sync with the develop branch #13

…leanup (#1355) * point to Man's ccpp-physics PR#944 branch: ccppv6 doc update

* Point FV3 to my branch upp_update_aug: Update inline post for RRFS and HAFS

* Update CDEPS

* * add 2 new MOM6 files in cmake * switch to use infra/FMS2 code in cmake * using MOM6 testing branch

…id for sea ice dynamics (was #1390) (#1381) * update ice_in and submodules * cesm_ponds is deprecated so remove from ice_in * fix hafs-wav configurations * turn ice coupling off for all hafs+wav tests * turn current coupling off for hafs-atm-wav test * add a cdeps test using c-grid for CICE6 (#27)

* Run inline post in two hafs tests * Update two hafs tests that run inline post

* acorn and common .lua changes, hera.intel (not hera.gnu) .lua changes * CMake_Platform --> CMAKE_Platform * jet and wcoss2 .lua changes, cheyenne.gnu/intel lua updates, orion lua updates, typo in jet.lua files, Orion fixes for .lua files * Set proper number of non-advected tracers in regional_atmaq regression test. * Add proper convective scavenging coefficients to the regional_ataqm regression test. * Update ufs_s4.intel.lua, Update ufs_s4.intel_debug.lua

* update .gitmodules and FV3 submodule pointer for RTs: Misc NRL bugfixes

…include s2swa tests (#1401) * update GNU to include s2swa tests * switch to MOM6 testing branch: update MOM6 to its main branch 20220902 commit

…itch three HPC's to epic's HPC Stack (#1405) * Bring in barry's AQM changes for fengsha * Update to PIO 2.5.7 and add EPIC Stack locations for Orion, Gaea and Jet Co-authored-by: jkbk2004 <[email protected]>

* update/condense Ch2 Code Overview, Ch2 links, formatting, add Glossary terms, etc.

* point to WW3 feature branch * update submodule and branch used for WW3 * update WW3 to latest meshcap_stripped commit Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Moving nest inline post fix * Enable hafs_regional_specified_moving_1nest_atm test on orion and wcoss2. Update BL_DATE Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

…sics ufs/dev branch for fv3atm (#1429) * Officially changed the ccpp-physics pointer from NCAR/ccpp-physics main branch to ufs-community/ccpp-physics ufs/dev branch for fv3atm

* update crtm-2.4.0 library and remove yaFyaml * update GOCART Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

…th the Thompson microphysics scheme (#1438) * added test case merra2_thompson * version worked for producing nifa and nwfa * added mraerosol for testing * use ltaersol=.true. and merra2 * using field table instead of code change for mraerosol * DNATS value was traced to merra2_thompson.nml.IN * added field and diag tables for regression tests * gocart aerosol coupled with thompson microphysics * Made CmakeModules and GOCART point to the correct hash * Updated FV3 for modifying the Thompson scheme Co-authored-by: anning.cheng <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: AnningCheng-NOAA <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* update FV3: Use saved routehandles in fv3 cap init phase Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Add RRFS-A to weekly tests

* Update input-data and hpc-stack containers * Update Dockerfile and opnReqTest * Update Jenkinsfile to handle PRs properly Co-authored-by: JONG KIM <[email protected]>

* .gitmodules updates and hash to rmontuoro/bugfix/aqm-build-system for AQM Co-authored-by: jkbk2004 <[email protected]>

…he P8 physics suite) (#1451) * This is equivalent to PR66 in NCAR/ufs-weather-model: Bugfix and optimization of prognostic closure for the P8 physics suite Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

#1437) * fixes for rrfs debug tests (uninitialized memory in fv_regional_bc and module_bl_mynn) * rrfs 13km debug tests * smoke bug fixes for restart * RRFS tests, but smoke takes too long due to 2hr wallclock limit, needed for restart test * remove smoke test variants * remove workarounds and fix remaining known bugs in ps_reg * a few more surface pressure bug fixes; now the test case runs in debug mode * update conus13km test list * workarounds and bug fixes from gnu compiler testing * atmos_cubed_sphere fixes&tweaks; ccpp/physics fix for precision issue that fails gfortran -DDEBUG=ON * 120s timestep for conus13km tests * atmos_cubed_sphere: simplify comments and explain snan * move task calculations to compute_petbounds_and_tasks in rt_utils.sh; call it from rt.sh * disable conus13km decomp and restart tests that are known to not match the control * hera.gnu tests pass, except conus13km decomp and restart which are expected to fail * move sanity checks to lsm_ruc and add "snow on ice" check * use i-1 & j-1 for two-point averages, when available * hera.gnu tests pass against new baseline after atmos_cubed_sphere i-j change * Replace many changes with atmos_cubed_sphere PR #220 * update stochastic_physics url Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* update FV3 submodule pointer and .gitmodules for RTs * small cloud tuning from Greg Thompson (#1410) * Simplify Jenkins pipeline Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Jesse McFarland <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: JONG KIM <[email protected]>

* Sync WW3 develop with dev/ufs-weather-model, Oct 12th 2022 * fix needed for cheyenne lmod update * Update fv3_qsub.IN_cheyenne * acorn intel lua cray-mpich update * acorn intel debug lua cray mpich update Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* update components and add external land component support * use cubed_sphere_grid as output grid * point updated CMEPS fork * switch to another fix for inconsistent land sea mask issue * make grid file configurable for external land Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* Add a new RT for SDF FV3_WoFS_v0 * Update delta_srw210 branch in ccpp/physics and minor bug fix in CCPP_typedefs Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

…clouds, ESMF 8.4 support for AQM, Update WW3. (#1456) * Bring in AQM PR #24 changes * Update WW3 hash to DeniseWorthen/feature/updatewm * Update AQM hash, bringing in EXMF 8.4 support for AQM * remove bio from aqm.rc Co-authored-by: jkbk2004 <[email protected]>

* Improve radiative fluxes and cloud cover in FV3 for HR1 Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* Replace low resolution regression tests with high resolution. * Rename ICs and result directory * Remove "calendar" variable from namelists. * Remove unused scripts: gfdlmp_run.IN & gsd_run.IN * Add '--cpus-per-task=@[THRD]' to fv3_conf/fv3_slurm.IN_jet * add omplace to cheyenne qsub script Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>

… 550nm (#1475) * Adjust GFS diagnostic ADO output to the exact 550nm in ccpp/physics * Modify a few lines of code in FV3/ccpp/physics/physics/radiation_aerosols.f to make them properly indented Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

…reading for cpld_bmark control and restart (was #1483); Software module updates in hpc-stack for Hera (intel, gnu) (was #1468) (#1486) * update CMEPS submodule * bmark cpld tests use esmf-managed threading by default * remove version w/o esmf-managed threading * update hera hpc stack locations: intel/gnu Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: zach1221 <[email protected]>

…a 3D diagnostic tracer in UFSWM (#1494) * Adding extra tracer (PM2.5) from AQM * correct units on aqm_pm25 tracer * Bring in production and fengsha section, but only enable prod * Keep PM2.5 name consistent with production. Co-authored-by: jkbk2004 <[email protected]>

…#1492) * modify mom6_files.cmake to add 3 new files * specify KVML in MOM_input but the follow three will use new default values (by following MOM6-examples) KAPPA_SHEAR_VERTEX_PSURF_BUG BAROTROPIC_TIDAL_SAL_BUG LAYER_Z_INIT_IC_EXTRAP_BUG * add STORE_CORIOLIS_ACCEL = False in MOM_input Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Couple convective clouds to radiation (#1496) Co-authored-by: Grant Firl <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* update CICE * remove files from cice_files.cmake * remove modules for features which have been removed (cesm ponds and therm_0layer) * remove compiles of drivers not used in ufs Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* noahmp bugfix/noahmp_hr1 * Add a new varible 'ztmax' in NOAHMP-interface/noahmp * Change DT_ATMOS from 720s to 600s for RT merra2_thompson due to the instability issue Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

