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Feature/gfsv16b wave #2

Merged
merged 2 commits into from
Aug 25, 2020
Merged

Feature/gfsv16b wave #2

merged 2 commits into from
Aug 25, 2020

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KateFriedman-NOAA
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@JessicaMeixner-NOAA JessicaMeixner-NOAA merged commit f0e3ae5 into JessicaMeixner-NOAA:feature/gfsv16b-wave Aug 25, 2020
JessicaMeixner-NOAA added a commit that referenced this pull request Sep 9, 2020
@JianKuang-Intelsat @JessicaMeixner-NOAA
@ajhenrique @KateFriedman-NOAA @lgannoaa
wave configuration update (NOAA-EMC#81)
a329e10 
* Pointing to v3.1 tag for ufs-s2s-model
making readme consistant with user.yaml.default

* bug fix, POSTGRB2TBL undefined

* Squashing commits to wave2global

* Fix to JWAVE_PREP to look back a day for rtofs

* Moving standalone fv3 model_config exglobal_fcst block into if/else/fi cplwav model_config block. Reinstating config.wave block in JGLOBAL_FORECAST. Pointing EXECwave to HOMEgfs/exec directory for WW3 util executables (changed link_fv3gfs.sh accordingly). Removing debug options from compile.sh line in build_fv3.sh.

* Clean up exwave_post_sbs

* clean up unused schema
move default value into defaults/

* move all default values into /defaults from /schema

It's better if we have one place to manage default values
for configurable variables other than two

Default values only for reference.

Please throughly test to make sure it could reproduce.

* model_configure_DATM

* merge in the latest revision from IPD work

* add stoch variables to config.fcst
scripts update: CCPP and IPD works

* capital case CDUMP values in config.fv3

* stochy variable namelist update,
add hard-coded variables into config.fcst (fcst.yaml)

* OCNTIM and ICETIM are included in config.fv3
ice variable istep0 bug fix

* stochastic variables update

* delete falseful copy after namelist and model_configure parsing
add FNMSKH conditional clause, coupled vs non-coupled

* update on sandbox platform, for FIX_SCRUB settings

* turn off stochastic features in case file

* configuration update for CCPP scripts

* generalize fix file directory for imp_physics 8

* reiflag default value changed to 1

* port to Orion

* remove HERA-like paths in platform.yaml of Orion

* checkout and External.cfg update

* update checkout and External.cfg

* case file adjustment for Orion IC

* expand gitignore

* automate fix file linking, to this location:
/work/noaa/marine/jmeixner/tempFixICdir/fix/fix_prep_benchmark3

* updates to checkout, build and link to run prototype 4

* update UPP version to v1.0.8

* making Externals_coupled.cfg consistent with checkout.sh

* removing fix from .gitignore

* fixed error when linking on hera

* replace MOM6IC with BASE_CPLIC for base directory location of
IC for s2s model and made it platform dependent.
(Orion location is temporary and needs to be replaced, can also be
changed in cases/coupled_free_forecast.yaml to users prefered location)

* updates for copying ICs

* more updates for ICs

* updates for new fix (which includes prep for multiple resolutions) and some clean-up

* renaming exe to reflect updated build

* update diag_table for ocean

* updates for ice_in to match prototype 4

* updates for CCPP suite used in p4

* making a fix dir of all available ccpp suite files
copying suite xml file to rundirectory

* updating for reorganized tar files, pulling in changes from wcoss-p2 workflow

* last of archive updates for p4

* updating module files to match s2s model and ncep post modules

* we don't want to cycle/have 4 runs per day so setting the cases to be just 1 IC

* updating module files on hera

* updates to readme for orion

* mediator cold start succeeds on hera and forecast job starts
post jobs for atmosphere are no longer triggered on cold starts

* adding ncks, updating ocean post, some fixes for tar files

* updates for tar files and do not keep data

* fix typo

* updating module_base.orion that allows cold start to run.
Not sure if other jobs will now fail though or if what is in your
.bashrc file will effect the success/failure of the run.

