Merge remote-tracking branch 'origin/develop' into feature/dyn_dng

* 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.
AnnetteGibbs-NOAA · Jul 3, 2023 · 2286a16 · 2286a16
2 parents a531c85 + c6419ba
commit 2286a16
Show file tree

Hide file tree

Showing 341 changed files with 36,990 additions and 28,314 deletions.
diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
@@ -2,24 +2,32 @@
 
 - You may delete any sections labeled "optional".
 
-- If you are unclear on what should be written here, see https://github.com/NOAA-EMC/UFS_UTILS/wiki/9.-Creating-a-Pull-Request for some guidance. 
+- If you are unclear on what should be written here, see https://github.com/ufs-community/UFS_UTILS/wiki/9.-Creating-a-Pull-Request for some guidance. 
 
 - The title of this pull request should be a brief summary (ideally less than 100 characters) of the changes included in this PR. Please also include the branch to which this PR is being issued.
 
 - Use the "Preview" tab to see what your PR will look like when you hit "Create pull request"
 
-# --- Delete this line and those above before hitting "Create pull request" ---
+## --- Delete this line and those above before hitting "Create pull request" ---
 
 ## DESCRIPTION OF CHANGES: 
 One or more paragraphs describing the problem, solution, and required changes.
 
 ## TESTS CONDUCTED: 
-State whether the contingency tests were run or are pending, and if they were already run, state the result.  If contingency test baselines need to be updated as a result of this PR, please specify the machine(s) and path(s) to the new files.  Note that running the contigency tests is required for every PR and should be run at least once after all commits or changes have been made after review of the PR.  Make note of the compilers used, the platform/machine, and other relevant details as necessary.  Please also note whether new unit tests or updates to existing ones were required and their file names.
+If there are changes to the build or source code, the tests below must be conducted. Contact a repository manager if you need assistance.
+
+- [ ] Compile branch on all Tier 1 machines using Intel (Orion, Jet, Hera and WCOSS2).
+- [ ] Compile branch on Hera using GNU.
+- [ ] Compile branch in 'Debug' mode on WCOSS2.
+- [ ] Run unit tests locally on any Tier 1 machine.
+- [ ] Run relevant consistency tests locally on all Tier 1 machine.
+
+Describe any additional tests performed.
 
 ## DEPENDENCIES:
 Add any links to pending PRs that are required prior to merging this PR. For example:
 
-NOAA-EMC/UFS_UTILS/pull/<pr_number>
+ufs-community/UFS_UTILS/pull/<pr_number>
 
 ## DOCUMENTATION:
 If this PR is contributing new capabilities that need to be documented, please also include updates to the RST files in the docs/source directory as supporting material.

