NOAA-EMC · aerorahul · Aug 19, 2020 · Aug 18, 2020 · Aug 18, 2020 · Aug 18, 2020
diff --git a/build_stack.sh b/build_stack.sh
@@ -6,7 +6,7 @@
 # build_stack.sh -p "prefix" -c "config.sh" -y "stack.yaml" -m
 # build_stack.sh -h
 
-set -e
+set -eu
 
 # root directory for the repository
 HPC_BUILDSCRIPTS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
@@ -120,9 +120,9 @@ fi
 #----------------------
 # Compiler and MPI
 build_lib gnu
-$MODULES || { [[ ${STACK_gnu_build} =~ [yYtT] ]] && export PATH="$PREFIX/bin:$PATH"; }
+$MODULES || { [[ ${STACK_gnu_build:-} =~ [yYtT] ]] && export PATH="$PREFIX/bin:$PATH"; }
 build_lib mpi
-$MODULES || { [[ ${STACK_mpi_build} =~ [yYtT] ]] && export PATH="$PREFIX/bin:$PATH"; }
+$MODULES || { [[ ${STACK_mpi_build:-} =~ [yYtT] ]] && export PATH="$PREFIX/bin:$PATH"; }
 
 # ==============================================================================
 #----------------------

diff --git a/libs/build_boost.sh b/libs/build_boost.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -x
+set -eux
 
 name="boost"
 version=${1:-${STACK_boost_version}}

diff --git a/libs/build_cgal.sh b/libs/build_cgal.sh
@@ -18,7 +18,7 @@
 #
 #
 
-set -ex
+set -eux
 
 name="cgal"
 version=${1:-${STACK_cgal_version}}

diff --git a/libs/build_cmake.sh b/libs/build_cmake.sh
@@ -5,7 +5,7 @@
 # allows you to place it into a module context so you can experiment
 # with different versions
 
-set -ex
+set -eux
 
 name="cmake"
 version=${1:-${STACK_cmake_version}}

diff --git a/libs/build_eigen.sh b/libs/build_eigen.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="eigen"
 version=${1:-${STACK_eigen_version}}

diff --git a/libs/build_esmf.sh b/libs/build_esmf.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="esmf"
 version=${1:-${STACK_esmf_version}}
@@ -54,9 +54,9 @@ else
 fi
 
 export F9X=$FC
-export FFLAGS="${STACK_esmf_FFLAGS} -fPIC"
-export CFLAGS="${STACK_esmf_CFLAGS} -fPIC"
-export CXXFLAGS="${STACK_esmf_CXXFLAGS} -fPIC"
+export FFLAGS="${STACK_esmf_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_esmf_CFLAGS:-} -fPIC"
+export CXXFLAGS="${STACK_esmf_CXXFLAGS:-} -fPIC"
 export FCFLAGS="$FFLAGS"
 
 gitURL="https://github.com/esmf-org/esmf"

diff --git a/libs/build_fftw.sh b/libs/build_fftw.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="fftw"
 version=${1:-${STACK_fftw_version}}

diff --git a/libs/build_gnu.sh b/libs/build_gnu.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="gnu"
 version=${1:-${STACK_gnu_version}}

diff --git a/libs/build_gptl.sh b/libs/build_gptl.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="gptl"
 version=${1:-${STACK_gptl_version}}

diff --git a/libs/build_hdf5.sh b/libs/build_hdf5.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="hdf5"
 version=${1:-${STACK_hdf5_version}}
@@ -9,9 +9,9 @@ version=${1:-${STACK_hdf5_version}}
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
 mpi=$(echo $HPC_MPI | sed 's/\//-/g')
 
