Merge in CICE-Consortium/main: June 2024 #81
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* Fix CESMCOUPLED compile problem in icepack
… bug (CICE-Consortium#824) * Update global reduction implementation to improve performance, fix VP bug This was mainly done for situations like VP that need a fast global sum. The VP global sum is still slightly faster than the one computed in the infrastructure, so kept that implementation. Found a bug in the workspace_y calculation in VP that was fixed. Also found that the haloupdate call as part of the precondition step generally improves VP performance, so removed option to NOT call the haloupdate there. Separately, fixed a bug in the tripoleT global sum implementation, added a tripoleT global sum unit test, and resynced ice_exit.F90, ice_reprosum.F90, and ice_global_reductions.F90 between serial and mpi versions. - Refactor global sums to improve performance, move if checks outside do loops - Fix bug in tripoleT global sums, tripole seam masking - Update VP solver, use local global sum more often - Update VP solver, fix bug in workspace_y calculation - Update VP solver, always call haloupdate during precondition - Refactor ice_exit.F90 and sync serial and mpi versions - Sync ice_reprosum.F90 between serial and mpi versions - Update sumchk unit test to handle grids better - Add tripoleT sumchk test * Update VP global sum to exclude local implementation with tripole grids
…#827) * Add functionality to change hist_avg for each stream * Fix some documentation * Try to fix sphinx problem * Fix hist_avg documentation * Add some metadata changes to time and time_bounds
Remove trailing blanks via automated tool in some Fortran files
* Fix for mesh check in CESM driver * Slightly different way to evaluate longitude difference * Slightly different way to evaluate longitude difference * Put the abs inside the mod * Add abort calls back in
* update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf
* Add option to change location in interval of time axis * Only use hist_time_axis when hist_avg is true * Add more comments and information in the documentation * Add a check on hist_time_axis as well as a global attribute * Abort if hist_time_axis is not set correctly.
Remove deprecated COREII LYq forcing Remove deprecated print_points_state Update links in rst documentation to point to main, not master
* updating paths for local nrlssc builds * Add jra55do forcing option * Updated env.nrlssc_gnu for new local directory structure * Added JRA55do to file names. Added comments for each variable name at top of JRA55do_???_files subroutine * Make JRA55 forcing to use common subroutines. Search atm_data_type for specific cases * remove extraneous 'i' variable in JRA55_files * Changed JRA55 filename JRA55_grid instead of grid at end of filename * Add jra55do tests to base_suite and quick_suite. This is done via set_nml options. * Update forcing implementation to provide a little more flexibility for JRA55, JRA55do, and ncar bulk atm forcing files. * Update documentation * update Onyx port * Update forcing documentation Initial port to derecho_intel * clean up blank spaces --------- Co-authored-by: daveh150 <david.hebert@nrlssc.navy.mil>
…tium#846) - fix optional arguments issues - fix hsn_new(1) bug Update optargs unit test, add new test cases Add opticep unit test, to test CICE calls to Icepack without optional arguments. Add new comparison option to comparelog.csh to compare a unit test with a standard CICE test. Update unittest_suite Update documentation about optional arguments and unit tests
…al remapping (CICE-Consortium#833) * Use same method whether l_fixed_area=T or F to compute masks for edge fluxes * Corrected typo in comment * Cosmetic (indentation) change in ice_transport_remap.F90 * Set l_fixed_area value depending of grid type * Modifs to the doc for l_fixed_area * Use umask for uvel,vvel initialization for boxslotcyl and change grid avg type from S to A in init_state * Temporary changes before next PR: l_fixed_area=F for B and C grid * Temporary changes before next PR: remove paragraph in the doc * Small modifs: l_fixed_area and grid_ice are defined in module ice_transport_remap
…Consortium#853) * test ghactions * update master to main in github actions
* Replace tr_snow flag with snwredist, snwgrain in some places (tr_snow is still used more generally). Fix intent(out) compile issue in ice_read_write.F90. Replace badger with chicoma machine files. * update icepack to 86cae16d1b7c4c4f8 --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com>
* Deprecate zsalinity, mostly with ifdef and comments first for testing * Deprecate zsalinity, remove code * Add warning message for deprecated zsalinity * Update Icepack to #f5e093f5148554674 (deprecate zsalinity)
…ICE-Consortium#850) * Extend restart output controls, provide multiple streams for possible output frequencies. Convert dumpfreq, dumpfreq_n, dumpfreq_base to arrays. Modify histfreq_base to make it an array as well. Now each history stream can have it's own base time (init or zero). Update documentation. * Clean up implementation and documentation * Update PR to check github actions