* both forecast and atm post seem to be running okay on orion

* wave configuration files

* wave configuration update

* fix module-setup.sh.inc script, which causes module purge unsuccessful

* 1, Moved some of the variables into configuration system from JWAVE scripts
2, Wave configuration system built out
3, Modularized scripts updated to accomodate wave variables

* Fix suite name of CCPP
Move cplwav and cplwav2atm variable

* Revise CCPP_SUITE variable name, default option, to "IPD"

* wave post-process job update

* reg2grb2 for test on feature coupled-crow

* orion hera build test

* reg2grb2 Build on Hera and Orion

* Merged and ready for test

* add ocn-ice build to readme

* adding updates to wave scripts from gfsv16b branch by @ajhenrique

* cleaning up double cplwav

* changes to wave case

* bugfix in layout file

* bug fix in layout file

* move OCNPETS, ICEPETS and WAVEPETS into dedicated model-specific
sessions instead of fv3_gfs_settings

* first try for adding wave ICs

* fix bugs in config.wave and coupled_ic.sh

* updates for wave defaults for s2s p4

* updates for running wave jobs

* point WW3-related executables through HOMEgfs/fv3_coupled.fd/exec

* ocean post hours at boundary are processed twice, now fixed.

* wave init job now works on hera

* adding missing file from last commit

* add ocean, ice and wave configurable variables

* add ocean, ice and wave configurable variables

* put ic type variable into config.fv3ic

* wave init now works on orion

* updates to run wave prep for s2s case

* updating forecast job for wave jobs

* updates for forecast with waves

* at this point the ocean post is now running

* fix nems.configure for cold start

* updated wave-realted scripts to match gfsv16 branch
updated environment files env/ORION.env
updated configuration system

* S2s prototype4 (#2)

* add waves to jglobal forecast config

* updates - everything but wave post seems to run now, part of wave post does
updating model to latest tag

* change for lmod -> lmod/lmod on orion
updated README

* fixing syntax error in JWAVE_PREP job for variables that are not
actively being used

* adding cycle definition to wave post job

* cleanup from duplications

Co-authored-by: Jessica.Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Henrique Alves <henrique.alves@noaa.gov>
Co-authored-by: kate.friedman <kate.friedman@noaa.gov>
Co-authored-by: Jose-Henrique Alves <47567389+ajhenrique@users.noreply.github.com>
Co-authored-by: Lin.Gan <lin.gan@noaa.gov>
JessicaMeixner-NOAA pushed a commit that referenced this pull request Dec 3, 2020
@jkhender
merge 26Mar20 develop branch into gmtb_ccpp_hera
a847acc 
Squashed commit of the following:

commit 0e0dc87
Merge: b133700 95a6343
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Thu Mar 26 10:54:44 2020 -0400

    Merge pull request NOAA-EMC#42 from NOAA-EMC/hotfix/viewer

    Issue NOAA-EMC#41 - Update PRODUTIL paths for WCOSS in viewer

commit 95a6343
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Thu Mar 26 14:43:44 2020 +0000

    Issue NOAA-EMC#41 - Update PRODUTIL paths for WCOSS in viewer

commit b133700
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Thu Mar 26 13:01:38 2020 +0000

    Issue NOAA-EMC#21 - correct syntax for machine if-blocks in setup_expt scripts

commit f4ee509
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Mar 25 20:52:49 2020 +0000

    Issue NOAA-EMC#21 - remove unneeded logic from partition check

commit 4acc80f
Merge: accb6f4 fb1c79f
Author: Hang-Lei-NOAA <44901908+Hang-Lei-NOAA@users.noreply.github.com>
Date:   Wed Mar 25 15:22:51 2020 -0400

    Merge pull request NOAA-EMC#40 from NOAA-EMC/port2wcoss3p5

    Issue NOAA-EMC#21 - Add support for WCOSS phase 3.5

commit fb1c79f
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Mar 25 16:06:54 2020 +0000

    Issue NOAA-EMC#21 - updated WCOSS phase 3.5 queues

commit 08a5354
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Mar 25 14:58:14 2020 +0000

    Issue NOAA-EMC#21 - add phase 3.5 support

    - add partition option to setup scripts
    - remove machine if-blocks from config.base and add variable population to setup_expt*py scripts
    - add phase 3.5 ppn value to WCOSS_DELL_P3 env and config.resources files

commit accb6f4
Merge: 057b2a8 8b51b56
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Mon Mar 23 14:01:30 2020 -0400

