Update develop branch: new versions, packages, package locations, fixes

README.md

@@ -37,7 +37,7 @@ S4          | David Huber
 
 ## Contributors
 
-Mark Potts, Steve Lawrence, Ed Hartnett, Guoqing Ge, Raffaele Montuoro, David Huber
+Mark Potts, Steve Lawrence, Ed Hartnett, Guoqing Ge, Raffaele Montuoro, David Huber, Natalie Perlin
 
 ## Prerequisites:
 

build_stack.sh

@@ -145,6 +145,7 @@ build_lib sqlite
 build_lib libtiff
 build_lib proj
 build_lib geos
+build_lib openblas
 
 # Also build serial versions of HDF5 and netCDF, if using MODULES
 if $MODULES; then
@@ -262,6 +263,7 @@ build_lib metplus
 # UFS 3rd party dependencies
 
 build_lib esmf
+build_lib scotch
 build_lib fms
 build_lib cmakemodules
 build_lib esma_cmake

config/config_macos_gnu.sh

@@ -5,16 +5,16 @@ LMOD=$(brew --prefix lmod)
 source $LMOD/init/profile
 
 # Compiler/MPI combination
-export HPC_COMPILER="gnu/11.3.0"
-export HPC_MPI="openmpi/4.1.2"
-export HPC_PYTHON="python/3.9.13"
+export HPC_COMPILER="gnu/12.3.0"
+export HPC_MPI="openmpi/4.1.5"
+export HPC_PYTHON="python/3.11.6"
 
 # Build options
 export USE_SUDO=N
 export PKGDIR=pkg
 export LOGDIR=log
 export OVERWRITE=N
-export NTHREADS=8
+export NTHREADS=4
 export   MAKE_CHECK=N
 export MAKE_VERBOSE=Y
 export   MAKE_CLEAN=N
@@ -24,8 +24,12 @@ export WGET="wget -nv "
 
 #
 # gfortran-10 needs the following
-export STACK_FFLAGS="-fallow-argument-mismatch -fallow-invalid-boz"
+export STACK_FFLAGS="-fallow-argument-mismatch -fallow-invalid-boz -march=native "
+export STACK_CFLAGS="-march=native"
 export STACK_CXXFLAGS="-march=native"
+export STACK_mpi_FFLAGS="-fopenmp"
+export STACK_mpi_CFLAGS="-fopenmp"
+export STACK_mpi_CXXFLAGS="-fopenmp"
 
 BREW=$(brew --prefix)
 

libs/build_esmf.sh

@@ -13,7 +13,9 @@ compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
 mpi=$(echo $HPC_MPI | sed 's/\//-/g')
 
 COMPILER=$(echo $HPC_COMPILER | cut -d/ -f1)
+[[ "$COMPILER" = *"intel"* ]] && COMPILER="intel"
 MPI=$(echo $HPC_MPI | cut -d/ -f1)
+[[ "$MPI" = *"oneapi-mpi"* ]] && MPI="impi"
 
 host=$(uname -s)
 abi64=$(uname -m)

libs/build_met.sh

@@ -5,18 +5,19 @@ set -eux
 name="met"
 version=${1:-${STACK_met_version}}
 release_date=${2:-${STACK_met_release_date}}
-install_as=${STACK_met_install_as:-${version}}
 
 # Hyphenated version used for install prefix
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+mpi=$(echo $HPC_MPI | sed 's/\//-/g')
 
 [[ ${STACK_met_enable_python:-} =~ [yYtT] ]] && enable_python=YES || enable_python=NO
 
 if $MODULES; then
     set +x
     source $MODULESHOME/init/bash
     module load hpc-$HPC_COMPILER
-    module load hpc-$HPC_PYTHON
+    [[ ! -z $mpi ]] && module load hpc-$HPC_MPI
+    [[ ${STACK_met_enable_python:-} =~ [yYtT] ]] &&  module load hpc-$HPC_PYTHON
     module load gsl
     module load bufr
     module load zlib
@@ -29,6 +30,8 @@ if $MODULES; then
     set -x
 
     prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version"
+    [[ ! -z $mpi ]] && prefix="${PREFIX:-"/opt/modules"}/$compiler/$mpi/$name/$version"
+
     if [[ -d $prefix ]]; then
       if [[ $OVERWRITE =~ [yYtT] ]]; then
           echo "WARNING: $prefix EXISTS: OVERWRITING!"
@@ -44,20 +47,27 @@ else
 