-[[ ${STACK_hdf5_enable_szip} =~ [yYtT] ]] && enable_szip=YES || enable_szip=NO
-[[ ${STACK_hdf5_enable_zlib} =~ [yYtT] ]] && enable_zlib=YES || enable_zlib=NO
-[[ ${STACK_hdf5_shared} =~ [yYtT] ]] && enable_shared=YES || enable_shared=NO
+[[ ${STACK_hdf5_enable_szip:-} =~ [yYtT] ]] && enable_szip=YES || enable_szip=NO
+[[ ${STACK_hdf5_enable_zlib:-} =~ [yYtT] ]] && enable_zlib=YES || enable_zlib=NO
+[[ ${STACK_hdf5_shared:-} =~ [yYtT] ]] && enable_shared=YES || enable_shared=NO
 
 if $MODULES; then
   set +x
@@ -44,9 +44,9 @@ else
 fi
 
 export F9X=$FC
-export FFLAGS="${STACK_hdf5_FFLAGS} -fPIC -w"
-export CFLAGS="${STACK_hdf5_CFLAGS} -fPIC -w"
-export CXXFLAGS="${STACK_hdf5_CXXFLAGS} -fPIC -w"
+export FFLAGS="${STACK_hdf5_FFLAGS:-} -fPIC -w"
+export CFLAGS="${STACK_hdf5_CFLAGS:-} -fPIC -w"
+export CXXFLAGS="${STACK_hdf5_CXXFLAGS:-} -fPIC -w"
 export FCFLAGS="$FFLAGS"
 
 gitURL="https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git"
@@ -68,7 +68,7 @@ mkdir -p build && cd build
 
 ../configure --prefix=$prefix \
              --enable-fortran --enable-cxx \
-             $szip_flags $zlib_flags $shared_flags $extra_conf
+             ${szip_flags:-} ${zlib_flags:-} ${shared_flags:-} ${extra_conf:-}
 
 VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}
 [[ $MAKE_CHECK =~ [yYtT] ]] && make check

diff --git a/libs/build_jasper.sh b/libs/build_jasper.sh
@@ -1,14 +1,14 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="jasper"
 version=${1:-${STACK_jasper_version}}
 
 # Hyphenated version used for install prefix
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
 
-[[ ${STACK_jasper_shared} =~ [yYtT] ]] && enable_shared=YES || enable_shared=NO
+[[ ${STACK_jasper_shared:-} =~ [yYtT] ]] && enable_shared=YES || enable_shared=NO
 
 if $MODULES; then
   set +x
@@ -30,8 +30,8 @@ export CC=$SERIAL_CC
 export CXX=$SERIAL_CXX
 
 export F77=$FC
-export FFLAGS="${STACK_jasper_FFLAGS} -fPIC"
-export CFLAGS="${STACK_jasper_CFLAGS} -fPIC"
+export FFLAGS="${STACK_jasper_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_jasper_CFLAGS:-} -fPIC"
 
 cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
 

diff --git a/libs/build_jpeg.sh b/libs/build_jpeg.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="jpeg"
 version=${1:-${STACK_jpeg_version}}
@@ -27,7 +27,7 @@ else
 fi
 
 export CC=$SERIAL_CC
-export CFLAGS="${STACK_jpeg_CFLAGS} -fPIC"
+export CFLAGS="${STACK_jpeg_CFLAGS:-} -fPIC"
 
 cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
 

diff --git a/libs/build_lapack.sh b/libs/build_lapack.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="lapack"
 version=${1:-${STACK_lapack_version}}

diff --git a/libs/build_lmod.sh b/libs/build_lmod.sh
@@ -7,7 +7,7 @@
 # usage:
 # build_lmod.sh <prefix>
 
-set -ex
+set -eux
 
 if [[ $# -lt 1 ]]; then
     mods_path=/opt

diff --git a/libs/build_mpi.sh b/libs/build_mpi.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name=${1:-${STACK_mpi_flavor}}
 version=${2:-${STACK_mpi_version}}

diff --git a/libs/build_nccmp.sh b/libs/build_nccmp.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="nccmp"
 version=${1:-${STACK_nccmp_version}}
@@ -52,19 +52,19 @@ else
     export CXX=$SERIAL_CXX
 fi
 
-export CFLAGS="${STACK_nccmp_CFLAGS} -fPIC"
+export CFLAGS="${STACK_nccmp_CFLAGS:-} -fPIC"
 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 $LDFLAGS5"
+export LDFLAGS="${LDFLAGS1:-} ${LDFLAGS2:-} ${LDFLAGS3:-} ${LDFLAGS4:-} ${LDFLAGS5:-}"
 
