Bring Feature/ufo geovals up to date.

.github/workflows/gcc.yml

@@ -15,21 +15,21 @@ env:
 
 # 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-gsi
+      - name: checkout
         if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-            path: GSI
+            path: gsi
 
       # Cache spack, compiler and dependencies
       - name: cache-env
@@ -39,33 +39,34 @@ jobs:
           path: |
             spack
             ~/.spack
-          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
+          key: spack-${{ 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: |
           sudo apt-get install cmake
-          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          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 mpich@3.4.2
           spack concretize
           spack install -v --fail-fast --dirty
           spack clean -a
 
-  build:
+  gsi:
     needs: setup
     runs-on: ubuntu-latest
 
     steps:
-      - name: checkout-gsi
-        uses: actions/checkout@v3
+      - name: checkout
+        uses: actions/checkout@v4
         with:
-            path: GSI
+            path: gsi
 
       - name: cache-env
         id: cache-env
@@ -74,13 +75,13 @@ jobs:
           path: |
             spack
             ~/.spack
-          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
+          key: spack-${{ 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
-          cd GSI
+          cd gsi
           mkdir -p build && cd build
           cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
           make -j2 VERBOSE=1

.github/workflows/intel.yml

@@ -18,21 +18,30 @@ env:
 
 # 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-gsi
+      - name: checkout
         if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-            path: GSI
+            path: gsi
 
       # Cache spack, compiler and dependencies
       - name: cache-env
@@ -43,16 +52,15 @@ jobs:
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
+          key: spack-${{ 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
 
@@ -62,31 +70,32 @@ jobs:
         run: |
           sudo mv /usr/local/ /usr_local_mv
           sudo apt-get install cmake
-          git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
+          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 -v --fail-fast --dirty
           spack clean -a
 
-  build:
+  gsi:
     needs: setup
     runs-on: ubuntu-latest
 
     steps:
-      - name: checkout-gsi
-        uses: actions/checkout@v3
-        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@v3
@@ -95,13 +104,13 @@ jobs:
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
+          key: spack-${{ 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
-          cd GSI
+          cd gsi
           mkdir -p build && cd build
           cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
           make -j2 VERBOSE=1

CMakeLists.txt

@@ -29,6 +29,7 @@ endif()
 option(OPENMP "Enable OpenMP Threading" OFF)
 option(ENABLE_MKL "Use MKL for LAPACK implementation (if available)" ON)
 option(BUILD_GSDCLOUD "Build GSD Cloud Analysis Library" OFF)
+option(BUILD_MGBF "Build MGBF Library" ON)
 option(BUILD_GSI "Build GSI" ON)
 option(BUILD_ENKF "Build EnKF" ON)
 option(BUILD_REG_TESTING "Build the Regression Testing Suite" OFF)
@@ -37,6 +38,7 @@ option(BUILD_REG_TESTING "Build the Regression Testing Suite" OFF)
 message(STATUS "OPENMP ................. ${OPENMP}")
 message(STATUS "ENABLE_MKL ............. ${ENABLE_MKL}")
 message(STATUS "BUILD_GSDCLOUD ......... ${BUILD_GSDCLOUD}")
+message(STATUS "BUILD_MGBF ............. ${BUILD_MGBF}")
 message(STATUS "BUILD_GSI .............. ${BUILD_GSI}")
 message(STATUS "BUILD_ENKF ............. ${BUILD_ENKF}")
 message(STATUS "BUILD_REG_TESTING ...... ${BUILD_REG_TESTING}")

INSTALL.md

@@ -79,6 +79,7 @@ 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_GSDCLOUD`      | Build GSD Cloud Library (`OFF`)                      |
+| `BUILD_MGBF`          | Build MGBF Library (`ON`)                            |
 | `BUILD_GSI`           | Build GSI library and executable (`ON`)              |
 | `BUILD_ENKF`          | Build EnKF library and executable (`ON`)             |
 | `BUILD_REG_TESTING`   | Enable Regression Testing (`ON`)                     |

LICENSE.md

@@ -0,0 +1,157 @@
+### GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+This version of the GNU Lesser General Public License incorporates the
+terms and conditions of version 3 of the GNU General Public License,
+supplemented by the additional permissions listed below.
+
+#### 0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the
+GNU General Public License.
+
+"The Library" refers to a covered work governed by this License, other
+than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
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+Version".
+
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+based on the Application, and not on the Linked Version.
+
+The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+#### 1. Exception to Section 3 of the GNU GPL.
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+#### 2. Conveying Modified Versions.
+
+If you modify a copy of the Library, and, in your modifications, a
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+#### 3. Object Code Incorporating Material from Library Header Files.
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+    the Library is used in it and that the Library and its use are
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