Add Climate Data Operators (CDO) to stack.

README.md

@@ -128,6 +128,7 @@ script.
   - [ParallelIO](https://github.com/NCAR/ParallelIO)
   - [nccmp](https://gitlab.com/remikz/nccmp)
   - [nco](http://nco.sourceforge.net/)
+  - [CDO](https://code.mpimet.mpg.de/projects/cdo)
   - [FFTW](http://www.fftw.org/)
   - [GPTL](https://jmrosinski.github.io/GPTL/)
   - [Tau2]()

build_stack.sh

@@ -147,6 +147,7 @@ build_lib pnetcdf
 build_lib netcdf
 build_lib nccmp
 build_lib nco
+build_lib cdo
 build_lib pio
 
 # UFS 3rd party dependencies

config/stack_custom.yaml

@@ -63,6 +63,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: YES
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

config/stack_gaea.yaml

@@ -60,6 +60,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: YES
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

config/stack_mac.yaml

@@ -64,6 +64,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: YES
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

config/stack_ncar.yaml

@@ -60,6 +60,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: YES
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

config/stack_noaa.yaml

@@ -60,6 +60,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: YES
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

config/stack_ufs_weather_ci.yaml

@@ -63,6 +63,10 @@ nco:
   build: NO
   version: 4.9.3
 
+cdo:
+  build: NO
+  version: 1.9.8
+
 pio:
   build: YES
   version: 2.5.1

libs/build_cdo.sh

@@ -0,0 +1,105 @@
+#!/bin/bash
+
+set -eux
+
+name="cdo"
+version=${1:-${STACK_cdo_version}}
+
+# Hyphenated version used for install prefix
+compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+mpi=$(echo $HPC_MPI | sed 's/\//-/g')
+
+if $MODULES; then
+  set +x
+  source $MODULESHOME/init/bash
+  module load hpc-$HPC_COMPILER
+  [[ -z $mpi ]] || module load hpc-$HPC_MPI
+  module try-load zlib
+  module try-load szip
+  module load hdf5
+  module load netcdf
+  module try-load udunits
+  module list
+  set -x
+  enable_pnetcdf=$(nc-config --has-pnetcdf)
+  set +x
+    [[ $enable_pnetcdf =~ [yYtT] ]] && module load pnetcdf
+  set -x
+
+  prefix="${PREFIX:-"/opt/modules"}/$compiler/$mpi/$name/$version"
+
+  if [[ -d $prefix ]]; then
+    [[ $OVERWRITE =~ [yYtT] ]] && ( echo "WARNING: $prefix EXISTS: OVERWRITING!"; $SUDO rm -rf $prefix ) \
+                               || ( echo "WARNING: $prefix EXISTS, SKIPPING"; exit 1 )
+  fi
+else
+  prefix=${CDO_ROOT:-"/usr/local"}
+  enable_pnetcdf=$(nc-config --has-pnetcdf)
+fi
+
+if [[ ! -z $mpi ]]; then
+    export FC=$MPI_FC
+    export CC=$MPI_CC
+    export CXX=$MPI_CXX
+else
+    export FC=$SERIAL_FC
+    export CC=$SERIAL_CC
+    export CXX=$SERIAL_CXX
+fi
+
+export FFLAGS="${STACK_FFLAGS:-} ${STACK_cdo_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_CFLAGS:-} ${STACK_cdo_CFLAGS:-} -fPIC"
+export CXXFLAGS="${STACK_CXXFLAGS:-} ${STACK_cdo_CXXFLAGS:-} -fPIC"
+
+export F77=$FC
+export FCFLAGS=$FFLAGS
+
+LDFLAGS1="-L$HDF5_ROOT/lib -lhdf5_hl -lhdf5"
+LDFLAGS2=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep AM_LDFLAGS | cut -d: -f2)
+LDFLAGS3=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep "Extra libraries" | cut -d: -f2)
+if [[ ! -z $mpi ]]; then
+  [[ $enable_pnetcdf =~ [yYtT] ]] && LDFLAGS4="-L$PNETCDF_ROOT/lib -lpnetcdf"
+fi
+LDFLAGS5="-L$NETCDF_ROOT/lib -lnetcdf"
+export LDFLAGS="${LDFLAGS1:-} ${LDFLAGS2:-} ${LDFLAGS3:-} ${LDFLAGS4:-} ${LDFLAGS5:-}"
+
+cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+
+case $version in
+  1.9.9 )
+    url="https://code.mpimet.mpg.de/attachments/download/23323/cdo-1.9.9.tar.gz"
+  ;;
+  1.9.8 )
+    url="https://code.mpimet.mpg.de/attachments/download/20826/cdo-1.9.8.tar.gz"
+  ;;
+  1.9.7.1 )
+    url="https://code.mpimet.mpg.de/attachments/download/20124/cdo-1.9.7.1.tar.gz"
+  ;;
+  1.9.6 )
+    url="https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz"
+  ;;
+  * )
+    echo "Try using CDO version 1.9.6 and above, ABORT!"
+    exit 1
+  ;;
+esac
+
+software=$name-$version
+[[ -d $software ]] || ( $WGET $url; tar -xzf $software.tar.gz && rm -f $software.tar.gz )
+[[ ${DOWNLOAD_ONLY} =~ [yYtT] ]] && exit 0
+[[ -d $software ]] && cd $software || ( echo "$software does not exist, ABORT!"; exit 1 )
+[[ -d build ]] && rm -rf build
+mkdir -p build && cd build
+
+../configure --prefix=$prefix \
+             --with-hdf5=$HDF5_ROOT \
+             --with-netcdf=$NETCDF_ROOT
+
+VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}
+[[ $MAKE_CHECK =~ [yYtT] ]] && make check
+$SUDO make install
+
+# generate modulefile from template
+[[ -z $mpi ]] && modpath=compiler || modpath=mpi
+$MODULES && update_modules $modpath $name $version \
+         || echo $name $version >> ${HPC_STACK_ROOT}/hpc-stack-contents.log

