add spack-based ci. (#528)

* add spack-based ci.
replace dependency on w3nco with w3emc.
Update w3emc to 2.9.2 on all machines (wcoss2 is already at 2.9.2)

* remove deprecated hera and orion env. modulefiles

* update nemsio version to 2.5.4. Flush cache

.github/workflows/gcc.yml

@@ -0,0 +1,96 @@
+name: GCC Linux Build
+on: [push, pull_request, workflow_dispatch]
+
+
+# Use custom shell with -l so .bash_profile is sourced
+# without having to do it in manually every step
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+env:
+  cache_key: gcc2  # The number (#) following the cache_key "gcc" is to flush Action cache.
+  CC: gcc-10
+  FC: gfortran-10
+  CXX: g++-10
+
+# A note on flushing Action cache and relevance to "cache_key" above.
+# There is no way to flush the Action cache, and hence a number (#) is appended
+# to the "cache_key" (gcc).
+# If the dependencies change, increment this number and a new cache will be
+# generated by the dependency build step "setup"
+# There is a Github issue to force clear the cache.
+# See discussion on:
+# https://stackoverflow.com/questions/63521430/clear-cache-in-github-actions
+
+# The jobs are split into:
+# 1. a dependency build step (setup), and
+# 2. a UPP build step (build)
+# The setup is run once and the environment is cached,
+# so each build of UPP can reuse the cached dependencies to save time (and compute).
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Cache spack, compiler and dependencies
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v2
+        with:
+          path: |
+            spack
+            ~/.spack
+          key: spack-${{ runner.os }}-${{ env.cache_key }}
+
+      - name: checkout-upp  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
+      # Install dependencies using Spack
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create upp-env UPP/ci/spack.yaml
+          spack env activate upp-env
+          spack compiler find
+          spack external find
+          spack add mpich@3.4.2
+          spack concretize
+          spack install --dirty -v
+
+  build:
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout-upp
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v2
+        with:
+          path: |
+            spack
+            ~/.spack
+          key: spack-${{ runner.os }}-${{ env.cache_key }}
+
+      - name: build-upp
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate upp-env
+          export CC=mpicc
+          export FC=mpif90
+          cd UPP
+          mkdir -p build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=../install ..
+          make -j2 VERBOSE=1
+          make install

.github/workflows/intel.yml

@@ -0,0 +1,114 @@
+name: Intel Linux Build
+on: [push, pull_request, workflow_dispatch]
+
+# 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}
+
+# Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
+env:
+  cache_key: intel2  # The number (#) following the cache_key "intel" is to flush Action cache.
+  CC: icc
+  FC: ifort
+  CXX: icpc
+  I_MPI_CC: icc
+  I_MPI_F90: ifort
+
+# A note on flushing Action cache and relevance to "cache_key" above.
+# There is no way to flush the Action cache, and hence a number (#) is appended
+# to the "cache_key" (intel).
+# If the dependencies change, increment this number and a new cache will be
+# generated by the dependency build step "setup"
+# There is a Github issue to force clear the cache.
+# See discussion on:
+# https://stackoverflow.com/questions/63521430/clear-cache-in-github-actions
+
+# The jobs are split into:
+# 1. a dependency build step (setup), and
+# 2. a UPP build step (build)
+# The setup is run once and the environment is cached,
+# so each build of UPP can reuse the cached dependencies to save time (and compute).
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Cache spack, compiler and dependencies
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v2
+        with:
+          path: |
+            spack
+            ~/.spack
+            /opt/intel
+          key: spack-${{ runner.os }}-${{ env.cache_key }}
+
+      - name: install-intel-compilers
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          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
+          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: checkout-upp  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
+      # Install dependencies using Spack
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create upp-env UPP/ci/spack.yaml
+          spack env activate upp-env
+          spack compiler find
+          spack external find
+          spack add intel-oneapi-mpi
+          spack concretize
+          spack install --dirty -v
+
+  build:
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout-upp
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
+      - name: install-intel
+        run: |
+          echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v2
+        with:
+          path: |
+            spack
+            ~/.spack
+            /opt/intel
+          key: spack-${{ runner.os }}-${{ env.cache_key }}
+
+      - name: build-upp
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate upp-env
+          export CC=mpiicc
+          export FC=mpiifort
+          cd UPP
+          mkdir -p build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=../install ..
+          make -j2 VERBOSE=1
+          make install