diff --git a/.github/workflows/Intel1.yml b/.github/workflows/Intel1.yml
@@ -0,0 +1,202 @@
+# UFS_UTILS test workflow.
+#
+# This workflow tests UFS_UTILS with the Intel compiler.
+#
+# Ed Hartnett 12/14/22
+name: Intel1
+on:
+  push:
+    branches:
+    - develop
+    paths-ignore:
+    - README.md
+  pull_request:
+    branches:
+    - develop
+    paths-ignore:
+    - README.md
+
+# Use custom shell with -l so .bash_profile is sourced which loads intel/oneapi/setvars.sh
+# without having to do it in manually every step. 
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  Intel:
+    runs-on: ubuntu-latest
+    env:
+      CC: icc
+      FC: ifort
+
+    steps:
+
+    # See https://software.intel.com/content/www/us/en/develop/articles/oneapi-repo-instructions.html
+    - name: install-intel
+      run: |
+        cd /tmp
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        sudo apt-get update
+        sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+        echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
+
+    - name: cache-netcdf
+      id: cache-netcdf
+      uses: actions/cache@v2
+      with:
+        path: ~/netcdf
+        key: Intel-netcdf-c-$4.7.4-{{ runner.os }}-intel3
+
+    - name: build-hdf5
+      if: steps.cache-netcdf.outputs.cache-hit != 'true'
+      run: |
+        export CC=mpiicc
+        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz &> /dev/null
+        tar -xzf hdf5-1.10.7.tar.gz
+        pushd hdf5-1.10.7
+        ./configure --prefix=${HOME}/netcdf --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests --disable-shared --disable-shared --enable-static
+        make -j2
+        make install
+           
+    - name: build-netcdf-c
+      if: steps.cache-netcdf.outputs.cache-hit != 'true'
+      run: |
+        export CC=mpiicc
+        export CPPFLAGS=-I${HOME}/netcdf/include
+        export LDFLAGS=-L${HOME}/netcdf/lib
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz &> /dev/null
+        tar -xzf v4.7.4.tar.gz
+        pushd netcdf-c-4.7.4
+        ./configure --prefix=${HOME}/netcdf --disable-dap --disable-utilities --disable-shared
+        make -j2
+        make install
+
+    - name: build-netcdf-fortran
+      if: steps.cache-netcdf.outputs.cache-hit != 'true'
+      run: |
+        export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${HOME}/netcdf/lib"
+        export PATH="${HOME}/netcdf/bin:$PATH"
+        export CC=mpiicc
+        export FC=mpiifort
+        export CPPFLAGS=-I${HOME}/netcdf/include
+        export LDFLAGS=-L${HOME}/netcdf/lib
+        export LIBS=`nc-config --libs`
+        wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.3.tar.gz &> /dev/null
+        tar -xzf v4.5.3.tar.gz
+        pushd netcdf-fortran-4.5.3
+        ./configure --prefix=${HOME}/netcdf --disable-shared
+        make -j2
+        make install
+
+    - name: cache-esmf
+      id: cache-esmf
+      uses: actions/cache@v2
+      with:
+        path: ~/esmf
+        key: Intel-esmf-8.2.0-${{ runner.os }}-intel3
+
+    - name: build-esmf
+      if: steps.cache-esmf.outputs.cache-hit != 'true'
+      run: |
+        pushd ~
+        export ESMF_DIR=~/esmf-ESMF_8_2_0
+        wget https://github.com/esmf-org/esmf/archive/ESMF_8_2_0.tar.gz &> /dev/null
+        tar zxf ESMF_8_2_0.tar.gz
+        cd esmf-ESMF_8_2_0
+        export ESMF_COMM=intelmpi
+        export ESMF_INSTALL_BINDIR=bin
+        export ESMF_INSTALL_LIBDIR=lib
+        export ESMF_INSTALL_MODDIR=mod
+        export ESMF_COMPILER=intel
+        export ESMF_INSTALL_PREFIX=~/esmf
+        export ESMF_NETCDF=split
+        export ESMF_NETCDF_INCLUDE=${HOME}/netcdf/include
+        export ESMF_NETCDF_LIBPATH=${HOME}/netcdf/lib
+        export ESMF_NETCDF_LIBS="-lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz"
+        make -j2
+        make install
+
+    - name: cache-jasper
+      id: cache-jasper
+      uses: actions/cache@v2
+      with:
+        path: ~/jasper
+        key: Intel-jasper-2.0.25-${{ runner.os }}-intel3
+
+    - name: build-jasper
+      if: steps.cache-jasper.outputs.cache-hit != 'true'
+      run: |
+        wget https://github.com/jasper-software/jasper/archive/version-2.0.25.tar.gz &> /dev/null
+        tar zxf version-2.0.25.tar.gz
+        cd jasper-version-2.0.25
+        mkdir build-jasper && cd build-jasper
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper -DJAS_ENABLE_SHARED=OFF
+        make -j2
+        make install
+
+    - name: checkout-nceplibs
+      uses: actions/checkout@v2
+      with:
+        repository: NOAA-EMC/NCEPLIBS
+        path: nceplibs
+
+    - name: cache-nceplibs
+      id: cache-nceplibs
+      uses: actions/cache@v2
+      with:
+        path: ~/nceplibs
+        key: Intel-nceplibs-1.4.0-${{ runner.os }}-intel3
+
+    - name: build-nceplibs
+      if: steps.cache-nceplibs.outputs.cache-hit != 'true'
+      run: |
+        export ESMFMKFILE=~/esmf/lib/esmf.mk
+        wget https://github.com/NOAA-EMC/NCEPLIBS/archive/v1.4.0.tar.gz &> /dev/null
+        tar zxf v1.4.0.tar.gz
+        cd NCEPLIBS-1.4.0
+        mkdir build && cd build
+        cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper;~/netcdf' -DCMAKE_INSTALL_PREFIX='~/nceplibs' -DFLAT=ON
+        make -j2
+       
+    - name: checkout-ufs-utils
+      uses: actions/checkout@v2
+      with: 
+        path: ufs_utils
+        submodules: recursive
+
+    - name: cache-data
+      id: cache-data
+      uses: actions/cache@v2
+      with:
+        path: ~/data
+        key: data-1
+
+    - name: build
+      run: |
+        export ESMFMKFILE=~/esmf/lib/esmf.mk
+        cd ufs_utils
+        mkdir build && cd build
+        export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
+        cmake -DTEST_FILE_DIR=/home/runner/data -DCMAKE_PREFIX_PATH='~;~/jasper;~/nceplibs;~/netcdf' ..
+        make -j2
+    
+    - name: test
+      run: |
+        cd ufs_utils/build
+        ctest --rerun-failed --output-on-failure
+
+    - name: cache-data
+      if: steps.cache-data.outputs.cache-hit != 'true'
+      run: |
+        mkdir ~/data
+        cp ufs_utils/build/tests/chgres_cube/data/* ~/data
+        cp ufs_utils/build/tests/sfc_climo_gen/data/* ~/data
+        cp ufs_utils/build/tests/cpld_gridgen/data/* ~/data
+        cp ufs_utils/tests/filter_topo/data/* ~/data
+        cp ufs_utils/tests/emcsfc_snow2mdl/data/* ~/data
+        cp ufs_utils/tests/chgres_cube/data/* ~/data
+        ls -l ~/data
+