…ICE-Consortium#856) * merge latest master (NOAA-EMC#4) * Isotopes for CICE (CICE-Consortium#423) Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> * 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 * Convergence on ustar for CICE. (CICE-Consortium#452) (NOAA-EMC#5) * Add atmiter_conv to CICE * Add documentation * trigger build the docs Co-authored-by: David A. Bailey <dbailey@ucar.edu> * 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 icepack submodule * change Orion to orion in backend remove duplicate print lines from ice_transport_driver * add -link_mpi=dbg to debug flags (NOAA-EMC#8) * cice6 compile (NOAA-EMC#6) * enable debug build. fix to remove errors * fix an error in comp_ice.backend.libcice * change Orion to orion for machine identification * changes for consistency w/ current emc-cice5 (NOAA-EMC#13) Update to emc/develop fork to current CICE consortium Co-authored-by: David A. Bailey <dbailey@ucar.edu> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> * Fixcommit (NOAA-EMC#14) Align commit history between emc/develop and cice-consortium/master * Update CICE6 for integration to S2S * add wcoss_dell_p3 compiler macro * update to icepack w/ debug fix * replace SITE with MACHINE_ID * update compile scripts * Support TACC stampede (NOAA-EMC#19) * update icepack * add ice_dyn_vp module to CICE_InitMod * update gitmodules, update icepack * Update CICE to consortium master (NOAA-EMC#23) updates include: * deprecate upwind advection (CICE-Consortium#508) * add implicit VP solver (CICE-Consortium#491) * update icepack * switch icepack branches * update to icepack master but set abort flag in ITD routine to false * update icepack * Update CICE to latest Consortium master (NOAA-EMC#26) update CICE and Icepack * changes the criteria for aborting ice for thermo-conservation errors * updates the time manager * fixes two bugs in ice_therm_mushy * updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases * add cice changes for zlvs (NOAA-EMC#29) * update icepack and pointer * update icepack and revert gitmodules * 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 * update icepack * update icepack * add memory profiling (NOAA-EMC#36) * add profile_memory calls to CICE cap * update icepack * fix rhoa when lowest_temp is 0.0 * provide default value for rhoa when imported temp_height_lowest (Tair) is 0.0 * resolves seg fault when frac_grid=false and do_ca=true * update icepack submodule * Update CICE for latest Consortium master (NOAA-EMC#38) * Implement advanced snow physics in icepack and CICE * Fix time-stamping of CICE history files * Fix CICE history file precision * Use CICE-Consortium/Icepack master (NOAA-EMC#40) * switch to icepack master at consortium * recreate cap update branch (NOAA-EMC#42) * add debug_model feature * add required variables and calls for tr_snow * remove 2 extraneous lines * remove two log print lines that were removed prior to merge of driver updates to consortium * duplicate gitmodule style for icepack * Update CICE to latest Consortium/main (NOAA-EMC#45) * Update CICE to Consortium/main (NOAA-EMC#48) Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics. Refactored eap puny/pi lookups to improve scalar performance Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp Update for sea bed stress calculations * fix comment, fix env for orion and hera * replace save_init with step_prep in CICE_RunMod * fixes for cgrid repro * remove added haloupdates * baselines pass with these extra halo updates removed * change F->S for ocean velocities and tilts * fix debug failure when grid_ice=C * compiling in debug mode using -init=snan,arrays requires initialization of variables * respond to review comments * remove inserted whitespace for uvelE,N and vvelE,N * Add wave-cice coupling; update to Consortium main (NOAA-EMC#51) * add wave-ice fields * initialize aicen_init, which turns up as NaN in calc of floediam export * add call to icepack_init_wave to initialize wavefreq and dwavefreq * update to latest consortium main (PR 752) * add initializationsin ice_state * initialize vsnon/vsnon_init and vicen/vicen_init * Update CICE (NOAA-EMC#54) * update to include recent PRs to Consortium/main * fix for nudiag_set allow nudiag_set to be available outside of cesm; may prefer to fix in coupling interface * Update CICE for latest Consortium/main (NOAA-EMC#56) * add run time info * change real(8) to real(dbl)kind) * fix syntax * fix write unit * use cice_wrapper for ufs timer functionality * add elapsed model time for logtime * tidy up the wrapper * fix case for 'time since' at the first advance * add timer and forecast log * write timer values to timer log, not nu_diag * write log.ice.fXXX * only one time is needed * modify message written for log.ice.fXXX * change info in fXXX log file * Update CICE from Consortium/main (NOAA-EMC#62) * Fix CESMCOUPLED compile issue in icepack. (CICE-Consortium#823) * Update global reduction implementation to improve performance, fix VP bug (CICE-Consortium#824) * Update VP global sum to exclude local implementation with tripole grids * Add functionality to change hist_avg for each stream (CICE-Consortium#827) * Update Icepack to #6703bc533c968 May 22, 2023 (CICE-Consortium#829) * Fix for mesh check in CESM driver (CICE-Consortium#830) * Namelist option for time axis position. (CICE-Consortium#839) * reset timer after Advance to retrieve "wait time" * add logical control for enabling runtime info * remove zsal items from cap * fix typo --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>
Includes thin ice enthalpy fix, not bit-for-bit.