@rmontuoro

… WCOSS2 MAPL Enable Tests (#1507) (#1505) * Inline post is now compiled by default on all supported platforms * Create Debug RT for AQM, Bring in fixes from debug testing and @rmontuoro small updates to AQM * update wcoss2 module files with esmf/mapl and turn on gocart in coupled runs * disable regional_atmaq_debug on jet: time out issue Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Change fv3atm branch to bugfix/noahmp_tq2m Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

…ototype 8, and turn on prognostic closure. (#1480) * Generation of gfsv17 tests for RT's beyond P8, updates in FV3 and ccpp submodules * Added DNATS=0 flag to not exclude any tracers from advection * update TKE contribution from cu for progsigma in deep and shallow cu * Correct noareo tests to set DNATS=0 to ensure advection of all tracers * Address review comments - clean out P7 and P8 labels in GFSv17 tests * update rt.conf removing old control tests, adding a cpld gfsv17 test * add outerloop wave coupling to a gfsv17 test * remove duplicate test Co-authored-by: Jessica Meixner <[email protected]> Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* adding hr_ave_chem_v1 * aqm diag_table changes Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: JONG KIM <[email protected]>

* removed control_2dwrtdecomp, control_fhzero, control_2threads_debug

* Update Jenkinsfile * Update ci.test * add a mixed-mode test Co-authored-by: zach1221 <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Performance optimization of moving nest. * Turn on HAFS RTs on WCOSS2 and switch to use the netcdf (instead of netcdf_parallel) write_grid_component option for HAFS RTs. * Update submodule FV3, which points to latest UPP develop branch. * Update submodule FV3, which will only call atmosphere_fill_nest_cpl at the cap driver time steps (coupling time steps) * Adding upoff as a namelist parameter * Update submodule HYCOM after the momentum flux fix for HAFS FV3ATM-HYCOM coupling. * Update submodule FV3 and rename HAFS_V0 CCPP physics suites into HAFS_V1. * Cleanup of CMakefile for moving nest, and added fv_timers namelist option Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: Biju Thomas <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

… indices. (#1497) * fv3 surface restart io: turn some calls into loops * turn many loops into subroutine calls, and remove nt_save * Refactor surface restart logic in FV3GFS_io.F90 to not use hard-coded indices Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Enhanced stability of drag_suite module and added diagnostics * Added new UGWP diagnostic variables to parm/diag_table/diag_table_rap * Bug fixes to rap, hrrr and rrfs test description files and tests/parm/rap.nml.IN * Updated standard_names for do_gsl_drag_ls_bl, do_gsl_drag_ss, do_gsl_drag_tofd and ugwp_seq_update * Incorporated dustinswales suggestions in ccpp-physics PR#22 * Assumed-shape in gwdps.f * Added logical flag 'ugwp_seq_update' to gfs_physics_nml namelist * Modified calculation of dtfac in drag_suite.F90 and revised various long_name's of diagnostic variables * Removed passage of variables 'ak' and 'bk' to drag_suite -- these are no longer used * Removed unused variables from GFS_typedefs.F90 and added clarifying comments in ccpp-physics Co-authored-by: JONG KIM <[email protected]>

* Convert all regression tests to use esmf-managed threading * update CMakeLists.txt * update rt.conf * Comment out unneeded steps in workflows/aux.yml * turn off control_c384 on cheyenne: all others passed Co-authored-by: Bin.Li <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* allow option no updated sub-components * Run control_c384 and control_c384gdas tests on Gaea using TPN=18 Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* clean up gitaction yml * Update build_test.yml, aux.yml

* fix fd_nems.yaml * cmeps restart will appear as different because field names changes * set TPN=18 on cheyenne: cpld_control_c192_p8, cpld_restart_c192_p8, hafs_global_multiple_4nests_atm Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* MYNNsfc uniform real kind Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* Updated FV3 hash, Bring in Fengsha and Pt Source input files, bring in updated aqm.rc Co-authored-by: Raffaele Montuoro <[email protected]>

…ade (#1554) * SUPAFAST option sets build flags ideal for HAFS * add test for HAFS with -DSUPAFAST=ON * SUPAFAST=>TEST_FASTER_INTEL and add -no-ip to CMAKE_Fortran_FLAGS_RELEASE * TEST_FASTER_INTEL => FASTER * Update rt_single function in rt.sh to parse correct .conf file * Remove fail_test file after model run only if Rocoto is used * Use -xSSE4.2 on GAEA * turn off regional_atmaq_debug on gaea: time limit Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: JONG KIM <[email protected]>

…dates (#1544) * Update submodule FV3/upp and use a newer version of g2tmpl/1.10.2. * Update submodule FV3 and switch to use the unified ugwp scheme for HAFS regression tests. * Update submodule HYCOM-interface/HYCOM and HYCOM-interface/CMakeLists.txt so that the debug build options will work properly for the HYCOM subcomponent. * Update tests/parm/postxconfig-NT-hafs.txt by using FV3/upp/parm/postxconfig-NT-hafs_nosat.txt * Fixed bug in calculation of nest halo weights identified by Biju Thomas in DDEBUG=ON builds. Co-authored-by: William Ramstrom <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* Remove -xHOST from CICE CMakeLists.txt. #1262 Co-authored-by: [David Huber] <[[email protected]]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* reverting the bug fix for ktherm=2 allows all cpld tests to pass and the single datm test using ktherm=2 (datm_cdeps_gfs) to also pass all other datm tests which use ktherm=1 fail Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

…#1566) * adding regional control back to jenkins-ci (#37) * Create ESMF field attributes using the same kind as field data values Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>

* AutoRT update for Jenkins.

* Bug fix for cloud effective radius for convective clouds (HR1)

* update CMEPS

* RRTMGP refactoring * Added RRTMGP p8 coupled RT. Update other GP RTs. * Adding GP physics blocking to UFS GP RT configurations * Trim old RRTMGP RTs * Interface changes for SP build in GP Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* hpc stack internal location changes and ORT fix Co-authored-by: JONG KIM <[email protected]>

… (3) hafs bug fix (#1606) * updates for movingnest debug mode * add hafs_regional_storm_following_1nest_atm_ocn_debug test * point MOM6 to test branch * remove cpld_esmfthreads_p8 Co-authored-by: Jun Wang <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: zach1221 <[email protected]>

…OAH and NOAH MP LSM, and rename nsradar_reset (#1529) * Six new winter wx diags, new precip ice density for RUC, NOAH MP and NOAH LSMs, new namelist parameter for nsradar_reset, new flat files for GFS and fv3lam to properly handle new winter wx diags. * remove six winter wx diags from f00 xml file * Remove commented out lines related to old computation of precip ice density * Added 6 winter weather diagnostics + precip ice density (all 2D fields) to select diag_tables * Use correct postxconfig files * Include Grant's winter wx mods Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: zach1221 <[email protected]>

…ces and turning off output; update FAQ documentation (was 1608); update drag suite intent mods (was 1612) (#1597) * update cdeps * use fv3atm from PR 1612 * Changed UGWP diagnostic variable declaration intents from out to inout * Docs/faqupdate (#8) Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: Brian Curtis <[email protected]>

* MOM6 writes restarts in YYYYMMDD.HHMMSS.MOM*nc format * the final restart is timestamped * make changes in scripts to remove 'suffix-hours' strings * remove STORE_CORIOLIS from MOM_input templates * add timestamp in the end forecast restart filenames for GFS * FV3atm restart filename format

* Update FV3 * Merge pull request #67 from dustinswales/accumulated_cleanup * Updated physics * Reverting DISKNM/gaea to original * add new BL_DATE

* Faster Compile option turned on for a compile and test per project * added sample tests from each project to be tested with faster compile * HAFS app to be compiled with 64bit

…ble usage of shared pio (#1645) * Gaea system: change in hpc-stack location, miniconda3 (EPIC-managed) * move DISABLE_FMA to one if at the end * only disable fma on wcoss if FASTER=ON * Update CMakeModules to develop; remove STATIC requirement from PIO find. Co-authored-by: Natalie Perlin <[email protected]> Co-authored-by: ulmononian <[email protected]>

* update WW3

* fix clock initialization for a restart in WW3 * update WW3 submodule * update to develop WW3

