Supported Stages/2024 and added a basic CI test (#27)

Supported Stages/2024 and added a basic CI test Summary of changes: - Added `Stages/2024` environment script `env/jsc.2024_Intel.sh`. - Added basic CI test for verifying eCLM-ParFlow build on GNU toolchain. - Updates to the ff. model components, mostly to fix IntelLLVM 2023.2.0 compiler (e.g. `icx`, `ifx`) issues: * parflow @ ed39749 * CLM3.5 @ 15dba17 * parflow_pdaf @ 24fd719 * pdaf @ 555d5b4 - Various minor changes to `build_tsmp2.sh`: * Align y/n input to the same line as question * Only source env file if on JSC or --tsmp2_env is supplied * Added flag `-v` for enabling verbose output from Makefile builds * Fixed checking for alternative `parflow` - README updates corresponding to the changes above. Co-authored-by: Johannes Keller <[email protected]> Co-authored-by: Johannes Keller <[email protected]>
HPSCTerrSys · Dec 5, 2024 · 5b29084 · 5b29084
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -0,0 +1,235 @@
+name: TSMP2 Build
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  eclm_build_job:
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-22.04 ]
+        config:
+        - {
+            name: "eCLM-ParFlow",
+          }
+
+    env:
+      CC: mpicc
+      CXX: mpicxx
+      FC: mpifort
+      F77: mpif77
+      BUILD_DIR: bld
+      INSTALL_DIR: install
+      MODEL_DIR: ${{ github.workspace }}/component-models
+      VER_OASIS: tsmp-patches-v0.1
+      VER_eCLM: beta-0.1
+      VER_PARFLOW: ed3974987902ef24c1f7519eb0ba5f8f66380c8c # points to commit "Supported Ubuntu 24.04 and added LLVM to CI"
+      VER_HYPRE: 2.26.0
+      VER_NETCDF_C: 4.9.2
+      VER_NETCDF_F90: 4.6.1
+      CMAKE_PREFIX_PATH: ${{ github.workspace }}/dependencies
+      SYSTEMNAME: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install TSMP2 dependencies on Ubuntu
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: libxml++2.6-dev pylint wget cmake libpnetcdf-dev tcl-dev tk-dev
+          version: 1.0
+          execute_install_scripts: true
+
+      - name: Download HDF5 headers and MPI Fortran compiler
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libhdf5-openmpi-103 hdf5-helpers
+
+      - name: Create directories for component model and dependencies
+        run: |
+          mkdir -p ${CMAKE_PREFIX_PATH} ${MODEL_DIR}
+
+      #
+      # NetCDF C
+      #
+      - name: Restore cached NetCDF C ${{ env.VER_NETCDF_C }}
+        uses: actions/cache/restore@v4
+        id: cache-netcdf-restore
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_NETCDF_C }}
+
+      - if: steps.cache-netcdf-restore.outputs.cache-hit != 'true'
+        name: Install NetCDF C ${{ env.VER_NETCDF_C }}
+        run: |
+          wget https://github.com/Unidata/netcdf-c/archive/v${VER_NETCDF_C}.tar.gz
+          tar xf v${VER_NETCDF_C}.tar.gz
+          cd netcdf-c-${VER_NETCDF_C}
+          export CPPFLAGS=-I/usr/include/hdf5/openmpi
