Add MADIS to hpc-stack

README.md

@@ -138,6 +138,7 @@ script.
   - [JSON for C++](https://github.com/nlohmann/json/)
   - [JSON Schema Validator for C++](https://github.com/pboettch/json-schema-validator)
   - [pybind11](https://github.com/pybind/pybind11)
+  - [MADIS](https://madis-data.ncep.noaa.gov)
 
 * UFS Dependencies
   - [ESMF](https://www.earthsystemcog.org/projects/esmf/)

build_stack.sh

@@ -206,6 +206,9 @@ build_lib eckit
 build_lib fckit
 build_lib atlas
 
+# Other
+build_lib madis
+
 # ==============================================================================
 # optionally clean up
 [[ $MAKE_CLEAN =~ [yYtT] ]] && \

config/stack_custom.yaml

@@ -270,3 +270,7 @@ atlas:
   build: YES
   version: release-stable
   repo: jcsda
+
+madis:
+  build: YES
+  version: 4.3

config/stack_mac.yaml

@@ -271,3 +271,7 @@ atlas:
   build: YES
   version: release-stable
   repo: jcsda
+
+madis:
+  build: YES
+  version: 4.3

config/stack_noaa.yaml

@@ -267,3 +267,7 @@ atlas:
   build: YES
   version: release-stable
   repo: jcsda
+
+madis:
+  build: YES
+  version: 4.3

libs/build_madis.sh

@@ -0,0 +1,118 @@
+#!/bin/bash
+
+set -eux
+
+name="madis"
+version=${1:-${STACK_madis_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 szip
+  module load hdf5
+  module load netcdf
+  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: $prefix EXISTS, SKIPPING"; exit 1 )
+  fi
+else
+  prefix=${MADIS_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=$SERIAL_CXX
+fi
+
+export F77=$FC
+export FFLAGS="${STACK_FFLAGS:-} ${STACK_madis_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_CFLAGS:-} ${STACK_madis_CFLAGS:-} -fPIC"
+
+HDF5_LDFLAGS="-L$HDF5_ROOT/lib"
+HDF5_LIBS="-lhdf5_hl -lhdf5"
+
+AM_LDFLAGS=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep AM_LDFLAGS | cut -d: -f2)
+EXTRA_LIBS=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep "Extra libraries" | cut -d: -f2)
+
+if [[ ! -z $mpi ]]; then
+  if [[ $enable_pnetcdf =~ [yYtT] ]]; then
+    PNETCDF_LDFLAGS="-L$PNETCDF_ROOT/lib"
+    PNETCDF_LIBS="-lpnetcdf"
+  fi
+fi
+
+NETCDF_LDFLAGS="-L$NETCDF_ROOT/lib"
+NETCDF_LIBS="-lnetcdf -lnetcdff"
+
+export LDFLAGS="${PNETCDF_LDFLAGS:-} ${NETCDF_LDFLAGS:-} ${HDF5_LDFLAGS} ${AM_LDFLAGS:-}"
+export LIBS="${PNETCDF_LIBS:-} ${NETCDF_LIBS} ${HDF5_LIBS} ${EXTRA_LIBS:-}"
+export CPPFLAGS="-I${NETCDF_ROOT}/include"
+
+cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+
+software=$name-$version
+URL="https://madis-data.ncep.noaa.gov/source/$software.tar.gz"
+[[ -f $software.tar.gz ]] || ( $WGET $URL )
+[[ ${DOWNLOAD_ONLY} =~ [yYtT] ]] && exit 0
+rm -rf $software && mkdir -p $software && cd $software
+tar -xf ../$software.tar.gz
+
+# cd into src/ directory where the makefile is
+cd src
+
+# Use sed to comment out the following hard-wired assignments in makefile
+# NETCDF_LIB, NETCDF_INC
+# FC, FFLAGS, LDFLAGS
+
+sed -i -e 's/NETCDF_LIB=/#NETCDF_LIB/g' makefile
+sed -i -e 's/NETCDF_INC=/#NETCDF_INC/g' makefile
+sed -i -e 's/FC=/#FC/g'                 makefile
+sed -i -e 's/FFLAGS=/#FFLAGS/g'         makefile
+sed -i -e 's/LDFLAGS=/#LDFLAGS/g'       makefile
+
+export NETCDF_LIB=$LIBS
+export NETCDF_INC="${NETCDF_ROOT}/include"
+
+# make in MADIS does not support parallel build
+VERBOSE=$MAKE_VERBOSE make #-j${NTHREADS:-4}
+
+# `make` builds and installs in predefined paths hard-wired in makefile
+# ../bin/ ../include/ ../lib/
+# ../doc/ and ../static/ are already populated prior to build
+# move them to $prefix
+cd ..
+$SUDO mkdir -p     $prefix/bin
+$SUDO mkdir -p     $prefix/include
+$SUDO mkdir -p     $prefix/lib
+$SUDO mkdir -p     $prefix/doc
+$SUDO mkdir -p     $prefix/static
+
+$SUDO mv bin/*     $prefix/bin/
+$SUDO mv include/* $prefix/include/
+$SUDO mv lib/*     $prefix/lib/
+$SUDO mv doc/*     $prefix/doc/
+$SUDO mv static/*  $prefix/static/
+
+# generate modulefile from template
+[[ -z $mpi ]] && modpath=compiler || modpath=mpi
+$MODULES && update_modules $modpath $name $version
+echo $name $version $URL >> ${HPC_STACK_ROOT}/hpc-stack-contents.log

libs/build_nccmp.sh

@@ -61,10 +61,10 @@ AM_LDFLAGS=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep AM_LDFLAGS | cut -d: -f2
 EXTRA_LIBS=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep "Extra libraries" | cut -d: -f2)
 
 if [[ ! -z $mpi ]]; then
-    if [[ $enable_pnetcdf =~ [yYtT] ]]; then
-	PNETCDF_LDFLAGS="-L$PNETCDF_ROOT/lib"
-	PNETCDF_LIBS="-lpnetcdf"
-    fi
+  if [[ $enable_pnetcdf =~ [yYtT] ]]; then
+    PNETCDF_LDFLAGS="-L$PNETCDF_ROOT/lib"
+    PNETCDF_LIBS="-lpnetcdf"
+  fi
 fi
 
 NETCDF_LDFLAGS="-L$NETCDF_ROOT/lib"

modulefiles/compiler/compilerName/compilerVersion/madis/madis.lua

@@ -0,0 +1,31 @@
+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"))
+prepend_path("LD_LIBRARY_PATH", pathJoin(base,"lib"))
+prepend_path("MANPATH", pathJoin(base,"share","man"))
+
+setenv("MADIS_ROOT", base)
+setenv("MADIS_VERSION", pkgVersion)
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: library")
+whatis("Description: MADIS Library and Utilities")

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

@@ -0,0 +1,33 @@
+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)
+
+always_load("netcdf")
+prereq("netcdf")
+
+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"))
+prepend_path("LD_LIBRARY_PATH", pathJoin(base,"lib"))
+prepend_path("MANPATH", pathJoin(base,"share","man"))
+
+setenv("MADIS_ROOT", base)
+setenv("MADIS_VERSION", pkgVersion)
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: library")
+whatis("Description: MADIS library and utilities")