diff --git a/tools/toolchain/install_cp2k_toolchain.sh b/tools/toolchain/install_cp2k_toolchain.sh
index 70ea700bce..78b993e25a 100755
--- a/tools/toolchain/install_cp2k_toolchain.sh
+++ b/tools/toolchain/install_cp2k_toolchain.sh
@@ -389,9 +389,13 @@ while [ $# -ge 1 ]; do
       export DOWNLOADER_FLAGS="-n"
       ;;
     --install-all)
-      # set all package to __INSTALL__ status
+      # set all package to the default installation status
       for ii in ${package_list}; do
-        [ "${ii}" != "intel" ] && eval with_${ii}="__INSTALL__"
+        if [ "${ii}" = "intel" ]; then
+          eval with_${ii}="__SYSTEM__"
+        else
+          eval with_${ii}="__INSTALL__"
+        fi
       done
       # default mpi-mode to MPICH
       export MPI_MODE=mpich
@@ -400,16 +404,16 @@ while [ $# -ge 1 ]; do
       user_input="${1#*=}"
       case "$user_input" in
         mpich)
-          export MPI_MODE=mpich
+          export MPI_MODE="mpich"
           ;;
         openmpi)
-          export MPI_MODE=openmpi
+          export MPI_MODE="openmpi"
           ;;
         intelmpi)
-          export MPI_MODE=intelmpi
+          export MPI_MODE="intelmpi"
           ;;
         no)
-          export MPI_MODE=no
+          export MPI_MODE="no"
           ;;
         *)
           report_error ${LINENO} \
@@ -441,36 +445,11 @@ while [ $# -ge 1 ]; do
       ;;
     --gpu-ver=*)
       user_input="${1#*=}"
-      case "$user_input" in
-        K20X)
-          export GPUVER=K20X
-          ;;
-        K40)
-          export GPUVER=K40
-          ;;
-        K80)
-          export GPUVER=K80
-          ;;
-        P100)
-          export GPUVER=P100
-          ;;
-        V100)
-          export GPUVER=V100
-          ;;
-        A100)
-          export GPUVER=A100
-          ;;
-        Mi50)
-          export GPUVER=Mi50
-          ;;
-        Mi100)
-          export GPUVER=Mi100
-          ;;
-        no)
-          export GPUVER=no
+      case "${user_input}" in
+        K20X | K40 | K80 | P100 | V100 | A100 | Mi50 | Mi100 | no)
+          export GPUVER="${user_input}"
           ;;
         *)
-          export GPUVER=no
           report_error ${LINENO} \
             "--gpu-ver currently only supports K20X, K40, K80, P100, V100, A100, Mi50, Mi100 and no as options"
           exit 1
@@ -534,112 +513,112 @@ while [ $# -ge 1 ]; do
       fi
       ;;
     --with-gcc*)
-      with_gcc=$(read_with $1)
+      with_gcc=$(read_with "${1}")
       ;;
     --with-cmake*)
-      with_cmake=$(read_with $1)
+      with_cmake=$(read_with "${1}")
       ;;
     --with-mpich*)
-      with_mpich=$(read_with $1)
-      if [ $with_mpich != "__DONTUSE__" ]; then
+      with_mpich=$(read_with "${1}")
+      if [ "${with_mpich}" != "__DONTUSE__" ]; then
         export MPI_MODE=mpich
       fi
       ;;
     --with-openmpi*)
-      with_openmpi=$(read_with $1)
+      with_openmpi=$(read_with "${1}")
       if [ "${with_openmpi}" != "__DONTUSE__" ]; then
         export MPI_MODE=openmpi
       fi
       ;;
     --with-intelmpi*)
-      with_intelmpi=$(read_with $1)
+      with_intelmpi=$(read_with "${1}" "__SYSTEM__")
       if [ "${with_intelmpi}" != "__DONTUSE__" ]; then
         export MPI_MODE=intelmpi
       fi
       ;;
     --with-intel*)
-      with_intel=$(read_with $1)
+      with_intel=$(read_with "${1}" "__SYSTEM__")
