Update modules with hpc-stack v1.1.0 #319

kgerheiser · 2020-12-04T16:05:54Z

hpc-stack v1.1.0 has been installed and tested on Orion, Hera (GNU and Intel), WCOSS Dell and WCOSS Cray.

Description

Update modules to use hpc-stack v1.1.0

Issue(s) addressed

The model has been using an unofficial test version of hpc-stack

Testing

The full set of regression tests was run on all machines included in this PR, and all passed.

Orion, Hera (GNU and Intel), WCOSS Dell and WCOSS Cray.

Note

There is an issue with WCOSS Dell. On that machine LMOD_EXACT_MATCH is set to yes. That causes problems when trying to load the fv3 module (when it loads NetCDF). LMOD_EXACT_MATCH is set from the default loaded module EnvVars/1.0.3.

Running module unload EnvVars/1.0.3, or setenv LMOD_EXACT_MATCH no from within the fv3 module does not work. However, running it from your shell and then loading fv3 does work. The regression tests run module purge before loading so they aren't affected.

This means that if you want to manually load fv3, you either unload EnvVars/1.0.3 or set LMOD_EXACT_MATCH=no before.

Any advice on this?

junwang-noaa · 2020-12-04T16:15:42Z

In general, we do ask developers to do "module purge" before load fv3 as you never know what user's env is, there might be many conflicted modules loaded.

climbfuji · 2020-12-04T16:18:05Z

In general, we do ask developers to do "module purge" before load fv3 as you never know what user's env is, there might be many conflicted modules loaded.

Except for gaea. You cannot do module purge there or your environment is broken. I have been/am making sure that the module files contain the necessary switches.

@kgerheiser you'll soon see a PR from me to your feature/hpc-v1.1.0 branch with the updates for Cheyenne and Gaea.

We'll need to rerun the regression tests once it is your turn in the commit queue.

DusanJovic-NOAA · 2020-12-04T16:41:12Z

Will this version be installed on WCOSS2 Acorn?

kgerheiser · 2020-12-04T17:30:12Z

I'm sure we can get something on Acorn. I haven't tried it myself, but I know other people have.

There's an in-progress PR to bring hpc-stack to WCOSS2.

Update:

Trying it now

climbfuji · 2020-12-04T21:04:09Z

@kgerheiser please merge my PR https://github.com/kgerheiser/ufs-weather-model/pull/1 into your branch - thanks!

kgerheiser · 2020-12-05T00:18:38Z

@DusanJovic-NOAA I was able to get hpc-stack with LMod to build on WCOSS2. I'll do an official installation next week.

kgerheiser · 2020-12-15T22:09:01Z

@DusanJovic-NOAA

hpc-stack v1.1.0 is available on WCOSS2 at module use /lfs/h1/emc/nceplibs/noscrub/hpc-stack/libs/v1.1.0/modulefiles/stack

climbfuji · 2020-12-16T15:34:44Z

@kgerheiser this PR is scheduled for Friday 12/18/2020, together with minor bugfixes for the CCPP Unified Gravity Wave Drag parameterization. The update should require a new baseline on hera (date tag in rt.sh will likely be develop-20201218), for all other platforms we should be able to copy over the at that time current baselines.

Please pull in the latest code changes from the ufs-weather-model develop (on Thursday after #323 was merged), update .gitmodules and the submodule pointer for fv3atm to point to https://github.com/climbfuji/fv3atm, branch "ugwp_bugfix_fv3atm" (this is a temporary change that will be reverted and the submodule pointer updated after the fv3atm PR was merged). See NOAA-EMC/fv3atm#216.

junwang-noaa

It seems jet module file is missing. Otherwise, it is good.

kgerheiser · 2020-12-16T15:43:07Z

Dom included that in a different commit where he fixed something else on Jet.

climbfuji · 2020-12-16T15:51:33Z

Dom included that in a different commit where he fixed something else on Jet.

That's right. The modulefile still says

# At this time (2020/11/30), this is the pre-release version 1.0.0

but it is actually the final version (because the pre-release was declared the release after all tests passed on the various platforms). I suggest removing that one line. (ignore that it says 1.0.0 when it actually is 1.1.0)

climbfuji · 2020-12-17T14:19:31Z

@kgerheiser it is time to start updating your branch, if possible. We have just one more round of commits to come in before it is turn for your commit (with Mike's ccpp-physics/my fv3atm branches). I updated the fv3atm PR yesterday. Do you know what to do?

hpc-stack v1.1.0 has been installed and tested on all machines

kgerheiser · 2020-12-17T14:55:20Z

Alright, so I re-based my commits to the head of develop and have the latest changes. I also need to point to a different fv3 submodule?

climbfuji · 2020-12-17T14:59:12Z

Alright, so I re-based my commits to the head of develop and have the latest changes. I also need to point to a different fv3 submodule?

Yes please:

cd FV3
git remote add dom https://github.com/climbfuji/fv3atm
git remote update
git checkout dom/ugwp_bugfix_fv3atm
cd ..

# edit .gitmodules and change the FV3 section so that it reads:
[submodule "FV3"]
  path = FV3
  url = https://github.com/climbfuji/fv3atm
  branch = ugwp_bugfix_fv3atm

git add FV3 .gitmodules
git commit -m "Update .gitmodules and submodule pointer for fv3atm for code review and testing"
git push your_fork your_branch

Make sense?

…nd testing

kgerheiser · 2020-12-17T15:08:04Z

Done

climbfuji · 2020-12-17T15:10:29Z

Done

Looks great, thanks! Once the current PRs are in, I will update fv3atm one more time. You'll need to check out my branch again and update the submodule pointer, and pull in the latest changes into ufs-weather-model. Should be ready in a few hours, I'll let you know.

kgerheiser · 2020-12-18T15:08:24Z

Done

Does everything look correct? FV3 should point back to the actual repository now, right?

Should I cleanup the branch history at all?

climbfuji · 2020-12-18T15:15:19Z

Done

Does everything look correct? FV3 should point back to the actual repository now, right?

Should I cleanup the branch history at all?

Actually, no. fv3atm still needs to point to my PR (hash 067e1ce593b059bbe6235b95e59f4d9c69aef84a), same as .gitmodules. No need to cleanup the history, this will be done in the squashed merge. Thanks!

…r-model into feature/hpc-v1.1.0

climbfuji · 2020-12-18T15:36:55Z

Thanks, Kyle, looks good now.

climbfuji · 2020-12-18T15:37:44Z

I will run the tests for: hera.{gnu,intel}, cheyenne.{gnu,intel}. jet.intel, gaea.intel, orion.intel - somebody needs to do wcoss_cray and wcoss_dell_p3, please. @junwang-noaa @DusanJovic-NOAA

junwang-noaa · 2020-12-18T16:04:14Z

@DusanJovic-NOAA <https://github.com/DusanJovic-NOAA>can you help?