…er update for #462 (#1654) * update FV3 submodule and .gitmodules for testing of 20230313_combo * turn off cpld_control_p8_faster cheyenne

* aqm init_concentrations=false * ATMAQ tests are 32BIT

* use the latest postxconfig-NT-fv3lam.txt to run ifi * rename postxconfig-NT-fv3lam-ifi.txt to postxconfig-NT-fv3lam-new.txt since it is, in fact, the new postxconfig-NT-fv3lam.txt * add lightning threat indexes to rrfs 13km tests * pass w to model & fixes to ccpp/physics changes * FV3: turn off lightning_threat by default since it allocates wgrs and passes w * do not output ltg*_max variables since they're all zeroes anyway because the 13km run cannot make enough graupel * FV3: missing `active = (lightning_threat_indices_enabled)` for wgrd * enable ltg*_max variables in diag_table_hrrr * alternative POSTAPP for C96 versions of regional configurations * rap & hrrr variants use POSTAPP=fv3lam_global * new tests for ifi on acorn * fix out-of-bounds access in upp calslr_roebbr * fix another out-of-bounds access and move a message to stdout

* "merge RRFS-SD to the community repository" * "include the MYNN-EDMF update PR #1636" * add new control_p8_mynn test to exercise the FV3_GFS_v17_p8_mynn suite * change some variables to environment-controlled in cpld_control.nml.IN; add satmedmf=T for export_cpl() in default_vars.sh; add satmedmf=T for tests that use cpld_control.nml.IN, but not export_cpl * add new smoke_dir_fdb_coef to rrfs test namelist Co-authored-by: joeolson42 <[email protected]> Co-authored-by: Haiqin.Li <[email protected]> Co-authored-by: Grant Firl <[email protected]>

… update #1673 (#1633) * Add 4 new quilting restart tests * Remove tests/qr.conf * Fix fv3_conf/regional_run.IN script to correctly copy restart files from dependent directory * Clean up Thompson table files (#38) * update control_qr_p8 control_restart_qr_p8 * Disable cpld_control_ciceC_p8 and cpld_control_c192_p8/cpld_restart_c192_p8 on Gaea * Update FV3 and WW3 Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Jessica Meixner <[email protected]>

* reverting the bug fix for ktherm=2 allows all cpld tests to pass and the single datm test using ktherm=2 (datm_cdeps_gfs) to also pass all other datm tests which use ktherm=1 fail * confirm cice testb16d7fd is b4b for all datm/cpld tests * update CICE and CICE gitmodule * fix alignments in rt.conf, rt_gnu.conf

@tanyasmirnova

* bug fix from @tanyasmirnova for rrfs crashes during restart * new regression test rrfs_conus13km_hrrr_warm_restart_mismatch * Update CMEPS with ufsdev_ruclsm * point to top of ufsdev_ruclsm for FV3 and FV3/ccpp/physics * FV3: incorrect character lengths in two calls Co-authored-by: samuel.trahan <[email protected]> Co-authored-by: Ratko Vasic <[email protected]> Co-authored-by: joeolson42 <[email protected]> Co-authored-by: tanya Smirnova <[email protected]>

…pplication; utilize custom restart names for WW3 (was #1684) (#1692) * set configuration variable true to use non-default restart file names in WW3 * change name of WW3 used for restart tests * change name of WW3 in hafs wav tests * update CMEPS

…KMPI (#1681) * Remove DEBUG_LINKMPI logic

…astic perturbations) needed for GFS/GEFS prototypes (#1677) * Bugfix for convection (prog closure) and gravity wave drag (for stochastic perturbations) needed for GFS/GEFS prototypes Co-authored-by: Michael Toy <[email protected]>

* orginal version is atmwm (m=multi); atmw = cmeps/mesh cap * input_nml for control_p8 and atmwave p8 test are different only in cplwav and cplwav2atm logicals

* fix the fdiag for GEFS EP4 * update fv3 with atm.logf file

* Rename global fv3 inline post itag and control files. * Set read merra2 as default; add SDEN in gfs control file. * Update cpld_control_run.IN for changing post_itag name.

… develop (#1669) * Updates to new unified convection, cleaning etc --------- Co-authored-by: Jessica Meixner <[email protected]>

* "update to run RRFS with GF"

…ines. Update WW3 (#1702) * Use nccmp to compare netcdf files * Use nccmp only on NOAA R&D systems * Do not skip checking fv_core.res.nc when GNU compiler is used * Update ufs_common.lua * Update ufs_hera modulefiles * Cleanup compile.sh. Remove unnecessary FIXME for gnu compiler * Update WW3

setup RT for flake * add fv3-conf for flake * add clm lake to FV3 * bug fixes, clm lake restart, and clm lake suite * flake_control_run.IN => lake_control_run.IN

* Update FV3 to a new version: Dycore semi-implicit solver update

…sing and combined with #1730 WW3 update (#1715) * update FV3 to better handle data source for regional model LBC processing * update WW3: PR#1730

* Update default_vars.sh to add noaacloud * Update detect_machine.sh to add noaacloud * Update module-setup.sh to add noaacloud env variables * Add noaacloud and env variable to rt.sh * Update module-setup.sh * Create ufs_noaacloud.intel.lua * Create ufs_common_spack.lua * Create compile_slurm.IN_noaacloud * Create fv3_slurm.IN_noaacloud * Update rt_utils.sh * Adding Requesting if statement to default_vars adding -B option back to nccmp

* This PR is created due to the ccpp-physics update for HR2 * PBL, Convection and Microphysics Update for HR2

…r baseline on gaea (#1749) * New baseline, develop-20230510 created * gaea hpc stack update and gaea9 phase out

* cpld pdlib, cpld control pass against created baselines * remove "wise" from wave domain name * update WW3, modify rtwaves for testing * set dnats to 0 in pdlib tests * remove scotch from ufs_common and add scotch module only for hera,cheyenne and orion

…r S4 (#1728) * update build for gfsv17 test with 32BIT * s4 option in rt.conf

* Add hafs tests that use quilting restart * Change Orion log file permissions

* pointing MOM6 to test branch, modify mom6_files.cmake to reflect new files being added

…t format as the global workflow; Update CDEPS (was #1741) (#1699) * Update cpld_control.nml.IN * Update model_configure.IN * Update nems.configure.cpld_noaero.IN * Update field_table_thompson_noaero_tke * Rename diag_table_gfsv17_template to diag_table_cpld_template * Update CDEPS-interface/cdeps_files.cmake Co-authored-by: Bin.Li <[email protected]> Co-authored-by: SadeghTabas-NOAA <[email protected]>

…pdates (#1761) * update Code Overview ch; add supported platforms section * add land build options to Build/Run ch * add configuration chapter * add details for ATM/ATML/LND configs

…ests/ (#1718) * move logs to logs/ folder, and move rt_gnu tests to rt.conf and delete rt_gnu.conf * Remove Intel/GNU specific calls for MACHINE_ID or in config scripts * default_vars machine name updates * ORT will continue and not exit if a test is unsupported * Logs will now contain the hashes of the UFSWM and its submodules * Adjust AutoRT with new BLDIR and no need for the compiler information * Remove compiler information from machine log files * Add -a option to opnReqTest

* Revert 2c8363e057dde026e65ddcec1b62c18d5e260017 to allow compiler optimization. Also use minval/maxval intrinsic functions instead of a loop nest in range_check_3d() * Switch range_check_2d to use minval/maxval intrinsics as requested * need git 2.28 on orion

* Bugfixes for RRTMGP This reverts commit 0f12deb.

