Update PULL_REQUEST_TEMPLATE to request detailed information #931
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Please let me know if you prefer different wording. Once we converge on changes to the template, I'll do the same for Icepack. |
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Co-authored-by: Philippe Blain <[email protected]>
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…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 <[email protected]>
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commit f36559256eb08272cdfe0706c45e0824e00fb37b Author: Denise Worthen <[email protected]> Date: Sun Apr 7 09:50:39 2024 -0400 fix bad merge * this fixes a block of code w/in a CESMCOUPLED ifdef block commit cbac04dad1f79eb51900dab8bf6aaa7cddbe82a1 Merge: 5a56c38 7d4e5de Author: Denise Worthen <[email protected]> Date: Wed Apr 3 16:05:31 2024 -0400 Merge branch 'emc/develop' into feature/pio_options commit 5a56c38a0d73bf16ddf2024a23f3f3fe4432007a Author: Denise Worthen <[email protected]> Date: Wed Apr 3 15:44:33 2024 -0400 update with last emc/develop change commit aca835755aa82ead50040ea7e43ec63619667054 Author: Tony Craig <[email protected]> Date: Thu Feb 22 08:55:44 2024 -0800 Update IO formats and add new IO namelist controls (#928) 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, https://github.com/NCAR/ParallelIO/issues/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 <[email protected]> commit 9e9e5b3fabd88c429c4632baa8235187129e2dd7 Author: Philippe Blain <[email protected]> Date: Mon Feb 19 14:08:37 2024 -0500 ug_testing.rst: also mention checking the base suite results (#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 <[email protected]> commit 095e62a9342df74261b90fcb7a20d2ecdae2c5bc Author: Tony Craig <[email protected]> Date: Mon Feb 12 14:49:02 2024 -0800 Update PULL_REQUEST_TEMPLATE to request detailed information (#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 <[email protected]> commit 1a00e5e4e967c8429a7753ac3597f9c1476cf6b7 Author: David A. Bailey <[email protected]> Date: Mon Feb 5 16:22:11 2024 -0700 Fix for ice_mesh_mod with grid variables removed (#929) commit 7a4b95e6deec0ec72c1da35a23ae1eb3ffe3d077 Author: Tony Craig <[email protected]> Date: Mon Jan 22 11:12:13 2024 -0800 Update pio and netcdf error checks (#927) Update pio and netcdf error checks --------- Co-authored-by: anton-climate <[email protected]> Co-authored-by: Anton Steketee <[email protected]> commit 6449f40c41aa1a5c00096696202d7bd7ebd2a69a Author: JFLemieux73 <[email protected]> Date: Thu Jan 11 19:17:20 2024 +0000 Add vorticity as a diagnostic output (#924) * Added new variable vort for vorticity output * Added calc of diag vorticity for evp, vp and eap for B, C and CD grids * updated doc and ice_in file for new vorticity variable * Changed output frequency of vorticity from m to x * Added f_vort to set_nml.histall and set_nml.histdbg * Specified location of divu, shear and vort in ice_history.F90 --------- Co-authored-by: Tony Craig <[email protected]> commit a20bfddf7a1260dbb61241e0838c678d2eecf972 Author: David A. Bailey <[email protected]> Date: Thu Jan 11 11:07:36 2024 -0700 scamn bugfix for nuopc driver (#926) Co-authored-by: John Truesdale <[email protected]> commit 1314e17b4213c6ce9424eab80763edf4b2ae867f Author: TRasmussen <[email protected]> Date: Thu Jan 11 18:25:52 2024 +0100 First round of housekeeping on ice_grid (#921) * removal of unused variables. * moved xav to transport. Could remove commented code. Could remove xav and yav as they are zero * Move derived parameters and only allocate if needed * bugfixes for cxp, cyp... * fix index and remove commented code in ice_grid * new version of transport_remap. xav, yav array where needed. xxav, yyav parameter * Removed comments rom ice_transport_remap and arrays for nonuniform grids commit 37f9a98b1b6529bc957fb888bd00348ab61c8b32 Author: Tony Craig <[email protected]> Date: Thu Dec 21 07:15:02 2023 -0800 Fix single channel debug failure, Update github actions testing (#922) * update ghactions testing * refactor min/max global reductions, code away from huge which was giving MPI some problems. commit b14cedfaed8b81500fc5422cfc44b6d80e5893ef Author: David A. Bailey <[email protected]> Date: Tue Nov 28 15:10:16 2023 -0700 ice_history: allow per-stream suffix for history filenames (#912) * Add capability for h extension * Update documentation for hist_str * Change hist_str to hist_suffix * Change in default namelist * Update doc/source/cice_index.rst Co-authored-by: Philippe Blain <[email protected]> * One more hist_str --------- Co-authored-by: Philippe Blain <[email protected]> commit 21fab166fd2b8e903df366dbc1c518dabd08c23f Author: Tony Craig <[email protected]> Date: Tue Nov 28 10:04:36 2023 -0800 Update Icepack to #f6ff8f7c4d4cb6f (#913) * Update Icepack to #f6ff8f7c4d4cb6f Split the developer guide infrastructure section from the dynamics documentation Add a coding standard section to the documentation Add a couple sentences about the state of the parameter nghost to the documentation Update opticep to use the latest main code for the unit test * update documentation commit 509e2c33e95e3a2370dc406fb2fe4d06192420a6 Author: Philippe Blain <[email protected]> Date: Thu Nov 23 13:09:04 2023 -0500 ice_history: refactor CMIP history variables (#906) * ice_flux: zero-initialize divu and shear in init_history_dyn 'divu' and 'shear' are accessed in 'accum_hist' when writing the initial condition before they are initialized at the start of {eap, evp, implicit_solver}. This leads to runtime error when compiling with NaN initialization. Zero-initialize 'divu' and 'shear' in init_history_dyn, where the related variable 'strength' is already zero-initialized. * ice_history_shared: disallow 'x' in history frequency variables f_*' In the current code, nothing prevents users from leaving 'x' along with active frequencies in the individual namelist history frequency variables, for example: f_aice = 'xmd' This configuration does not work correctly, however. The corresponding history fields are correctly defined in ice_history_shared::define_hist_field, but since the calls to ice_history_shared::accum_hist_field in ice_history::accum_hist are only done after checking that the first element of each frequency variable is not 'x', the corresponding variables in the history files are all zero. Prevent that behaviour by actually disallowing 'x' in history frequency variables if any other frequencies are active. To implement that, add a check in the loop in define_hist_field, which loops through vhistfreq, (corresponding to f_aice, etc. in ice_history). Since this subroutine initializes 'id(:)' to zero and then writes a (non-zero) index in 'id' for any active frequency, it suffices to check that all previous indices are non-zero. * ice_history: remove uneeded conditions around CMIP history variables In ice_history::accum_hist, after the calls to accum_hist, we loop on the different output streams, and on the history variables in the avail_hist_fields array, to mask out land points and convert units for each output variable. Since 3c99e106 (Update CICE with CMIP changes. (#191), 2018-09-27), we also use this loop to do a special treatment for some CMIP variables (namely, averaging them only for time steps where ice is present, and masking points where ice is absent). This adjustment is done if the corresponding output frequency variable (f_sithick, etc.) does not have 'x' as its first element, and if the corresponding index in avail_hist_field for that variable/frequency (n_sithick(ns)) is not zero. Both conditions are in fact uneeded since they are always true. The first condition is always true because if the variable is found in the avail_hist_field array, which is ensured by the condition on line 3645, then necessarily its corresponding namelist output frequency won't have 'x' as its first character (since this is enforced in ice_history_shared::define_hist_field). The second condition is always true because if the variable is found in the avail_hist_field array, then necessarily its index in that array, n_<var>(ns), is non-zero (see ice_history_shared::define_hist_field). Remove these uneeded conditions. This commit is best viewed with git show --color-moved --color-moved-ws=allow-indentation-change * ice_history: use loop index directly for CMIP variables In ice_history::accum_hist, there is a special treatment for some CMIP variables where they are averaged only for time steps where ice is