* Update cheyenne and derecho ports cheyenne_intel updated to intel/19/1/1, mpt/2.25 cheyenne_gnu updated to gnu/8.3.0, mpt/2.25 cheyenne_pgi updated to pgi/19.9, mpt/2.22 derecho_intel minor updates derecho_intelclassic added derecho_inteloneapi added (not working) derecho_gnu added derecho_cray added derecho_nvhpc added cheyenne_pgi changed answers derecho_inteloneapi is not working, compiler issues fixes automated qc testing on cheyenne * Update permissions on env.chicoma_intel
Update License and Copyright Update Icepack for version/copyright
* Modified doc to specify that l_fixed_area is T for C-grid * Initial modifs to calc areafact based on linear interpolation of left and rigth values * put back l_fixed_area = .true. for C-grid * added temporary comments for PR review * Modified areafac calc for case 1 and case 2 * Corrected minor compilation issues * Corrected conditions for case 1 to make sure areas add up * Small modif in l_fixed_area section to ensure only one condition is true * Modified conditions in locate triangle to be consistent with previous changes for case 1 * Use other edge areafac_c for TL, BL, TR and BR triangles * Some comments removed * Fixed out of bounds areafac_ce and now use earea and narea * Replaced ib,ie,jb,je in locate_triangle using ilo,ihi,jlo,jhi * Modified areafac for TL1, BL2, TR1 and BR2 for area flux consistency * Cosmetic changes * Added comment to explain latest change * Modification of bugcheck condition for l_fixed_area=T * update areafac_c, areafac_ce in halo in dynamics --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com>
…um#875) * Added code for transport in one grid cell wide channels * Update remap advection to support transport in single gridcell channels Add single grid east and north channel configurations and tests * Update documentation * Remove temporary code comments --------- Co-authored-by: Jean-Francois Lemieux <jean-francois.lemieux@canada.ca>
* Update CICE to run with eclare108213/Icepack branch snicar (CICE-Consortium#100) * Update CICE to run with eclare108213/Icepack branch snicar - including eclare108213/Icepack#13, Sept 11, 2022 - Passes full CICE test suite on cheyenne with 3 compilers except alt04 changes answers for all compilers and all tests. CICE #fea412a55f was baseline. - Icepack submodule still points to standard version on main, need to be swapped manually to appropriate development version. * Remove faero_optics * update ciceexe string to account for USE_SNICARHC CPP * Update documentation * Update test suite to add modal testing * Point Icepack submodule to cice-consortium/E3SM-icepack-initial-integration Update to snicar branch merge, #8aef3f785ce * Add E3SM namelists for CICE. (CICE-Consortium#101) * New e3sm and e3smbgc namelist options * Update E3SM test options * Add a simple e3sm test suite * atmbndy is not actually different * Additional changes * add Tliquidus_max namelist parameter to CICE * Add Tf argument to icepack interfaces * Add constant option for tfrz_option * Fix some diagnostic prints and add to additional drivers * Update messages and change option in alt01 * Update implementation for latest version of Icepack - Update tfrz_option, add _old options for backwards bit-for-bit - Fix unittests - Add hi_min to namelist and tests * Update Icepack * Update to E3SM-Project/Icepack/cice-consortium/E3SM-icepack-initial-integration including Icepack1.3.3 release, Dec 15, 2022. * Update Icepack to E3SM-Project/Icepack #87db73ba6d93747a9, current head of cice-consortium/E3SM-icepack-initial-integration Feb 3, 2023 * Update boxchan1e and boxchan1n tests to tfrz_option = 'mushy_old' to recover Consortium main results Update Icepack to the latest hash on E3SM-Project Icepack cice-consortium/E3SM-icepack-initial-integration, #96f2fc707fc743d7 Prior commit was a merge from CICE Consortium Main, #d466031001cf447bcd64220c842dcd2707f61e9, Sept 29, 2023 * remove icepack * update icepack --------- Co-authored-by: David A. Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov>
…is (CICE-Consortium#883) changes answers for some test cases, as expected. Update tfrz_option implementation to not allow _old options.