*removal of the snow mixing, reverting back to the RRFS Base E configuration. *change to table values of Leaf Area Index * increase resource to fix gaea out-of-memory issue * Reset default TPN=24 on gaea

…n (was #1758) (#1752) * update CMEPS w/ fix for error condition * adding atmw to ORT *update cmeps build to implement check4nans feature using module stored in cdeps repo * Gaea software stack location update after C3 and C4 partition upgrades * added CMP_DATAONLY variable for ORT FHZ test * added CMEPS and WAVE restart file for ATMW ORT RST test * add ORT log for atmwav_control_noaero_p8 ORT test ----- Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: Sadegh Sadeghi Tabas <[email protected]> Co-authored-by: Natalie Perlin <[email protected]>

@tanyasmirnova

…sd and clm lake to quilt restart. (#1769) * refactor FV3GFS restart, add clm lake and rrfs-sd to quilt restart * rrfs sd restart in quilt (still under testing) * explicitly write axis values (from DusanJovic-NOAA), and clean up code * rename FV3GFS to fv3atm in code, except output metadata * refactor a bit more, putting history into fv3atm_history_io.F90 and restart into fv3atm_restart_io.F90 * add the two qr hurr_control tests * Even longer explanation of RUC LSM axes from @tanyasmirnova * missing dependency for rrfs_smoke_conus13km_hrrr_warm_restart * do not delete tests/lock directory when another rt.sh is running * Set THRD variable in rrfs 2threads tests * bug fix to "alt check" code: add -S -q to avoid infinite output * 32-bit quilt restart tests * use process id instead of $delete_lock to decide3 whether to delete the lock file * Remove THRD= from smoke tests * no THRD in non-smoke conus13km tests * save restarts in rrfs_conus13km_hrrr_warm test * disable four broken tests

* Update GEFS tests * Update nems.configure.datm_cdeps.IN

…d (C3) scheme (#1795) * Updates for the Community Convective Cloud (C3) scheme

* Remove unused ccpp suites

* send evap from atm * instead of converting from lat->evap in prep_ocn, send evap from atm directly. Sign change still needed. * turn off c48-5deg warm start test * disable hrrr tests on wcoss2

#1797) * refactor FV3GFS restart, add clm lake and rrfs-sd to quilt restart * rrfs sd restart in quilt (still under testing) * explicitly write axis values (from DusanJovic-NOAA), and clean up code * rename FV3GFS to fv3atm in code, except output metadata * refactor a bit more, putting history into fv3atm_history_io.F90 and restart into fv3atm_restart_io.F90 * add the two qr hurr_control tests * bug fix to "alt check" code: add -S -q to avoid infinite output * 32-bit quilt restart tests

* add iopt_diag for 2m t/q diagnostic option * land surface upgrades for hr2 * fixed a typo for soil color file flag * change FNSOCC setting * update cmake of NOAHMP-interface * soil data for datm_cdeps_lnd_gswp test * Update rt.conf remove baselines for hrrr_control_qr

…(branch Maie) (#1815) * establish maie * optimized the code and decrease the stratosphere warm bias for mraerosol=T * Update detect_machine.sh * Update compile.sh --------- Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Anning Cheng <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Wen Meng <[email protected]>

…3-jun-27 (#1811) * WW3: updates

* Add new BL_DATE Update inline post with: *Clean up legacy code in inline post interface *Relocate computation of diagnostic variables *Sync changes from offline post interface *Update upp revision

* Update empty_output_bundle * Update pull_request_template.md from 1813 Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>

* Update control_CubedSphereGrid_parallel test * The control_CubedSphereGrid_parallel test has been updated to run post and create native grid history files

* reverting the bug fix for ktherm=2 allows all cpld tests to pass and the single datm test using ktherm=2 (datm_cdeps_gfs) to also pass all other datm tests which use ktherm=1 fail * update CICE * change freq in for ice_diag.d global values * remove unused history* settings * update DISKNM with epic and rt log * Update bl.py for new Hera blstore

* add gridtype to gocart CAP.rc * move to GOCART 20230227 version with threading capability * udpate to netcdf/4.9.2 and add threading capability for gocart * update esmf library * update GOCART to allow no-Nitrates run

…r CMEPS (#1807) * commit changes for sensible heat flux * add sensible heat changes * update submodules and fd for evap fields * backup to pre-evap changes to test

) * modify mom6_files.cmake to reflect files being removed/added

* update FV3 submodule pointer after GT combined his physics PRs

…ng PR#1863) (#1844) * Changes to logging and initialization of the CLM Lake Model. * merge ccpp-physics #91 (UFS-SRW v3.0.0 SciDoc updates) 1. Use ice thickness hice(i) to find the level in the lake where ice is zero. 2. Do not allow lake temperature to be below freezing point if there is no ice. 3. If there is no snow or ice, do not allow surface lake temperature to be below freezing point. These changes fixed the problem with large errors in the energy budget at the beginning of the cold-start run with lakes. 4. Added flag to turn on debug print statements in the CLM lake model. * explicitly turn of frac_ice for flake * t_grnd(i) should be t_grnd(c) ------------------------------------------------------------------- Co-authored-by: Samuel Trahan <[email protected]> Co-authored-by: Grant Firl <[email protected]>

*Modulefiles to be updated through this PR include: Acorn, Gaea, Hera, Jet, Linux, MacOSX, Orion, NOAA Cloud (Parallelworks), and S4 to spack-stack 1.4.1. *Update Cheyenne's fv3_conf files to address switch from mpt to impi, * Update hdf5 version in ufs_common; * Update ufs_common, ufs_orion.intel; cherry-pick GOCART parm file and hash updates from Jun's newmapl branch.

* update CMEPS w/ fix for error condition update cmeps build to implement check4nans feature using module stored in cdeps repo * make pio rearranger=box the default for all tests * update configurations for ocnalb changes * set the ocean albedo limit in config and use it to set logical flag * albdir and albdif can be set as non-std values in nems.configure will default to 0.07 and 0.06 if not set * ocean albedo changes were merged at ESCOMP * fix variable name in 2 nems.configure files * update CMEPs with fioi_swpen fix * remove albedo limiter for DATM cases

… & FV3_HRRR_gf (#1880) * replacement 13km conus regtests * delete old conus13km tests * temporary file with list of new tests * fix errors in new compile lines * simplify test specifications for hrrr and conus13km * bug fix to quilt servers & use clm lake in hrrr c3 & gf * correct errors in rt.conf for new tests * revert bug fix to avoid a GFDL_atmos_cubed_sphere PR * missing a "+ hera cheyenne" for one new test

…bining PRs #1853 & 1834) (#1467) * Update fms to 2022.04. Update acorn modulefiles * Remove fms_io_nml and mpp_io_nml namelists from input.nml templates * Update FMS to 2023.01 * Use netcdf4 fms2_io option * replace tabs with spaces * Update rt.sh to allow creating new baselines only for a subset of tests * Update rt.sh to run compile tasks only if needed during baseline creation (-b option) * Revert MAX_BUILDS back to 10 * Fix hrrr qutlting restart tests.

* update module file * update rt.conf with pdlib tests on wcoss2

* 2D advection of cellular automata * add Configuration.rst change from 1804 * add Glossary.rst change from 1804 * Delete doc/UsersGuide/build/.gitignore

…1823) * add fv3atm/mom6/cice6 run time info * update fv3 and cice * fix mom6 output * use Denises cice6 branch and fix atm log file * using stdout for mom6 timing info * update mom6 runtime * update CICE and mom6 output log file * remove icepack_zsalinity.F90

* add stochastic parameterization perturbations to support to Grell-Freitas deep convection * fix reproducibility issue in G-F deep convection

* WW3: CI fix

* MYNN SFC OpenACC directives

* Update rt.sh * Create RegressionTests_noaacloud.log * Create Jenkinsfile.noaacloud * Update rt.conf * Update bl.py

* Update several RT files to add Hercules support. Add hercules intel lua file. * Update rt.sh * Use dusan's formatting in ufs_common. Change hdf5 version. * Update rt_utils.sh * Remove git diff syntax from rt_utils.sh * Add regnerated cdeps_share files; add DCPRGNU and DCPRINTEL flags to CMEPS and CDEPS CMakeliststo allow for GNU builds; remove the Intel compiler directive in the current cdeps_share files. * turn off control_wam_debug for intel as well move CPRGNU CPP flag to apply to all gnu versions (fixes hera failures) * Add Hercules as a machine in pull_request_template.md

* update CICE * remove comment lines from genf90.pl preprocessing * Update bl_date.conf

…a variables (#1903) * Update fv3atm io routines to use same type kind for both axes and data variables