 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
 
 cd  ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+software=MET-$version
 software=$name-$version.$release_date
 pkg_name=$name-$version
 URL="https://github.com/dtcenter/MET/releases/download/v$version/$software.tar.gz"
-[[ -d $software ]] || ( $WGET $URL; tar -xf $software.tar.gz )
+[[ -d $pkg_name || -f $software.tar.gz ]] || ( $WGET $URL )
+[[ -d $pkg_name ]] ||  tar -xf $software.tar.gz
 [[ ${DOWNLOAD_ONLY} =~ [yYtT] ]] && exit 0
 
 export MET_BASE=$prefix/share/met
 
-export FC=$SERIAL_FC
-export CC=$SERIAL_CC
-export CXX=$SERIAL_CXX
-
 export F77=$FC
 export FFLAGS="${STACK_FFLAGS:-} ${STACK_met_FFLAGS:-}"
 export CFLAGS="${STACK_CFLAGS:-} ${STACK_met_CFLAGS:-}"
@@ -119,5 +129,6 @@ make
 $SUDO make install
 
 # generate modulefile from template
-$MODULES && update_modules compiler $name $install_as
+[[ -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_met.sh_11.0.2

@@ -0,0 +1,121 @@
+#!/bin/bash    
+
+set -eux
+
+name="met"
+version=${1:-${STACK_met_version}}
+install_as=${STACK_met_install_as:-${version}}
+
+# Hyphenated version used for install prefix
+compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+
+[[ ${STACK_met_enable_python:-} =~ [yYtT] ]] && enable_python=YES || enable_python=NO
+
+if $MODULES; then
+    set +x
+    source $MODULESHOME/init/bash
+    module load hpc-$HPC_COMPILER
+    [[ ${STACK_met_enable_python:-} =~ [yYtT] ]] && module load hpc-$HPC_PYTHON
+    module load gsl
+    module load bufr
+    module load zlib
+    module load jasper
+    module try-load libpng
+    module load g2c
+    module load hdf5
+    module load netcdf
+    module list
+    set -x
+
+    prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version"
+    if [[ -d $prefix ]]; then
+      if [[ $OVERWRITE =~ [yYtT] ]]; then
+          echo "WARNING: $prefix EXISTS: OVERWRITING!"
+          $SUDO rm -rf $prefix
+      else
+          echo "WARNING: $prefix EXISTS, SKIPPING"
+          exit 0
+      fi
+    fi
+else
+
+    prefix=${MET_ROOT:-"/usr/local"}
+
+fi
+
+
+cd  ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+software=MET-$version
+URL="https://github.com/dtcenter/MET/archive/refs/tags/v$version.tar.gz"
+[[ -d $software ]] || ( $WGET $URL; tar -xf v$version.tar.gz )
+[[ ${DOWNLOAD_ONLY} =~ [yYtT] ]] && exit 0
+
+export MET_BASE=$prefix/share/met
+
+export FC=$SERIAL_FC
+export CC=$SERIAL_CC
+export CXX=$SERIAL_CXX
+
+export F77=$FC
+export FFLAGS="${STACK_FFLAGS:-} ${STACK_met_FFLAGS:-}"
+export CFLAGS="${STACK_CFLAGS:-} ${STACK_met_CFLAGS:-}"
+
+export CFLAGS+="-D__64BIT__"
+export CXXFLAGS+="-D__64BIT__"
+
+export MET_NETCDF=${NETCDF_ROOT}
+export MET_HDF5=${HDF5_ROOT}
+