…

On Fri, Dec 18, 2020 at 10:38 AM Dom Heinzeller ***@***.***> wrote: I will run the tests for: hera.{gnu,intel}, cheyenne.{gnu,intel}. jet.intel, gaea.intel, orion.intel - somebody needs to do wcoss_cray and wcoss_dell_p3, please. @junwang-noaa <https://github.com/junwang-noaa> @DusanJovic-NOAA <https://github.com/DusanJovic-NOAA> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#319 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI7D6TK7C7SYMACVYCAQ5XDSVNZNVANCNFSM4UNUFXBQ> .

climbfuji · 2020-12-18T17:10:54Z

Note: gaea is not behaving well today (filesystem issues, as per email from the sysadmins last night). We may have to skip that platform if they don't fix it in time.

DusanJovic-NOAA · 2020-12-18T17:15:43Z

I'll run tests on Cray and Dell.

climbfuji · 2020-12-18T17:29:52Z

Update. So far I have completed:

	modified:   tests/RegressionTests_cheyenne.gnu.log
	modified:   tests/RegressionTests_cheyenne.intel.log
	modified:   tests/RegressionTests_hera.gnu.log
	modified:   tests/RegressionTests_hera.intel.log
	modified:   tests/RegressionTests_orion.intel.log

Will wait for jet before sending those to @kgerheiser

climbfuji · 2020-12-18T18:22:34Z

Update: jet.intel tests finished. I will merge ccpp-physics now and update my fv3atm submodule pointer. Once the fv3atm PR is merged, I will send a PR to @kgerheiser with my log files, Dusan's log files (please send them me), and the fv3atm/.gitmodules update. This should kick off the final CI tests when it gets merged.

junwang-noaa

fv3 needs to point back to the EMC develop branch.

climbfuji · 2020-12-18T20:01:14Z

fv3 needs to point back to the EMC develop branch.

I'll take care of this when I send Kyle my regression test logs (after I got the wcoss logs from Dusan).

climbfuji · 2020-12-18T20:19:06Z

@kgerheiser please merge https://github.com/kgerheiser/ufs-weather-model/pull/2 into your branch, final step for this PR. Thanks!

….intel, jet.intel, orion.intel, wcoss_cray, wcoss_dell_p3

kgerheiser · 2020-12-18T20:22:19Z

Merged

climbfuji · 2020-12-18T20:23:43Z

Merged

Thanks! All we have to do now is wait for 150mins or so until the tests are complete. Happy weekend and Happy Holidays!

climbfuji · 2020-12-18T20:49:06Z

gaea seems to have recovered. I am running the tests now just for the sake of completeness. If it works, I'll just attach them to this PR in form of a comment.

climbfuji · 2020-12-18T21:38:26Z

gaea seems to have recovered. I am running the tests now just for the sake of completeness. If it works, I'll just attach them to this PR in form of a comment.

Regression tests on gaea passed. Attaching here.

RegressionTests_gaea.intel.log

climbfuji · 2020-12-18T22:57:30Z

@DusanJovic-NOAA Green light - CI tests passed, Jun and I already approved.

@SMoorthi-emc

* Updates to stochastic_physics_wrapper (ufs-community#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 <[email protected]> * Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T (ufs-community#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 (ufs-community#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 (ufs-community#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 ufs-community#312) Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Updates to build for JEDI linking/control, add wcoss2 (ufs-community#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 <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * Final-final GFS v16 updates / restart reproducibility bugfixes (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#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 ufs-community#323 for jet.intel (ufs-community#336) * Update modules with hpc-stack v1.1.0 (ufs-community#319) * Update modules with hpc-stack v1.1.0 * Minor bug fixes to CCPP UGWP Co-authored-by: Dom Heinzeller <[email protected]> * Replace old regional SDF with FV3_GFS_v15_thompson_mynn (ufs-community#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 (ufs-community#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) (ufs-community#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 ufs-community#341 ("Update MOM6 to GFDL's 20201218 commit") Add modulefiles/wcoss_cray/fv3_debug (identical to modulefiles/wcoss_cray/fv3) Fix broken utest (see ufs-community#348) * Update the format of rt.conf (ufs-community#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 (ufs-community#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 (ufs-community#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) (ufs-community#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 (ufs-community#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 (ufs-community#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 <[email protected]> * Remove IPD steps 3 and 5 (ufs-community#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 (ufs-community#377) * update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (ufs-community#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 <[email protected]> Co-authored-by: Jun Wang <[email protected]> * Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (ufs-community#386) * Update .gitmodules and submodule pointer for fv3atm for gsl/develop branch * RUC ice for gsl/develop (replaces #47) (#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 (#50) * Updates to stochastic_physics_wrapper (ufs-community#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 (ufs-community#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 (#57) * dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (ufs-community#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 <[email protected]> Co-authored-by: MinsukJi-NOAA <[email protected]> Co-authored-by: Jun Wang <[email protected]> * 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 (ufs-community#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 <[email protected]> * Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (ufs-community#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 (ufs-community#401) * Add HAFS support in NOAA-EMC/CMEPS * Add coupled and datm tests for Gaea.intel Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Bin Li <[email protected]> * Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2) (ufs-community#407) * Regression test logs for all tier=1 platforms * updates FMS to 2020.04.01 (ufs-community#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 <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> * add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (ufs-community#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 (ufs-community#396) - combines the changes in PRs ufs-community#360 and ufs-community#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 <[email protected]> Co-authored-by: Michael Toy <[email protected]> Co-authored-by: MinsukJi-NOAA <[email protected]> * Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (ufs-community#419)" (ufs-community#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 <[email protected]> Co-authored-by: jiandewang <[email protected]> Co-authored-by: Denise Worthen <[email protected]> Co-authored-by: Dusan Jovic <[email protected]> Co-authored-by: Mark Potts <[email protected]> Co-authored-by: BinLi-NOAA <[email protected]> Co-authored-by: dustinswales <[email protected]> Co-authored-by: Kyle Gerheiser <[email protected]> Co-authored-by: RatkoVasic-NOAA <[email protected]> Co-authored-by: Ali.Abdolali <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Jun Wang <[email protected]> Co-authored-by: XiaqiongZhou-NOAA <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Bin Li <[email protected]> Co-authored-by: MiKyung Lee <[email protected]> Co-authored-by: valery.yudin <[email protected]> Co-authored-by: Michael Toy <[email protected]> Co-authored-by: MinsukJi-NOAA <[email protected]>