*add pbl_tapering for SPPT *Add possibility to run the CA on a single tile, ensure decomposition of domain is proportional between the atmosphere domain and the higher resolution CA domain

…sics, and string length mismatch in dycore (plus PR #1913, #1917, and #1926) (#1893) * GFDL_atmos_cubed_sphere: consistent string lengths in array * stop FV3_HRRR_c3 from crashing with gnu debug * 1hr forecast limit for conus13km_debug_qr * fv3atm: bug fix from Dusan to recover_fields crash * disable conus13km_debug_qr_gnu due to 25% failure rate on Hera * FV3 dycore: initialize srf_wnd_var2 and tracers_var3 arrays * enable conus13km_debug_qr_gnu * Fix race condition in GFS_phys_time_vary.fv3.F90 error detection * More bug fixes to GFS_phys_time_vary.fv3.F90: 1. detect empty errmsg from subroutines 2. Initialize err variables in set_soilveg.f, which is called from GFS_phys_time_vary.fv3.F90 * ccpp-physics: initialize errmsg & errflg in noahmp_tables.f90 * ccpp-physics: only read h2odata, ozdata and noahmp table when they are needed * "point to the dimension fix of smc for dust emission" * FV3: more dycore bug fixes from GFDL_atmos_cubed_sphere PR 285 * merge #1926 * merge GFDL_atmos_cubed_sphere #276 * bugfix: 12hr hrrr tests * add GAEA rocoto support * fv3: merge GF radar fixes * check that baseline directory exists and is non-empty --------- Co-authored-by: Haiqin.Li <[email protected]>

* update CMEPS * update CMEPS w/ fix for error condition * turning off regional_atmaq_debug: time-out issue on cheyenne.intel *update cmeps build to implement check4nans feature using module stored in cdeps repo * initial sw fix branch * make pio rearranger=box the default for all tests * update configurations for ocnalb changes

* update CMEPS w/ fix for error condition * turning off regional_atmaq_debug: time-out issue on cheyenne.intel *update cmeps build to implement check4nans feature using module stored in cdeps repo * make pio rearranger=box the default for all tests * update configurations for ocnalb changes * set the ocean albedo limit in config and use it to set logical flag * albdir and albdif can be set as non-std values in nems.configure will default to 0.07 and 0.06 if not set * swap signs for latent heat flux used by HYCOM * test latent flux change for hycom

remove mean prefix for fields imported to FV3atm from CICE or CMEPS rename fv3atm export fields for snow and rain as inst

* add cpld_bmark_p8_iau test * set up cpld_gfsv17 c96 iau test * add tests/cpld_control_gfsv17_iau * remove cpld_bmark_p8_iau * sync MOM input template with global-workflow * add a diag_table that works with fms fix

* establish mrfd * bug fixed for mraerosol * updated upp * sync up CICE/CMEPS/MOM6/Stoch

…e-opening #1943) (#1947) * Allow instantaneous SW and LW fluxes to be used when cpllnd=.true. (re-opening #1943) (#1947)

* Updated fv3atm and ccpp-physics submodules as part of fixing ccpp UGWP OGWD stability issues in the upper atmosphere * Change RF damping parameters and n_split for HR3 * Corrected new 'ugwpv1' SDF's in fv3atm * Added UGWPv1 tests: control_p8_ugwpv1 and cpld_control_gfsv17_ugwpv1 * Changed n_split from 4 to 5 in tests/parm/cpld_control.nml.IN and cpld_control_ugwpv1.nml.IN

…#1922) * update to gocart hash f7b34e - important updates for FENGSHA * Add additional inputs in GOCART control file for FENGSHA

… compile, also re-enable 3 hafs tests for WCOSS2. (#1907) * Adjust timestep to 120 second to avoid saturation vapor pressure table issue * Update rt.conf to re-enable regional_atmaq_faster for wcoss2 and acorn * re-enable 3 hafs tests for WCOSS2 to fix issue #1896

* Update modulefiles/ufs_common.lua modulefiles/ufs_hera.gnu.lua modulefiles/ufs_hera.intel.lua for testing ESMF 8.5.0 and MAPL 2.40.3 * Replace [email protected] with [email protected] in ufs_common.lau * Remove miniconda from tests/rt.sh for spack-stack systems * Switch to mvapich2 on Hercules with GNU * Add gfortran-10 argument mismatch compatibility flags in CICE-interface/CMakeLists.txt, needed for mvapich2 * Add export MV2_SHMEM_COLL_NUM_COMM=128 to hercules gnu job card

… "ufs", allow file clobbering for GOCART history files (was #1948) (#1932) * Enable zstd compression in several tests * update FD and some nems configs * all except lnd sbs run * update aero_history to allow file clobber

* FV3 changes for refactored ozone physics scheme * SDF cleanup. physics updates * Some polishing. Merge 2006 ozone into module_ozphys

* Add -mcmodel=medium for builds targeting multiple cores (prevents link failure on jet) * Updated FV3/ccpp/physics (NSSL MP)

* update FD and some nems configs * all except lnd sbs run * update FD and nems.configure * remove temporary test settings * remove history_n settings from one more test

…active (#1953) Added new condition turning off samfdeepcnv, when the MYNN shallow convection is active.

…tart (#1946) * Convert most global (uncoupled) and regional tests to use quilting restart * use MOM6 test branch, modify mom6_files.cmake * update MOM6 to include 20231106 NOAA-GFDL/rtd_fix * Update cpld_control_p8 remove hera_gnu wall clock stipulation --------- Co-authored-by: jiandewang <[email protected]> Co-authored-by: WenMeng-NOAA <[email protected]>

@lisa-bengtsson

* update FD and nems.configure * add new suite_FV3_global_nest_v1 to FV3 * new tests for global_nest_v1 suite * update tests to match new gwd scheme * Namelist changes from Mike Toy & adapt to changes from develop in FV3 * Merge FV3 NOAA-EMC/fv3atm#715 from @lisa-bengtsson * remove unused tests/rap_clm_lake * Update bl_date.conf * note that gnv1_nested might work on s4 * Update cpld_control_p8 remove hera_gnu wall clock stipulation

#1945) .* MYNN-EDMF, MYNN surface layer, and Thompson AA updates (combines 1940) (#1945) --------- Co-authored-by: tanyasmirnova <[email protected]> Co-authored-by: Grant Firl <[email protected]>

*fixed grv function used by NST *point to FV3 with grv fix

* enable pdlib tests on more platforms * fix bug and use scotch 7.0.4

* Convert tests to use netcdf quantize options

* point to nst kind fix branch

* Convective reflectivity added for NSSL,Thompson mp,SAS,GF shal/deep * Bug fix: htop intent set to in, modified if condition for convective refl. * if do_deep is false, set deep and shal parameters to -1. This will prevent conv refl from being computed. * Revert imfhsalcnv and imfdeepcnv changes * Bug fix for conv refl,remove conv refl computation from the cu_gf driver * change imfshallow and imfdeep to -1 since no convection is used, otherwise it will try to compute convective reflectivity * Replace 273.16 with already defined physical constant, con_t0c

…pport RRFS multiphysics ensemble and add tob in ocean output)(Includes PR #1997) (#1784) * Reinstate all the c5 changes that I botched with my git ignorance. * Update ufs_common. Upate c5 modulefile. * TPN adjustments for C5 regional_atmaq tests. * Remove set -eu from module-setup.sh * Update rt.sh adding new DISKNM for Gaea_C5 * updates for gaea-c5 modulefiles, scripts * Update rt.conf fix gaea machine name

…chunk sizes in restart files (#2021) * Acorn RT Log, failure due to Acorn queue limits, not system or code issue * revert change in cpld_debug_p8 and increase wlclk for cpld_debug_pdlib_p8/jet

…1979) * Update MOM templates to be in sync with recent additions to g-w and update 5 deg template to be in line with g-w and OM4 settings * Revert manual copying of file now that new file is in input directory

… for application, cleanup tests (#2010) * additional template variables for CICE namelist * rename templates, add component level defaults * clean up unnecessary quotes in tests * add cmeps restart directory variable * add MOM6 variables to some standalone tests * add missing mom6 variables for two restart tests

* Add cpld_s2sa_p8 regression test * Reduce output in cpld_s2sa_p8

UFS: - Remove Cheyenne (retiring UCAR HPC) support. - Add UCAR's new Derecho HPC system to supported Tier 1 Platforms.

