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Port g-w for GEFS to WCOSS2/acorn #345

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XianwuXue-NOAA opened this issue Jun 14, 2021 · 6 comments
Closed

Port g-w for GEFS to WCOSS2/acorn #345

XianwuXue-NOAA opened this issue Jun 14, 2021 · 6 comments
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@XianwuXue-NOAA
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GEFS Update for GEFS branch port Porting the system to a new platform

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@XianwuXue-NOAA
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No description provided.

@XianwuXue-NOAA XianwuXue-NOAA self-assigned this Jun 14, 2021
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 14, 2021
@XianwuXue-NOAA
Port program enkf_chgres_recenter_nc to acorn
3bda226 
 On branch release/gefs_v12_github_port2acorn
	new file:   modulefiles/fv3gfs/enkf_chgres_recenter_nc.acorn
	modified:   sorc/machine-setup.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 15, 2021
@XianwuXue-NOAA
Port gfs_bufr & tocsbufr to acorn
13d4540 
Issue is there is no SIGIO_LIB4 & SIGIO_INC4 in module sigio/2.3.2
	I use SIGIO_INC and SIGIO_LIB to assign values to them

 On branch release/gefs_v12_github_port2acorn
	new file:   modulefiles/gfs_bufr.acorn

Refs: NOAA-EMC#345
@WalterKolczynski-NOAA
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This should be two separate issues.

@XianwuXue-NOAA
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Thanks. Walter, could you separate it two issues?

@WalterKolczynski-NOAA WalterKolczynski-NOAA changed the title Port g-w for GEFS to WCOSS2/acorn and update some components in g-w from vlab to GitHub Port g-w for GEFS to WCOSS2/acorn Jun 22, 2021
@WalterKolczynski-NOAA WalterKolczynski-NOAA added port Porting the system to a new platform GEFS Update for GEFS branch labels Jun 22, 2021
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 24, 2021
@XianwuXue-NOAA
Change the components in g-w to use my repo
cd784f5 
For the next porting to acorn

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 25, 2021
@XianwuXue-NOAA
Add acorn to sorc/machine-setup.sh
28959d2 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/machine-setup.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 25, 2021
@XianwuXue-NOAA
Port program enkf_chgres_recenter_nc to acorn
6455a1b 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	new file:   modulefiles/fv3gfs/enkf_chgres_recenter_nc.acorn

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 25, 2021
@XianwuXue-NOAA
Port gfs_bufr & tocsbufr to acorn
9a073b7 
Issue is there is no SIGIO_LIB4 & SIGIO_INC4 in module sigio/2.3.2
	I use SIGIO_INC and SIGIO_LIB to assign values to them

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	new file:   modulefiles/gfs_bufr.acorn

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jun 25, 2021
@XianwuXue-NOAA
Port sorc/build_gsd_prep_chem.sh to acorn
35ab5a5 
 On branch feature/gefs_v12_github_port2acorn
	modified:   sorc/build_gsd_prep_chem.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jul 22, 2021
@XianwuXue-NOAA
Add acorn to build_ufs_utils.sh
41fdb45 
 On branch feature/gefs_v12_github_port2acorn
	modified:   sorc/build_ufs_utils.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jul 30, 2021
@XianwuXue-NOAA
Update modules after Acorn environment changed
2b9a2d2 
 On branch feature/gefs_v12_github_port2acorn
	modified:   modulefiles/fv3gfs/enkf_chgres_recenter_nc.acorn
	modified:   modulefiles/gfs_bufr.acorn
	modified:   sorc/machine-setup.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Jul 30, 2021
@XianwuXue-NOAA
Update the checkout repo/branches for transition
606afde 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Aug 10, 2021
@XianwuXue-NOAA
Change acorn to wcoss2
76d6b69 
 On branch feature/gefs_v12_github_port2acorn
	renamed:    modulefiles/fv3gfs/enkf_chgres_recenter_nc.acorn -> modulefiles/fv3gfs/enkf_chgres_recenter_nc.wcoss2
	renamed:    modulefiles/gfs_bufr.acorn -> modulefiles/gfs_bufr.wcoss2
	modified:   sorc/build_gsd_prep_chem.sh
	modified:   sorc/build_ufs_utils.sh
	modified:   sorc/machine-setup.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 9, 2021
@XianwuXue-NOAA
Remove jlogfile and modify format of wavempexec
f1929b8 
1) Remote jlogfile
2) Modify format of wavempexec, however, may be changed
	in the future