* upstream/develop: update MOM6 to GFDL 20210224 main branch commit (ufs-community#439) Add GNU and Cheyenne Support to Automated RT (ufs-community#444) Move Noah MP init to CCPP and update Noah MP regression tests, ice flux init bug fix in CCPP (ufs-community#425) Feature/rt automation (ufs-community#403) Update ccpp-physics. Make RRTMGP thread safe (ufs-community#418) Update regression tests from GFSv15+Thompson to GFSv16+Thompson, include "Add one regional regression test in DEBUG mode. (ufs-community#419)" (ufs-community#421) UGWP v0 v1 combined (ufs-community#396) add optional mesh in MOM6; add dz_min and min_seaice as configurable variables for coupled model (ufs-community#399) updates FMS to 2020.04.01 (ufs-community#392) Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization (remove IPD step 2) (ufs-community#407) Update CMEPS for HAFS integration; add datm and coupled-model tests on Gaea (ufs-community#401) Remove legacy gnumake build from fv3atm and NEMS, remove legacy Python 2.7 support, rename v16beta to v16 and RT updates (ufs-community#384) 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 (ufs-community#379) dycore options to add zero-gradient BC to reconstruct interface u/v and change dz_min as input (ufs-community#369) Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (ufs-community#386) update cpl gfsv16 tests, rrtmgp fix and bug fixes in cmeps (ufs-community#378) point fv3 to EMC develop branch (ufs-community#377) Remove IPD steps 3 and 5 (ufs-community#357) Update CMEPS (ufs-community#345) Implementation of CCPP timestep_init and timestep_final phases (ufs-community#337) Remove unnecessary SIMD instruction sets for Jet, first round of cleanup in rt.conf, initialize cld_amt to zero for regional runs (dycore) (ufs-community#353) add frac grid input, update and add additional cpld tests (ufs-community#354) Add checkpoint restarts for ufs-cpld (ufs-community#342) Update the format of rt.conf (ufs-community#349) Remove IPD (step 1) (ufs-community#331) Feature/ww3update (ufs-community#334) Replace old regional SDF with FV3_GFS_v15_thompson_mynn (ufs-community#333) Update modules with hpc-stack v1.1.0 (ufs-community#319) Regression test log for PR ufs-community#323 for jet.intel (ufs-community#336) RRTMGP and Thompson MP coupling (ufs-community#323) Add 2 new tests for DATM-MOM6-CICE6 application (ufs-community#332) Add optional bulk flux calculation in ufs-datm (ufs-community#266) Final-final GFS v16 updates / restart reproducibility bugfixes (ufs-community#325) Updates to build for JEDI linking/control, add wcoss2 (ufs-community#295) Update CICE, Move regression test input outside baseline directory (ufs-community#270) Feature/update mom6 and retain b4b results for 025x025 resolution (ufs-community#290) Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, and in restarting with frac_grid=T (ufs-community#304) Updates to stochastic_physics_wrapper (ufs-community#280) Update develop from gsd/develop 2020/11/20: Unified gravity wave drag, updates to other GSL physics (ufs-community#297) Fix to allow quilting with non-factors for layout (ufs-community#250) rt update (ufs-community#261)

…parameterization in the SDF and if so, adjusts certain workflow arrays to contain the names and other associated values of the fixed files needed by this parameterization so that those files are automatically copied and/or linked to. (#319) ## DESCRIPTION OF CHANGES: Add and call a function that checks for use of Thompson microphysics parameterization in the suite definition file (SDF). If not, do nothing. If so, add to the appropriate workflow arrays the names and other associated values of the fixed files needed by this parameterization so that they are automatically copied and/or linked to instead of being regenerated from scratch in the run_fcst task. ## TESTS CONDUCTED: On hera, ran two WE2E tests, one in NCO mode (nco_RRFS_CONUS_25km_HRRRX_RAPX) and the other in community mode (suite_FV3_GSD_v0). These use suites FV3_GSD_SAR and FV3_GSD_v0, respectively, and both of these call Thompson microphysics. Both succeeded. ## ISSUE (optional): This PR resolves issue #297.