 # Enable header pad comparison, if netcdf-c src directory exists!
-[[ -d "netcdf-c-$NETCDF_VERSION" ]] && netcdf_src="$PWD/netcdf-c-$NETCDF_VERSION"
-[[ -d "netcdf-c-$NETCDF_VERSION" ]] && extra_confs="--with-netcdf=$netcdf_src"
+[[ -d "netcdf-c-${NETCDF_VERSION:-}" ]] && netcdf_src="$PWD/netcdf-c-$NETCDF_VERSION"
+[[ -d "netcdf-c-${NETCDF_VERSION:-}" ]] && extra_confs="--with-netcdf=$netcdf_src"
 
 [[ -d $software ]] && cd $software || ( echo "$software does not exist, ABORT!"; exit 1 )
 [[ -d build ]] && rm -rf build
@@ -79,7 +79,7 @@ cmake .. \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DNETCDF_INC_DIR=$NETCDF_ROOT/include \
   -DNETCDF_LIB_PATH=$NETCDF_ROOT/lib/libnetcdf.a \
-  -DWITH_NETCDF=$netcdf_src
+  -DWITH_NETCDF=${netcdf_src:-}
 
 make -j${NTHREADS:-4}
 [[ $MAKE_CHECK =~ [yYtT] ]] && make check

diff --git a/libs/build_nceplibs.sh b/libs/build_nceplibs.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name=$1
 eval s_version="\${STACK_${name}_version}"
@@ -13,6 +13,7 @@ openmp=${4:-${s_openmp:-"OFF"}}
 # Hyphenated version used for install prefix
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
 mpi_check=$(echo $HPC_MPI | sed 's/\//-/g')
+mpi=''
 
 if $MODULES; then
   set +x
@@ -121,9 +122,9 @@ else
   export CXX=$SERIAL_CXX
 fi
 
-eval fflags="\${STACK_${name}_FFLAGS}"
-eval cflags="\${STACK_${name}_CFLAGS}"
-eval cxxflags="\${STACK_${name}_CXXFLAGS}"
+eval fflags="\${STACK_${name}_FFLAGS:-}"
+eval cflags="\${STACK_${name}_CFLAGS:-}"
+eval cxxflags="\${STACK_${name}_CXXFLAGS:-}"
 
 export F9X=$FC
 export FFLAGS="$fflags -fPIC -w"
@@ -143,8 +144,8 @@ case $name in
     gitURL="https://github.com/noaa-emc/emc_crtm"
     ;;
   wgrib2)
-    [[ -z $STACK_wgrib2_ipolates ]] && ipolates=0   || ipolates=$STACK_wgrib2_ipolates
-    [[ -z $STACK_wgrib2_spectral ]] && spectral=OFF || spectral=$STACK_wgrib2_spectral
+    [[ -z ${STACK_wgrib2_ipolates:-} ]] && ipolates=0   || ipolates=$STACK_wgrib2_ipolates
+    [[ -z ${STACK_wgrib2_spectral:-} ]] && spectral=OFF || spectral=$STACK_wgrib2_spectral
     extraCMakeFlags="-DUSE_SPECTRAL=$spectral -DUSE_IPOLATES=$ipolates"
     ;;
 esac
@@ -168,7 +169,7 @@ mkdir -p build && cd build
 cmake .. \
   -DCMAKE_INSTALL_PREFIX=$prefix \
   -DENABLE_TESTS=OFF \
-  $extraCMakeFlags \
+  ${extraCMakeFlags:-} \
   -DOPENMP=${openmp}
 
 VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}

diff --git a/libs/build_nco.sh b/libs/build_nco.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="nco"
 version=${1:-${STACK_nco_version}}
@@ -47,9 +47,9 @@ else
     export CXX=$SERIAL_CXX
 fi
 
-export FFLAGS="${STACK_nco_FFLAGS} -fPIC"
-export CFLAGS="${STACK_nco_CFLAGS} -fPIC"
-export CXXFLAGS="${STACK_nco_CXXFLAGS} -fPIC"
+export FFLAGS="${STACK_nco_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_nco_CFLAGS:-} -fPIC"
+export CXXFLAGS="${STACK_nco_CXXFLAGS:-} -fPIC"
 
 export F77=$FC
 export FCFLAGS=$FFLAGS

diff --git a/libs/build_netcdf.sh b/libs/build_netcdf.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -ex
+set -eux
 
 name="netcdf"
 c_version=${1:-${STACK_netcdf_version_c}}
@@ -11,7 +11,7 @@ cxx_version=${3:-${STACK_netcdf_version_cxx}}
 compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
 mpi=$(echo $HPC_MPI | sed 's/\//-/g')
 