+bufr_libdir=`find ${bufr_ROOT:-${BUFR_ROOT}} -name libbufr_4.a -exec dirname {} \;`
+export MET_BUFRLIB=$bufr_libdir
+g2c_libdir=`find ${g2c_ROOT:-${G2C_ROOT}} -name libg2c.a -exec dirname {} \;`
+export MET_GRIB2CLIB=$g2c_libdir
+export MET_GRIB2CINC=${G2C_ROOT:-${g2c_ROOT}}/include
+export MET_GSL=${GSL_ROOT}
+export BUFRLIB_NAME=-lbufr_4
+export GRIB2CLIB_NAME=-lg2c
+jasper_libdir=`find ${JASPER_ROOT} -name libjasper.a -exec dirname {} \;`
+export LIB_JASPER=$jasper_libdir
+
+export LIB_LIBPNG=${PNG_LIBRARIES}
+export LIB_Z=${ZLIB_ROOT}/lib
+
+if [[ $enable_python =~ [yYtT] ]]; then
+    export MET_PYTHON=${MET_PYTHON:-`which python3`}
+
+    if [[ -z ${MET_PYTHON_CC+x} ]]; then
+        #export MET_PYTHON_CC=`$MET_PYTHON_CONFIG --cflags`
+        echo "Set MET_PYTHON_CC to include 'Python.h' usually found through 'python3-config --cflfags'"
+        exit 1
+    fi
+
+    if [[ -z ${MET_PYTHON_LD+x} ]]; then
+        #export MET_PYTHON_LD=`$MET_PYTHON_CONFIG --ldflags`
+        echo "Set MET_PYTHON_LD to to link to libpython found through 'python3-config --ldflags"
+        exit 1
+    fi
+fi
+
+LDFLAGS2="-L${MET_NETCDF}/lib -L${MET_HDF5}/lib -L${MET_BUFRLIB}"
+LDFLAGS3="-L${MET_GRIB2CLIB} -L${MET_GSL}/lib"
+LDFLAGS4="-L${LIB_JASPER} -L${MET_HDF5}/lib -L${LIB_LIBPNG} -L${LIB_Z}"
+
+export LDFLAGS="-fPIE ${LDFLAGS2:-} ${LDFLAGS3:-} ${LDFLAGS4:-}"
+export LIBS="-lhdf5_hl -lhdf5 -lz -ldl"
+
+[[ -d $software ]] && cd $software || ( echo "$software does not exist, ABORT!"; exit 1 )
+
+cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}/${software}
+curr_dir=$(pwd)
+
+extra_flags="--enable-grib2 "
+[[ $enable_python =~ [yYtT] ]] && extra_flags+="--enable-python "
+./configure --prefix=$prefix BUFRLIB_NAME=${BUFRLIB_NAME} GRIB2CLIB_NAME=${GRIB2CLIB_NAME} ${extra_flags:-}
+
+make
+[[ $MAKE_CHECK =~ [yYtT] ]] && make check
+$SUDO make install
+
+# generate modulefile from template
+$MODULES && update_modules compiler $name $install_as
+echo $name $version $URL >> ${HPC_STACK_ROOT}/hpc-stack-contents.log

libs/build_metplus.sh

@@ -7,18 +7,30 @@ version=${1:-${STACK_metplus_version}}
 
 # Hyphenated version used for install prefix
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+mpi=$(echo $HPC_MPI | sed 's/\//-/g')
 
 cd  ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
 software="v"$version
 pkg_name=METplus-$version
 met_version=${1:-${STACK_met_version}}
 URL="https://github.com/dtcenter/METplus/archive/$software.tar.gz"
-[[ -d $software ]] || ( $WGET $URL; tar -xf $software.tar.gz )
+[[ -d $software || -f $software.tar.gz ]]  || ( $WGET $URL )
+[[ -d $software ]] ||  tar -xf $software.tar.gz 
 [[ -d $pkg_name ]] && cd $pkg_name || ( echo "$pkg_name does not exist, ABORT!"; exit 1 )
 
