortium#589) - Update set_nml.histall to include hourly output (CICE-Consortium#589) - Update test scripts to cleanly abort if run fails where possible (CICE-Consortium#608) - Update decomp test so it's rerunable, remove restart at start of run (CICE-Consortium#601) - Add ability to do bfbcomp tests with additional options set on command line (CICE-Consortium#569) - Update documentation of calendar frequency computation, calendar types, and closed boundaries (CICE-Consortium#541) - Add optional doabort flag to abort_ice to control whether the method aborts. This is useful for testing and code coverage statistics, although doabort=.false. will not call the actual abort method, but we can test the interfaces and rest of the code. - Add histfreq_base and dumpfreq_base ('init' or 'zero') to specify reference data for history and restart output. Defaults are 'zero' and 'init' respectively for hist and dump. Setting histfreq_base to 'zero' allows for consistent output across multiple runs. Setting dumpfreq_base to 'init' allows the standard testing which requires restarts be written, for example, 5 days after the start of the run. - Remove extra abort calls in bcstchk and sumchk on runs that complete fine but don't pass checks. These aborts should never have been there. - Update documentation. - Clean up some of the unit tests to better support regression testing - modify initial/restart implementation - restart namelist is deprecated, now computed internally - modify initial/continue init checks and set restart and use_restart_time as needed - create compute_relative_elapsed method in ice_calendar to improve code reuse - update documentation with regard to initial/continue modes - Set default use_restart_time to false
…ium#617) - Update unit test output and scripts to differentiate completed runs and successful testing better - sumchk is not passing on Onyx due to issues in the global reduction at real*16 and real*4. This seems to be a software bug in mpich and a report has been issued to Onyx admins.
- Fix 1x1 and 2x2 non-bit-for-bit results. It turns out the 1x1 and 2x2 blocks were bit-for-bit physicallly. The problem was that a set of blocks were "land block eliminated" near the equator incorrectly. These blocks never have sea ice form, so it's not a problem scientifically, but it changes the masking and restart files. The fix is a one line change in ice_domain.F90 which that sets the minimum "flat" value to 1. This error could only happen in cases where the blocks were within 0.5 degrees of the equator, and a set of conditions were required where an active gridcell was set to inactive which then resulted in the entire block being eliminated. - Update the initialization of ARRAY_G in the gather_global_ext interfaces. Get rid of older, more complex approach which left some blocks uninitialized. - Set psalt(n) to zero by default. Was uninitialized in cases where vice=0. - Add a test to check bit-for-bit in log files for 1x1 blocks with bfbflag set to reprosum.
* port to gaea
* Initialization of global HTE and HTN arrays with ghost cells on master task to avoid gathering constant arrays when running EVP 1D implementation. This solves issue with departure errors resulting from erroneous initialization of full land blocks in EVP 1D gathering. Correct initialization of remaining variables for full land blocks in EVP 1D gathering. * Reverted configuration/scripts/cice.batch.csh to resolve bad auto merge of file. Machine 'freya' was double in file. * Spell error corrected (CICE-Consortium#568 (comment)). * Redundant initializations to default values removed (CICE-Consortium#568 (comment)). @mhrib questions to default value settings removed. * Subroutine primary_grid_lengths_global_ext moved from ice_grid module to MPI and serial implementations of ice_boundary modules (CICE-Consortium#568 (comment)). Please note duplication of subroutine. * Added 1d solver to be fully integrated. Removed kevp=102 bypass. Clean up. Changed namelist parameter kevp to evp_algorithm * General cleanup of ice_dyn_evp_1d module (CICE-Consortium#568 (comment) and CICE-Consortium#568 (comment)) * Modified documentation in order to comply with modifications of evp 1d * Uncommenting of numainit parallelization removed and domp_init moved before numainit to ensure correct initialization. Additional cleanup of code. * renamed set_nml.evp_algorithm to set_nml.evp1d added test to base test * rm set_nml.kevp102 * Naming of variable se is not logical. Changed to sse which is the same as the global variable * Alignment of NUMA-aware array splitting between threads * Initialization of global HTE and HTN arrays with ghost cells on master task to avoid gathering constant arrays when running EVP 1D implementation. This solves issue with departure errors resulting from erroneous initialization of full land blocks in EVP 1D gathering. Correct initialization of remaining variables for full land blocks in EVP 1D gathering. * Reverted configuration/scripts/cice.batch.csh to resolve bad auto merge of file. Machine 'freya' was double in file. * Spell error corrected (CICE-Consortium#568 (comment)). * Redundant initializations to default values removed (CICE-Consortium#568 (comment)). @mhrib questions to default value settings removed. * Subroutine primary_grid_lengths_global_ext moved from ice_grid module to MPI and serial implementations of ice_boundary modules (CICE-Consortium#568 (comment)). Please note duplication of subroutine. * Added 1d solver to be fully integrated. Removed kevp=102 bypass. Clean up. Changed namelist parameter kevp to evp_algorithm * General cleanup of ice_dyn_evp_1d module (CICE-Consortium#568 (comment) and CICE-Consortium#568 (comment)) * Modified documentation in order to comply with modifications of evp 1d * Uncommenting of numainit parallelization removed and domp_init moved before numainit to ensure correct initialization. Additional cleanup of code. * renamed set_nml.evp_algorithm to set_nml.evp1d added test to base test * rm set_nml.kevp102 * Naming of variable se is not logical. Changed to sse which is the same as the global variable * Alignment of NUMA-aware array splitting between threads * Fix bad scaling of calculation of tinyarea. Different order of multiplication causes small differences in result * Fix evp 1d masking issues - There are relatively rare cases/gridcells where stress (tmask) and stepu (umask) are advanced without the other. The 1d evp implementation was not addressing this issue, so skiptcell was added to the 1d evp (similar to skipucell) to mask out cells separately for stress and stepu. This fixed a few non bit-for-bit cases in testing. - Cleaned up some indentation and other minor issues in 1d evp. - Updated the evp_algorithm log output in ice_init. * Some minor revisions in the documentation as suggested by @apcraig (CICE-Consortium#568 (review)) plus some additional minor spelling corrections. Co-authored-by: Stefan Rethmeier <[email protected]> Co-authored-by: Till Rasmussen <[email protected]> Co-authored-by: Stefan Rethmeier <[email protected]> Co-authored-by: apcraig <[email protected]>
* initial snow redist/metamorph tracer implementation (no physics) * add rhosmin, snwlvlfac to namelist, change init_snow to init_snowtracers * updating format labels due to changes in Consortium master * add calls to new snow physics routines * update_state after step_snow * fix optional in update_state * wrap step_snow and update_state with tr_snow conditional * snow interactions with thermo (except dEdd) * conflict warning * adding snwgrain namelist flag * use snwredist=bulk instead of 30percent, fix array errors, init snow tracer values, add namelist flags to ice_in * aging lookup table for dry metamorphism (version for testing) * add/clean up diagnostics, begin debugging restart implementation * fixing restarts * add snow tests to base_suite * add history; minor cleanup * fix step_therm1 interface * io fixes for snow1 * bug fix for snow diagnostics * fix line continuation * refactor bgc diagnostics as in Icepack * add snowtable implementation * cleaning up snow test options * send rsnw tracer to dEdd; initialize snow tracers; update -s options for snow * broadcast new snow diagnostics * new snow tests require 5 snow layers and therefore can not start from standard initial condition files with nslyr=1 * update icepack * use local variable for rsnow to prevent array out-of-bound error; cleanup * updating documentation and some code comments * documentation: index * fix history output; include but comment out code for averaging based on snow presence; set rsnw_fall in ice_in for default dEdd and include relevant snow parameters in options files; update doc; clean up * minor cleanup, especially documentation * update icepack Co-authored-by: Andrew Roberts <[email protected]> Co-authored-by: Elizabeth Hunke <[email protected]> Co-authored-by: apcraig <[email protected]>
…ng for timestep output (CICE-Consortium#624) * Fix history features - Fix bug in history time axis when sec_init is not zero. - Fix issue with time_beg and time_end uninitialized values. - Add support for averaging with histfreq='1' by allowing histfreq_n to be any value in that case. Extend and clean up construct_filename for history files. More could be done, but wanted to preserve backwards compatibility. - Add new calendar_sec2hms to converts daily seconds to hh:mm:ss. Update the calchk calendar unit tester to check this method - Remove abort test in bcstchk, this was just causing problems in regression testing - Remove known problems documentation about problems writing when istep=1. This issue does not exist anymore with the updated time manager. - Add new tests with hist_avg = false. Add set_nml.histinst. * revert set_nml.histall * fix implementation error * update model log output in ice_init * Fix QC issues - Add netcdf ststus checks and aborts in ice_read_write.F90 - Check for end of file when reading records in ice_read_write.F90 for ice_read_nc methods - Update set_nml.qc to better specify the test, turn off leap years since we're cycling 2005 data - Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data - Add QC run to base_suite.ts to verify qc runs to completion and possibility to use those results directly for QC validation - Clean up error messages and some indentation in ice_read_write.F90 * Update testing - Add prod suite including 10 year gx1prod and qc test - Update unit test compare scripts * update documentation * reset calchk to 100000 years * update evp1d test
* Fix history single/double precision issues - Fix io_netcdf. Double precision output was passed thru a single precision variable before writing so the precision in the output was lost. This is now fixed. Single and double precision netcdf output now reflects the internal model data correctly. - Fix io_pio2. Single precision output with pio2 was producing garbage for both netcdf and pnetcdf cases. This is not the case with pio1. Several changes were needed. - The iodesc initialization has to differentiate single or double target variables - The write_darray has to explicitly send a single or double array - Migrated to spval_dbl fills everywhere data is a double type, mostly in ice_history.F90. - Created a ice_write_hist_fill method in both io_netcdf and io_pio2 to improve reuse. Ran io_suite on cheyenne and checked that values are produced correctly for each case. * update formatting
* update gx1prod, update version number to 6.3 * update Icepack * update gx1prod15 to start at 1995
This was referenced Sep 15, 2021
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this pull request encapsulates all the changes you made in https://github.com/ayumifuji/ADC-WW3-NWM-NEMS/tree/master/CICE, but in this repository (dedicated CICE repository) instead of in the greater
CoastalApprepositorythis is paired with ayumifuji/ADC-WW3-NWM-NEMS#1; together, these two pull requests act to move your CICE changes from:
https://github.com/ayumifuji/ADC-WW3-NWM-NEMS/tree/master/CICE -> https://github.com/ayumifuji/CICE