+          export LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+          ./configure --prefix=$(realpath $CMAKE_PREFIX_PATH)
+          make -j4 install
+
+      - if: steps.cache-netcdf-restore.outputs.cache-hit != 'true'
+        name: Cache NetCDF ${{ env.VER_NETCDF_C }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_NETCDF_C }}
+
+      #
+      # NetCDF Fortran
+      #
+      - name: Restore cached NetCDF Fortran ${{ env.VER_NETCDF_F90 }}
+        uses: actions/cache/restore@v4
+        id: cache-netcdff90-restore
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_NETCDF_F90 }}
+
+      - if: steps.cache-netcdff90-restore.outputs.cache-hit != 'true'
+        name: Install NetCDF Fortran ${{ env.VER_NETCDF_F90 }}
+        run: |
+          wget https://github.com/Unidata/netcdf-fortran/archive/v${VER_NETCDF_F90}.tar.gz
+          tar xf v${VER_NETCDF_F90}.tar.gz
+          cd netcdf-fortran-${VER_NETCDF_F90}
+          export CPPFLAGS=-I${CMAKE_PREFIX_PATH}/include
+          export LDFLAGS=-L${CMAKE_PREFIX_PATH}/lib
+          ./configure --prefix=$(realpath $CMAKE_PREFIX_PATH)
+          make -j4 install
+
+      - if: steps.cache-netcdff90-restore.outputs.cache-hit != 'true'
+        name: Cache NetCDF Fortran ${{ env.VER_NETCDF_F90 }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_NETCDF_F90 }}
+
+      #
+      # OASIS3-MCT
+      #
+      - name: Restore cached OASIS3-MCT ${{ env.VER_OASIS }}
+        uses: actions/cache/restore@v4
+        id: cache-oasis-restore
+        with:
+          path: ${{ env.MODEL_DIR }}/oasis3-mct
+          key: cache-${{ matrix.config.name }}-${{ env.VER_OASIS }}
+
+      - if: steps.cache-oasis-restore.outputs.cache-hit != 'true'
+        name: Download OASIS3-MCT ${{ env.VER_OASIS }}
+        working-directory: ${{ env.MODEL_DIR }}
+        run: |
+          git clone -b $VER_OASIS https://icg4geo.icg.kfa-juelich.de/ExternalReposPublic/oasis3-mct.git
+          echo "OASIS3-MCT version: $(cd oasis3-mct && git describe --tags --always)"
+
+      - if: steps.cache-oasis-restore.outputs.cache-hit != 'true'
+        name: Cache OASIS3-MCT ${{ env.VER_OASIS }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.MODEL_DIR }}/oasis3-mct
+          key: cache-${{ matrix.config.name }}-${{ env.VER_OASIS }}
+
+      #
+      # eCLM
+      #
+      - name: Restore cached eCLM ${{ env.VER_eCLM }}
+        uses: actions/cache/restore@v4
+        id: cache-eclm-restore
+        with:
+          path: ${{ env.MODEL_DIR }}/eCLM
+          key: cache-${{ matrix.config.name }}-${{ env.VER_eCLM }}
+
+      - if: steps.cache-eclm-restore.outputs.cache-hit != 'true'
+        name: Download eCLM ${{ env.VER_eCLM }}
+        working-directory: ${{ env.MODEL_DIR }}
+        run: |
+          git clone -b $VER_eCLM https://github.com/HPSCTerrSys/eCLM.git
+          echo "eCLM version: $(cd eCLM && git describe --tags --always)"
+
+      - if: steps.cache-eclm-restore.outputs.cache-hit != 'true'