    Merge pull request NOAA-EMC#39 from NOAA-EMC/feature/verif-tag

    Issue NOAA-EMC#38 - update EMC_verif-global pointer from VLab to GitHub

commit 8b51b56
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Mon Mar 23 17:40:18 2020 +0000

    Issue NOAA-EMC#38 - update EMC_verif-global pointer from VLab to GitHub

commit 057b2a8
Merge: 0377d20 622167d
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Wed Mar 11 12:00:58 2020 -0400

    Merge pull request NOAA-EMC#29 from NOAA-EMC/feature/manage_externals

    Issue #3 - Introduce manage_externals as replacement for checkout.sh

commit 622167d
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 18:20:31 2020 +0000

    Issue #3 - added explicit config flag example for checkout_externals in README and blurb about this replacing checkout.sh

commit e83b90d
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 17:00:15 2020 +0000

    Issue #3 - remove prod_util and grib_util sections from build_all.sh, removed elsewhere already

commit 8699b46
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 16:30:54 2020 +0000

    Issue #3 - updated README with new manic version

commit e602cd3
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 16:27:57 2020 +0000

    Issue #3 - updated link_fv3gfs.sh to adjust wafs links

commit 830c73f
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 15:21:45 2020 +0000

    Issue #3 - update EMC_verif-global tag in Externals.cfg after sync with develop

commit 40084e6
Merge: f662fff 0377d20
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Mar 6 15:18:52 2020 +0000

    Issue #3 - Merge branch 'develop' into feature/manage_externals

commit 0377d20
Merge: 1b359db 2552467
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Thu Mar 5 08:43:16 2020 -0500

    Merge pull request NOAA-EMC#28 from NOAA-EMC/feature/metplus2

    Issue #8 - add switch for MET+ jobs

commit 2552467
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Thu Mar 5 13:31:02 2020 +0000

    Issue #8 - add switch for MET+ jobs

commit 1b359db
Merge: 0359d34 31bb7d3
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Wed Mar 4 10:19:36 2020 -0500

    Merge pull request NOAA-EMC#26 from NOAA-EMC/feature/metplus

    Feature/metplus - refactored MET+ jobs to resolve timing issues

commit 31bb7d3
Merge: eb73e52 0359d34
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Wed Feb 19 15:24:42 2020 +0000

    Merge branch 'develop' into feature/metplus

commit f662fff
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Feb 14 15:57:05 2020 +0000

    Issue #3 - Updated README with new manic tag v1.1.7

commit e3196a8
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Thu Feb 13 15:59:06 2020 -0500

    Update README.md

commit e46b175
Merge: 4bd0e20 0359d34
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Thu Feb 13 20:38:04 2020 +0000

    Issue #3 - sync merge with develop branch

commit 0359d34
Merge: 1d9a1f0 bd00cb9
Author: Hang-Lei-NOAA <44901908+Hang-Lei-NOAA@users.noreply.github.com>
Date:   Thu Feb 13 09:53:59 2020 -0500

    Merge pull request NOAA-EMC#19 from NOAA-EMC/feature/remove_theia

    Feature/remove theia

commit eb73e52
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Fri Feb 7 14:04:37 2020 +0000

    Update EMC_verif-global checkout to verif_global_v1.5.0

commit bd00cb9
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Fri Feb 7 13:41:05 2020 +0000

    Issue #4 - bug fix in getic.sh for v15

commit 1c85197
Merge: 67dae40 1d9a1f0
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Fri Feb 7 13:27:18 2020 +0000

    Issue # 4 - Sync merge branch 'develop' into feature/remove_theia

commit 1d9a1f0
Merge: 3ed9267 bdbecaa
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Fri Feb 7 08:11:21 2020 -0500

    Merge pull request NOAA-EMC#18 from lgannoaa/exception_handling

    Exception handling

commit 4bd0e20
Author: Kate Friedman <kate.friedman@noaa.gov>
Date:   Thu Feb 6 11:55:31 2020 -0500

    Update README.md

commit d9ea1ac
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Thu Feb 6 16:03:11 2020 +0000

    Issue #3 - reduce hashes down to minimum 8 characters

commit bdbecaa
Author: Lin.Gan <lin.gan@noaa.gov>
Date:   Wed Jan 29 15:15:52 2020 +0000

