Bring in HAFSv1 nesting needed changes from FRE-NCtools #752
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Initial commit to support conversion of atmospheric data from grib2 files
Bug fix for improper tracer loop in regridding section
Initial commit to support conversion of atmospheric data from grib2 files
Bug fix for improper tracer loop in regridding section
Add a module load command for wgrib2 for chgres_cube.theia
…to feature/chgres_cube_grib2_atmos
Conflicts (resolved): sorc/build_all_ufs_utils.sh sorc/partial_ufs_build.sh sorc/ufs_build.cfg ush/fv3gfs_driver_grid.sh
Conflicts (resolved): modulefiles/chgres_cube.jet modulefiles/fv3gfs/fre-nctools.jet modulefiles/fv3gfs/global_chgres.jet modulefiles/fv3gfs/orog.jet modulefiles/modulefile.sfc_climo_gen.jet sorc/fre-nctools.fd/tools/filter_topo/make.csh_jet sorc/fre-nctools.fd/tools/make_hgrid/fre-nctools.mk_jet sorc/fre-nctools.fd/tools/shave.fd/build_shave
Added check for bad namelist inputs for grib2 input. Improved varmap tables and how they're read. Bug Fixes.
Minor syntax/bug fixes.
chgres_cube.theia build module file - fix error in load of w3nco library. Update makefile to link the wgrib2 api last. This eliminates problems reading netcdf files which is the result of esmf and wgrib2 using different versions of netcdf (?) Change-Id: Ifee9f0986fb6664122acc5c32a7ece8a5e6a8143
Merge branch 'develop' into feature/chgres_cube_grib2_atmos. Change-Id: Ie4b94468ff2c46ed95f547c4ac8b07586cb59ec8
Fixed empty line in GFS varmap table and updated reading of varmap table to ignore empty lines.
…to feature/chgres_cube_grib2_atmos
Fix for proper RH->sphum computation.
dzdt is now properly converted to sigma coordinates and flipped vertically for non-native grib2 files
dzdt is now properly converted to sigma coordinates and flipped vertically for non-native grib2 files
Update build of 'fre-nctools', 'nst_tf_chg', 'nems_util' and 'orog' programs for Hera. Remove references to Theia.
Update 'emcsfc' and 'sfc_climo_gen' build for Hera. Add better logic to 'machine-setup.sh' to determine if on Hera.
Update 'chgres', 'chgres_cube' and 'global_cycle' to build on Hera. All programs can now be compiled on Hera.
Update to intel v15 for chgres on phase 1/2. This is required because other machines use newer versions that require the -qopenmp flag. v14 only recognized -openmp.
Update "link_fixdirs.sh" for Hera. Remove references to Theia.
@GeorgeGayno-NOAA, as for mppnccombine, I would like to check with @JacobCarley-NOAA and @JianpingHuang-NOAA to see if they actually still use/need this mppnccombine tool. For HAFS, we previously used it as a workaround for a slow IO issue for FV3 restart files. But, we currently no longer use it as the slow IO for FV3 restart files has been addressed from the ufs-weather-model/FV3 side. In terms of the fregrid, make_hgrid, make_solo_mosaic, and other fre-nctools.fd related changes, this set of changes are mainly a manual sync with the corresponding version from FRE-NCtools official repository as of 09/2021 to bring in the support for multiple static and moving nesting capabilities needed by HAFS. |
@GeorgeGayno-NOAA, this branch was originally branched out from UFS_UTILS master branch a while ago (at least 2 years or more). But, we have been keeping syncing with the UFS_UTILS's develop/master branch. And you can see the actual differences between this branch and the latest develop branch are relatively small (only 20+ files were changed/added). Also, if you would prefer to, all these changes can just be squashed and merged back on top of the latest develop branch, once the PR review and test are done. Thanks! |
|
@bin Liu - NOAA Affiliate ***@***.***> We used to
use mppnccombine utility to support UFS-AQM testing at the beginning. It is
fine for us without using it now.