…-Consortium#886) Update Icepack to version #0c548120ce44382 Oct 16, 2023 includes NO_SNICARHC
Update documentation
…nsortium#931) Update PULL_REQUEST_TEMPLATE to request detailed information about changes associated with the PR. This will be useful for the commit log when squash merging the PR. --------- Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com>
…nsortium#934) In the "End-To-End Testing Procedure" section of the user guide, we instruct users to run a base suite and a test suite, but only mention checking the results of the test suite. Also mention checking the results of the base suite first, to make sure everything passes before checking the test suite. Suggested-by: Jean-Francois Lemieux <jean-francois.lemieux@canada.ca>
This provides new features for CICE IO both thru netCDF and PIO. New namelist are added to control history and restart format, hdf5 compression and chunking, the PIO rearranger, and PIO IO task control. Separate controls are provided for history and restart files. The namelist changes are for _history_format, restart_format history_rearranger, restart_rearranger history_iotasks, history_root, history_stride, restart_iotasks, restart_root, and restart_stride history_chunksize, history_deflate, restart_chunksize, restart_deflate._ In particular, - Update restart_format and history_format options to 'cdf1', 'cdf2', 'cdf5', 'hdf5', 'pnetcdf1', 'pnetcdf2', 'pnetcdf5', 'default'. The old options, 'default', 'pio_netcdf', and 'pio_pnetcdf' are still supported and backwards compatible with lcdf64, but are deprecated and no longer documented. The old options and old namelist lcdf64 are covered by the new options. Support of the old options should be removed in the future. Note that some problems were discovered when opening files with hdf5 format but reading non-hdf5 files with a spack built PIO/netCDF. As a result, the format specified for the restart read is always 'cdf1' which provides flexibility and robustness across software installs, although it may result in serial reads of hdf5 files when a parallel read could be done. - Deprecate lcdf64 namelist. This namelist is no longer needed and is covered by the new restart_format and history_format options. The namelist still exists and is backwards compatible with the old 'default', 'pio_netcdf', and 'pio_pnetcdf' format options, but is no longer documented. This should be removed in the future. - Add new namelist to control PIO pe/task setup (iotasks, root, stride) for history and restart. These settings control the PIO IO tasks. The root, stride, and iotasks are consistent with the MPI communicator. root=0 is the first MPI task. These control PIO IO performance and are usually a function of things like the IO and node hardware. See PIO for more information. CICE computes PIO iotask, root, and stride defaults for cases where -99 is passed in for some or all of these namelist. Those defaults are somewhat constrained by a bug in PIO, NCAR/ParallelIO#1986. The current implementation avoids the bug by limiting the iotasks for some MPI task counts. This is noted in ice_pio.F90. - Add new namelist to control PIO rearranger (rearranger) for history and restart. Supports 'box', 'subset', and 'default'. These control how PIO rearrangment is carried out. default is equivalent to box and the box generally performs better. See PIO for more information. - Add new namelist to support hdf5 compression and chunking (deflate, chunksize) for history and restart. The deflate controls file compression and is an integer between 0 and 9 where 0 means no compression and 9 is maximum compression. Generally, the higher the number, the slower the IO and the smaller the file, but the optimal setting depends on the contents of the file. Chunksize provides a performance control for the hdf5 parallel writes. It is a 2d array and is associated with the size of the piece of the array written by hdf5. hdf5 can be read and written in parallel, but that depends on how netCDF and PIO are built. Note that prior version of PIO, including PIO1, do not support the hdf5 compression and chunking thru the PIO interface. - Add new namelist settings (set_nml files) and update the io_suite to cover the new IO options. Remove old namelist settings associated with the deprecated format options and the lcdf64 namelist. These deprecated feature are no longer tested. - Update documentation to add new namelist and IO features. - Update the nuopc/cmeps driver code to support the new features. - Update the default ice_in to add the new namelist. - Update the derecho netcdf module to a version that supports hdf5. - Clean up some code formatting (indentation) --------- Co-authored-by: Anton Steketee <anton.steketee@anu.edu.au>
* ice_history_shared: add namelist flags for coordinate variables
Users might not wish for all 8 coordinate variables to be written to
each history file, so add namelist flags allowing to disable each
coordinate variable independantly, following the approach used for the
other grid variables. Move the definition of 'ncoord' from each IO
backend to 'ice_history_shared'. Note that we already 'use' the whole of
ice_history_shared in ice_history_write, so we do not need to adjust the
use statement.