… AND #2040 and #2043 (#2041) General clean-up, and CCPP concurrency bug fixes 1. Remove nfhout, nfhmax_hf, nfhout_hf and nsout from fv3atm and the regression tests. ( Remove nfhout, nfhmax_hf, nfhout_hf etc configuration parameters NOAA-EMC/fv3atm#731 ) 2. Add comments to smc pert and fix bug in stc pert ( Fix bugs in soil temperature perturbation #2042 ) 3. Disable concurrency in NetCDF calls within CCPP GFS_phys_time_vary_init subroutine to avoid crashes

…nodi + #2047, #2053, and #2056 (#2044) FV3 diagnostic fixes, CCPP fixes for model crashes, new PR template - UFS: - commit message in PR template (#2053) - fix hercules crashes (#2015) - CMEPS & FV3: Bad data from in CCPP CLM Lake physics scheme caused model crashes - Communicate changes to lake ice (Closes #2055, NOAA-EMC/CMEPS#105, NOAA-EMC/fv3atm#741) - unit mismatch (NOAA-EMC/fv3atm#736) - FV3: correct errors in diagnostic calculations - snodi had weasdi data in it (NOAA-EMC/fv3atm#736) - revisions to RUC LSM snowfall melting and accumulation (NOAA-EMC/fv3atm#739)

* "update smoke/dust for RRFS code freeze" * "point to the chem3d dimension update in GF for hercules/gnu"

* Metafile cleanup * Move rte-rrtmgp submodule * Re-organization of physical parameterizations into process and scheme subdirectories * Modifications to CCPP metadata files to accommodate source file location changes * File location update referenced in CMEPS

…build system to allow CMAKE_<COMPILER>_FLAGS to be specified for submodules #2052 (#2013) * bmark time increase * spack-stack-151 & common updates * switch to fms/2023.02.01 * remove gaea c4 * switch to fv3/use_fms_mpp Reverts gaea TPN statement, this includes gaea c5 in its configuration. * WCOSS2 LUA changes to match updates in spack-stack 1.5.1 * Fixing CMAKE_Fortran_FLAGS to be passed from top level to submodules * fixed c flags for cice * turn off some gnu cases: hercules/gnu issue * Bring in lua changes on Acorn --------- Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Mark A Potts <[email protected]> Co-authored-by: jkbk2004 <[email protected]> Co-authored-by: zach1221 <[email protected]>

* update CICE * update CICE source file list * updates to ice_in.IN for use in global applications --------- Co-authored-by: Rahul Mahajan <[email protected]>

…dd stochastic physics pattern update frequency options within SPP and LNDP ('sppint' and 'lndpint') #2077 + Updates to ufs.configure for use in global applications #2074 + Doc Updates #2030 (#2080) * Update MOM6 to its main repository 20231218 updating (disable FPEs) * Updates ufs.configure templates for use in global-applications. * Adds the stochastic pattern interval (sppint) option to SPP and (lndpint) to the land perturbations (LNDP) * Doc update for LND & CDEPS Input files required for land configurations --------- Co-authored-by: “gspetro-NOAA” <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Jeff <[email protected]> Co-authored-by: Jong Kim <[email protected]> Co-authored-by: FernandoAndrade-NOAA <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: zach1221 <[email protected]>

* fix array out of bounds issue in physics aerinterpol.F90 (ufs-community/ccpp-physics#152)

@adams-selin

…FS on WCOSS2 (#2064) * Eliminate an out-of-bounds write in FV3 dynamical core hail diagnostic code. * FV3 component GFDL_atmos_cubed_sphere submodule: * The module_diag_hailcast.F90 has a KBAS index which can have the value of 1. When it has that value, a later line writes to address 0 of a 1-based array. This caused the RRFS ensemble to crash on WCOSS2. * fix out-of-bounds write in module_diag_hailcast * remove unused variable DO_MYJPBL from default_vars.sh (it has a typo in its value) * only correct RWA_new where RWA_adiabat(k).ge.1.E-12 * module_diag_hailcast.F90: update comments; changes from @adams-selin

…; Allow MOM6 to write non-interval restarts (was #2099) (#2085) fix potential divide by zero in WW3 appendtail routine add timers to WW3 mesh cap add non-interval restart capability to MOM6

…rent (#2059) use single MPI_Bcast (via mpp_broadcast()) instead of multiple point-to-point messages (via mpp_send/mpp_recv) address issue maxing out the SlingShot-10 link on the first node resulting in a .15s hit every fifth time step

…#2090) Update diag_able for global coupled iau test cpld_control_gfsv17_iau for mom6 history output

Enable fully could atmosphere-land configuration Supplementary physics updates (MYNN, GF, RUC_LSM, smoke and dust) for RRFS code freeze

CCPP physics code update for HR4 related to surface roughness, background diffusivity and shallow convection + CI fix

…es (#2098) fix NSSL MP init issue when initialized from other microphysics schemes

@binli2337

…osphere-ocean coupling (#2104) Enable the capability of considering sea surface current's impact on air-sea flux calculation for atmosphere-ocean coupling. A namelist option is added to control whether or not to use this feature (default is off). Fixes #1975 Co-authored by: @binli2337, @BinLiu-NOAA, @WeiguoWang-NOAA, @BijuThomas-NOAA, @hyunsookkim-NOAA, @XuLi-NOAA, @MariaAristizabal-NOAA, @JohnSteffen-NOAA

Developed and enabled using CMEPS with inline CDEPS capability for UFS regional coupling. Two HAFS regional moving nest atm_ocn_wav coupling regression tests were added to test this capability. Note: This is a collaborative effort among the ESMF team, EMC/EIB, and EMC hurricane project team.

- Add three new regression tests for version 2 of the surface coldstart file. (Closes #1977)

UPP will be brought to the commit to fix the missing reflectivity bug for NSSL MP cases.

…lock_atmos_copy routines in fv3atm #2124 (#2115) - Gaea C5 modulefile & DISKNM update: closes issues Gaea F2 to F5 file system migration #2101 - Bring in the global-workflow detect_machine.sh to keep consistent between projects. (Closes Bring in detect_machine.sh from global workflow for consistency across the community. #2096 ) - Fix out of bound errors in block_atmos_copy routines in fv3atm

Add ice temperature in CICE output

…file (#2062) Add option to write 3d soilt, soilw and soill variables to a history file

…f support, simplify RT logs. (#2061) * UFSWM * Re-work test verification in rt.sh for developers to use in PR process. (Closes #2058) * fail_<test_number> file name upgraded to use compile/test name instead of number. * Regression test logs do not clearly indicate when a test fails to run. (Closes #1821) * New test_changes.list file: * Verification of what tests change for each PR. * Used with './rt.sh -c -b test_changes.list` to help create new baselines for each PR.

…run compile jobs of regression test suite only & -mcmodel=medium gnu.cmake option (also includes #2142) (#2066) * UFSWM - Add option to `rt.sh` to run compile-only tests * FV3 - Update submodule pointer (NOAA-EMC/fv3atm#747) * ccpp-physics - Update submodule pointer (ufs-community/ccpp-physics#150) * ccpp-framework - Update submodule pointer (NCAR/ccpp-framework#519) * Update WM license and documentation logo * Update GNU.cmake: -mcmodel=medium

Changes to physics code such that the ice model is used to determine the ice temperature over both sea ice and lake ice

* MOM6 - update MOM6 to its main repo. 20240228 updating (which is the original GFDL 20231113 candidate PR)

…ll on macOS arm64 (also contains #2017) (#2164) * UFSWM - "Add conflict for MOVING_NEST option with GNU Fortran, use mcmodel=small on macOS arm64" * FV3 - "Bug fix for unallocated array sfcprop%wetness in GFS_diagnostics.F90" * ccpp-physics - * ccpp-framework - "Bug fix required to use chunked arrays and retain backward compatibility with blocked data structures in ccpp_prebuild.py" * Creation of UFS-WM jenkinsfile for pipeline integration * Jet Rocky8 updates * spack-stack module path * eflow location and version

…g templates for global apps and append _esmf for templates using ESMF-managed threading (was #2179) (#2172) * CICE and CMEPS - Remove compiler warnings. * UFSWM - Allow flexibility to use traditional or ESMF-managed threading for global apps.