@JeffBeck-NOAA

* Fix to post flat file. * Create MET and METplus config files under ush/templates/parm * Added script to pull and reorg ccpa data. Added a script to run gridstat with METplus. Updated MET and METplus config files. * Added new jjob for running grid-stat vx. Updated setup.sh to include grid-stat vx. Updated run_gridstatvx script. * Fixed typo on script name from ksh to sh * Moved some hard coded items out from the script to the XML * Updates to get METplus to run with fewer hard-coded paths. * Updates to add grid-stat task to XML generation. * Bug fixes for adding grid-stat to XML generation * Updates to remove hard-coded paths in config files * Change log dir to put master_metplus log file with other logs under log/, rather than default logs/. * Updates to generate xml without hard-coded paths for MET * Add hera gridstat module file * Add METplus point-stat task for both sfc and upper air * Small tweaks to remove hard coded paths and add some flexibility * Updates for adding point-stat into auto-generated xml * Add in function to set point-stat task to FALSE * Final tweaks to get it to generate the xml correctly * Minor updates to run ensure 0,6,12,18 * Tweaks to var list for Point-Stat * Add METplus settings to config_defaults * Move quote for end of settings and fix extra comment. * Fix typos to populate templates correctly * Updated to include SCRIPTSDIR and other MET specific settings along with updates to FHR syntax * Update module loads on hera * Fixed comment for BOTH_VARn_THRESH to avoid syntax issues * Added files to run grid_stat for a variety of accumulation intervals, including 3, 6, and 24h * Added module load hpss * Remove module load informatino from these scripts * Updated the method of turning on/off vx tasks using jinja template if statement * Remove commented out lines of code. Fixed typo. Removed gen_wflow.out file. * Updated pull scripts to have file names dependent on date to pull from HPSS. Updated to export a few more local variables that METplus conf needed in scripts. Updated workflow to use service queue (for now) to for 1h grid_stat and point_stat run and default for 3+h accumulation grid_stat runs) * moved common_hera.conf to common.conf - no platform specific information included that needs to be handled. * Remove common_hera.conf * Add scripts to pull and process MRMS data from NOAA HPSS * Updates for REFC vx tasks * updates to obs pull scripts * Update for adding in reflectivity verification using MRMS analyses and updating name of model output to RRFS rather than HRRR * Updates to account for CCPA issues on HPSS - day off for 00-05 UTC directories * Verification mods to feature/add metplus (#1) * Remove unused/outdated code (#313) ## DESCRIPTION OF CHANGES: * In setup.sh and generate_FV3LAM_wflow.sh, remove temporary codes that fix bugs in the FV3_GFS_2017_gfdlmp_regional suite definition file because those bugs have been fixed (in the ufs-weather-model repo). * In setup.sh, remove block of code that is no longer necessary because chgres_cube can now initialize from external model data with either 4 or 9 soil levels, and run with LSMs of either 4 or 9 soil levels. * Remove modifications to LD_LIBRARY_PATH in exregional_run_fcst.sh. * For the make_ics and make_lbcs tasks, move the setting of APRUN and other machine-specific actions from the J-job to the ex-script in order to be consistent with the other workflow tasks. * Fix indentation and edit comments. * Remove unused file load_fv3gfs_modules.sh. ## TESTS CONDUCTED: Ran two WE2E tests on hera, new_ESGgrid and new_GFDLgrid: * new_ESGgrid uses the FV3_GFS_2017_gfdlmp_regional suite. The test was successful. * new_GFDLgrid uses the FV3_GFS_2017_gfdlmp suite. The test was successful. ## ISSUE (optional): This resolves issue #198. * Add and call a function that checks for use of Thompson microphysics parameterization in the SDF and if so, adjusts certain workflow arrays to contain the names and other associated values of the fixed files needed by this parameterization so that those files are automatically copied and/or linked to. (#319) ## DESCRIPTION OF CHANGES: Add and call a function that checks for use of Thompson microphysics parameterization in the suite definition file (SDF). If not, do nothing. If so, add to the appropriate workflow arrays the names and other associated values of the fixed files needed by this parameterization so that they are automatically copied and/or linked to instead of being regenerated from scratch in the run_fcst task. ## TESTS CONDUCTED: On hera, ran two WE2E tests, one in NCO mode (nco_RRFS_CONUS_25km_HRRRX_RAPX) and the other in community mode (suite_FV3_GSD_v0). These use suites FV3_GSD_SAR and FV3_GSD_v0, respectively, and both of these call Thompson microphysics. Both succeeded. ## ISSUE (optional): This PR resolves issue #297. * RRFS_v1beta SDF changes after reverting from GSL to GFS GWD suite (#322) (#327) ## DESCRIPTION OF CHANGES: Removed checks on the RRFS_v1beta SDF implemented for use with the GSL GWD suite (now uses the GFS GWD suite). No longer copies staged orography files necessary for the GSL GWD suite. ## TESTS CONDUCTED: Runs to completion on Hera. End-to-end runs DOT_OR_USCORE and suite_FV3_RRFS_v1beta succeeded on Cheyenne. Co-authored-by: JeffBeck-NOAA <[email protected]> * Update FV3.input.nml for fhzero = 1.0 * Updated conf files for file name conventions. * Updated MET scripts and MRMS pull scripts. * Adjust RRFS_CONUS_... grids (#294) ## DESCRIPTION OF CHANGES: * Adjust RRFS_CONUS_25km, RRFS_CONUS_13km, and RRFS_CONUS_3km grid parameters so that: * All grids, including their 4-cell-wide halos, lie completely within the HRRRX domain. * All grids have dimensions nx and ny that factor "nicely", i.e. they don't have factors greather than 7. * The write-component grids corresponding to these three native grids cover as much of the native grids as possible without going outside of the native grid boundaries. The updated NCL scripts (see below) were used to generate the write-component grid parameters. * For the RRFS_CONUS_13km grid, reduce the time step (DT_ATMOS) from 180sec to 45sec. This is necessary to get a successful forecast with the GSD_SAR suite, and thus likely also the RRFS_v1beta suite. * Modify WE2E testing system as follows: * Add new tests with the RRFS_CONUS_25km, RRFS_CONUS_13km, and RRFS_CONUS_3km grids that use the GFS_v15p2 and RRFS_v1beta suites (which are now the ones officially supported in the first release of the short-range weather app) instead of the GFS_v16beta and GSD_SAR suites, respectively. * For clarity, rename the test configuration files that use the GFS_v16beta and GSD_SAR suites so they include the suite name. * Update list of WE2E tests (baselines_list.txt). * Update the NCL plotting scripts to be able to plot grids with the latest version of the workflow. ## TESTS CONDUCTED: On hera, ran tests with all three grids with the GFS_v15p2 and RRFS_v1beta suites (a total of 6 tests). All were successful. * Remove redundant model_configure.${CCPP_PHYS_SUITE} template files; use Jinja2 to create model_configure (#321) ## DESCRIPTION OF CHANGES: * Remove model_configure template files whose names depend on the physics suite, i.e. files with names of the form model_configure.${CCPP_PHYS_SUITE}. Only a single template file is needed because the contents of the model_configure file are not suite dependent. This leaves just one template file (named model_configure). * Change the function create_model_configure_file.sh and the template file model_configure so they use jinja2 instead of sed to replace placeholder values. * Absorb the contents of the write-component template files wrtcmp_lambert_conformal, wrtcmp_regional_latlon, and wrtcmp_rotated_latlon into the new jinja2-compliant model_configure file. We can do this because Jinja2 allows use of if-statements in the template file. * In the new model_configure jinja2 template file, include comments to explain the various write-component parameters. ## TESTS CONDUCTED: On Hera, ran the two WE2E tests new_ESGgrid and new_GFDLgrid. The first uses a "lambert_conformal" type of write-component grid, and the second uses a "rotated_latlon" type of write-component grid. (The write-component also allows "regional_latlon" type grids, which is just the usual earth-relative latlon coordinate system, but we do not have any cases that use that.) Both tests succeeded. ## ISSUE (optional): This PR resolves issue #281. * Add Thompson ice- and water-friendly aerosol climo file support (#332) * Add if statement in