CMakeLists.txt

@@ -57,18 +57,12 @@ if(BUILD_POSTEXEC)
   find_package(sfcio REQUIRED)
   find_package(sigio REQUIRED)
   find_package(sp REQUIRED)
-  find_package(w3nco REQUIRED)
+  find_package(w3emc REQUIRED)
   if(BUILD_WITH_WRFIO)
     find_package(wrf_io REQUIRED)
   endif()
 endif()
 
-### Switch RUNTIME DESTINATION DIR between bin and exec
-set(exec_dir bin)
-if(EMC_EXEC_DIR)
-  set(exec_dir exec)
-endif()
-
 add_subdirectory(sorc)
 add_subdirectory(parm)
 

ci/spack.yaml

@@ -0,0 +1,23 @@
+# Spack environment file to build UPP dependencies
+spack:
+  packages:
+    all:
+      compiler: [intel, gcc]
+  specs:
+  - netcdf-c@4.7.4
+  - netcdf-fortran@4.5.3
+  - bacio@2.4.1
+  - w3emc@2.9.2
+  - g2@3.4.5
+  - g2tmpl@1.10.0
+  - sp@2.3.3
+  - ip@3.3.3
+  - sigio@2.3.2
+  - sfcio@1.4.1
+  - nemsio@2.5.4
+  - wrf-io@1.2.0
+  - crtm@2.3.0
+  view: true
+  concretizer:
+    unify: true
+

cmake/PackageConfig.cmake.in

@@ -30,7 +30,7 @@ find_dependency(ip CONFIG)
 #find_dependency(sfcio CONFIG)
 #find_dependency(sigio CONFIG)
 #find_dependency(sp CONFIG)
-#find_dependency(w3nco CONFIG)
+#find_dependency(w3emc CONFIG)
 
 # Get the build type from library target
 get_target_property(@PROJECT_NAME@_BUILD_TYPES @PROJECT_NAME@::@PROJECT_NAME@ IMPORTED_CONFIGURATIONS)

modulefiles/cheyenne

@@ -35,6 +35,5 @@ module load nemsio/2.5.2
 module load sfcio/1.4.1
 module load sigio/2.3.2
 module load sp/2.3.3
-module load w3nco/2.4.1
-module load w3emc/2.7.3
+module load w3emc/2.9.2
 module load wrf_io/1.2.0

modulefiles/cheyenne_gnu

@@ -36,6 +36,5 @@ module load nemsio/2.5.2
 module load sfcio/1.4.1
 module load sigio/2.3.2
 module load sp/2.3.3
-module load w3nco/2.4.1
-module load w3emc/2.7.3
+module load w3emc/2.9.2
 module load wrf_io/1.2.0

modulefiles/hera.lua

@@ -31,8 +31,6 @@ g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.0"
 load(pathJoin("g2tmpl", g2tmpl_ver))
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 ip_ver=os.getenv("ip_ver") or "3.3.3"
@@ -44,7 +42,7 @@ load(pathJoin("crtm", crtm_ver))
 w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
 load(pathJoin("w3emc", w3emc_ver))
 
-nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 load(pathJoin("nemsio", nemsio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))

modulefiles/jet

@@ -30,6 +30,5 @@ module load nemsio/2.5.2
 module load sfcio/1.4.1
 module load sigio/2.3.2
 module load sp/2.3.3
-module load w3nco/2.4.1
-module load w3emc/2.7.3
+module load w3emc/2.9.2
 module load wrf_io/1.1.1

modulefiles/orion.lua

@@ -31,8 +31,6 @@ g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.0"
 load(pathJoin("g2tmpl", g2tmpl_ver))
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 ip_ver=os.getenv("ip_ver") or "3.3.3"

modulefiles/s4

@@ -29,6 +29,5 @@ module load nemsio/2.5.2
 module load sfcio/1.4.1
 module load sigio/2.3.2
 module load sp/2.3.3
-module load w3nco/2.4.1
-module load w3emc/2.7.3
+module load w3emc/2.9.2
 module load wrf_io/1.1.1