present, and points where there is no ice are masked. This is done on the loop on output streams (with loop index n). This special averaging is done by accessing a2D and a3Dc using the variable n_<var>(ns), which corresponds to the index in the avail_hist_field array where this history variable/frequency is defined. By construction, this index correponds to the loop index 'n', for both the 2D and the 3D loops. Simplify the code by using 'n' directly. * ice_history_shared: add two logical components to ice_hist_field At the end of ice_history::accum_hist, we do a special processing for some CMIP variables: we average them only for time steps where ice is present, and also mask ice-free points. The code to do that is repeated for each variable to which it applies. In order to reduce code duplication, let's introduce two new logical components to our 'ice_hist_field' type, defaulting them to .false., and make them optional arguments in ice_history_shared::define_hist_field. This allows us to avoid defining them for each output variable. We'll set them for CMIP variables in a following commit. * ice_history: set avg_ice_present, mask_ice_free_points for relevant CMIP variables In the previous commit, we added two components to type ice_hist_field (avg_ice_present and mask_ice_free_points), relating to some special treatment for CMIP variables (whether to average only for time steps where the ice is present and to mask ice-free points). Set these to .true. in the call to 'define_hist_field' for the relevant 2D variables [1], and set only 'avg_ice_present' to .true. for the 3D variables siitdthick and siitdsnthick, corresponding to the code under the "Mask out land points and convert units" loop in ice_history::accum_hist. [1] sithick siage sisnthick sitemptop sitempsnic sitempbot siu siv sidmasstranx sistrxdtop sistrydtop sistrxubot sistryubot sicompstren sispeed sidir sialb sihc siflswdtop siflswutop siflswdbot sifllwdtop sifllwutop siflsenstop siflsensupbot sifllatstop siflcondtop siflcondbot sipr sifb siflsaltbot siflfwbot siflfwdrain sidragtop sirdgthick siforcetiltx siforcetilty siforcecoriolx siforcecorioly siforceintstrx siforceintstry * ice_history: use avg_ice_present, mask_ice_free_points to reduce duplication Some CMIP variables are processed differently in ice_history::accum_hist: they are averaged only for time steps when ice is present, and points where ice is absent are masked. This processing is repeated for each of these variables in the 2D and 3Dc loops. To reduce code duplication, use the new components avg_ice_present and mask_ice_free_points of ice_hist_field to perform this processing only for variables that were defined accordingly. The relevant variables already have those components defined as of the previous commit. Note that we still need a separate loop for the variable 'sialb' (sea ice albedo) to mask points below the horizon. commit 1cf109b7c350f119e8e3cd8bd918fa31e61d829c Author: David A. Bailey <[email protected]> Date: Mon Nov 20 14:03:59 2023 -0700 Change to dealloc_grid in CICE_InitMod.F90 (#911) commit d14bb694f2f8df4e74361a9df999e82eaa44fc8b Author: Mads Hvid Ribergaard <[email protected]> Date: Fri Nov 17 16:39:01 2023 +0100 Add missing logical "timer_stats" (#910) Co-authored-by: Mads Hvid Ribergaard <[email protected]> commit 8573ba8ab196c1e357a101462b16bd92128461b1 Author: TRasmussen <[email protected]> Date: Thu Nov 16 22:12:07 2023 +0100 New 1d evp solver (#895) * New 1d evp solver * Small changes incl timer names and inclued private/publice in ice_dyn_core1d * fixed bug on gnu debug * moved halo update to evp1d, added deallocation, fixed bug * fixed deallocation dyn_evp1d * bugfix deallocate * Remove gather strintx and strinty * removed 4 test with evp1d and c/cd grid * Update of evp1d implementation - Rename halo_HTE_HTN to global_ext_halo and move into ice_grid.F90 - Generalize global_ext_halo to work with any nghost size (was hardcoded for nghost=1) - Remove argument from dyn_evp1d_init, change to "use" of global grid variables - rename pgl_global_ext to save_ghte_ghtn - Update allocation of G_HTE, G_HTN - Add dealloc_grid to deallocate G_HTE and G_HTN at end of initialization - Add calls to dealloc_grid to all CICE_InitMod.F90 subroutines - Make