MEGB added to one version before Sho's localization

.github/pull_request_template.md

@@ -0,0 +1,41 @@
+<!-- PLEASE READ -->
+<!--
+Before opening a PR, please note these guidelines:
+
+- Each PR should only address ONE topic and have an associated issue
+- No hardcoded or paths to personal directories should be present
+- No temporary or backup files should be committed
+- Any code that was disabled by being commented out should be removed
+-->
+
+**Description**
+
+<!-- Please include relevant motivation and context. -->
+<!-- Please include a summary of the change and which issue is fixed. -->
+<!-- List any dependencies that are required for this change. -->
+
+<!-- Please provide reference to the issue this pull request is addressing. -->
+<!-- For e.g. Fixes #IssueNumber -->
+
+**Type of change**
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+**How Has This Been Tested?**
+
+<!-- Please describe the tests that you ran to verify your changes and on the platforms these tests were conducted. -->
+<!-- Provide instructions so we can reproduce. -->
+<!-- Please also list any relevant details for your test configuration -->
+
+**Checklist**
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] New and existing tests pass with my changes
+- [ ] Any dependent changes have been merged and published

.github/workflows/gcc.yml

@@ -1,5 +1,5 @@
 name: GCC Linux Build
-on: [push, pull_request]
+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
@@ -8,88 +8,84 @@ defaults:
     shell: bash -leo pipefail {0}
 
 env:
-  cache_key: gcc3  # The number (#) following the cache_key "gcc" is to flush Action cache.
+  cache_key: gcc
   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)
+# 2. a GSI build step (gsi)
 # 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).
+# so each subsequent build of GSI can reuse the cached dependencies to save time (and compute).
 
 jobs:
   setup:
     runs-on: ubuntu-latest
 
     steps:
+      # Checkout the GSI to get the ci/spack.yaml file
+      - name: checkout
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
+        with:
+            path: gsi
+
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         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
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}
 
       # 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
+          sudo apt-get install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
           source spack/share/spack/setup-env.sh
-          spack env create gsi-env GSI/ci/spack.yaml
+          spack env create gsi-env gsi/ci/spack.yaml
           spack env activate gsi-env
           spack compiler find
+          sudo apt install cmake
           spack external find
           spack add [email protected]
           spack concretize
-          spack install --dirty -v
+          spack install -v --fail-fast --dirty
+          spack clean -a
 
-  build:
+  gsi:
     needs: setup
     runs-on: ubuntu-latest
 
     steps:
-      - name: checkout-gsi
-        uses: actions/checkout@v2
+      - name: checkout
+        uses: actions/checkout@v4
         with:
-            path: GSI
+            path: gsi
 
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
             ~/.spack
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}
 
-      - name: build-gsi
+      - name: build
         run: |
           source spack/share/spack/setup-env.sh
           spack env activate gsi-env
-          export CC=mpicc
-          export FC=mpif90
-          cd GSI
+          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 ..
+          cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
           make -j2 VERBOSE=1
           make install
+        env:
+          CC: mpicc
+          FC: mpif90

.github/workflows/intel.yml

@@ -1,5 +1,5 @@
 name: Intel Linux Build
-on: [push, pull_request]
+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
@@ -9,106 +9,112 @@ defaults:
 
 # 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.
+  cache_key: intel
   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)
+# 2. a GSI build step (gsi)
 # 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).
+# so each subsequent build of GSI can reuse the cached dependencies to save time (and compute).
 
 jobs:
   setup:
     runs-on: ubuntu-latest
 
     steps:
+      # Free up disk space
+      - name: free-disk-spack
+        run: |
+          df -h
+          sudo swapoff -a
+          sudo rm -f /swapfile
+          sudo apt clean
+          docker rmi $(docker image ls -aq)
+
+      # Checkout the GSI to get the ci/spack.yaml file
+      - name: checkout
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
+        with:
+            path: gsi
+
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}
 
