Merge branch 'feature/2mDA' into bugfix2mDA

.github/workflows/gcc.yml

@@ -0,0 +1,95 @@
+name: GCC Linux Build
+on: [push, pull_request]
+
+# 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: gcc3  # 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 GSI build step (build)
+# The setup is run once and the environment is cached,
+# so each build of GSI 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-gsi  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v2
+        with:
+            path: GSI
+
+      # 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 gsi-env GSI/ci/spack.yaml
+          spack env activate gsi-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-gsi
+        uses: actions/checkout@v2
+        with:
+            path: GSI
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v2
+        with:
+          path: |
+            spack
+            ~/.spack
+          key: spack-${{ runner.os }}-${{ env.cache_key }}
+
+      - name: build-gsi
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate gsi-env
+          export CC=mpicc
+          export FC=mpif90
+          cd GSI
+          mkdir -p build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF -DBUILD_NCDIAG=OFF ..
+          make -j2 VERBOSE=1
+          make install

.github/workflows/intel.yml

@@ -0,0 +1,114 @@
+name: Intel Linux Build
+on: [push, pull_request]
+
+# 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: intel3  # 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 GSI build step (build)
+# The setup is run once and the environment is cached,
+# so each build of GSI 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-gsi  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v2
+        with:
+            path: GSI
+
+      # 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 gsi-env GSI/ci/spack.yaml
+          spack env activate gsi-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-gsi
+        uses: actions/checkout@v2
+        with:
+            path: GSI
+
+      - 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-gsi
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate gsi-env
+          export CC=mpiicc
+          export FC=mpiifort
+          cd GSI
+          mkdir -p build && cd build
+          cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF -DBUILD_NCDIAG=OFF ..
+          make -j2 VERBOSE=1
+          make install

.gitignore

@@ -1,2 +1,34 @@
 build*/
+install*/
 .*.swp
+*.[aox]
+*.mod
+.DS_Store
+exec/
+lib/
+lib64/
+
+nohup.out
+log*
+build.log*
+install.log*
+
+# Ensure no one adds binary files to this repo. Not even by accident.
+# over-riding this file can be done in the subdirectory
+*.bin
+*.nc*
+*.tar*
+*.tgz
+*.gz
+*.png
+*.jp*g
+*.tiff
+
+# Python related
+_pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+

.gitmodules

@@ -1,7 +1,3 @@
 [submodule "fix"]
 	path = fix
 	url = gerrit:GSI-fix
-
-[submodule "libsrc"]
-	path = libsrc
-	url = gerrit:GSI-libsrc