dimension of evp1d arguments implicit size more consistently - Clean up indentation and formatting a bit * Clean up trailing blanks * resolved name conflicts * 1d grid var name change --------- Co-authored-by: apcraig <[email protected]> commit 5d09123865b5e8b47ba9d3c389b23743d84908c1 Author: Mads Hvid Ribergaard <[email protected]> Date: Fri Nov 10 01:17:24 2023 +0100 Rename sum to asum, as "sum" is also a generic fortran function (#905) Co-authored-by: Mads Hvid Ribergaard <[email protected]> commit 4450a3e8c64bc07d1173eb3e341cd8dea91d5068 Author: Tony Craig <[email protected]> Date: Fri Oct 27 22:22:43 2023 -0700 Update Icepack to latest version, does not affect CICE (#903) commit ea241fa81a53b614f54cf5c2dad93bda20b72a78 Author: Tony Craig <[email protected]> Date: Fri Oct 27 16:27:15 2023 -0700 Update version, remove trailing blanks (#901) commit 32f233d9728b4e453c0f02fb79a188517a8d5ed4 Author: Tony Craig <[email protected]> Date: Fri Oct 27 16:27:01 2023 -0700 Update Icepack, add snicar and snicartest tests (#902) commit 0484dcd1410920f26375b7c280500a5bd16173e9 Author: Tony Craig <[email protected]> Date: Fri Oct 27 09:24:52 2023 -0700 Split N/E grid computation out of Tlonlat, create NElonlat subroutine. (#899) * Split N/E grid computation out of Tlonlat, create NElonlat subroutine. See https://github.com/CICE-Consortium/CICE/issues/897 When TLON, TLAT, ANGLET are on the CICE grid, Tlonlat is NOT called. This meant N and E grid info was never computed. This would fail during history writing with invalid values in N and E grid arrays. And it would also cause problem if the C-grid were run with this type of CICE grid. There are no test grids that have TLON, TLAT, ANGLET on them, so this error was not found in standard test suites. This was detected by users. * Add gx3 grid/kmt files with TLON, TLAT, ANGLET netcdf grid test. The grid and kmt files were produced from a gx3 history file. Results are not bit-for-bit with the standard gx3 runs, but seem to be roundoff different initially (as expected). commit 0b5ca0911edaf6081ba891f4287af14ceb201c9f Author: Tony Craig <[email protected]> Date: Thu Oct 26 19:33:19 2023 -0700 Revert "Add 5-band dEdd shortwave tests (#896)" (#900) This reverts commit b4abca479cd548c3e600a6c645447d5ba9464422. commit 2e13606558f7ce71633274bc38630caa23de3392 Author: Philippe Blain <[email protected]> Date: Thu Oct 26 13:24:37 2023 -0400 doc: update histfreq_base and hist_avg descriptions (#898) * doc: ug_implementation.rst: do not use curly quotes The namelist excerpt in section 'History' of the Implementation part of the user guide uses curly quotes (’) instead of regular straight quotes ('). This is probably a remnant of the LaTeX version of the doc. These quotes can't be used in Fortran and so copy pasting from the doc to the namelist causes runtime failures. Use straigth quotes instead. * doc: ug_implementation.rst: align histfreq_n with histfreq Align frequencies with their respective streams, which makes the example clearer. * doc: ug_implementation.rst: avoid "now" and "still" The documentation talks about the current version of the code, so it is unnecessary to use words like "now" and "still" to talk about the model features. Remove them. * doc: ug_implementation.rst: mention histfreq_base and hist_avg are per-stream In 35ec167d (Add functionality to change hist_avg for each stream (#827), 2023-05-17), hist_avg was made into an array, allowing each stream to individually be set to instantaneous or averaged mode. The first paragraph of the "History" section of the user guide was updated, but another paragraph a little below was not. In 933b148c (Extend restart output controls, provide multiple frequency options (#850), 2023-08-24), histfreq_base was also made into an array, but the "History" section of the user guide was not updated. Adjust the wording of the doc to reflect the fact that both hist_avg and histfreq_base are per-stream. Also adjust the namelist excerpt to make histfreq_base an array, and align hist_avg with it. * doc: ug_implementation.rst: refer to 'timemanager' after mentioning histfreq_base In 34dc6670 (Namelist option for time axis position. (#839), 2023-07-06), the namelist option hist_time_axis was added, and the "History" section of the