Note that the code that writes these variables in module
'ice_history_write' in each of the IO backends is not modified, it will
be adjusted in a following commit.
* io_{netcdf,pio2}/ice_history_write: define coordinates attributes in a loop
In ice_history_write::ice_write_hist, we initialize the 'var_coord' and
'coord_bounds' arrays by manually incrementing 'ind' and initializing
each elements with the corresponding information for each coordinate
variable. The rest of the code in that subroutine instead uses a loop on
'ncoord', which is a parameter holding the number of coordinates
variable, along with 'select' statements.
The latter approach is more elegant and also more flexible if we change
the number of coordinates variables. Refactor the code to use a loop and
leverage the integers n_{u,t,n,e}{lon,lat} added in the previous commit,
in both io_netcdf and io_pio2, which have identical code in this part of
the subroutine.
* io_{netcdf,pio2}/ice_history_write: use namelist flags for coordinate variables
In order to enable the namelist flags for each coordinate variables
added in the previous commit, adjust the code of the io_netcdf and
io_pio2 backends by checking the value of 'icoord(i)' for each loop on
'ncoord' that calls NetCDF or PIO functions.
Add the new flags to the reference namelist.
For CESMCOUPLED, the pio_iotype is set though CMEPS. For completeness, we also need to check the ioformat set through CMEPS. ioformat is used to set the nmode0. nmode0 and clobber combine to set the nmode flag for pio_createfile / pio_openfile operations. Due a typo nmode0 was not being set for netcdf4 iotypes (before this change).
Set idate0 in nuopc cap, so that the history "time:units" attribute in netcdf output is consistent with other model components. Set use_leap_years in nuopc cap, so that netcdf output "time:calendar" is set correctly in history output Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Port CICE to Carpenter for intel, cray, and gnu compilers with mpich. Will add weekly testing on Carpenter, Onyx was recently decommissioned. During development, - It was discovered that the serial compilers and parallel compilers produce different results. This was reported to sys admins. Serial compilation is done with the parallel compilers to ensure bit-for-bit results with serial and mpi comm versions. - It was discovered that the openmpi and intel mpi options are not working properly. This was reported to sys admins. All testing is done with mpich for now.
* Add dvsdtd diagnostic for SIMIP sndmassdyn * Fix the units of SIMIP snow variables * Fix calls to update_state * Add present for dagedt and fix indents * This PR has been updated to include dvsdtt (thermodynamic tendency for snow). Also, the calls to update_state have been updated in all of the drivers. Note that I can only test the NUOPC/CMEPS and standalone drivers, so it would be good if others could test. * Update the opticep unit test to be consistent with the latest changes. --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com>
…E-Consortium#943) Add checks that individual history streams have unique filenames. If they do not, then streams will overwrite each other. With this change, abort in that case. Added in ice_history_shared.F90, subroutine construct_filename. The implementation tracks the latest filenames for each stream and checks versus those names. Because the file naming convention relies heavily on the current model date/time, this should be adequate (versus keeping track of all history filenames ever used). Updated the cstream string in subroutine construct_filename. It was hardwired to len=1 which probably was an error. Made it len=char_len to support longer hist_suffix character strings in filenames. Updated the ncfile variable implementation in ice_write_hist in io_binary, io_netcdf, and io_pio2. It was defined as an array of length max_nstrm, and was changed to a non-array character string. The array implementation served no purpose. Modified the set_nml.histinst to add hist_suffix values for each stream. The latest code modifications cause The current test suite to fail with "histall,histinst" because it creates multiple streams with the same filename. Setting hist_suffix for histinst fixes this (and tests hist_suffix). Clean up abort calls in ice_history_shared.F90, add space before "ERROR:". Update the documentation describing history streams. Some "_" formatting was changed to simply "_" where the backslash wasn't needed in ug_implementation.rst. Several namelist settings were tested to make sure the model would abort with identical filenames including the case where a time averaged file with output at each timestep conflicts with an instantaneous history stream of lower output frequency.