* UFSWM - Update the CS convection scheme * FV3 - Update the CS convection scheme * ccpp-physics - Update the CS convection scheme

…ure/capgen into main/20240308) Combined PR #2190 (#2181) * FV3 - Update submodule pointers for ccpp-framework and ccpp-physics. Change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes. * ccpp-physics - In physics/Interstitials/UFS_SCM_NEPTUNE/maximum_hourly_diagnostics.meta: change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes. * ccpp-framework - Update main from feature/capgen as of 2024-03-08 (includes optional argument updates in feature/capgen). Only commit on top of the merge is NCAR/ccpp-framework@6cdd38a which is required to parse the metadata in the Unified Forecast System / ccpp-physics (underscores in units, e.g. degree_north).

…allow-argument-mismatch' flag (#1147) * UFSWM - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag. * FV3 - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag. * ccpp-physics - Resolve various subroutine argument mismatches. * ccpp-framework - Add support to use mpi_f08 MPI module . * stochastic_physics - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.

- update module paths in Hera intel/gnu lua files for Rocky8 OS spack-stack libraries.

…d xr_cnvcld flag to FV3 (#2185) (#2202) * UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh. * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite * ccpp - physics-level changes to implement new namelist variable * MOM6 - update MOM6 code to eliminate all compiler warnings

* WW3 - Langmuir turbulence parameterization

* UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs

* CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files * CMEPS - fix mapping mask for lnd->atm * FV3 - add export of cpl_scalars * NOAHMP - add export of cpl_scalars

…2223) cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)

Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE

…m wrong for nests (#2201) * UFSWM - None. * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP. * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.

*doc/UserGuide *requirements.txt - updates inda version from 3.6 to 3.7

* UFSWM * doc/Userguide * source * conf.py * Configurations.rst * FAQ.rst * InputsOutputs.rst * Introduction.rst

…Adds -v Verbose option. (#2218) Remove nowarn Intel compiler flag (#2225) * UFSWM - Add bash linting to CI: - uses superlinter to check for consistent bash code writing - Cleans up .sh scripts to comply with superlinter - Cleans up .sh scripts to be more consistent, easier to read. - Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's. - Addresses smaller bugs - quota/timeout search logic adjusted. - check for dirs existing (DISKNM, STMP, PTMP) before starting. - adjustments/cleanup to ecflow/rocoto sections - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh. - fix for issue where run_dir will not delete properly. * FV3: Address compiler warnings * atmos_cubed_sphere: Address compiler warnings.

* UFSWM - Update inline post * FV3 - Update upp submodule for inline post

* UFSWM - global_control.nml_IN has been added as the new regression test namelist template for all global regression tests. The namelist now uses pointers (i.e. @[abc]) for variables and default values have been added to the default_vars.sh script. A new section in default_vars.sh has been added (export_tiled) to account for tiled RTs that pulls the correct parameter files using the ATMRES variable. Regression tests have been modified to account for these changes. Tests that were not compatible with the GFSv17_p8 core have been disabled for now. They will be turned on as they are updated from GFSv16 to GFSv17.

* UFSWM - * MOM6 - update MOM6 to its main repo. 20240401 commit (NCAR-candidate-20240319)

* UFSWM - fix fully coupled land component configuration * NOAHMP - get fixed information from surface file

@DusanJovic-NOAA

* NWFA Induced evaporation is turn off , but evaporation not related to aerosol is turned on to prevent excessive evaporation when Inner loop and mraerosol=T * ccpp/framework hash update * Cleanup unused code and variables, fix wcoss2 issue starting ecflow * Bring in @DusanJovic-NOAA trap changes * Merge some machine ecflow starts together and move to case statements

…2235) * UFSWM - update input data directory to fix CICE grid files for incorrect Bu angle, update C48 coupled warmstart files and remove 4-deg ocean files

…ion to specify fv3atm history and inline post files output directory #2254 + Bump jinja2 from 3.1.3 to 3.1.4 in /doc/UsersGuide #2270 (#2215) * UFSWM - Add several aliases in `fd_ufs.yaml` needed for JEDI-UFS. Add new model_configure option (fv3atm_output_dir) to specify directory in which all fv3atm history and inline post files will be saved. * FV3 - Add new model_configure option (fv3atm_output_dir) to specify directory in which all history and inline post files will be saved. --------- Co-authored-by: Fabio L R Diniz <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>

…epo. 20240508 commit #2275 (#2259) * UFSWM - Update CICE to CICE-Consortium (2024-05-01) and mom6 to its main repo (2024-05-08) * CICE - Update CICE to CICE-Consortium (2024-05-01) * MOM6 - Update mom6 to its main repo. 20240508 commit

* UFSWM - Add a RT for SFS with hydrostatic options * FV3 - Remove -DUSE_COND and -DMOIST_CAPPA compiling flags for hydrostatic runs; Fix the issue to write out geopotential height for inline post in hydrostatic runs; Use omega from the model if defined in diag_table instead calculated in post * atmos_cubed_sphere - Remove -DUSE_COND and -DMOIST_CAPPA compiling flags for hydrostatic runs

…gfixes, sfcsub.F landmask bugfix, and canopy resistance output (#2264) * UFSWM, CMEPS, FV3/ccpp_physics - CCPP Physics bugfixes for metadata intents and sfcsub.f landmask and output changes for ozone diagnostics and canopy resistance

…add end of run restart functionality to MOM6 (was #2286) (#2205) * UFSWM - Add support for optional arguments in ccpp physics and framework * FV3 - [Add support for optional arguments in ccpp physics and framework](NOAA-EMC/fv3atm#807 (comment)) * ccpp-physics - Introduce optional arguments in ccpp schemes and metadata * ccpp-framework - Add support (and tests) for optional arguments in ccpp_prebuild * atmos_cubed_sphere - Set cdata%thrd_cnt in driver/fvGFS/atmosphere.F90 * MOM6 - Add end of run restart functionality to MOM6 * stochastic_physics - Add optional attribute for variables where necessary

…2273) * MERRA2 climatology upgraded to 2014 to 2024 mean

…+ develop]: Minor documentation bug fixes #2296 (#2281) * UFSWM - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * FV3 - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * UFSWM - Update requirements.txt; fix EMC broken link in Glossary; fix sample rt.sh run command for single RT run (add compiler)

@BrianCurtis-NOAA

) * UFSWM - A few miscellaneous minor fixes to regression test scripts - Bring in changes for WCOSS2 to match the spack-stack 1.6.0 setup - Bring in updated pnetcdf/pio for CICE - Print 'ECFLOW Tasks Remaining' message only when the number of tasks changes - Remove explicit 'set -e'. Use -v command line option for verbose mode - Remove 'Computing PET bounds and tasks' message - Fix bugs with log generation script (from @BrianCurtis-NOAA) - Uncomment new_compile=true in rocoto_create_compile_task - Removed unneeded colonifnco

*UFSWM: *Updates modulefiles to spack-stack version 1.6.0 *Updates Hera GNU version to 13.3

…or perturbation/increments for cold starts #2271 (#2269) UFSWM - Update modulefiles/ufs_gaea.intel.lua to compile ufs_weather_model on Gaea-C5 FV3 - - atmos_cubed_sphere - move the call to read_da_inc outside the if external_ic/restart logic