user guide updated to mention it. The added sentence, however, separates the mention of 'histfreq_base' and the reference to the "Time manager" section, which explains the different allowed values for that variable. Move the reference up so both are next to each other. commit b4abca479cd548c3e600a6c645447d5ba9464422 Author: Tony Craig <[email protected]> Date: Thu Oct 26 08:54:40 2023 -0700 Add 5-band dEdd shortwave tests (#896) commit 624c28b19b443c031ea862e3e5d2c16387777ddc Author: Philippe Blain <[email protected]> Date: Thu Oct 26 11:52:26 2023 -0400 ice_dyn_evp: pass 'grid_location' for LKD seabed stress on C grid (#893) When the C grid support was added in 078aab48 (Merge cgridDEV branch including C grid implementation and other fixes (#715), 2022-05-10), subroutine ice_dyn_shared::seabed_stress_factor_LKD gained a 'grid_location' optional argument to indicate where to compute intermediate quantities and the seabed stress itself (originally added in 0f9f48b9 (ice_dyn_shared: add optional 'grid_location' argument to seabed_stress_factor_LKD, 2021-11-17)). This argument was however forgotten in ice_dyn_evp::evp when this subroutine was adapted for the C grid in 48c07c66 (ice_dyn_evp: compute seabed stress factor at CD-grid locations, 2021-11-17), such that currently the seabed stress is not computed at the correct grid location for the C and CD grids. Fix that by correctly passing the 'grid_location' argument. Note that the dummy argument is incorrectly declared as 'intent(inout)' in the subroutine, so change that to 'intent(in)' so we can pass in character constants. Closes: https://github.com/CICE-Consortium/CICE/issues/891 commit d3698fb46fc23a81b1df8dba676a5a74d7e96a39 Author: daveh150 <[email protected]> Date: Wed Oct 25 16:34:35 2023 -0500 Add atm_data_version to allow JRA55 forcing filenames to have a unique version string (#876) * Add jra55date to allow JRA55 forcing to have creation date in file name * Changed jra55_date to atm_data_date. Added atm_data_date to docs. * Change jra55_date to atm_data_date. Update JRA55_files to include atm_data_date in file. Update case scripts/namelist. * change atm_data_date to atm_data_version. Update set_nml.tx1 default to corrected forcing version * Update doc to have atm_data_version in proper alphabetical order * Re-add set_nml.jra55. Deleted accitentally * Fix type-o in atm_data_dir documentation * Add atm_data_version to set_nml.jra55 * fix spacing after changing atm_data_date to atm_data_version * Change atm_data_date to atm_data_version * Comment out JRA55 file debugging * Update dg_forcing docs to describe atm_data_version string * Uncomment JRA55 filename check. Added check for debug_forcing before writing output * Correct doc format/links in dg_forcing.rst commit 8916b9ff2c58a3a095235bb5b4ce7e8a68f76e87 Author: Tony Craig <[email protected]> Date: Wed Oct 18 14:08:21 2023 -0700 Update update_ocn_f implementation, Add cpl_frazil namelist (#889) * Update update_ocn_f implementation Add cpl_frazil namelist Add update_ocn_f and cpl_frazil to icepack_init_parameters call, set these values inside Icepack at initialization. Remove update_ocn_f argument from icepack_step_therm2 call Update runtime_diags and accum_hist to account for new Icepack and cpl_frazil implementation. These may need an addition update later. * Update documentation commit 6ba070f7e7027f9fd2cc32f2dbe10c9854511d93 Author: Tony Craig <[email protected]> Date: Wed Oct 18 12:35:08 2023 -0700 Update Documentation to clarify Namelist Inputs (#888) * Update Documentation to clarify Namelist Inputs * Update documentation commit a9d6dc75f47a2898f1800ad4ddd96c4992e3bed0 Author: Tony Craig <[email protected]> Date: Wed Oct 18 10:47:01 2023 -0700 Update input data area for Derecho, switch to campaign (#890) commit 5ddb74dfb8724ff90aa7e806d5bfcfb4a0990762 Author: Tony Craig <[email protected]> Date: Wed Oct 18 10:46:40 2023 -0700 Remove cicedynB link (#887) Update documentation commit 96b43fb458fe00696d9532e547a3c5bff113f9f9 Author: Tony Craig <[email protected]> Date: Wed Oct 18 10:46:25 2023 -0700 Update Icepack CPP USE_SNICARHC to NO_SNICARHC and update logic (#886) Update Icepack to version #0c548120ce44382 Oct 16, 2023 includes NO_SNICARHC commit 48a92ef6dd6bf7884ec8a16b2c082345accae385 