) (CICE-Consortium#944) * fix dummy arguments w/o values * fix missing j-loop in export 4d Resolve compiler warning arising from ice_prescribed_mod due to the intent(out) variable RC not being given an explicit value. This is an operational requirement for NOAA. Fix bug arising from missing j-loop index in ice_import_export
Github Actions broke again after default macos system update. Clang was not picking up the C system files. Had to change the implementation and add -isysroot to the CFLAGS option. At the same time, removed prior implementation where the system files were linked into /usr/local/include, this was no longer working.
Add standalone build config for gadi supercomputer --------- Co-authored-by: Anton Steketee <anton-seaice@noreply.users.github.org>
This change allows nprocs to be set to -1 in 'ice_in' and then the number of processors will be automatically detected. This change improves the automatic calculation of max_blocks to give a better (but still not foolproof) estimate of max_blocks if it is not set in ice_in.
…ium#953) Update the calculation of uvel and vvel in subroutine evp in file ice_dyn_evp.F90. Do an unmasked grid_average_X2Y when averaging from uvelE to uvel and from vvelN to vvel instead of a masked average. The masking is handled separately. This change is bit-for-bit and saves a few flops. Closes CICE-Consortium#952. Update the documentation to add the hemispheric sign dependence in the water stress terms in the dynamics equations. Closes CICE-Consortium#951.
Update version number to 6.5.1 in preparation for release Update copyright date and LICENSE.pdf
Update support for max_blocks=-1. This update computes the blocks required on each MPI task and then sets that as max_blocks if max_blocks=-1 in namelist. This is done in ice_distribution and is a function of the decomposition among other things. Refactor the decomposition computation to defer usage of max_blocks and eliminate the blockIndex array. Update some indentation formatting in ice_distribution.F90. Modify cice.setup and cice_decomp.csh to set max_blocks=-1 unless it's explicitly defined by the cice.setup -p setting. Fix a bug in ice_gather_scatter related to zero-ing out of the halo with the field_loc_noupdate setting. This was zero-ing out the blocks extra times and there were no problems as long as max_blocks was the same value on all MPI tasks. With the new implementation of max_blocks=-1, max_blocks can be different values on different MPI tasks. An error was generated and then the implementation was fixed so each block on each task is now zeroed out exactly once. Update diagnostics related to max_block information. Write out the min and max max_blocks values across MPI tasks. Add extra allocation/deallocation checks in ice_distribution.F90 and add a function, ice_memusage_allocErr, to ice_memusage.F90 that checks the alloc/dealloc return code, writes an error message, and aborts. This function could be used in other parts of the code as well. Fix a bug in the io_binary restart output where each task was writing some output when it should have just been the master task. Update test cases Update documentation
These changes are associated with the multi-machine pre-release testing for CICE. Update Hera port, new compiler version Add NO_CDF2, NO_CDF5, and NO_HDF5 CPP options to model to support older/other versions of netcdf. Several machines with only netcdf 4.4 do not support cdf5 format. Sometimes netcdf is not built with hdf5. We need a CPP to avoid that part of the code to allow the model to build on those machines. Set NO_CDF5 for gaffney, koehr, mustang machines Set NO_HDF5 for compy Update documentation
This only impacts single column CAM (CESM) runs.
…CE-Consortium#958) Update CICE plotting tools. Add ciceplots.csh and ciceplots2d.py. Update timeseries.py. Remove timeseries.csh. Have the plotting tools copied into case directories. Update documentation. ciceplots2d.py generates global and polar plots for fields on CICE history files. ciceplots.csh is a general script that calls timeseries.py and ciceplots2d.py to generate plots for a user defined case. Add basemap to the cice conda environment.yml file to support the plotting packages. Add output to JRA55_files in ice_forcing.F90 to make it easier to understand when/why JRA55 files are missing. Add NO_CDF5 CPP to izumi_nag Macros file. Change 10 year production test case to 8 year test. This will serve as basis for release results. Update Icepack to #083d6e3cf42198 from May 28, 2024. Includes updates to Icepack plotting tools.
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@NickSzapiro-NOAA Please create the associated issue w/ the upstream PRs that are being merged. |
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Merge CICE-Consortium/main into emc/develop (Sync and merge with Consortium/main (2024-09-01) #82)
Nicholas Szapiro
TODO
This is a git merge of CICE-Consortium/main into emc/develop with conflict resolved. The shared history then simplifies code management and pushing contributions back. For example, diffs to CICE-Consortium/main now show only new features added to emc/develop like ice prescribed cice for UFS