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   scripts/exwave_init.sh
	modified:   scripts/exwave_prep.sh
	modified:   ush/wave_grid_moddef.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 9, 2021
@XianwuXue-NOAA
Update the checkout.sh to checkout latest repos
c956245 
which have ported to WCOSS2

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 9, 2021
@XianwuXue-NOAA
Port link_fv3gfs.sh to WCOSS2 and improve it
e82f1c4 
To link needed parm file for chem to parm
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/link_fv3gfs.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 9, 2021
@XianwuXue-NOAA
Add calc_increment_ens_ncio.x to link_fv3gfs.sh
af38db9 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/link_fv3gfs.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 9, 2021
@XianwuXue-NOAA
Remove the unused sorc folders in link_fv3gfs.sh
b5c9d9b 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/link_fv3gfs.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 23, 2021
@XianwuXue-NOAA
Add version of PrgEnv-intel and use hdf5/netcdf
7ab32de 
1) Add version of PrgEnv-intel
2) Replace hdf5-parallel/netcdf-hdf5parallel using hdf5/netcdf

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   modulefiles/fv3gfs/enkf_chgres_recenter_nc.wcoss2
	modified:   modulefiles/gfs_bufr.wcoss2

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 24, 2021
@XianwuXue-NOAA
Remove jlogfile and modify waveexe for wcoss2
404edb3 
1) Remove jlogfile based on new standard for wcoss2
2) Modify the format of wavempexec for wcoss2

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   scripts/exglobal_fcst_nemsfv3gfs.sh
	modified:   scripts/exwave_init.sh
	modified:   scripts/exwave_post_sbs.sh
	modified:   scripts/exwave_prep.sh
	modified:   scripts/exwave_stat.sh
	modified:   ush/wave_ens_bull.sh
	modified:   ush/wave_ens_stat.sh
	modified:   ush/wave_grib2_sbs.sh
	modified:   ush/wave_grid_interp_sbs.sh
	modified:   ush/wave_grid_moddef.sh
	modified:   ush/wave_outp_spec.sh
	modified:   ush/wave_prnc_ice.sh
	modified:   ush/wave_tar.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Sep 30, 2021
@XianwuXue-NOAA
Change back for scripts/exwave_stat.sh
98a5a9f 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   scripts/exwave_stat.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Oct 15, 2021
@XianwuXue-NOAA
Change NETCDF4 to NETCDF,remove "-lhdf5_hl -lhdf5"
8ac03a5 
Due to the new NetCDF lib
1) Change NETCDF4 to NETCDF
2) Remove "-lhdf5_hl -lhdf5"
Update gfsfix path to Kate's path

 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   enkf_chgres_recenter_nc.fd/CMakeLists.txt
	modified:   enkf_chgres_recenter_nc.fd/src/makefile
	modified:   link_fv3gfs.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Oct 16, 2021
@XianwuXue-NOAA
Update some modules using new versions
3f4a5de 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   ../modulefiles/fv3gfs/enkf_chgres_recenter_nc.wcoss2
	modified:   ../modulefiles/gfs_bufr.wcoss2

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Oct 16, 2021
@XianwuXue-NOAA
Update modules to new version in gfs_bufr
d4ad994 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   modulefiles/gfs_bufr.wcoss2

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Oct 20, 2021
@XianwuXue-NOAA
Update build modules to remove hardwired ver nums
b3ad62b 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   modulefiles/fv3gfs/enkf_chgres_recenter_nc.wcoss2
	modified:   modulefiles/gfs_bufr.wcoss2

