Merge branch 'develop' into feature/new_ip

Fixes ufs-community#242.
GeorgeGayno-NOAA · Sep 7, 2022 · 292be97 · 292be97
2 parents 2b2a235 + c33ea52
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diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
@@ -0,0 +1,32 @@
+- Use this template to give a detailed message describing the change you want to make to the code.
+
+- You may delete any sections labeled "optional".
+
+- 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" ---
+
+## 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.
+
+## DEPENDENCIES:
+Add any links to pending PRs that are required prior to merging this PR. For example:
+
+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.
+
+## ISSUE: 
+If this PR is resolving or referencing one or more issues, in this repository or elsewhere, list them here. For example, "Fixes issue mentioned in #123" or "Related to bug in https://github.com/NOAA-EMC/other_repository/pull/63"
+
+## CONTRIBUTORS (optional): 
+If others have contributed to this work aside from the PR author, list them here
+
diff --git a/.github/workflows/debug-docs-test_coverage.yml b/.github/workflows/debug-docs-test_coverage.yml
@@ -26,16 +26,16 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/esmf
-        key: esmf-8.0.1-${{ runner.os }}
+        key: esmf-8.2.0-${{ runner.os }}3
 
     - name: build-esmf
       if: steps.cache-esmf.outputs.cache-hit != 'true'
       run: |
         pushd ~
-        export ESMF_DIR=~/esmf-ESMF_8_0_1
-        wget https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz &> /dev/null
-        tar zxf ESMF_8_0_1.tar.gz
-        cd esmf-ESMF_8_0_1
+        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=mpich3
         export ESMF_INSTALL_BINDIR=bin
         export ESMF_INSTALL_LIBDIR=lib
@@ -53,7 +53,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/jasper
-        key: jasper-2.0.25-${{ runner.os }}
+        key: jasper-2.0.25-${{ runner.os }}3
 
     - name: build-jasper
       if: steps.cache-jasper.outputs.cache-hit != 'true'
@@ -62,7 +62,7 @@ jobs:
         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
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper -DJAS_ENABLE_SHARED=OFF
         make -j2
         make install
 
@@ -71,14 +71,14 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/nceplibs
-        key: nceplibs-1.3.0-${{ runner.os }}
+        key: nceplibs-1.4.0-${{ runner.os }}3
 
     - name: build-nceplibs
       if: steps.cache-nceplibs.outputs.cache-hit != 'true'
       run: |
-        wget https://github.com/NOAA-EMC/NCEPLIBS/archive/v1.3.0.tar.gz &> /dev/null
-        tar zxf v1.3.0.tar.gz
-        cd NCEPLIBS-1.3.0
+        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
         export ESMFMKFILE=~/esmf/lib/esmf.mk
         mkdir build && cd build
         cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper' -DCMAKE_INSTALL_PREFIX='~/nceplibs' -DFLAT=ON
@@ -88,6 +88,7 @@ jobs:
       uses: actions/checkout@v2
       with: 
         path: ufs_utils
+        submodules: recursive
 
     - name: build
       run: |
@@ -97,15 +98,13 @@ jobs:
         export CC=mpicc
         export CXX=mpicxx
         export FC=mpifort
+        export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
         cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs' -DCMAKE_BUILD_TYPE=Debug -DENABLE_DOCS=On -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0"
         make -j2
 
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         export LSAN_OPTIONS=suppressions=LSanSuppress.supp
         ctest --rerun-failed --output-on-failure
         export PATH="/home/runner/.local/bin:$PATH"

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -16,7 +16,7 @@ jobs:
       CXX: icpc
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-latest]
 
     steps:
 
@@ -37,7 +37,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/netcdf
-        key: netcdf-c-$4.7.4-{{ runner.os }}-intel
+        key: netcdf-c-$4.7.4-{{ runner.os }}-intel3
 
     - name: build-hdf5
       if: steps.cache-netcdf.outputs.cache-hit != 'true'
@@ -46,7 +46,7 @@ jobs:
         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=${HOME}/netcdf --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
+        ./configure --prefix=${HOME}/netcdf --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests --disable-shared --disable-shared --enable-static
         make -j2
         make install
            
@@ -56,10 +56,10 @@ jobs:
         export CC=mpiicc
         export CPPFLAGS=-I${HOME}/netcdf/include
         export LDFLAGS=-L${HOME}/netcdf/lib
-        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
-        tar -xzf netcdf-c-4.7.4.tar.gz
+        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=${HOME}/netcdf --disable-dap --disable-utilities
+        ./configure --prefix=${HOME}/netcdf --disable-dap --disable-utilities --disable-shared
         make -j2
         make install
 
@@ -72,10 +72,11 @@ jobs:
         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=${HOME}/netcdf
+        ./configure --prefix=${HOME}/netcdf --disable-shared
         make -j2
         make install
 
@@ -84,16 +85,16 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/esmf
-        key: esmf-8.0.1-${{ runner.os }}-intel
+        key: esmf-8.2.0-${{ runner.os }}-intel3
 
     - name: build-esmf
       if: steps.cache-esmf.outputs.cache-hit != 'true'
       run: |
         pushd ~
-        export ESMF_DIR=~/esmf-ESMF_8_0_1
-        wget https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz &> /dev/null
-        tar zxf ESMF_8_0_1.tar.gz
-        cd esmf-ESMF_8_0_1
+        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
@@ -103,6 +104,7 @@ jobs:
         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
 
@@ -111,7 +113,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/jasper
-        key: jasper-2.0.25-${{ runner.os }}-intel
+        key: jasper-2.0.25-${{ runner.os }}-intel3
 
     - name: build-jasper
       if: steps.cache-jasper.outputs.cache-hit != 'true'
@@ -120,7 +122,7 @@ jobs:
         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
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper -DJAS_ENABLE_SHARED=OFF
         make -j2
         make install
 
@@ -135,15 +137,15 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/nceplibs
-        key: nceplibs-1.3.0-${{ runner.os }}-intel
+        key: nceplibs-1.4.0-${{ 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/v1.3.0.tar.gz &> /dev/null
-        tar zxf v1.3.0.tar.gz
-        cd NCEPLIBS-1.3.0
+        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
@@ -152,19 +154,18 @@ jobs:
       uses: actions/checkout@v2
       with: 
         path: ufs_utils
+        submodules: recursive
 
     - 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 .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_PREFIX_PATH='~;~/jasper;~/nceplibs;~/netcdf'
         make -j2
     
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         ctest --rerun-failed --output-on-failure