modulefiles/compiler/compilerName/compilerVersion/cdo/cdo.lua

@@ -0,0 +1,28 @@
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+local hierA        = hierarchyA(pkgNameVer,1)
+local compNameVer  = hierA[1]
+local compNameVerD = compNameVer:gsub("/","-")
+
+conflict(pkgName)
+
+always_load("netcdf")
+prereq("netcdf")
+
+local opt = os.getenv("HPC_OPT") or os.getenv("OPT") or "/opt/modules"
+
+local base = pathJoin(opt,compNameVerD,pkgName,pkgVersion)
+
+prepend_path("PATH", pathJoin(base,"bin"))
+setenv("CDO_ROOT", base)
+setenv("CDO_VERSION", pkgVersion)
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: Utility")
+whatis("Description: Climate Data Operators (CDO) Utility")

modulefiles/mpi/compilerName/compilerVersion/mpiName/mpiVersion/cdo/cdo.lua

@@ -0,0 +1,28 @@
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+local hierA        = hierarchyA(pkgNameVer,2)
+local mpiNameVer   = hierA[1]
+local compNameVer  = hierA[2]
+local mpiNameVerD  = mpiNameVer:gsub("/","-")
+local compNameVerD = compNameVer:gsub("/","-")
+
+conflict(pkgName)
+
+local opt = os.getenv("HPC_OPT") or os.getenv("OPT") or "/opt/modules"
+
+local base = pathJoin(opt,compNameVerD,mpiNameVerD,pkgName,pkgVersion)
+
+prepend_path("PATH", pathJoin(base,"bin"))
+
+setenv("CDO_ROOT", base)
+setenv("CDO_VERSION", pkgVersion)
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: Utilities")
+whatis("Description: Climate Data Operators (CDO) Utility")