Author: Tony Craig <[email protected]> Date: Fri Oct 13 14:22:03 2023 -0700 Remove use of the deprecated "_old" tfrz_options in set_nml files. This (#883) changes answers for some test cases, as expected. Update tfrz_option implementation to not allow _old options. commit 276563041ea6a2b6b4c70cbfa5173fb85db7b47f Author: Tony Craig <[email protected]> Date: Thu Oct 12 12:41:17 2023 -0700 Add perlmutter gnu, intel, cray port (#882) commit deb247bcec381615d01006bfa15dddf3a4f068fd Author: Tony Craig <[email protected]> Date: Thu Oct 5 12:50:32 2023 -0700 Update CICE for E3SM Icepack modifications (#879) * Update CICE to run with eclare108213/Icepack branch snicar (#100) * Update CICE to run with eclare108213/Icepack branch snicar - including https://github.com/eclare108213/Icepack/pull/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. (#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 <[email protected]> Co-authored-by: Elizabeth Hunke <[email protected]> commit d466031001cf447bcd64220c842dcd2707f61e90 Author: Tony Craig <[email protected]> Date: Fri Sep 29 12:08:53 2023 -0700 Add single grid channel capability and test for C-grid (#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 <[email protected]> commit 55342ca7cb4a1be511ade6249e349cb8a8095881 Author: Dougie Squire <[email protected]> Date: Tue Sep 26 03:49:09 2023 +1000 Fix mesh mask check in nuopc/cmeps cap (#873) commit a5bb4f9a0c180e325e2a5480832f588dbfdd25ec Author: Denise Worthen <[email protected]> Date: Fri Sep 15 16:01:00 2023 -0400 switch to cesm-style field names (#869) commit 01ed4db7c4e5857768a37e8b1fd7472ab5121827 Author: JFLemieux73 <[email protected]> Date: Fri Sep 15 19:59:55 2023 +0000 More accurate calculation of areafact in remapping (#849) * 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 <[email protected]> commit 06282a538e03599aed27bc3c5506ccc31a590069 Author: Tony Craig <[email protected]> Date: Fri Sep 8 11:26:45 2023 -0700 Update version to 6.4.2 (#864) Update License and Copyright Update Icepack for version/copyright commit 714bab97540e5b75c0f2b6c11cd061277cdb322d Author: Tony Craig <[email protected]> Date: Thu Sep 7 14:20:29 2023 -0700 Update Cheyenne and Derecho ports (#863) * 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 commit cbbac74cd9073dce8eb44fa23cabb573913aa44f Author: David A. Bailey <[email protected]> Date: Tue Sep 5 14:22:59 2023 -0600 Only print messages in CAP on master task (#861) commit 32dc48eae101749b437bd777c18830e3c397b17a Author: Tony Craig <[email protected]> Date: Thu Aug 31 13:05:54 2023 -0700 Update Icepack to #23b6c1272b50d42ca, Aug 30, 2023 (#857) Includes thin ice enthalpy fix, not bit-for-bit. commit e8a69abde90b99fc6528d469b8698506a99f6e2a Author: Denise Worthen <[email protected]> Date: Mon Aug 28 16:00:41 2023 -0400 Add logging features to nuopc/cmeps cap; deprecates zsalinity in cap (#856) * merge latest master (#4) * Isotopes for CICE (#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. (#452) (#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 e70d1abcbeb4351195a2b81c6ce3f623c936426c. * 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 (#8) * cice6 compile (#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 (#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 (#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 (#19) * update icepack * add ice_dyn_vp module to CICE_InitMod * update gitmodules, update icepack * Update CICE to consortium master (#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 (#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 (#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 (#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 (#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 (#40) * switch to icepack master at consortium * recreate cap update branch (#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 (#45) * Update CICE to Consortium/main (#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 (#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 (#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 (#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 (#62) * Fix CESMCOUPLED compile issue in icepack. (#823) * Update global reduction implementation to improve