       ;;
     --with-libint*)
-      with_libint=$(read_with $1)
+      with_libint=$(read_with "${1}")
       ;;
     --with-libxc*)
-      with_libxc=$(read_with $1)
+      with_libxc=$(read_with "${1}")
       ;;
     --with-fftw*)
-      with_fftw=$(read_with $1)
+      with_fftw=$(read_with "${1}")
       ;;
     --with-mkl*)
-      with_mkl=$(read_with $1)
-      if [ $with_mkl != "__DONTUSE__" ]; then
+      with_mkl=$(read_with "${1}" "__SYSTEM__")
+      if [ "${with_mkl}" != "__DONTUSE__" ]; then
         export MATH_MODE="mkl"
       fi
       ;;
     --with-acml*)
-      with_acml=$(read_with $1)
-      if [ $with_acml != __DONTUSE__ ]; then
+      with_acml=$(read_with "${1}")
+      if [ "${with_acml}" != "__DONTUSE__" ]; then
         export MATH_MODE="acml"
       fi
       ;;
     --with-openblas*)
-      with_openblas=$(read_with $1)
-      if [ "${with_openblas}" != __DONTUSE__ ]; then
+      with_openblas=$(read_with "${1}")
+      if [ "${with_openblas}" != "__DONTUSE__" ]; then
         export MATH_MODE="openblas"
       fi
       ;;
     --with-scalapack*)
-      with_scalapack=$(read_with $1)
+      with_scalapack=$(read_with "${1}")
       ;;
     --with-libsmm*)
-      with_libsmm=$(read_with $1)
+      with_libsmm=$(read_with "${1}")
       ;;
     --with-libxsmm*)
-      with_libxsmm=$(read_with $1)
+      with_libxsmm=$(read_with "${1}")
       ;;
     --with-elpa*)
-      with_elpa=$(read_with $1)
+      with_elpa=$(read_with "${1}")
       ;;
     --with-ptscotch*)
-      with_ptscotch=$(read_with $1)
+      with_ptscotch=$(read_with "${1}")
       ;;
     --with-superlu*)
-      with_superlu=$(read_with $1)
+      with_superlu=$(read_with "${1}")
       ;;
     --with-pexsi*)
-      with_pexsi=$(read_with $1)
+      with_pexsi=$(read_with "${1}")
       ;;
     --with-quip*)
-      with_quip=$(read_with $1)
+      with_quip=$(read_with "${1}")
       ;;
     --with-plumed*)
-      with_plumed=$(read_with $1)
+      with_plumed=$(read_with "${1}")
       ;;
     --with-sirius*)
-      with_sirius=$(read_with $1)
+      with_sirius=$(read_with "${1}")
       ;;
     --with-gsl*)
-      with_gsl=$(read_with $1)
+      with_gsl=$(read_with "${1}")
       ;;
     --with-spglib*)
-      with_spglib=$(read_with $1)
+      with_spglib=$(read_with "${1}")
       ;;
     --with-hdf5*)
-      with_hdf5=$(read_with $1)
+      with_hdf5=$(read_with "${1}")
       ;;
     --with-libvdwxc*)
-      with_libvdwxc=$(read_with $1)
+      with_libvdwxc=$(read_with "${1}")
       ;;
     --with-spfft*)
-      with_spfft=$(read_with $1)
+      with_spfft=$(read_with "${1}")
       ;;
     --with-cosma*)
-      with_cosma=$(read_with $1)
+      with_cosma=$(read_with "${1}")
       ;;
     --with-libvori*)
-      with_libvori=$(read_with $1)
+      with_libvori=$(read_with "${1}")
       ;;
     --with-spla*)
-      with_spla=$(read_with $1)
+      with_spla=$(read_with "${1}")
       ;;
     --help*)
       show_help
diff --git a/tools/toolchain/scripts/stage1/install_intelmpi.sh b/tools/toolchain/scripts/stage1/install_intelmpi.sh
index de6f2ab1c9..3cc5274f15 100755
--- a/tools/toolchain/scripts/stage1/install_intelmpi.sh
+++ b/tools/toolchain/scripts/stage1/install_intelmpi.sh
@@ -24,8 +24,9 @@ INTELMPI_LIBS=""
 mkdir -p "${BUILDDIR}"
 cd "${BUILDDIR}"
 