set_thompson_mp_fix_files.sh to source Thompson climo file when using a combination of a Thompson-based SDF and non-RAP/HRRR external model data * Modify if statement based on external models for Thompson climo file * Remove workflow variable EMC_GRID_NAME (#333) ## DESCRIPTION OF CHANGES: * Remove the workflow variable EMC_GRID_NAME. Henceforth, PREDEF_GRID_NAME is the only variable that can be used to set the name of the predefined grid to use. * Make appropriate change of variable name (EMC_GRID_NAME --> PREDEF_GRID_NAME) in the WE2E test configuration files. * Change anywhere the "conus" and "conus_c96" grids are specified to "EMC_CONUS_3km" and "EMC_CONUS_coarse", respectively. * Rename WE2E test configuration files with names containing the strings "conus" and "conus_c96" by replacing these strings with "EMC_CONUS_3km" and "EMC_CONUS_coarse", respectively. * Update the list of WE2E test names (tests/baselines_list.txt). * Bug fixes not directly related to grids: * In config.nco.sh, remove settings of QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST since these are now set automatically (due to another PR). * In the template file FV3LAM_wflow.xml, add the ensemble member name after RUN_FCST_TN in the dependency of the run_post metatask. ## TESTS CONDUCTED: Since this change only affects runs in NCO mode, the following NCO-mode WE2E tests were rerun on hera, all successfully: ``` nco_EMC_CONUS_3km SUCCESS nco_EMC_CONUS_coarse SUCCESS nco_EMC_CONUS_coarse__suite_FV3_GFS_2017_gfdlmp SUCCESS nco_RRFS_CONUS_25km_HRRRX_RAPX SUCCESS nco_RRFS_CONUS_3km_FV3GFS_FV3GFS SUCCESS nco_RRFS_CONUS_3km_HRRRX_RAPX SUCCESS nco_ensemble SUCCESS ``` * Port workflow to Orion (#309) ## DESCRIPTION OF CHANGES: * Add stanzas for Orion where necessary. * Add new module files for Orion. * On Orion, both the slurm partition and the slurm QOS need to be specified in the rocoto XML in order to be able to have wall times longer than 30 mins (the partition needs to be specified because it is by default "debug", which has a limit of 30 mins). Thus, introduce modifications to more easily specify slurm partitions: * Remove the workflow variables QUEUE_DEFAULT_TAG, QUEUE_HPSS_TAG, and QUEUE_FCST_TAG that are currently used to determine whether QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST specify the names of queue/QOS's or slurm partitions. * Add the workflow variables PARTITION_DEFAULT_TAG, PARTITION_HPSS_TAG, and PARTITION_FCST_TAG. These will be used to specify slurm partitions only, and the variables QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST will be used to specify queues/QOS's only. IMPORTANT NOTE: On Orion, in order to load the regional_workflow environment needed for generating an experiment, the user must first issue the following commands: ``` module use -a /apps/contrib/miniconda3-noaa-gsl/modulefiles module load miniconda3 conda activate regional_workflow ``` ## TESTS CONDUCTED: Ran 11 WE2E tests on Orion, Hera, and Cheyenne. Results on Orion: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km FAILURE - In the run_fcst task. * Error message: !!! (1) Error in subr radiation_aerosols: unrealistic surface pressure = 1 NaN new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` Results on Hera: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km SUCCESS new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` Results on Cheyenne: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km FAILURE - In run_fcst task. * Error message: !!! (1) Error in subr radiation_aerosols: unrealistic surface pressure = 1 NaN new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` All succeed except GSD_HRRR_AK_50km on Orion and Cheyenne. It is not clear why grid_GSD_HRRR_AK_50km fails on Orion and Cheyenne but not Hera. Seems to point to a bug in the forecast model. These two failures are not so important since this grid will soon be deprecated. Also tested successfully on Jet by @JeffBeck-NOAA and on Odin and Stampede by @ywangwof. ## ISSUE: This resolves Issue #152. ## CONTRIBUTORS: @JeffBeck-NOAA @ywangwof @christinaholtNOAA * Removed comments from exregional_get_mrms_files.sh and removed fhzero from FV3.input.yml * Update FV3.input.nml for fhzero = 1.0 * Updated conf files for file name conventions. * Updated MET scripts and MRMS pull scripts. * Removed comments from exregional_get_mrms_files.sh and removed fhzero from FV3.input.yml Co-authored-by: gsketefian <[email protected]> Co-authored-by: Michael Kavulich <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: Jamie Wolff <[email protected]> * Change cov_thresh for REFL to be a true max in nbrhood as SPC does. * Separated Pull Data Scripts from Run Vx Scripts: Feature/add_metplus (#2) * Job script for get_obs_ccpa * Jobs script for get_obs_mrms * Jobs script for get_obs_ndas * Added external variables necessary to get_ccpa script * Updated workflow template with separate get obs tasks * Separated pull scripts from run scripts * Added necessary defaults/values for defining pull tasks * Added module files, default config.sh options, and changed dependencies for vx tasks * Changed name of new workflow to FV3LAM_wflow.xml * Added task get_obs_tn, removed config.sh, updated config_defaults and config.community.sh * Adjusted the community and default config files based on comments * Updated FV3LAM workflow * Fixed discrepancies in config.community.sh * Fixed discrepancies in config_defaults.sh * Fixed discrepancies in config_defaults.sh round 2 * Fixed discrepancies in config_defaults.sh round 3 * Fixed discrepancies in config_defaults.sh round 4 * Fixed discrepancies in config.community.sh round 2 * Fixed discrepancies in config.community.sh round 3 * Fixed discrepancies in generate_FV3LAM_wflow.sh * Fixed discrepancies in generate_FV3LAM_wflow.sh round 2 * Fixed discrepancies in generate_FV3LAM_wflow.sh round 3 * Updated FV3LAM_wflow template * Fixed Vx Task Dependencies in Workflow: Feature/add metplus (#3) * Job script for get_obs_ccpa * Jobs script for get_obs_mrms * Jobs script for get_obs_ndas * Added external variables necessary to get_ccpa script * Updated workflow template with separate get obs tasks * Separated pull scripts from run scripts * Added necessary defaults/values for defining pull tasks * Added module files, default config.sh options, and changed dependencies for vx tasks * Changed name of new workflow to FV3LAM_wflow.xml * Added task get_obs_tn, removed config.sh, updated config_defaults and config.community.sh * Adjusted the community and default config files based on comments * Updated FV3LAM workflow * Fixed discrepancies in config.community.sh * Fixed discrepancies in config_defaults.sh * Fixed discrepancies in config_defaults.sh round 2 * Fixed discrepancies in config_defaults.sh round 3 * Fixed discrepancies in config_defaults.sh round 4 * Fixed discrepancies in config.community.sh round 2 * Fixed discrepancies in config.community.sh round 3 * Fixed discrepancies in generate_FV3LAM_wflow.sh * Fixed discrepancies in generate_FV3LAM_wflow.sh round 2 * Fixed discrepancies in generate_FV3LAM_wflow.sh round 3 * Updated FV3LAM_wflow template * Fixed the dependencies of the vx tasks * Manual merge with develop that didn't seem to work before. Trying to get feature branch updated so it will run again! * Add local module files * Add environment variable for SCRIPTSDIR * Remove echo statement * Remove old module files * Update to config_default for walltime for ndas pull. Update to metplus parm for obs file template. Update to FV3LAM xml to not include 00 hour for verification * Update template to remove full path * Verification channges for obs. (#4) * Verification channges for obs. * Update config_defaults.sh for vx description * Update config_defaults.sh to remove extraneous MET info. Co-authored-by: Michelle Harrold <[email protected]> * Pull in updates from develop that were not merging properly. Small change to config.community to turn off vx tasks by default. * Did manual merge of these files because it was not handled properly automatically * Adding additional variables to METplus for regional workflow (#5) * Updates to address comments in PR review * Changed name of get_obs to remove _tn * Missed removal of on get_obs Co-authored-by: michelleharrold <[email protected]> Co-authored-by: gsketefian <[email protected]> Co-authored-by: Michael Kavulich <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: Lindsay <[email protected]> Co-authored-by: Michelle Harrold <[email protected]> Co-authored-by: PerryShafran-NOAA <[email protected]>