…On Wed, Jan 4, 2023 at 8:53 AM Bin Liu ***@***.***> wrote:
Any new codes, such as mppnccombine, will need a test.
Any new functions to existing codes will also need a test. What exactly
changed with 'fregrid', 'make_hgrid' and 'make_solo_mosaic'?
@GeorgeGayno-NOAA <https://github.com/GeorgeGayno-NOAA>, as for
mppnccombine, I would like to check with @JacobCarley-NOAA
<https://github.com/JacobCarley-NOAA> and @JianpingHuang-NOAA
<https://github.com/JianpingHuang-NOAA> to see if they actually still
use/need this mppnccombine tool. For HAFS, we previously used it as a
workaround for a slow IO issue for FV3 restart files. But, we currently no
longer use it as the slow IO for FV3 restart files has been addressed from
the ufs-weather-model/FV3 side.
In terms of the fregrid, make_hgrid, make_solo_mosaic, and other
fre-nctools.fd related changes, this set of changes are mainly a manual
sync with the corresponding version from FRE-NCtools official repository
<https://github.com/NOAA-GFDL/FRE-NCtools> as of 09/2021 to bring in the
support for multiple static and moving nesting capabilities needed by HAFS.
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@JianpingHuang-NOAA, thanks for confirming you are no longer using this mppnccombine tool! @GeorgeGayno-NOAA I am trying to check with the RRFS group. If they also do not use it. I will just go ahead take out the mppnccombine changes. Thanks! |
Thank you for not adding unneeded programs to the repository. |
The test that checks a GFDL regional grid (See https://github.com/ufs-community/UFS_UTILS/blob/develop/reg_tests/grid_gen/gfdl.regional.sh) failed. Differences in the 'grid' file are small, however: This lead to downstream changes in the 'orog' files (which are also small) |
BinLiu-NOAA
changed the title
…ir will be genearated during the cmake build anyway.
@GeorgeGayno-NOAA, I have checked with developers for other applications (RRFS, AQM), and they no longer use this mppnccombine tool. So I have just removed it from this PR. PR title and description are also updated now. Thanks! |
@GeorgeGayno-NOAA, I think these differences are due to the sync with the fre-nctools official repository, which probably included some bug fixes/updates. I hope this result changing can be considered as acceptable. Thanks! |
These differences are very small and will not prevent a merge. I am not seeing any differences with global uniform grids. (I tried C96 and C768). |
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Does this merge support a HAFS implementation? If so, will you need a UFS_UTILS tag or will you create a tag from the HAFS fork? |
@GeorgeGayno-NOAA, yes. If possible, we would prefer your help to create a support/production branch (say production/hafs.v1.0.0 branch or support/hafs.v1.0.0 branch depending upon ufs_utils side branch naming convention) from the develop branch once this PR is merged. This is just in case any further changes might be needed before the HAFSv1 code freeze and code delivery to NCO. And for the NCO code delivery, you can then help to tag this branch into a tag like ops-hafsv1.0.0 (or simply hafs.v1.0.0 or something similar). Please feel free to let us know if you would prefer to something else. Thanks! |
We have been asked to do versioned tags - v1.8 etc. So, after the merge we can create v1.9. If further changes are required, we can create another tag - v1.10 - or if the fix is small, add it to v1.9 and then create a v1.9.1 tag. |
@GeorgeGayno-NOAA, I saw there are tags like ops-gfsv16.3.0. So, this tag naming convention is no longer recommended? If not, we can use whatever the UFS_UTILS repository side preferred tag/branch names. Thanks! |
We were told to stop naming tags after the specific operational implementation. You are seeing some tags with the old naming convention that we need to maintain. |
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@GeorgeGayno-NOAA, Thanks for the context and explanation! And we can go with the UFS_UTILS repository preferred naming convention for tagging/branching. Thanks! |
