* 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 <[email protected]>

…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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: apcraig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>

* 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 <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: Minsuk Ji <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>
Co-authored-by: Jun.Wang <[email protected]>

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