@JeffBeck-NOAA

* Fix to post flat file. * Create MET and METplus config files under ush/templates/parm * Added script to pull and reorg ccpa data. Added a script to run gridstat with METplus. Updated MET and METplus config files. * Added new jjob for running grid-stat vx. Updated setup.sh to include grid-stat vx. Updated run_gridstatvx script. * Fixed typo on script name from ksh to sh * Moved some hard coded items out from the script to the XML * Updates to get METplus to run with fewer hard-coded paths. * Updates to add grid-stat task to XML generation. * Bug fixes for adding grid-stat to XML generation * Updates to remove hard-coded paths in config files * Change log dir to put master_metplus log file with other logs under log/, rather than default logs/. * Updates to generate xml without hard-coded paths for MET * Add hera gridstat module file * Add METplus point-stat task for both sfc and upper air * Small tweaks to remove hard coded paths and add some flexibility * Updates for adding point-stat into auto-generated xml * Add in function to set point-stat task to FALSE * Final tweaks to get it to generate the xml correctly * Minor updates to run ensure 0,6,12,18 * Tweaks to var list for Point-Stat * Add METplus settings to config_defaults * Move quote for end of settings and fix extra comment. * Fix typos to populate templates correctly * Updated to include SCRIPTSDIR and other MET specific settings along with updates to FHR syntax * Update module loads on hera * Fixed comment for BOTH_VARn_THRESH to avoid syntax issues * Added files to run grid_stat for a variety of accumulation intervals, including 3, 6, and 24h * Added module load hpss * Remove module load informatino from these scripts * Updated the method of turning on/off vx tasks using jinja template if statement * Remove commented out lines of code. Fixed typo. Removed gen_wflow.out file. * Updated pull scripts to have file names dependent on date to pull from HPSS. Updated to export a few more local variables that METplus conf needed in scripts. Updated workflow to use service queue (for now) to for 1h grid_stat and point_stat run and default for 3+h accumulation grid_stat runs) * moved common_hera.conf to common.conf - no platform specific information included that needs to be handled. * Remove common_hera.conf * Add scripts to pull and process MRMS data from NOAA HPSS * Updates for REFC vx tasks * updates to obs pull scripts * Update for adding in reflectivity verification using MRMS analyses and updating name of model output to RRFS rather than HRRR * Updates to account for CCPA issues on HPSS - day off for 00-05 UTC directories * Verification mods to feature/add metplus (#1) * Remove unused/outdated code (#313) ## DESCRIPTION OF CHANGES: * In setup.sh and generate_FV3LAM_wflow.sh, remove temporary codes that fix bugs in the FV3_GFS_2017_gfdlmp_regional suite definition file because those bugs have been fixed (in the ufs-weather-model repo). * In setup.sh, remove block of code that is no longer necessary because chgres_cube can now initialize from external model data with either 4 or 9 soil levels, and run with LSMs of either 4 or 9 soil levels. * Remove modifications to LD_LIBRARY_PATH in exregional_run_fcst.sh. * For the make_ics and make_lbcs tasks, move the setting of APRUN and other machine-specific actions from the J-job to the ex-script in order to be consistent with the other workflow tasks. * Fix indentation and edit comments. * Remove unused file load_fv3gfs_modules.sh. ## TESTS CONDUCTED: Ran two WE2E tests on hera, new_ESGgrid and new_GFDLgrid: * new_ESGgrid uses the FV3_GFS_2017_gfdlmp_regional suite. The test was successful. * new_GFDLgrid uses the FV3_GFS_2017_gfdlmp suite. The test was successful. ## ISSUE (optional): This resolves issue #198. * Add and call a function that checks for use of Thompson microphysics parameterization in the SDF and if so, adjusts certain workflow arrays to contain the names and other associated values of the fixed files needed by this parameterization so that those files are automatically copied and/or linked to. (#319) ## DESCRIPTION OF CHANGES: Add and call a function that checks for use of Thompson microphysics parameterization in the suite definition file (SDF). If not, do nothing. If so, add to the appropriate workflow arrays the names and other associated values of the fixed files needed by this parameterization so that they are automatically copied and/or linked to instead of being regenerated from scratch in the run_fcst task. ## TESTS CONDUCTED: On hera, ran two WE2E tests, one in NCO mode (nco_RRFS_CONUS_25km_HRRRX_RAPX) and the other in community mode (suite_FV3_GSD_v0). These use suites FV3_GSD_SAR and FV3_GSD_v0, respectively, and both of these call Thompson microphysics. Both succeeded. ## ISSUE (optional): This PR resolves issue #297. * RRFS_v1beta SDF changes after reverting from GSL to GFS GWD suite (#322) (#327) ## DESCRIPTION OF CHANGES: Removed checks on the RRFS_v1beta SDF implemented for use with the GSL GWD suite (now uses the GFS GWD suite). No longer copies staged orography files necessary for the GSL GWD suite. ## TESTS CONDUCTED: Runs to completion on Hera. End-to-end runs DOT_OR_USCORE and suite_FV3_RRFS_v1beta succeeded on Cheyenne. Co-authored-by: JeffBeck-NOAA <[email protected]> * Update FV3.input.nml for fhzero = 1.0 * Updated conf files for file name conventions. * Updated MET scripts and MRMS pull scripts. * Adjust RRFS_CONUS_... grids (#294) ## DESCRIPTION OF CHANGES: * Adjust RRFS_CONUS_25km, RRFS_CONUS_13km, and RRFS_CONUS_3km grid parameters so that: * All grids, including their 4-cell-wide halos, lie completely within the HRRRX domain. * All grids have dimensions nx and ny that factor "nicely", i.e. they don't have factors greather than 7. * The write-component grids corresponding to these three native grids cover as much of the native grids as possible without going outside of the native grid boundaries. The updated NCL scripts (see below) were used to generate the write-component grid parameters. * For the RRFS_CONUS_13km grid, reduce the time step (DT_ATMOS) from 180sec to 45sec. This is necessary to get a successful forecast with the GSD_SAR suite, and thus likely also the RRFS_v1beta suite. * Modify WE2E testing system as follows: * Add new tests with the RRFS_CONUS_25km, RRFS_CONUS_13km, and RRFS_CONUS_3km grids that use the GFS_v15p2 and RRFS_v1beta suites (which are now the ones officially supported in the first release of the short-range weather app) instead of the GFS_v16beta and GSD_SAR suites, respectively. * For clarity, rename the test configuration files that use the GFS_v16beta and GSD_SAR suites so they include the suite name. * Update list of WE2E tests (baselines_list.txt). * Update the NCL plotting scripts to be able to plot grids with the latest version of the workflow. ## TESTS CONDUCTED: On hera, ran tests with all three grids with the GFS_v15p2 and RRFS_v1beta suites (a total of 6 tests). All were successful. * Remove redundant model_configure.${CCPP_PHYS_SUITE} template files; use Jinja2 to create model_configure (#321) ## DESCRIPTION OF CHANGES: * Remove model_configure template files whose names depend on the physics suite, i.e. files with names of the form model_configure.