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Oct 27, 2021
@XianwuXue-NOAA
Change UPP from Xianwu.Xue repo to EMC repo
5539bfb 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 4, 2021
@XianwuXue-NOAA
Update checkout.sh to use new gsi branch
59feb05 
 On branch feature/gefs_v12_github_port2acorn
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 5, 2021
@XianwuXue-NOAA
Update gsd-prep-chem to use NOAA-GSL repo
c330c2e 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 8, 2021
@XianwuXue-NOAA
Update checkout.sh to switch back to EMC repo
c025be3 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 10, 2021
@XianwuXue-NOAA
Update gsi back to EMC repo in checkout.sh
f170fe9 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 13, 2021
@XianwuXue-NOAA
Update checkout.sh to use tag of UPP
f310f3c 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 13, 2021
@XianwuXue-NOAA
Change FV3-GSDCHEM-WW3 back to EMC repo
3e39692 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 15, 2021
@XianwuXue-NOAA
Clean up the unused statements
7c12d40 
 On branch feature/gefs_v12_github_port2acorn
	modified:   scripts/exwave_init.sh
	modified:   scripts/exwave_post_sbs.sh
	modified:   scripts/exwave_prep.sh
	modified:   sorc/machine-setup.sh
	modified:   ush/wave_grid_moddef.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 16, 2021
@XianwuXue-NOAA
Change checkout branch to tag for FV3-GSDCHEM-WW3
402b83f 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/checkout.sh

Refs: NOAA-EMC#345
XianwuXue-NOAA added a commit to XianwuXue-NOAA/global-workflow that referenced this issue Nov 16, 2021
@XianwuXue-NOAA
Remove unused statements
5368f4d 
 On branch feature/gefs_v12_github_port2acorn
 Changes to be committed:
	modified:   sorc/enkf_chgres_recenter_nc.fd/src/makefile
	modified:   sorc/link_fv3gfs.sh

Refs: NOAA-EMC#345
@arunchawla-NOAA
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@XianwuXue-NOAA is this issue complete ?

@XianwuXue-NOAA
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Almost done, since we have the MPI-allreduce issue in GSI, though this is a system issue, we can fix it, however, we need to work with Steven and George to finalize it next week. After this fix, I will close this issue.

@XianwuXue-NOAA
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@arunchawla-NOAA The issue I mentioned in the previous comment is NOAA-EMC/GSI#289

@XianwuXue-NOAA
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@arunchawla-NOAA I will close this issue since NCO has updated the gsi code using our modified file. And I am merged my changes to the branch and update the tag.

zhanglikate pushed a commit to zhanglikate/global-workflow that referenced this issue Oct 6, 2022
@DeniseWorthen @junwang-noaa
Update CMEPS (NOAA-EMC#345)
6daad90 
* Update CMEPS for recent changes, including addition of new run "post" run phases to eliminate redundant mapping, multiple ice sheet capability and ocn->land ice dynamic mapping
* Add a new test fv3_gfs_v16_RRTMGP_c192L127

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
zhanglikate pushed a commit to zhanglikate/global-workflow that referenced this issue Oct 6, 2022
@climbfuji @pjpegion
@jiandewang @DeniseWorthen @DusanJovic-NOAA @mark-a-potts @binli2337 @dustinswales @kgerheiser @RatkoVasic-NOAA @aliabdolali @junwang-noaa @XiaqiongZhou-NOAA @mlee03 @ValeryYudin-NOAA @mdtoyNOAA @MinsukJi-NOAA
Update gsl develop from master (NOAA-EMC#63)
56e9901 
* Updates to stochastic_physics_wrapper (NOAA-EMC#280)

Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (NOAA-EMC#304)

Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms).

The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc).