-[[ ${STACK_netcdf_enable_pnetcdf} =~ [yYtT] ]] && enable_pnetcdf=YES || enable_pnetcdf=NO
+[[ ${STACK_netcdf_enable_pnetcdf:-} =~ [yYtT] ]] && enable_pnetcdf=YES || enable_pnetcdf=NO
 
 if $MODULES; then
     set +x
@@ -48,9 +48,9 @@ fi
 
 export F77=$FC
 export F9X=$FC
-export FFLAGS="${STACK_netcdf_FFLAGS} -fPIC"
-export CFLAGS="${STACK_netcdf_CFLAGS} -fPIC"
-export CXXFLAGS="${STACK_netcdf_CXXFLAGS} -fPIC -std=c++11"
+export FFLAGS="${STACK_netcdf_FFLAGS:-} -fPIC"
+export CFLAGS="${STACK_netcdf_CFLAGS:-} -fPIC"
+export CXXFLAGS="${STACK_netcdf_CXXFLAGS:-} -fPIC -std=c++11"
 export FCFLAGS="$FFLAGS"
 
 gitURLroot="https://github.com/Unidata"
@@ -61,12 +61,12 @@ curr_dir=$(pwd)
 LDFLAGS1="-L$HDF5_ROOT/lib"
 LDFLAGS2=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep AM_LDFLAGS | cut -d: -f2)
 [[ $enable_pnetcdf =~ [yYtT] ]] && LDFLAGS4="-L$PNETCDF_ROOT/lib"
-if [[ ${STACK_netcdf_shared} != [yYtT] ]]; then
+if [[ ${STACK_netcdf_shared:-} != [yYtT] ]]; then
   LDFLAGS1+=" -lhdf5_hl -lhdf5"
   LDFLAGS3=$(cat $HDF5_ROOT/lib/libhdf5.settings | grep "Extra libraries" | cut -d: -f2)
   [[ $enable_pnetcdf =~ [yYtT] ]] && LDFLAGS4+=" -lpnetcdf"
 fi
-export LDFLAGS="$LDFLAGS1 $LDFLAGS2 $LDFLAGS3 $LDFLAGS4"
+export LDFLAGS="${LDFLAGS1:-} ${LDFLAGS2:-} ${LDFLAGS3:-} ${LDFLAGS4:-}"
 
 export CFLAGS+=" -I$HDF5_ROOT/include"
 export CPPFLAGS+=" -I$HDF5_ROOT/include"
@@ -118,7 +118,7 @@ mkdir -p build && cd build
              --disable-dap \
              --enable-netcdf-4 \
              --disable-doxygen \
-             $shared_flags $pnetcdf_conf $extra_conf
+             ${shared_flags:-} ${pnetcdf_conf:-} ${extra_conf:-}
 
 VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}
 [[ $MAKE_CHECK =~ [yYtT] ]] && make check
@@ -167,7 +167,7 @@ software=$name-"fortran"-$version
 mkdir -p build && cd build
 
 ../configure --prefix=$prefix \
-             $shared_flags
+             ${shared_flags:-}
 
 #VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}
 VERBOSE=$MAKE_VERBOSE make -j1 #NetCDF-Fortran-4.5.2 & intel/20 have a linker bug if built with j>1
@@ -192,7 +192,7 @@ software=$name-"cxx4"-$version
 mkdir -p build && cd build
 
 ../configure --prefix=$prefix \
-             $shared_flags
+             ${shared_flags:-}
 
 VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}
 [[ $MAKE_CHECK =~ [yYtT] ]] && make check
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,7 +18,7 @@ @@
     #
     #
-    set -ex
+    set -eux
     name="cgal"
     version=${1:-${STACK_cgal_version}}
@@ Expand Down @@