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@GeorgeGayno-NOAA, wondering if it is possible to merge this PR back to develop branch and create a tag for HAFSv1 code freeze saying before the end of this week. Much appreciated. |
Yes, I can create your tag before the end of this week. |
The branch at af65b7e was compiled on Hera, Jet, Orion and Cactus. The grid_gen consistency test were run. All test passed expect the GFDL regional test. It failed on all machines with the very small errors as described above. I can't explain these differences, but they are too small to worry about. |
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@BinLiu-NOAA I have one final small question. Otherwise, everything looks OK. |
* origin/develop: Update ccpp submodule (ufs-community#827) Change length of character variable "mosaic_name" in "make_solo_mosaic.c" (ufs-community#824) Update GDAS INIT utility for GFS COM reorganization (ufs-community#820) Add backup calculation for orography and mask generation (ufs-community#713) Improve repository build script (ufs-community#819) Use latest wgrib2 executable on Jet. (ufs-community#816) chgres_cube - Minor update for high-resolution grids . (ufs-community#814) Update PR template (ufs-community#813) global_cycle - Add soil moisture nudging for NoahMP option (ufs-community#809) Release v1.10.0 (ufs-community#807) Run sfc_climo_gen utility on Hera (ufs-community#791) Fix bug in chgres_cube subroutine search_many (ufs-community#808) sfc_climo_gen - Output fractions of each vegetation/soil type category (ufs-community#748) Replace w3nco library with w3emc (ufs-community#802) Fix Debug compilation (ufs-community#800) Update WCOSS2 build module to use new ESMF v8.4.1 library. (ufs-community#799) Update chgres_cube documentation for duplicate grib2 records (ufs-community#795) Use latest Cray modules on WCOSS2 (ufs-community#792) Remove checksum attribute from global_cycle restart files (ufs-community#794) Remove goto statements from chgres_cube (ufs-community#775) FVCOM_TOOLS - Remove dependency on module_nwp_base.f90 (ufs-community#790) Remove "gcovr" step from the 'developer' workflow (ufs-community#785) Update build module for Cheyenne (ufs-community#783) GDAS Init utility - consolidate the copy of coldstart files (ufs-community#773) Remove support for ODIN machine (ufs-community#782) Update GDAS INIT utility to optionally use fracoro data (ufs-community#741) Option to build only application specific utilities (e.g. GFS) (ufs-community#777) Use combined IP/IP2 library (ufs-community#695) Initial updates to global_cycle for Noah-MP land model (ufs-community#774) New resolution options for the cpld_gridgen utility (ufs-community#769) Use new EPIC-maintained hpc-stack on Jet (ufs-community#771) Update GDAS initialization scripts for the new ENKF directory (ufs-community#764) Reduce memory usage in chgres_cube (ufs-community#766) Detect duplicate vertical levels in chgres_cube. (ufs-community#767) Point to new input orography directory. (ufs-community#758) Release version 1.9 (ufs-community#754) HAFSv1 grid nesting updates (ufs-community#752) Remove compiler warnings from chgres_cube (ufs-community#747) chgres_cube: Split input_data module into to 3 separate modules (ufs-community#744) More work on CI, checking with different versions of ESMF (ufs-community#742) Add processing of soil color to sfc_climo_gen (ufs-community#721) more work on CI - added Linux_versions workflow (ufs-community#739) Add TEST_FILE_DIR option to CMake build, where test data files can be found instead of using FTP. (ufs-community#732) adding developer workflow (ufs-community#724) Update GDAS INIT utility for v16.3. (ufs-community#723) OROG_GSL - Remove negative bias in orographic asymmetery (OA) fields (ufs-community#718) Incorporate BNU soil type data (ufs-community#717) High-resolution MODIS and STATSGO veg/soil data. (ufs-community#703) Run WCOSS2 consistency tests under role account (ufs-community#711) Fix macOS CI workflow (ufs-community#715) Add utility codes to create BNU soil texture data (ufs-community#707) Update chgres_cube to output netcdf4 file. (ufs-community#704) Incorporate high-res global VIIRS vegetation data. (ufs-community#699) Run grid_gen consistency tests in parallel. (ufs-community#697) Fix