* Feature/update mom6 and retain b4b results for 025x025 resolution (NOAA-EMC#290)

* point MOM6 to new branch which corresponding to GFDL 20201022 commit
* modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM6 code as this version of MOM6 contains some file deletion, new files being added and renaming of files
* manually set MOM6 parameters in order to retain origonal results for 0.25x0.25 resolution
* update MOM6 to include Bugfix for mom6solo to be built
* modify compile.sh to allow mom6solo compiling
* modify MOM_input_template for all resolutions based on GFDL MOM6-example main branch update on 20201022
* change executable permissions for CMakeLists.txt
* chmod 644 to 6 files Dom pointed out
* chmod for CMakeLists.txt and tests/compile.sh
* change baseline directpory to 20201202 in rt.sh

* Update CICE, Move regression test input outside baseline directory (NOAA-EMC#270)

*Updates CICE to most recent develop branch of NOAA-EMC
* Sets n_aero (number of aerosols) in ice_in_template to 0.
* removes trailing whitespace from ice_in
* moves regression test input outside baseline directory (ufs-weather PR NOAA-EMC#312)

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

* Updates to build for JEDI linking/control, add wcoss2 (#295)

* Build on wcoss2 (acorn)
* Use -march=core-avx2 instead of -xCORE-AVX2 on wcoss2
* Updates to build for JEDI linking/control
* Removed unnecessary include files and INLINE POST setting
* Updated to address PR suggestions.
* Add rt_acorn.conf. Change /lfs/h2 to /lfs/h1.
* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* regression test results
* Updated .gitmodules and removed extraneous file
* Fixed .gitmodules and updated pointer for FV3
* Updated pointer to NEMS repo
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Final-final GFS v16 updates / restart reproducibility bugfixes (NOAA-EMC#325)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Add GFS v16 beta restart test, update stochastics test
* Update regression test baseline date tag to 20201214; skip-ci
* tests/rt.conf: bugfix, add missing 'fv3' to new stochy tests; skip-ci
* Regression test logs for gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci
* Run GFS v16beta tests also on wcoss; regression test logs for wcoss; skip-ci
* Regression test logs for cheyenne.intel and cheyenne.gnu
* Revert change to .gitmodules and update submodule pointer for fv3atm

* Add optional bulk flux calculation in ufs-datm (NOAA-EMC#266)


* Update NEMS DATM and CMEPS to allow the optional bulk flux formulation; add two tests using the option
* Update top level CMakeList.txt to have compile flags for MOM6 and CICE6 identical for ufs-cpld and ufs-datm
* Add optional configuration variable to nems.configure to specify the directory where CMEPS will write restarts
* Adds cheyenne tasking variables to default_vars and sets WW3_COMP to cheyenne for platform cheyenne.intel 

*NOTE: Baselines develop-20201215 exist on all platforms, regression tests were run against exactly that baseline on all systems except cheyenne.intel. On cheyenne.intel the tests were run against 20201214, and this baseline is identical to 20201215 (as per "diff -r develop-20201214 develop-20201215").

Co-authors:
@DusanJovic-NOAA
@aerorahul
@JessicaMeixner-NOAA

skip-ci

* Add 2 new tests for DATM-MOM6-CICE6 application (NOAA-EMC#332)

* Add the following 2 tests: datm_restart_cfsr, datm_debug_cfsr
* Add wcoss_dell_p3.log.
* Add Hera log, Orion log, wcoss_dell_p3 log.

* RRTMGP and Thompson MP coupling (NOAA-EMC#323)

* Feature branch with RRTMGP and Thompson MP
* Updated FV3/ccpp-physics. Added namelist and configuration for RRTMGP RTs using GSD physics.
* Updated FV3
* Update physics in FV3
* Updated baselines in rt.sh
* Updated RT logs. Updated FV3 physics submodule pointer.
* Updated FV3 hash and .gitmodules

* Regression test log for PR NOAA-EMC#323 for jet.intel (NOAA-EMC#336)

* Update modules with hpc-stack v1.1.0 (NOAA-EMC#319)