       - 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
+          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1
+          sudo apt-get clean
           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
+          sudo mv /usr/local/ /usr_local_mv
+          sudo apt-get install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
           source spack/share/spack/setup-env.sh
-          spack env create gsi-env GSI/ci/spack.yaml
+          spack env create gsi-env gsi/ci/spack.yaml
           spack env activate gsi-env
           spack compiler find
+          sudo apt install cmake
           spack external find
           spack add intel-oneapi-mpi
           spack concretize
-          spack install --dirty -v
+          spack install -v --fail-fast --dirty
+          spack clean -a
 
-  build:
+  gsi:
     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: checkout
+        uses: actions/checkout@v4
+        with:
+            path: gsi
+
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}
 
-      - name: build-gsi
+      - name: build
         run: |
           source spack/share/spack/setup-env.sh
           spack env activate gsi-env
-          export CC=mpiicc
-          export FC=mpiifort
-          cd GSI
+          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 ..
+          cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
           make -j2 VERBOSE=1
           make install
+        env:
+          CC: mpiicc
+          FC: mpiifort

.gitmodules

@@ -1,7 +1,4 @@
 [submodule "fix"]
-	path = fix
-	url = gerrit:GSI-fix
-[submodule "ncdiag"]
-	path = src/ncdiag
-	url = https://github.com/NOAA-EMC/GSI-ncdiag
-	branch = v1.0.0
+  path = fix
+  url = https://github.com/NOAA-EMC/GSI-fix
+  branch = develop

CMakeLists.txt

@@ -28,7 +28,6 @@ endif()
 # User options
 option(OPENMP "Enable OpenMP Threading" OFF)
 option(ENABLE_MKL "Use MKL for LAPACK implementation (if available)" ON)
-option(BUILD_NCDIAG "Build GSI NetCDF Diagnostic Library" ON)
 option(BUILD_GSDCLOUD "Build GSD Cloud Analysis Library" OFF)
 option(BUILD_GSI "Build GSI" ON)
 option(BUILD_ENKF "Build EnKF" ON)
@@ -37,7 +36,6 @@ option(BUILD_REG_TESTING "Build the Regression Testing Suite" OFF)
 # Echo user options
 message(STATUS "OPENMP ................. ${OPENMP}")
 message(STATUS "ENABLE_MKL ............. ${ENABLE_MKL}")
-message(STATUS "BUILD_NCDIAG ........... ${BUILD_NCDIAG}")
 message(STATUS "BUILD_GSDCLOUD ......... ${BUILD_GSDCLOUD}")
 message(STATUS "BUILD_GSI .............. ${BUILD_GSI}")
 message(STATUS "BUILD_ENKF ............. ${BUILD_ENKF}")
@@ -46,6 +44,11 @@ message(STATUS "BUILD_REG_TESTING ...... ${BUILD_REG_TESTING}")
 # Build components
 add_subdirectory(src)
 
+# Download and copy binary fix files if submodule has been cloned
+if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/fix/CMakeLists.txt)
+  add_subdirectory(fix)
+endif()
+
 if(BUILD_REG_TESTING)
   add_subdirectory(regression)
 endif()

INSTALL.md

@@ -40,6 +40,7 @@ NCEP Libraries (NCEPLibs) compiled with the same compiler and MPI library (where
 | SFCIO           | 1.4.1 and above                                            |
 | NEMSIO          | 2.5.2 and above                                            |
 | NCIO            | 1.0.0 and above                                            |
+| NCDIAG          | 1.0.0 and above                                            |
 | WRF_IO          | 1.2.0 and above                                            |
 
 ### Building the GSI
@@ -77,7 +78,6 @@ CMake allows for various options that can be specified on the command line via `
 |---------------------|--------------------------------------------------------|
 | `OPENMP`              | Enable OpenMP Threading (`OFF`)                      |
 | `ENABLE_MKL`          | Use MKL (`ON`), If not found use LAPACK              |
-| `BUILD_NCDIAG`        | Build GSI NetCDF Diagnostics Library (`ON`)          |
 | `BUILD_GSDCLOUD`      | Build GSD Cloud Library (`OFF`)                      |
 | `BUILD_GSI`           | Build GSI library and executable (`ON`)              |
 | `BUILD_ENKF`          | Build EnKF library and executable (`ON`)             |