error handling in "link_fixdirs.sh". Add -L to the copy command. (ufs-community#701) Update for new fixed data directory structure (ufs-community#688) Add WCOSS2 support for tests (ufs-community#693) Increase test data pull timeout (ufs-community#692) Option to install binaries to any directory. (ufs-community#685) Update global_cycle to use the latest CCPP version of sfcsub.F (ufs-community#671) Incorporate weight_gen program. (ufs-community#677) Add install of jpeg-turbo to macos workflows (ufs-community#684) Improve logic in regression test driver script (ufs-community#681) Release v1.8 (ufs-community#679) Update link_fixdirs.sh for new data directories (ufs-community#672) Update default ice climatology in ./ush/global_cycle.sh. (ufs-community#664) Remove all references to WCOSS 1 from UFS_UTILS (ufs-community#667) Update workflows to use latest macOS and ubuntu (ufs-community#675) Update GDAS Initialization utility for recent HPSS tarball name change (ufs-community#666) Port UFS_UTILS to WCOSS2 (ufs-community#642) Fix chgres_cube to process GEFS GRIB2 data (ufs-community#658) Update global_cycle_driver.sh for GFS OPS directory convention (ufs-community#655) Update documentation for SRW App (ufs-community#656) New coupled model utility (ufs-community#647) Update support for S4 and enable regression testing (ufs-community#654) global_cycle - Link to CCPP version of sfcsub.F (ufs-community#636) Add processing of new global AFWA snow data to emcsfc_snow2mdl. (ufs-community#648) Update build module on Cheyenne (ufs-community#646) Move to Intel 2022 on Jet, Hera and Orion (ufs-community#650) Host doxygen documentation for multiple releases (ufs-community#644) Download unit test data as part of the CMake build (ufs-community#630) chgres_cube - Complete removal of wgrib2 library (ufs-community#641) Eliminate circular dependency in chgres_cube Update workflow files to pull netcdf-c library from GitHub chgres_cube - Remove the wgrib2 library from the GRIB2 data read routines. Undefined symbols on macOS with Intel compiler (ufs-community#628) Update FVCOM code to handle sub-domain restart files using multiple cores. (ufs-community#624) chgres_cube - Run routine 'convert_omega' on all tasks. (ufs-community#627) Use ESMF 8.2.0 library Automate update of consistency test baseline data. (ufs-community#603) Update workflow files to use newer versions of ESMF and NCEPLIBS. (ufs-community#617) Update build modules to be lua compliant (ufs-community#614) Allow FVCOM tools to Update Ice Surface Roughness Length (ufs-community#604) Update the requested memory in the Orion chgres_cube consistency test script (ufs-community#611) Use copy of grib_util under Jet role account. (ufs-community#608) Run consistency tests on Orion using role account (ufs-community#606) Run consistency tests on Hera using role account (ufs-community#605) Run consistency tests on Jet using role account. (ufs-community#607) Update more documentation after move to ufs-community (ufs-community#597) fvcom_tools - Add option to process 'cold' or 'warm' restart files (ufs-community#595) Update documentation after move to ufs-community (ufs-community#594) chgres_cube - Eliminate segmentation fault in input_data.F90 (ufs-community#585) Update to language of unit test README to match that in unit test. chgres_cube - Simplify surface processing using field bundles (ufs-community#572) Add compiler flags for GNU Fortran v10 or newer compilers. (ufs-community#583) Move verbose output from example unit test to be commented to streamline test output. Updates to test README to add instructions for use of example unit test. Add Findwgrib2.cmake (ufs-community#578) Added unit test to be used as an instructional example for new users.
DESCRIPTION OF CHANGES:
TESTS CONDUCTED:
All the changes have been tested with the UFS HAFS application.
The grid_gen consistency tests were run. Results documented below.
DEPENDENCIES:
N/A
DOCUMENTATION:
N/A
ISSUE:
Fixes issue mentioned in #751
CONTRIBUTORS:
FRE-NCtools changes are mainly from https://github.com/NOAA-GFDL/FRE-NCtools. The FRE-NCtools related porting were mainly done by @BinLiu-NOAA and @BijuThomas-NOAA.