* Update modules with hpc-stack v1.1.0
* Minor bug fixes to CCPP UGWP

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* Replace old regional SDF with FV3_GFS_v15_thompson_mynn (NOAA-EMC#333)

* Replace old FV3_GFS_2017_gfdlmp_regional SDF for regional tests with FV3_GFS_v15_thompson_mynn.
* Final path to IC's and new results.  Also, input.nml updated.
* Update RegressionTests_wcoss_dell_p3.log
* Update RegressionTests_wcoss_cray.log
* Update RegressionTests_hera.intel.log
* Update RegressionTests_jet.intel.log
* Update RegressionTests_orion.intel.log
* Update RegressionTests_cheyenne* logs.
* Update RegressionTests_hera.gnu.log

* Feature/ww3update (NOAA-EMC#334)

This updates the WW3 submodule pointer to point to the top of the WW3 develop branch.
The path to WW3 inputs is changed to input-data-20201201/WW3_input_data_20201207/

* Remove IPD (step 1) (NOAA-EMC#331)

Make CCPP=Y the default in tests/compile.sh. Remove CCPP=Y from tests/rt*.conf and adjust formatting.
Update submodule pointer for MOM6 to include PR NOAA-EMC#341 ("Update MOM6 to GFDL's 20201218 commit")
Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3)
Fix broken utest (see NOAA-EMC#348)

* Update the format of rt.conf (NOAA-EMC#349)

Update the format of MACHINES column in rt.conf (and other .conf files). This column can be either empty, which means a test will run on all supported machines, or start with - or + sign to exclude or include specified machines explicitly.

* Add checkpoint restarts for ufs-cpld (NOAA-EMC#342)


* Adds 3 checkpoint restart tests for the ufs-cpld model
* Drops the existing c92mx025 restart test
* Adds cheyenne.intel as tested configuration for ufs-cpld and ufs-datm
* Fixes instances of srf_data* in various fv3_conf files

* add frac grid input, update and add additional cpld tests (NOAA-EMC#354)


* Updates FV3_input_frac to add both benchmark dates and L127 files
* Adds additional tests and restart tests for coupled model
* Sets all cpld tests to use frac grid input by default
* Removes all instances of  USE_LA_LI2016=True except for benchmark+wave configurations

* Remove unnecessary SIMD instruction sets for Jet, first round of cleanup in rt.conf, initialize cld_amt to zero for regional runs (dycore) (NOAA-EMC#353)

* Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake
* First cleanup of regression test config tests/rt.conf
* tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5
* Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files
* Remove tests/rt_acorn.conf and run GFS v15p2 and GFS v16beta DEBUG tests on all platforms

* Implementation of CCPP timestep_init and timestep_final phases (NOAA-EMC#337)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Update submodule pointer for fv3atm; skip-ci
* Don't try to compile all suites in DEBUG mode on cheyenne.intel, weird bug on compute nodes; skip-ci
* Don't try to compile all suites in DEBUG mode on wcoss_cray; skip-ci
* Regression test logs for cheyenne.gnu, cheyenne.intel, gaea.intel, hera.gnu, hera.intel, jet.intel, orion.intel; skip-ci
* Don't try to compile all suites in DEBUG mode on wcoss_dell_p3; skip-ci
* Regression test logs for wcoss_cray and wcoss_dell_p3
* Revert change to .gitmodules and update submodule pointer for fv3atm

* Update CMEPS  (NOAA-EMC#345)


* Update CMEPS for recent changes, including addition of new run "post" run phases to eliminate redundant mapping, multiple ice sheet capability and ocn->land ice dynamic mapping
* Add a new test fv3_gfs_v16_RRTMGP_c192L127

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Remove IPD steps 3 and 5 (NOAA-EMC#357)