performance, fix VP bug (#824) * Update VP global sum to exclude local implementation with tripole grids * Add functionality to change hist_avg for each stream (#827) * Update Icepack to #6703bc533c968 May 22, 2023 (#829) * Fix for mesh check in CESM driver (#830) * Namelist option for time axis position. (#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]> commit 933b148cb141a16d74615092af62c3e8d36777a2 Author: Tony Craig <[email protected]> Date: Thu Aug 24 10:23:56 2023 -0700 Extend restart output controls, provide multiple frequency options (#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 commit 357103a2df0428089d54bdacf9eab621a5e1f710 Author: Tony Craig <[email protected]> Date: Tue Aug 22 11:27:28 2023 -0700 Deprecate zsalinity (#851) * 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) commit 8322416793ae2b76c2bafa9c7b9b108c289ede9d Author: Elizabeth Hunke <[email protected]> Date: Fri Aug 18 17:34:24 2023 -0600 Updates to advanced snow physics implementation (#852) * 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]> commit 7e8dc5b2aeffe98a6a7fd91dbb8e93ced1e3369c Author: Tony Craig <[email protected]> Date: Thu Aug 10 13:06:41 2023 -0700 Update conda_macos to fix problems with Github Actions testing (#853) * test ghactions * update master to main in github actions commit 4cb296c4003014fe57d6d00f86868a78a532fc95 Author: JFLemieux73 <[email protected]> Date: Tue Jul 25 16:11:33 2023 +0000 Modification of edge mask computation when l_fixed_area=T in horizontal remapping (#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 commit 9f42a620e9e642c637d8f04441bacb5835ebf0b7 Author: Tony Craig <[email protected]> Date: Thu Jul 20 14:59:42 2023 -0700 Update Icepack to Consortium main #4728746, July 18 2023 (#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 commit f9d3002c86e11ca18b06382fc2d0676c9a945223 Author: Tony Craig <[email protected]> Date: Thu Jul 13 16:01:26 2023 -0700 Add support for JRA55do (#843) * 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]> commit 766ff8d9606ae08bdd34ac2b36b6b068464c7e71 Author: Tony Craig <[email protected]> Date: Tue Jul 11 07:53:22 2023 -0700 Update Icepack to #d024340f19676b July 6, 2023 (#841) Remove deprecated COREII LYq forcing Remove deprecated print_points_state Update links in rst documentation to point to main, not master commit 34dc66707f6b691b1689bf36689591af3e8df270 Author: David A. Bailey <[email protected]> Date: Thu Jul 6 21:46:58 2023 -0600 Namelist option for time axis position. (#839) * 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. commit 7eb4dd7e7e2796c5718061d06b86ff602b9d29cc Author: Tony Craig <[email protected]> Date: Tue Jun 20 09:40:55 2023 -0700 Update .readthedocs.yaml, add pdf (#837) * update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf * update readthedocs.yaml, turn on pdf commit 8e2aab217ece5fae933a1f2ad6e0d6ab81ecad8a Author: David A. Bailey <[email protected]> Date: Tue Jun 20 08:54:25 2023 -0600 Fix for mesh check in CESM driver (#830) * 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 commit b98b8ae899fb2a1af816105e05470b829f8b3294 Author: Tony Craig <[email protected]> Date: Wed May 24 09:56:10 2023 -0700 Update Icepack to #6703bc533c968 May 22, 2023 (#829) Remove trailing blanks via automated tool in some Fortran files commit 35ec167dc6beee685a6e9485b8a1db3604d566bd Author: David A. Bailey <[email protected]> Date: Wed May 17 14:56:26 2023 -0600 Add functionality to change hist_avg for each stream (#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 commit 5b0418a9f6d181d668ddebdc2c540566529e4125 Author: Tony Craig <[email protected]> Date: Wed Apr 5 13:29:21 2023 -0700 Update global reduction implementation to improve performance, fix VP bug (#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 commit 942449751275ebd884abb5752d03d7ea64b72664 Author: David A. Bailey <[email protected]> Date: Thu Mar 23 16:46:05 2023 -0600 Fix CESMCOUPLED compile issue in icepack. (#823) * Fix CESMCOUPLED compile problem in icepack
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…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 <[email protected]>
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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.
Closes #930