+        name: Cache eCLM ${{ env.VER_eCLM }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.MODEL_DIR }}/eCLM
+          key: cache-${{ matrix.config.name }}-${{ env.VER_eCLM }}
+
+      #
+      # ParFlow
+      #
+      - name: Restore cached ParFlow ${{ env.VER_PARFLOW }}
+        uses: actions/cache/restore@v4
+        id: cache-parflow-restore
+        with:
+          path: ${{ env.MODEL_DIR }}/parflow
+          key: cache-${{ matrix.config.name }}-${{ env.VER_PARFLOW }}
+
+      # TODO: Must use upstream repo https://github.com/parflow/parflow.git
+      - if: steps.cache-parflow-restore.outputs.cache-hit != 'true'
+        name: Download ParFlow ${{ env.VER_PARFLOW }}
+        working-directory: ${{ env.MODEL_DIR }}
+        run: |
+          git clone https://github.com/parflow/parflow.git
+          cd parflow
+          git checkout $VER_PARFLOW
+          echo "ParFlow version: $(git describe --tags --always)"
+
+      - if: steps.cache-parflow-restore.outputs.cache-hit != 'true'
+        name: Cache ParFlow ${{ env.VER_PARFLOW }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.MODEL_DIR }}/parflow
+          key: cache-${{ matrix.config.name }}-${{ env.VER_PARFLOW }}
+
+      #
+      # Hypre
+      #
+      - name: Restore cached Hypre ${{ env.VER_HYPRE }}
+        uses: actions/cache/restore@v4
+        id: cache-hypre-restore
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_HYPRE }}
+
+      - if: steps.cache-hypre-restore.outputs.cache-hit != 'true'
+        name: Install Hypre ${{ env.VER_HYPRE }}
+        run: |
+          wget https://github.com/hypre-space/hypre/archive/v${VER_HYPRE}.tar.gz
+          tar xf v${VER_HYPRE}.tar.gz
+          cd hypre-${VER_HYPRE}/src
+          ./configure --prefix=$(realpath $CMAKE_PREFIX_PATH)
+          make -j4 install
+
+      - if: steps.cache-hypre-restore.outputs.cache-hit != 'true'
+        name: Cache Hypre ${{ env.VER_HYPRE }}
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.CMAKE_PREFIX_PATH }}
+          key: cache-${{ matrix.config.name }}-${{ env.VER_HYPRE }}
+
+      #
+      # TSMP2
+      #
+      - name: Configure TSMP2
+        run: >-
+          cmake -S . -B ${BUILD_DIR}
+          -DCMAKE_BUILD_TYPE="RELEASE"
+          -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR}
+          -DOASIS_SRC=${MODEL_DIR}/oasis3-mct
+          -DeCLM="ON"
+          -DeCLM_SRC=${MODEL_DIR}/eCLM
+          -DParFlow="ON"
+          -DPARFLOW_SRC=${MODEL_DIR}/parflow
+
+      - name: Build TSMP2
+        run: |
+          cmake --build ${BUILD_DIR}
+
+      - name: Install TSMP2
+        run: |
+          cmake --install ${BUILD_DIR}
diff --git a/.gitmodules b/.gitmodules
@@ -9,7 +9,7 @@
 [submodule "models/parflow_pdaf"]
 	path = models/parflow_pdaf
 	url = https://github.com/HPSCTerrSys/parflow
-	branch = tsmp-pdaf
+	branch = tsmp-pdaf-patched
 [submodule "models/pdaf"]
 	path = models/pdaf
 	url = https://github.com/HPSCTerrSys/pdaf.git