…nts (ATM_DS2S and ATM_DS2S-PCICE) and regression tests (atm_ds2s_docn_dice and atm_ds2s_docn_pcice) (#2186) * UFSWM - Add ATM_DS2S and ATM_DS2S-PCICE applications by adding CDEPS dice and enabling prescribed ice CICE. Add corresponding atm_ds2s_docn_dice and atm_ds2s_docn_dice-pcice regression tests. New gnv1_nested regression test with Water in the West domain at C96 resolution using templates compatible with global-workflow * CDEPS - Add dice cplhist datamode * CICE - Enable ice prescribed CICE mode

*UFSWM - update WAM RT compatible with v17 *UFSWM - fix derecho modulefile path for Spack Stackv1.6

…s_cubed_sphere to fix a typo when printing out the nest grid corner locations #2323+Bump urllib3 from 2.2.1 to 2.2.2 in /doc/UsersGuide #2329 + Orion changes for switch to new OS - Rocky-9 #2336 (#2324) * CICE - Adds restart write capability at the end of a run for CICE * FV3 - * atmos_cubed_sphere - Update submodule FV3/atmos_cubed_sphere to fix a typo when printing out the nest grid corner locations * doc/UsersGuide/requirements.txt: Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.1 to 2.2.2. * Orion Spack stack modulefile update: Rocky-9 * update detect_machine.sh: hercules

… similar to hydrostatic method (#2327) * atmos_cubed_sphere - A new parameter, pass_full_omega_to_physics_in_non_hydrostatic_mode, has been added in dycore. When set to true, the omega calculation will match that of hydrostatic runs, using the formula omega = dp/dt. The default value is false, where the calculation remains omega = w * dp/dz as before.

* HR4 GWD update for FV3 * point to PR#549 of ccpp-framework * Update default_vars.sh: GWD parameters * Update global_control.nml.IN * update cpld case GWD parameters: gfsv17 * Update Jenkinsfile.combined fix multi-label removal * Update Jenkinsfile for ORT Pipeline * update input oro files for control_run.IN: gsfv17 --------- Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Jong Kim <[email protected]> Co-authored-by: Dustin Swales <[email protected]> Co-authored-by: zach1221 <[email protected]>

* UFSWM - * FV3 - * atmos_cubed_sphere - bug fix to address debug mode crashes caused by floating-point exception in subroutine a2b_ord2 in model/a2b_edge.F90

…nd PR#2265) (#2335) * UFSWM - restore error checking to regression test system and add a self-test suite - Detect_machine.sh identifies Frontera --------- Co-authored-by: Sam Trahan <[email protected]> Co-authored-by: Benjamin Cash <[email protected]>

… in the GFS physics suite (#2340) * ccpp-physics - update convection and PBL schemes to improve cloud/convection interaction * Output updraft value of convective cloud condensate in FV3 and CCPP * update xkinv1 to 0.15 * add check if progsigma is true

* HR4 land surface upgrades to address surface cold biases * update noahmp table

* CMEPS - Sync CMEPS with ESCOMP/main.

* UFSWM - Fix dumpfields=true option in FV3 by using ESMF_FieldBundleWrite * FV3 - Fix dumpfields=true option by using ESMF_FieldBundleWrite * Update rt_utils.sh. Set ECF_HOST on wcoss2 explicitly

* UFSWM - Adds pass_full_omega_to_physics_in_non_hydrostatic_model parameter in the global_control.nml.IN namelist and sets it to true for non-hydrostatic runs. An additional field (omga) has been added to the diag_tables.

…omponents (#2370) * UFSWM - * CICE - initialize scalar field when created * MOM6 - initialize scalar field when created * WW3 - initialize scalar field when created

…s arrays (#2183) * UFSWM - In fv3atm and submodules, convert internal GFS DDTs from blocked data structures to contiguous arrays. This excludes the (external) `GFS_extdiag` and `GFS_restart` DDTs. * AQM - * CDEPS - * CICE - * CMEPS - * CMakeModules - * FV3 - Convert GFS DDTs from blocked data structures to contiguous arrays (not including GFS_restart and GFS_extdiag DDTs) * ccpp-physics - Convert GFS DDTs from blocked data structures to contiguous arrays (affects `GFS_debug.{F90,meta} only`) * atmos_cubed_sphere - Convert GFS DDTs from blocked data structures to contiguous arrays and remove IPD_Data super DDT * GOCART - * HYCOM - * MOM6 - * NOAHMP - * WW3 - * stochastic_physics -

… FV3 diag table documentation #2277 + SKEB fix with d_con = zero #2374 (#2278) * UFSWM - python scripts for yaml and rocoto-xml conversion, experiment setup, and test log output * Add python superlint option * Documentation update: doc/UsersGuide/source/tables/fv3_diag_table.rst * FV3 - * atmos_cubed_sphere - bugfix: allocates heat_source when skeb is True and d_con is zero

* using MOM6 test branch add MOM_dynamics_split_RK2b.F90 and MOM_EOS_base_type.F90 in cmake list add extra 8PE for cpld_debug_pdlib job set DEFAULT_ANSWER_DATE=20231231 in 5x5 case add USE_HUYNH_STENCIL_BUG = True in MOM_input using MOM6 restart file as BL for sfs and hafs_mom jobs * remove USE_HUYNH_STENCIL_BUG = True in MOM_input switch FIX_USTAR_GUSTLESS_BUG=F to USTAR_GUSTLESS_BUG=T * switch FIX_USTAR_GUSTLESS_BUG to USTAR_GUSTLESS_BUG for MOM_input_hafs * set USE_HUYNH_STENCIL_BUG = True

) * UFSWM - Update the MOM_input templates and RT scripts to allow use of downscaled MOM6 and CICE6 warmstarts. * update script variables and sfs test

* UFSWM - update g2tmpl library, g2 library, UPP hash. Sync parm files with new UPP version. * FV3 - update inline post for UPP, point UPP submodule to head of develop, revise spack.yaml

…ng in rt.sh (2388) + Add ability to read increment files on native cubed sphere grid (2304) (#2389) * UFSWM - Unify CDEPS gfs, cfsr, and gefs datm datamodes. Add ability to read increment files on native cubed sphere grid. Update rt scripts to fix checking the job exit status from Slurm and PBS schedulers. * FV3 - Add namelist parameter for cubed sphere increment read and update atmos_cubed_sphere hash for GFDL Atmospheric Cubed Sphere PR #[342](NOAA-GFDL/GFDL_atmos_cubed_sphere#342) * atmos_cubed_sphere - Add ability to read increments from files on native cubed sphere grid * CDEPS - Unify CDEPS gfs, cfsr, and gefs datm datamodes. Rename CDEPS-related FILENAME_BASE to FILEBASE_DATM in tests. Sunset gfs_hafs datamode.

…3/SAS/MYNN fix) (#2408) * UFSWM - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme * FV3 - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme * ccpp-physics - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from the MYNN PBL scheme

…Switch to using Aux history files in atm_ds2s_docn_dice test; Remove IFI tests (was #2417) (#2395) * UFSWM - * CMEPS - fix aux history functionality; sync with ESCOMP * UFSWM - use auxiliary history files as input for atm_ds2s_docn_dice; remove the IFI tests

*MOM6 - update MOM6 to its main repo. 20240824 updating (GFDL's FMA PR)

* UFSWM - Update default parameter values for damping based off of work done for GW

* UFSWM - The fire_behavior component has been added and a new application created 'ATMF'. This work also includes a new regression test 'cpld_regional_atm_fbh' for testing two-way coupling of the atm component (fv3atm) and fbh component (fire_behavior) * CMEPS - CMEPS required modifications to be aligned with the changes to the ccpp physics package * FV3 - the fv3 cap has been modified to export atmosphere forcing data to the fire component when 'cpl_fire' is set to true. It will also import new fields for physics. * ccpp-physics - the ccpp physics package has been modified to add heat fluxes, upward specific humidity flux, and a smoke tracer from the fire component.

…#2430) * UFSWM - Use EMC/CICE:develop branch from CICE-Consortium:main * CICE - Use EMC/CICE:develop branch from CICE-Consortium:main

Commits on Feb 1, 2023

update CMEPS (#1570 )

* update CMEPS

DeniseWorthen committed Feb 1, 2023

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sync with the develop branch #13

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