Merge branch 'develop' into gaea_build

.github/workflows/gcc.yml

@@ -48,7 +48,8 @@ jobs:
           df -h
 
       - name: checkout  # This is for getting spack.yaml
-        uses: actions/checkout@v3
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
         with:
             path: gsi-utils
 
@@ -70,19 +71,21 @@ jobs:
           source spack/share/spack/setup-env.sh
           spack env create gsiutils-env gsi-utils/ci/spack.yaml
           spack env activate gsiutils-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 --all
 
-  gsi-monitor:
+  gsi-utils:
     needs: setup
     runs-on: ubuntu-latest
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             path: gsi-utils
 
@@ -99,10 +102,11 @@ jobs:
         run: |
           source spack/share/spack/setup-env.sh
           spack env activate gsiutils-env
-          export CC=mpicc
-          export FC=mpif90
           cd gsi-utils
           mkdir -p build && cd build
           cmake -DCMAKE_INSTALL_PREFIX=../install -DBUILD_UTIL_ALL=ON ..
           make -j2 VERBOSE=1
           make install
+        env:
+          CC: mpicc
+          FC: mpif90

.github/workflows/intel.yml

@@ -33,15 +33,16 @@ env:
 
 jobs:
   setup:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
       # Free up disk space
       - name: free-disk-spack
         run: |
           df -h
           sudo swapoff -a
-          sudo rm -f /swapfile
+          sudo rm -rf /swapfile
+          sudo rm -rf /usr_local_mv
           sudo rm -rf /usr/share/dotnet
           sudo rm -rf /opt/ghc
           sudo rm -rf "/usr/local/share/boost"
@@ -51,7 +52,8 @@ jobs:
           df -h
 
       - name: checkout # This is for getting spack.yaml
-        uses: actions/checkout@v3
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v4
         with:
             path: gsi-utils
 
@@ -73,17 +75,21 @@ jobs:
           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-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
 
       # Install dependencies using Spack
       - name: install-dependencies-with-spack
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
+          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 gsiutils-env gsi-utils/ci/spack.yaml
           spack env activate gsiutils-env
           spack compiler find
+          sudo apt install cmake
           spack external find
           spack add intel-oneapi-mpi
           spack concretize
@@ -92,15 +98,15 @@ jobs:
 
   gsi-utils:
     needs: setup
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
       - name: install-intel
         run: |
           echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
 
       - name: checkout-gsiutils
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
             path: gsi-utils
 
@@ -118,10 +124,11 @@ jobs:
         run: |
           source spack/share/spack/setup-env.sh
           spack env activate gsiutils-env
-          export CC=mpiicc
-          export FC=mpiifort
           cd gsi-utils
           mkdir -p build && cd build
           cmake -DCMAKE_INSTALL_PREFIX=../install -DBUILD_UTIL_ALL=ON ..
           make -j2 VERBOSE=1
           make install
+        env:
+          CC: mpiicc
+          FC: mpiifort

ci/spack.yaml

@@ -21,7 +21,6 @@ spack:
   - crtm@2.4.0.1
   - ncio@1.1.2
   - gsi-ncdiag@1.1.2
-  - cmake@3.20.1
   view: true
   concretizer:
     unify: when_possible

modulefiles/gsiutils_wcoss2.intel.lua

@@ -7,20 +7,21 @@ local craype_ver=os.getenv("craype_ver") or "2.7.8"
 local cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.7"
 local cmake_ver= os.getenv("cmake_ver") or "3.20.2"
 local python_ver=os.getenv("python_ver") or "3.8.6"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.0.10"
 
 local netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
-
 local bufr_ver=os.getenv("bufr_ver") or "11.7.0"
 local bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-local w3emc_ver=os.getenv("w3emc_ver") or "2.9.1"
+local w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
 local sp_ver=os.getenv("sp_ver") or "2.3.3"
 local ip_ver=os.getenv("ip_ver") or "3.3.3"
 local sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 local sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
-local nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
+local nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 local wrf_io_ver=os.getenv("wrf_io_ver") or "1.2.0"
+local ncio_ver=os.getenv("ncio_ver") or "1.1.2"
 local crtm_ver=os.getenv("crtm_ver") or "2.4.0.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "2.0.10"
+local ncdiag_ver=os.getenv("ncdiag_ver") or "1.1.1"
 
 load(pathJoin("PrgEnv-intel", PrgEnv_intel_ver))
 load(pathJoin("intel", intel_ver))
@@ -29,8 +30,9 @@ load(pathJoin("cray-mpich", cray_mpich_ver))
 load(pathJoin("cmake", cmake_ver))
 load(pathJoin("python", python_ver))
 
-load(pathJoin("netcdf", netcdf_ver))
+load(pathJoin("prod_util", prod_util_ver))
 
+load(pathJoin("netcdf", netcdf_ver))
 load(pathJoin("bufr", bufr_ver))
 load(pathJoin("bacio", bacio_ver))
 load(pathJoin("w3emc", w3emc_ver))
@@ -40,15 +42,8 @@ load(pathJoin("sigio", sigio_ver))
 load(pathJoin("sfcio", sfcio_ver))
 load(pathJoin("nemsio", nemsio_ver))
 load(pathJoin("wrf_io", wrf_io_ver))
+load(pathJoin("ncio", ncio_ver))
 load(pathJoin("crtm", crtm_ver))
-
-load(pathJoin("prod_util", prod_util_ver))
-
-pushenv("HPC_OPT", "/apps/ops/para/libs")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/compiler/intel/19.1.3.304")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.7")
-
-load("ncio/1.1.2")
-load("ncdiag/1.0.0")
+load(pathJoin("ncdiag",ncdiag_ver))
 
 whatis("Description: GSI utilities environment on WCOSS2")