-case "$with_intelmpi" in
+case "${with_intelmpi}" in
   __INSTALL__)
+    echo "==================== Installing Intel MPI ===================="
     echo '__INSTALL__ is not supported; please manually install Intel MPI'
     exit 1
     ;;
diff --git a/tools/toolchain/scripts/stage2/install_mkl.sh b/tools/toolchain/scripts/stage2/install_mkl.sh
index 65b402355f..566c3d1acc 100755
--- a/tools/toolchain/scripts/stage2/install_mkl.sh
+++ b/tools/toolchain/scripts/stage2/install_mkl.sh
@@ -22,15 +22,15 @@ MKL_LDFLAGS=""
 MKL_LIBS=""
 
 MKL_FFTW="yes"
-if [ "$with_libvdwxc" != "__DONTUSE__" ] && [ "$MPI_MODE" != "no" ]; then
-  report_warning ${LINENO} "MKL FFTW3 interface is present, but FFTW library is needed (FFTW-MPI)"
+if [ "${with_libvdwxc}" != "__DONTUSE__" ] && [ "${MPI_MODE}" != "no" ]; then
+  report_warning ${LINENO} "MKL FFTW3 interface is present, but FFTW library is needed for FFTW-MPI wrappers."
   MKL_FFTW="no"
 fi
 
 ! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
 cd "${BUILDDIR}"
 
-case "$with_mkl" in
+case "${with_mkl}" in
   __INSTALL__)
     echo "==================== Installing MKL ===================="
     report_error ${LINENO} "To install MKL, please contact your system administrator."
@@ -47,22 +47,23 @@ case "$with_mkl" in
     check_lib -lm
     check_lib -ldl
     ;;
-  __DONTUSE__) ;;
-
+  __DONTUSE__)
+    # Nothing to do
+    ;;
   *)
     echo "==================== Linking MKL to user paths ===================="
-    check_dir "$with_mkl"
-    MKLROOT="$with_mkl"
+    check_dir "${with_mkl}"
+    MKLROOT="${with_mkl}"
     ;;
 esac
-if [ "$with_mkl" != "__DONTUSE__" ]; then
-  case $OPENBLAS_ARCH in
+if [ "${with_mkl}" != "__DONTUSE__" ]; then
+  case ${OPENBLAS_ARCH} in
     x86_64)
-      mkl_arch_dir=intel64
+      mkl_arch_dir="intel64"
       MKL_CFLAGS="-m64"
       ;;
     i386)
-      mkl_arch_dir=ia32
+      mkl_arch_dir="ia32"
       MKL_CFLAGS="-m32"
       ;;
     *)
@@ -80,7 +81,7 @@ if [ "$with_mkl" != "__DONTUSE__" ]; then
     fi
   done
 
-  case $MPI_MODE in
+  case ${MPI_MODE} in
     intelmpi | mpich)
       mkl_scalapack_lib="IF_MPI(-lmkl_scalapack_lp64|)"
       mkl_blacs_lib="IF_MPI(-lmkl_blacs_intelmpi_lp64|)"
@@ -109,9 +110,6 @@ if [ "$with_mkl" != "__DONTUSE__" ]; then
   # write setup files
   cat << EOF > "${BUILDDIR}/setup_mkl"
 export MKLROOT="${MKLROOT}"
-EOF
-  cat "${BUILDDIR}/setup_mkl" >> ${SETUPFILE}
-  cat << EOF >> "${BUILDDIR}/setup_mkl"
 export MKL_CFLAGS="${MKL_CFLAGS}"
 export MKL_LIBS="${MKL_LIBS}"
 export MATH_CFLAGS="\${MATH_CFLAGS} ${MKL_CFLAGS}"
@@ -134,6 +132,7 @@ export FFTW_LDFLAGS="${MKL_LDFLAGS}"
 export FFTW_LIBS="${MKL_LIBS}"
 EOF
   fi
+  cat "${BUILDDIR}/setup_mkl" >> ${SETUPFILE}
 fi
 
 load "${BUILDDIR}/setup_mkl"
diff --git a/tools/toolchain/scripts/tool_kit.sh b/tools/toolchain/scripts/tool_kit.sh
index 51dcb5017c..b588063b0b 100644
--- a/tools/toolchain/scripts/tool_kit.sh
+++ b/tools/toolchain/scripts/tool_kit.sh
@@ -580,18 +580,22 @@ read_enable() {
 read_with() {
   local __input_var="${1#--with*=}"
   case $__input_var in
-    "$1")
+    "${1}")
       # if there is no "=" then treat as "install"
-      echo '__INSTALL__'
+      if [ ${#} -gt 1 ]; then
+        echo "${2}"
+      else
+        echo "__INSTALL__"
+      fi
       ;;
     install)
-      echo '__INSTALL__'
+      echo "__INSTALL__"
       ;;
     system)
-      echo '__SYSTEM__'
+      echo "__SYSTEM__"
       ;;
     no)
-      echo '__DONTUSE__'
+      echo "__DONTUSE__"
       ;;
     *)
       echo "${__input_var//\~/$HOME}"