 if $MODULES; then
-    prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version" 
-    met_prefix="${PREFIX:-"/opt/modules"}/$compiler"
+    source $MODULESHOME/init/bash
+    module load hpc-$HPC_COMPILER
+    [[ ! -z $mpi ]] && module load hpc-$HPC_MPI
+    module try-load met
+    echo "Using module met version (none if blank) = ${MET_VERSION:-:}"
+    if [[ -z $mpi ]]; then
+      prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version" 
+      met_prefix=${MET_ROOT:-"${PREFIX:-"/opt/modules"}/$compiler"}
+    else
+      prefix="${PREFIX:-"/opt/modules"}/$compiler/$mpi/$name/$version"
+      met_prefix=${MET_ROOT:-"${PREFIX:-"/opt/modules"}/$compiler/$mpi"}
+    fi
 else
     prefix=${MET_ROOT:-"/usr/local"}
     met_prefix=$prefix
@@ -43,12 +55,12 @@ curr_dir=$(pwd)
 
 # Update the path to the MET tools for the users
 cd ${curr_dir}/parm/metplus_config
-cat metplus_system.conf | \
+cat defaults.conf | \
   sed "s%MET_INSTALL_DIR = /path/to%MET_INSTALL_DIR = $met_prefix/met/$met_version%g" \
   > metplus_system_new.conf
 mv metplus_system_new.conf metplus_system.conf
 
-
 # generate modulefile from template
-$MODULES && update_modules compiler $name $version
+[[ -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_metplus.sh_5.0.2

@@ -0,0 +1,58 @@
+#!/bin/bash                                                                                                                              
+
+set -eux
+
+name="metplus"
+version=${1:-${STACK_metplus_version}}
+
+# Hyphenated version used for install prefix
+compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+
+cd  ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+software="v"$version
+pkg_name=METplus-$version
+met_version=${1:-${STACK_met_version}}
+URL="https://github.com/dtcenter/METplus/archive/$software.tar.gz"
+[[ -d $software ]] || ( $WGET $URL; tar -xf $software.tar.gz )
+[[ -d $pkg_name ]] && cd $pkg_name || ( echo "$pkg_name does not exist, ABORT!"; exit 1 )
+
+if $MODULES; then
+  source $MODULESHOME/init/bash
+    module load hpc-$HPC_COMPILER
+    module try-load met
+    echo "Using module met version (none if blank) = ${MET_VERSION:-:}"
+    prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version" 
+    met_prefix=${MET_ROOT:-"${PREFIX:-"/opt/modules"}/$compiler"}
+else
+    prefix=${MET_ROOT:-"/usr/local"}
+    met_prefix=$prefix
+fi
+
+if [[ -d $prefix ]]; then
+    if [[ $OVERWRITE =~ [yYtT] ]]; then
+        echo "WARNING: $prefix EXISTS: OVERWRITING!"
+        $SUDO rm -rf $prefix
+    else
+        echo "WARNING: $prefix EXISTS, SKIPPING"
+        exit 0
+    fi
+fi
+
+mkdir -p $prefix
+
+# Install is simply copying over the unpacked package to the install location
+cp -r ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}/${pkg_name}/* $prefix
+cd $prefix
+curr_dir=$(pwd)
+
+# Update the path to the MET tools for the users
+cd ${curr_dir}/parm/metplus_config
+cat defaults.conf | \
+  sed "s%MET_INSTALL_DIR = /path/to%MET_INSTALL_DIR = $met_prefix/met/$met_version%g" \
+  > metplus_system_new.conf
+mv metplus_system_new.conf metplus_system.conf
+
+
+# generate modulefile from template
+$MODULES && update_modules compiler $name $version
+echo $name $version $URL >> ${HPC_STACK_ROOT}/hpc-stack-contents.log