    Display exception handling message for individual package with location of the log file

commit b64fd5f
Merge: cf00863 3ed9267
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Tue Jan 28 15:24:37 2020 +0000

    Merge branch 'develop' into feature/manage_externals

commit cf00863
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Tue Jan 28 15:23:14 2020 +0000

    Issue #3 - remove copy of manage_externals under util and add README.md file

commit c12e879
Author: Lin.Gan <lin.gan@noaa.gov>
Date:   Mon Jan 27 19:38:19 2020 +0000

    Implement exception handling in build_all script

commit bfc7bb0
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Mon Jan 27 19:06:17 2020 +0000

    Issue #3 - initial add of manage_externals and needed Externals.cfg. Also added .gitignore file and removed scripts/files associated with no-longer-used prod_util and grid_util builds.

commit 4d5713d
Author: Lin.Gan <lin.gan@noaa.gov>
Date:   Fri Jan 24 15:51:28 2020 +0000

    Testing github commit

commit 786806f
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Fri Jan 24 15:04:16 2020 +0000

    Missed file format updates in a few places in config.metp

commit d0a3b53
Author: Lin.Gan <lin.gan@noaa.gov>
Date:   Fri Jan 24 14:30:29 2020 +0000

    init commit for exception handling branch

commit c11dfef
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Fri Jan 24 14:07:29 2020 +0000

    Update EMC_verif-global tag to verif_global_v1.4.1

commit 0ea809c
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Thu Jan 23 13:29:56 2020 +0000

    Update file format variable in config.metp of online archive files

commit c0d7179
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Tue Jan 21 16:37:16 2020 +0000

    Add updated env machine files for gfsmetp

commit 82e6907
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Tue Jan 21 16:29:23 2020 +0000

    Update config.resources for gfsmetp

commit 72e8adf
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Tue Jan 21 16:19:31 2020 +0000

    Update EMC_verif-global tag checkout to 1.4.0

commit 6872f79
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Tue Jan 21 16:14:25 2020 +0000

    Add rocoto METplus job script

commit 9c94156
Author: Mallory Row <mallory.row@noaa.gov>
Date:   Tue Jan 21 16:09:13 2020 +0000

    Changes to setup_workflow.py for gfsmetp metatask

commit 3ed9267
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Tue Jan 14 19:32:36 2020 +0000

    Issue #10 - mid-year update to bufr station list (develop)

commit 1915aa9
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Fri Jan 10 18:36:32 2020 +0000

    Issue #8 - pulled in config.metp and modifications to two setup scripts

commit 67dae40
Merge: f78eb1b 091f4ba
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Jan 8 20:15:45 2020 +0000

    Merge branch 'develop' into feature/remove_theia

commit f78eb1b
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Jan 8 20:13:08 2020 +0000

    Issue #4 - removed references to Theia and Theia scripts

commit 091f4ba
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Wed Jan 8 19:37:45 2020 +0000

    Issue #7 - missed update to gdas transfer file from GFSv15.2.5 updates

commit 3fd4bcf
Author: kate.friedman <kate.friedman@noaa.gov>
Date:   Tue Dec 17 19:12:28 2019 +0000

    GitHub Issue #2 - GFSv15.2.6 obsproc version update, earc bug fix, and tracker path update

commit 5307952
Author: Kate.Friedman <Kate.Friedman@noaa.gov>
Date:   Wed Dec 11 20:47:44 2019 +0000

    HOTFIX - VLab Issue #72346 - fix to rocoto_viewer on Hera
JessicaMeixner-NOAA pushed a commit that referenced this pull request Dec 3, 2020
@lgannoaa
Merge pull request #2 from KateFriedman-NOAA/ccpp
32a004a 
Adjust efcs walltime and eupd thread value on Orion
JessicaMeixner-NOAA pushed a commit that referenced this pull request Jan 28, 2021
@KateFriedman-NOAA
GitHub Issue #2 - GFSv15.2.6 changes
b1dcb4f
JessicaMeixner-NOAA pushed a commit that referenced this pull request Apr 1, 2022
@WalterKolczynski-NOAA
Merge pull request #2 from RobertoPadilla-NOAA/feature/gefs_wave_statgem
7450b17 
Feature/gefs wave statgem
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@KateFriedman-NOAA @JessicaMeixner-NOAA