${CCPP_PHYS_SUITE}. Only a single template file is needed because the contents of the model_configure file are not suite dependent. This leaves just one template file (named model_configure). * Change the function create_model_configure_file.sh and the template file model_configure so they use jinja2 instead of sed to replace placeholder values. * Absorb the contents of the write-component template files wrtcmp_lambert_conformal, wrtcmp_regional_latlon, and wrtcmp_rotated_latlon into the new jinja2-compliant model_configure file. We can do this because Jinja2 allows use of if-statements in the template file. * In the new model_configure jinja2 template file, include comments to explain the various write-component parameters. ## TESTS CONDUCTED: On Hera, ran the two WE2E tests new_ESGgrid and new_GFDLgrid. The first uses a "lambert_conformal" type of write-component grid, and the second uses a "rotated_latlon" type of write-component grid. (The write-component also allows "regional_latlon" type grids, which is just the usual earth-relative latlon coordinate system, but we do not have any cases that use that.) Both tests succeeded. ## ISSUE (optional): This PR resolves issue #281. * Add Thompson ice- and water-friendly aerosol climo file support (#332) * Add if statement in set_thompson_mp_fix_files.sh to source Thompson climo file when using a combination of a Thompson-based SDF and non-RAP/HRRR external model data * Modify if statement based on external models for Thompson climo file * Remove workflow variable EMC_GRID_NAME (#333) ## DESCRIPTION OF CHANGES: * Remove the workflow variable EMC_GRID_NAME. Henceforth, PREDEF_GRID_NAME is the only variable that can be used to set the name of the predefined grid to use. * Make appropriate change of variable name (EMC_GRID_NAME --> PREDEF_GRID_NAME) in the WE2E test configuration files. * Change anywhere the "conus" and "conus_c96" grids are specified to "EMC_CONUS_3km" and "EMC_CONUS_coarse", respectively. * Rename WE2E test configuration files with names containing the strings "conus" and "conus_c96" by replacing these strings with "EMC_CONUS_3km" and "EMC_CONUS_coarse", respectively. * Update the list of WE2E test names (tests/baselines_list.txt). * Bug fixes not directly related to grids: * In config.nco.sh, remove settings of QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST since these are now set automatically (due to another PR). * In the template file FV3LAM_wflow.xml, add the ensemble member name after RUN_FCST_TN in the dependency of the run_post metatask. ## TESTS CONDUCTED: Since this change only affects runs in NCO mode, the following NCO-mode WE2E tests were rerun on hera, all successfully: ``` nco_EMC_CONUS_3km SUCCESS nco_EMC_CONUS_coarse SUCCESS nco_EMC_CONUS_coarse__suite_FV3_GFS_2017_gfdlmp SUCCESS nco_RRFS_CONUS_25km_HRRRX_RAPX SUCCESS nco_RRFS_CONUS_3km_FV3GFS_FV3GFS SUCCESS nco_RRFS_CONUS_3km_HRRRX_RAPX SUCCESS nco_ensemble SUCCESS ``` * Port workflow to Orion (#309) ## DESCRIPTION OF CHANGES: * Add stanzas for Orion where necessary. * Add new module files for Orion. * On Orion, both the slurm partition and the slurm QOS need to be specified in the rocoto XML in order to be able to have wall times longer than 30 mins (the partition needs to be specified because it is by default "debug", which has a limit of 30 mins). Thus, introduce modifications to more easily specify slurm partitions: * Remove the workflow variables QUEUE_DEFAULT_TAG, QUEUE_HPSS_TAG, and QUEUE_FCST_TAG that are currently used to determine whether QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST specify the names of queue/QOS's or slurm partitions. * Add the workflow variables PARTITION_DEFAULT_TAG, PARTITION_HPSS_TAG, and PARTITION_FCST_TAG. These will be used to specify slurm partitions only, and the variables QUEUE_DEFAULT, QUEUE_HPSS, and QUEUE_FCST will be used to specify queues/QOS's only. IMPORTANT NOTE: On Orion, in order to load the regional_workflow environment needed for generating an experiment, the user must first issue the following commands: ``` module use -a /apps/contrib/miniconda3-noaa-gsl/modulefiles module load miniconda3 conda activate regional_workflow ``` ## TESTS CONDUCTED: Ran 11 WE2E tests on Orion, Hera, and Cheyenne. Results on Orion: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km FAILURE - In the run_fcst task. * Error message: !!! (1) Error in subr radiation_aerosols: unrealistic surface pressure = 1 NaN new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` Results on Hera: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km SUCCESS new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` Results on Cheyenne: ``` community_ensemble_2mems SUCCESS DOT_OR_USCORE SUCCESS grid_GSD_HRRR_AK_50km FAILURE - In run_fcst task. * Error message: !!! (1) Error in subr radiation_aerosols: unrealistic surface pressure = 1 NaN new_ESGgrid SUCCESS new_GFDLgrid SUCCESS regional_001 SUCCESS regional_002 SUCCESS suite_FV3_GFS_v15p2 SUCCESS suite_FV3_GFS_v16beta SUCCESS suite_FV3_GSD_SAR SUCCESS suite_FV3_GSD_v0 SUCCESS ``` All succeed except GSD_HRRR_AK_50km on Orion and Cheyenne. It is not clear why grid_GSD_HRRR_AK_50km fails on Orion and Cheyenne but not Hera. Seems to point to a bug in the forecast model. These two failures are not so important since this grid will soon be deprecated. Also tested successfully on Jet by @JeffBeck-NOAA and on Odin and Stampede by @ywangwof. ## ISSUE: This resolves Issue #152. ## CONTRIBUTORS: @JeffBeck-NOAA @ywangwof @christinaholtNOAA * Removed comments from exregional_get_mrms_files.sh and removed fhzero from FV3.input.yml * Update FV3.input.nml for fhzero = 1.0 * Updated conf files for file name conventions. * Updated MET scripts and MRMS pull scripts. * Removed comments from exregional_get_mrms_files.sh and removed fhzero from FV3.input.yml Co-authored-by: gsketefian <[email protected]> Co-authored-by: Michael Kavulich <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: Jamie Wolff <[email protected]> * Change cov_thresh for REFL to be a true max in nbrhood as SPC does. * Job script for get_obs_ccpa * Jobs script for get_obs_mrms * Jobs script for get_obs_ndas * Added external variables necessary to get_ccpa script * Updated workflow template with separate get obs tasks * Separated pull scripts from run scripts * Added necessary defaults/values for defining pull tasks * Added module files, default config.sh options, and changed dependencies for vx tasks * Changed name of new workflow to FV3LAM_wflow.xml * Added task get_obs_tn, removed config.sh, updated config_defaults and config.community.sh * Adjusted the community and default config files based on comments * Updated FV3LAM workflow * Fixed discrepancies in config.community.sh * Fixed discrepancies in config_defaults.sh * Fixed discrepancies in config_defaults.sh round 2 * Fixed discrepancies in config_defaults.sh round 3 * Fixed discrepancies in config_defaults.sh round 4 * Fixed discrepancies in config.community.sh round 2 * Fixed discrepancies in config.community.sh round 3 * Fixed discrepancies in generate_FV3LAM_wflow.sh * Fixed discrepancies in generate_FV3LAM_wflow.sh round 2 * Fixed discrepancies in generate_FV3LAM_wflow.sh round 3 * Updated FV3LAM_wflow template * Separated Pull Data Scripts from Run Vx Scripts: Feature/add_metplus (#2) * Job script for get_obs_ccpa * Jobs script for get_obs_mrms * Jobs script for get_obs_ndas * Added external variables necessary to get_ccpa script * Updated workflow template with separate get obs tasks * Separated pull scripts from run scripts * Added necessary defaults/values for defining pull tasks * Added module files, default config.sh options, and changed dependencies for vx tasks * Changed name of new workflow to FV3LAM_wflow.xml * Added task get_obs_tn, removed config.sh, updated config_defaults and config.community.sh * Adjusted the community and default config files based on comments * Updated FV3LAM workflow * Fixed discrepancies in config.community.sh * Fixed discrepancies in config_defaults.sh * Fixed discrepancies in config_defaults.sh round 2 * Fixed discrepancies in config_defaults.sh round 3 * Fixed discrepancies in config_defaults.sh round 4 * Fixed