Reduce SIMDMULTIARCH sets from four to two in cmake/Intel.cmake
* First cleanup of regression test config tests/rt.conf
* tests/rt.sh: reduce number of build jobs on jet.intel from 10 to 5; skip-ci
* Remove flags -f and -s from rt.sh, remove SET logic, remove corresponding column in all rt*conf files
* Update usage in rt.sh, add modulefiles/jet.intel/fv3_debug; skip-ci
* CCPP is default in cmake build
* Add debug modulefiles for linux.gnu and macosx.gnu
* Update submodule pointer for fv3atm
* Change logic in CMakeLists.txt and tests/compile.sh so that 32BIT=ON automatically sets DYN32=ON; skip-ci
* Move logic to set DYN32 - depending on 32BIT setting - to fv3atm
* Remove -DCCPP=ON from tests/compile.sh; update submodule pointer for fv3atm; skip-ci

* point fv3 to EMC develop branch (NOAA-EMC#377)

* update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (NOAA-EMC#378)

* update CMEPS, fix character length error for gnu compile
* add Dusan's fix for rt_utils.sh
* update cpl gfsv16 tests, replace seaice_newland.grb with global_slmask.t1534.3072.1536.grb, recover input.mom6.nml.IN, update input directory, update global thread and decomp tests, update fdiag for global control
* point to Dustins rrtmgp fix branch
* update input directory

Co-authored-by: denise.worthen <Denise.Worthen@noaa.gov>
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (NOAA-EMC#386)

* Update .gitmodules and submodule pointer for fv3atm for gsl/develop branch
* RUC ice for gsl/develop (replaces NOAA-EMC#47) (NOAA-EMC#49)Implementation of RUC LSM ice model in CCPP
* Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop
* Add kice=9 to tests/tests/fv3_ccpp_rap and tests/tests/fv3_ccpp_hrrr
* Change NEW_BASELINE directory for gsl/develop to avoid conflicts with development work on the authoritative branches
* Add KICE=9 to tests/tests/fv3_ccpp_gsd_unified_ugwp and tests/tests/fv3_ccpp_gsd_drag_suite_unified_ugwp
* Revert change to .gitmodules and update submodule pointer for fv3atm
* Update gsl/develop from develop 2020/12/08 (NOAA-EMC#50)
* Updates to stochastic_physics_wrapper (NOAA-EMC#280)
Fix to stochastic_physics_wrapper to allow for random patterns to update at a longer time-step than model
* Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T  (NOAA-EMC#304)
Update the modulefile for jet.intel to enable UPP v10.0.0. The hpc-stack v1.0.0 pre-release is used for this. Small changes are made to tests.rt.sh for jet.intel and gaea.intel (consistency with other platforms).
The submodule pointer update for fv3atm addresses bugs in the ufs-weather-model with frac_grid=T and GFDL microphysics, and with restarting the model when frac_grid=T (from @shansun6 and @SMoorthi-emc).
* Land stochastic perturbations (NOAA-EMC#57)

* dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (NOAA-EMC#369)

* Update fv3atm
* update ccpp control test forecast length to 24h
* remove rename command
* Add CI related changes
* Update RT logs
* Update RT log files
* Add the gaea RT log file
* Update the point of fv3atm
* Update fv3atm
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>

* MOM6 bugfixes, GFDL update, update CDMBGWD settings; fix for restart reproducibility (without waves) when USE_LA_LI2016=True, sign error on fprec passed to ocean, GFDL update, resolution dependent cdmbgwd settings (NOAA-EMC#379)


* implements two MOM6 bugfixes in the NUOPC MOM6 cap to allow restart reproducibility when USE_LA_LI2016=True and to change the sign of the latent heat flux associated with frozen precipitation (fprec) exported to MOM6

* updates MOM6 to include the GFDL 20210120 main branch which contains EMC's wave coupling code, alone with some minor code standardization and documentation

* updates the cdmbgwd namelist settings for FV3 standalone tests at C96 and implements resolution dependent values for ufs-cpld tests

Co-authored-by: Ali <ali.abdolali@noaa.gov>

* Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (NOAA-EMC#384)