diff --git a/README.md b/README.md
@@ -56,7 +56,7 @@ cd $TSMP2_DIR
 2. Load the environment variables required for the build.
 
 ```bash
-source env/jsc.2023_Intel.sh
+source env/jsc.2024_Intel.sh
 ```
 
 3. Specify build and install directories.
@@ -82,19 +82,19 @@ mkdir -p ${BUILD_DIR} ${INSTALL_DIR}
 ## NOTE: Download only the component models that you need! ##
 
 # eCLM
-git clone https://github.com/HPSCTerrSys/eCLM.git models/eCLM
+git clone -b beta-0.1 https://github.com/HPSCTerrSys/eCLM.git models/eCLM
 eCLM_SRC=`realpath models/eCLM`
 
 # ICON
 git clone https://icg4geo.icg.kfa-juelich.de/spoll/icon2.6.4_oascoup.git models/icon
 ICON_SRC=`realpath models/icon`
 
 # ParFlow
-git clone -b v3.12.0 https://github.com/parflow/parflow.git models/parflow
+git clone https://github.com/parflow/parflow.git models/parflow
 PARFLOW_SRC=`realpath models/parflow`
 
 # ParFlow (PDAF-patched)
-git clone -b v3.12.0-tsmp https://github.com/HPSCTerrSys/parflow models/parflow_pdaf
+git clone -b v3.13.0-pdaf https://github.com/HPSCTerrSys/parflow models/parflow_pdaf
 PARFLOW_SRC=`realpath models/parflow_pdaf`
 
 # CLM3.5

diff --git a/build_tsmp2.sh b/build_tsmp2.sh
@@ -72,8 +72,7 @@ if [ -n "${comp_namey}" ] && [ -z "${comp_srcname}" ];then
      submodule_name=$(echo "models/"${sub_srcname})
   fi
   if [ "$( ls -A ${cmake_tsmp2_dir}/${submodule_name} | wc -l)" -ne 0 ];then
-     echo "submodule ${submodule_name} aleady exist. Do you want overwrite it? (y/n)"
-     read yn
+     read -p "submodule ${submodule_name} aleady exists. Do you want overwrite it? (y/n) " yn
      if [ "${yn,}" = "y" ];then
         message "Overwrite submodule ${submodule_name}"
         git submodule update --init --force -- ${submodule_name}
@@ -188,7 +187,7 @@ else
 fi
 
 # set INSTALL and BUILD DIR (neccesary for building)
-if [ -z "${SYSTEMNAME}" ]; then SYSTEMNAME="UNKN"; fi
+if [ -z "${SYSTEMNAME}" ]; then export SYSTEMNAME=$(hostname); fi
 
 if [ -z "${build_dir}" ]; then
   cmake_build_dir="${cmake_tsmp2_dir}/bld/${SYSTEMNAME^^}_${model_id}" 
@@ -210,14 +209,16 @@ fi # Makefile verbosity
 
 build_log="$(dirname ${cmake_build_dir})/${model_id}_$(date +%Y-%m-%d_%H-%M).log"
 
-## source environment
-message "source environment"
-if [ -z "${tsmp2_env}" ]; then
-  tsmp2_env="${cmake_tsmp2_dir}/env/jsc.2023_Intel.sh"
+## source environment if on JSC or env file is provided
+if [[ -z "${tsmp2_env}" && ($SYSTEMNAME = "jurecadc" || $SYSTEMNAME = "juwels" || $SYSTEMNAME = "jusuf") ]]; then
+  tsmp2_env="${cmake_tsmp2_dir}/env/jsc.2024_Intel.sh"
 else
   tsmp2_env="$(realpath ${tsmp2_env})"
 fi # tsmp2_env
-source $tsmp2_env
+if [ ! -z "${tsmp2_env}" ]; then
+  message "source environment"
+  source $tsmp2_env
+fi
 
 ## CMAKE config
 # rm -rf ${cmake_build_dir}

diff --git a/cmake/BuildCOSMO.cmake b/cmake/BuildCOSMO.cmake
@@ -1,5 +1,6 @@
 find_package(ecCodes REQUIRED)
 find_package(NetCDF REQUIRED)
+find_package(OpenMP REQUIRED)
 
 set(COSMO_BLD_DIR ${CMAKE_BINARY_DIR}/COSMO5_1/bld)
 set(COSMO_Fopts ${COSMO_BLD_DIR}/Fopts)
@@ -15,7 +16,7 @@ file(APPEND ${COSMO_Fopts} "COMFLG4      = $(COMFLG1)\n")
 file(APPEND ${COSMO_Fopts} "COMFLG       = $(COMFLG1)\n")
 file(APPEND ${COSMO_Fopts} "COMFLG5      = $(COMFLG1)\n")
 file(APPEND ${COSMO_Fopts} "LDPAR        = ${CMAKE_Fortran_COMPILER}\n")
-file(APPEND ${COSMO_Fopts} "LDFLG        = -qopenmp\n")
+file(APPEND ${COSMO_Fopts} "LDFLG        = ${OpenMP_Fortran_FLAGS}\n")
 file(APPEND ${COSMO_Fopts} "PROGRAM      = lmparbin\n")
 file(APPEND ${COSMO_Fopts} "LIBPATH      = ${ecCodes_LIBRARIES} ${NetCDF_LIBRARIES} ${OASIS_LIBRARIES}\n")
 