discrepancies in config.community.sh round 2 * Fixed discrepancies in config.community.sh round 3 * Fixed discrepancies in generate_FV3LAM_wflow.sh * Fixed discrepancies in generate_FV3LAM_wflow.sh round 2 * Fixed discrepancies in generate_FV3LAM_wflow.sh round 3 * Updated FV3LAM_wflow template * Fixed the dependencies of the vx tasks * Fixed Vx Task Dependencies in Workflow: Feature/add metplus (#3) * Job script for get_obs_ccpa * Jobs script for get_obs_mrms * Jobs script for get_obs_ndas * Added external variables necessary to get_ccpa script * Updated workflow template with separate get obs tasks * Separated pull scripts from run scripts * Added necessary defaults/values for defining pull tasks * Added module files, default config.sh options, and changed dependencies for vx tasks * Changed name of new workflow to FV3LAM_wflow.xml * Added task get_obs_tn, removed config.sh, updated config_defaults and config.community.sh * Adjusted the community and default config files based on comments * Updated FV3LAM workflow * Fixed discrepancies in config.community.sh * Fixed discrepancies in config_defaults.sh * Fixed discrepancies in config_defaults.sh round 2 * Fixed discrepancies in config_defaults.sh round 3 * Fixed discrepancies in config_defaults.sh round 4 * Fixed discrepancies in config.community.sh round 2 * Fixed discrepancies in config.community.sh round 3 * Fixed discrepancies in generate_FV3LAM_wflow.sh * Fixed discrepancies in generate_FV3LAM_wflow.sh round 2 * Fixed discrepancies in generate_FV3LAM_wflow.sh round 3 * Updated FV3LAM_wflow template * Fixed the dependencies of the vx tasks * Manual merge with develop that didn't seem to work before. Trying to get feature branch updated so it will run again! * Add local module files * Add environment variable for SCRIPTSDIR * Remove echo statement * Remove old module files * Update to config_default for walltime for ndas pull. Update to metplus parm for obs file template. Update to FV3LAM xml to not include 00 hour for verification * Update template to remove full path * Verification channges for obs. (#4) * Verification channges for obs. * Update config_defaults.sh for vx description * Update config_defaults.sh to remove extraneous MET info. Co-authored-by: Michelle Harrold <[email protected]> * Initial METplus .confs and MET config files for EnsembleStat APCP * J-Job script for running ensemble stat * Exregional script for ensemble-stat * Added EnsembleStat.conf for A6 and A24. Added PCPCombine to A3, A6, and A24. * Added EnsembleStatConfig files for 6 and 24h * Copy of workflow template with precipitation ensemble tasks added. Will become main template when testing is complete * Added export statement for number of ensemble members * Added necessary task definitions in ush * Updated workflow to included ENTITY definitions for ensstat * Fixed typo * Added ens vx configs * Pull in updates from develop that were not merging properly. Small change to config.community to turn off vx tasks by default. * Added/mod files for point ens vx. * Updated metplus conf files for ens point vx * Did manual merge of these files because it was not handled properly automatically * Adding additional variables to METplus for regional workflow (#5) * Changes made based on meeting with Michelle and Jamie * Updating fork * Cleanup after merge * Added additional ens vx * Ensemble point vx mods * Additional updates for ens and det vx * ensgrid_mean and ensgrid_prob .conf files for APCP * Updates for ensemble vx. * Added mean and prob point-stat configs * Updates to ensgrid_vx * Updates for mean/prob vx. * Updates to FV3LAM_wflow.xml * Deterministic and ensembel vx updates. * Ensgrid mean * Update setup.sh * Changed workflow template title * Updates to deterministic and ensemble verification * Created EnsembleStat METplus conf and MET config files for REFC * Added reflectivity mean and prob METplus and MET config files. Updated APCP mean and prob METplus and MET config files. * Added all J-job scripts, exregional scripts, and necessary definitons for workflow generation for all ensgrid_mean and ensgrid_prob tasks * Updates to workflow to add ensgrid_vx * Changes I made to account for runtime errors. * Made changes to directory structures * Made changes to directory structures and variables * Changed log files and stage dir. * Changes for grid- and point-vx. * Updated METplus ensemble precip conf files. * Mods for ensemble and deterministic vx. * Change to GridStatConfig_REFC_mean * Updated EnsembleStat_REFC.conf * Updated to METv10.0.0 * Updated conf files for paths. * Updated FV3LAM_wflow.xml template. * Mods for vx dependencies * Updated for censor thresh in METplus conf files; changes to FV3LAM_wflow.xml after sync with develop. * Updated exregional_run_fcst.sh generate_FV3LAM_wflow.sh to address merge with develop. * Mods for ensemble precip vx, handling padded/non-padded ensemble member names, fixes for python environment for obs pull. * Changes to RETOP (units) and REFC (naming and level) verification. * Fix OUTPUT_BASE for deterministic vx. * Changes to some verification ex-scripts for syntax and path fixes. Included start end dates of incorrect 01-h CCPA data. Removed some extra lines in FV3LAM_wflow.xml template. * Changed comp. ref. variable name in GridStat_REFC_prob.conf * Changed comp. ref. level in GridStat_REFC_prob.conf * Updated logic for number padding in the directory name when running in ensemble mode. * Added MET ensemble vx WE2E test. * Modified location of obs to live outside cycle dir, allowing for obs to be shared across cycles. * Mods to address comments on PR575. * Updated ensemble METPlus conf files for changes to post output name. * Addessed comments in PR and mods for 10-m WIND. * Addressing final comments in PR. Co-authored-by: Jamie Wolff <[email protected]> Co-authored-by: gsketefian <[email protected]> Co-authored-by: Michael Kavulich <[email protected]> Co-authored-by: JeffBeck-NOAA <[email protected]> Co-authored-by: lindsayrblank <[email protected]> Co-authored-by: Michelle Harrold <[email protected]> Co-authored-by: PerryShafran-NOAA <[email protected]>

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Minor bug fixes to CCPP UGWP (update submodule pointer for ccpp-physics) NOAA-EMC/fv3atm#216

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Minor bug fixes to unified_ugwp.F90 and drag_suite.F90 NCAR/ccpp-physics#532

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climbfuji requested review from DusanJovic-NOAA, junwang-noaa, climbfuji and aerorahul and removed request for DusanJovic-NOAA and junwang-noaa December 16, 2020 15:29

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kgerheiser and others added 3 commits December 17, 2020 09:49

Update modules with hpc-stack v1.1.0

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hpc-stack v1.1.0 has been installed and tested on all machines

Modulefilesusing hpc-stack v1.1.0 on Cheyenne and Gaea

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Remove pre-release notes from Jet module

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Update .gitmodules and submodule pointer for fv3atm for code review a…

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climbfuji added No Baseline Change No Baseline Change and removed Baseline Updates Current baselines will be updated. labels Dec 18, 2020

Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…

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Update modules with hpc-stack v1.1.0 #319

Update modules with hpc-stack v1.1.0 #319

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Update modules with hpc-stack v1.1.0 #319

Update modules with hpc-stack v1.1.0 #319

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