* Update .gitmodules and submodule pointers for fv3atm and NEMS
* Remove Python 2.7 support from top-level CMakeLists.txt
* Reduce forecast length of test fv3_ccpp_gfs_v16_RRTMGP_c192L127 from 24h to 12h
* Rename v16beta to v16 everywhere except the public release documentation
* Bugfixes and missing changes
* Remove 'export CCPP_LIB_DIR=ccpp/lib' from all regression tests
* Update regression test baseline date tag to 20210128; skip-ci
* Update ecflow-python environment on cheyenne and jet; skip-ci

* Update CMEPS for HAFS integration; add datm and coupled-model tests on Gaea (NOAA-EMC#401)


* Add HAFS support in NOAA-EMC/CMEPS 
* Add coupled and datm tests for Gaea.intel

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov>

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2)  (NOAA-EMC#407)

* Regression test logs for all tier=1 platforms

* updates FMS to 2020.04.01 (NOAA-EMC#392)

* updates FMS to 2020.04.01
* fixes fms_files.cmake
* removes extra horiz_interp
* Workaround for FMS 2020.04.01 for Cheyenne with GNU 9.1.0, incl. regression test log
Co-authored-by: Mikyung Lee <mlee@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

* add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (NOAA-EMC#399)

*Implements an optional setting in the cpld and datm nems.configure files to specify whether the MOM6 cap should use a mesh or a grid

*Adds configurable settings for min_seaice to gfs_physics_nml and dz_min to fv_core_nml.

* UGWP v0 v1 combined (NOAA-EMC#396)

- combines the changes in PRs NOAA-EMC#360 and NOAA-EMC#382
- adds three regression tests `fv3_ccpp_gfsv16_ugwpv1 `, `fv3_ccpp_gfsv16_ugwpv1_warmstart` and `fv3_ccpp_gfsv16_ugwpv1_debug`
- contains updates and bugfixes for `nc_compare.py` and the CI tests from @MinsukJi-NOAA 
- update Python3 environment on jet.intel, gaea.intel, cheyenne.{intel,gnu}
- turn off (again) test `fv3_ccpp_decomp` on jet.intel, this test didn't work in the past, but recently it "passed", because the error checking with `nc_compare.py` failed silently and we didn't notice it

Co-authored-by: valery.yudin <valery.yudin@noaa.gov>
Co-authored-by: Michael Toy <michael.toy@noaa.gov>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>

* Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (NOAA-EMC#419)" (NOAA-EMC#421)

* Add one regional regression test in DEBUG mode.
* Update .gitmodules and submodule pointer for fv3atm for code review and testing
* Update regression tests from GFSv15+Thompson to GFSv16+Thompson
* Combine several COMPILE lines in tests/rt.conf and tests/rt_gnu.conf
* Regression test log for cheyenne.{gnu,intel},gaea.intel, hera.gnu, jet.intel,hera.intel,orion.intel;wcoss_cray and wcoss_dell_p3;

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
Co-authored-by: dustinswales <dustin.swales@noaa.gov>
Co-authored-by: Kyle Gerheiser <3209794+kgerheiser@users.noreply.github.com>
Co-authored-by: RatkoVasic-NOAA <37597874+RatkoVasic-NOAA@users.noreply.github.com>
Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com>
Co-authored-by: Ali <ali.abdolali@noaa.gov>
Co-authored-by: Bin Li <Bin.Li@gaea13.ncrc.gov>
Co-authored-by: MiKyung Lee <58964324+mlee03@users.noreply.github.com>
Co-authored-by: valery.yudin <valery.yudin@noaa.gov>
Co-authored-by: Michael Toy <michael.toy@noaa.gov>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
kayeekayee pushed a commit to kayeekayee/global-workflow that referenced this issue May 30, 2024
@junwang-noaa
Flexible output hour for history files (NOAA-EMC#345)
f8732ff 
* add flexibile output time
* add fcst_mpi_comm to GFS_init_type Init_parm in atmos_model_init, remove commglobal communicator
* update output_fh for fms history output,  fix output_startfh initialization
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