diff --git a/cmake/BuildOASIS3MCT.cmake b/cmake/BuildOASIS3MCT.cmake
@@ -1,4 +1,5 @@
 find_package(NetCDF REQUIRED)
+find_package(OpenMP REQUIRED)
 
 if (CMAKE_BUILD_TYPE STREQUAL "DEBUG")
   set(OPTIM "-g")
@@ -20,7 +21,7 @@ file(WRITE   ${OASIS_MAKE_INC} "CHAN            = MPI1\n")
 file(APPEND  ${OASIS_MAKE_INC} "COUPLE          = ${OASIS_SRC}\n")
 file(APPEND  ${OASIS_MAKE_INC} "BUILD_DIR       = ${OASIS_BLD_DIR}\n")
 file(APPEND  ${OASIS_MAKE_INC} "ARCHDIR         = ${OASIS_INSTALL_PREFIX}\n")
-file(APPEND  ${OASIS_MAKE_INC} "NETCDF_INCLUDE  = ${NetCDF_ROOT}/include\n")
+file(APPEND  ${OASIS_MAKE_INC} "NETCDF_INCLUDE  = ${NetCDF_F90_ROOT}/include\n")
 file(APPEND  ${OASIS_MAKE_INC} "NETCDF_LIBRARY  = ${NetCDF_LIBRARIES}\n")
 file(APPEND  ${OASIS_MAKE_INC} "MPI_INCLUDE     = ${MPI_Fortran_INCLUDE_DIRS}\n")
 file(APPEND  ${OASIS_MAKE_INC} "MAKE            = make\n")
@@ -39,8 +40,14 @@ if(${PDAF})
 else()
   file(APPEND  ${OASIS_MAKE_INC} "CPPDEF          = -Duse_netCDF -Duse_comm_$(CHAN) -D__VERBOSE  -DTREAT_OVERLAY\n")
 endif()
-file(APPEND  ${OASIS_MAKE_INC} "FCBASEFLAGS     = ${OPTIM} -xCORE-AVX2 -I. -assume byterecl -mt_mpi -qopenmp\n")
-file(APPEND  ${OASIS_MAKE_INC} "CCBASEFLAGS     = ${OPTIM} -qopenmp\n")
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+  file(APPEND  ${OASIS_MAKE_INC} "FCBASEFLAGS     = ${OPTIM} -I. -ffree-line-length-none -fallow-argument-mismatch ${OpenMP_Fortran_FLAGS}\n")
+elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel" OR CMAKE_Fortran_COMPILER_ID STREQUAL "IntelLLVM")
+  file(APPEND  ${OASIS_MAKE_INC} "FCBASEFLAGS     = ${OPTIM} -I. -xCORE-AVX2 -assume byterecl -mt_mpi ${OpenMP_Fortran_FLAGS}\n")
+else()
+  message(FATAL_ERROR "Fortran compiler '${CMAKE_Fortran_COMPILER_ID}' is not supported.")
+endif()
+file(APPEND  ${OASIS_MAKE_INC} "CCBASEFLAGS     = ${OPTIM} ${OpenMP_Fortran_FLAGS}\n")
 file(APPEND  ${OASIS_MAKE_INC} "MCT_DEBUGFLAG   = ${MCT_DEBUGFLAG}\n")
 file(APPEND  ${OASIS_MAKE_INC} "FLIBS           = ${NetCDF_LIBRARIES}\n")
 file(APPEND  ${OASIS_MAKE_INC} "INC_DIRS        = -I$(ARCHDIR)/include -I$(NETCDF_INCLUDE)\n")