diff --git a/setup_modules.sh b/setup_modules.sh
index bc5039bc..00bb3558 100755
--- a/setup_modules.sh
+++ b/setup_modules.sh
@@ -89,50 +89,87 @@ $SUDO mkdir -p $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion
 $SUDO mkdir -p $PREFIX/modulefiles/mpi/$compilerName/$compilerVersion/$mpiName/$mpiVersion
 
 $SUDO mkdir -p $PREFIX/modulefiles/core/hpc-$compilerName
-$SUDO cp $HPC_STACK_ROOT/modulefiles/core/hpc-$compilerName/hpc-$compilerName.lua \
-         $PREFIX/modulefiles/core/hpc-$compilerName/$compilerVersion.lua
-
 $SUDO mkdir -p $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName
-$SUDO cp $HPC_STACK_ROOT/modulefiles/compiler/compilerName/compilerVersion/hpc-$mpiName/hpc-$mpiName.lua \
-         $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName/$mpiVersion.lua
+
+$SUDO mkdir -p $PREFIX/modulefiles/stack/hpc
 
 #===============================================================================
-# Query the user if using native compiler and MPI
-echo "Are you using native compiler $compilerName [yes|YES|no|NO]: (DEFAULT: NO)  "
-read responseCompiler
-if [[ $responseCompiler =~ [yYtT] ]]; then
-  echo -e "==========================\n USING NATIVE COMPILER"
-  cd $PREFIX/modulefiles/core/hpc-$compilerName
-  $SUDO sed -i -e '/load(compiler)/d' $compilerVersion.lua
-  $SUDO sed -i -e '/prereq(compiler)/d' $compilerVersion.lua
-  [[ -f $compilerVersion.lua-e ]] && $SUDO rm -f "$compilerVersion.lua-e" # Stupid macOS does not understand -i, and creates a backup with -e (-e is the next sed option)
-  echo
+# Are the hpc-$compilerName.lua, hpc-$mpiName.lua or hpc/stack.lua modulefiles present at $PREFIX?
+# If yes, query the user to ask to over-write
+if [[ -f $PREFIX/modulefiles/core/hpc-$compilerName/$compilerVersion.lua ]]; then
+  echo "WARNING: $PREFIX/modulefiles/core/hpc-$compilerName/$compilerVersion.lua exists!"
+  echo "Do you wish to over-write? [yes|YES|no|NO]: (DEFAULT: NO)  "
+  read response
+else
+  response="YES"
 fi
+[[ $response =~ [yYtT] ]] && overwriteCompilerModulefile=YES
+unset response
 
-echo "Are you using native MPI $mpiName [yes|YES|no|NO]: (DEFAULT: NO)  "
-read responseMPI
-if [[ $responseMPI =~ [yYtT] ]]; then
-  echo -e "===========================\n USING NATIVE MPI"
-  cd $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName
-  $SUDO sed -i -e '/load(mpi)/d' $mpiVersion.lua
-  $SUDO sed -i -e '/prereq(mpi)/d' $mpiVersion.lua
-  [[ -f $mpiVersion.lua-e ]] && $SUDO rm -f "$mpiVersion.lua-e"
-  echo
+if [[ -f $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName/$mpiVersion.lua ]]; then
+  echo "WARNING: $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName/$mpiVersion.lua exists!"
+  echo "Do you wish to over-write? [yes|YES|no|NO]: (DEFAULT: NO)  "
+  read response
+else
+  response="YES"
 fi
+[[ $response =~ [yYtT] ]] && overwriteMPIModulefile=YES
+unset response
+
+if [[ -f $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua ]]; then
+  echo "WARNING: $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua exists!"
+  echo "Do you wish to over-write? [yes|YES|no|NO]: (DEFAULT: NO)  "
+  read response
+else
+  response="YES"
+fi
+[[ $response =~ [yYtT] ]] && overwriteStackModulefile=YES
+unset response
 
 #===============================================================================
+# Query the user if using native compiler and MPI, if overwriting (or writing for first time)
+if [[ ${overwriteCompilerModulefile:-} =~ [yYtT] ]]; then
+  $SUDO cp $HPC_STACK_ROOT/modulefiles/core/hpc-$compilerName/hpc-$compilerName.lua \
+           $PREFIX/modulefiles/core/hpc-$compilerName/$compilerVersion.lua
+  echo "Are you using native compiler $compilerName [yes|YES|no|NO]: (DEFAULT: NO)  "
+  read response
+  if [[ $response =~ [yYtT] ]]; then
+    echo -e "==========================\n USING NATIVE COMPILER"
+    cd $PREFIX/modulefiles/core/hpc-$compilerName
+    $SUDO sed -i -e '/load(compiler)/d' $compilerVersion.lua
+    $SUDO sed -i -e '/prereq(compiler)/d' $compilerVersion.lua
+    [[ -f $compilerVersion.lua-e ]] && $SUDO rm -f "$compilerVersion.lua-e" # Stupid macOS does not understand -i, and creates a backup with -e (-e is the next sed option)
+    echo
+  fi
+  unset response
+fi
 
-# Deploy directory for stack modulefile
-$SUDO mkdir -p $PREFIX/modulefiles/stack/hpc
-$SUDO cp $HPC_STACK_ROOT/modulefiles/stack/hpc/hpc.lua \
-         $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua
-
-# Replace #PREFIX# from template with $PREFIX,
-# sed does not like delimiter (/) to be a part of replacement string, do magic!
-cd $PREFIX/modulefiles/stack/hpc
-repl=$(echo ${PREFIX} | sed -e "s#/#\\\/#g")
-$SUDO sed -i -e "s/#HPC_OPT#/${repl}/g" $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua
-[[ -f $HPC_STACK_VERSION.lua-e ]] && $SUDO rm -f "$HPC_STACK_VERSION.lua-e"
+if [[ ${overwriteMPIModulefile:-} =~ [yYtT] ]]; then
+  $SUDO cp $HPC_STACK_ROOT/modulefiles/compiler/compilerName/compilerVersion/hpc-$mpiName/hpc-$mpiName.lua \
+           $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName/$mpiVersion.lua
+  echo "Are you using native MPI $mpiName [yes|YES|no|NO]: (DEFAULT: NO)  "
+  read response
+  if [[ $response =~ [yYtT] ]]; then
+    echo -e "===========================\n USING NATIVE MPI"
+    cd $PREFIX/modulefiles/compiler/$compilerName/$compilerVersion/hpc-$mpiName
+    $SUDO sed -i -e '/load(mpi)/d' $mpiVersion.lua
+    $SUDO sed -i -e '/prereq(mpi)/d' $mpiVersion.lua
+    [[ -f $mpiVersion.lua-e ]] && $SUDO rm -f "$mpiVersion.lua-e"
+    echo
+  fi
+  unset response
+fi
+
+if [[ ${overwriteStackModulefile:-} =~ [yYtT] ]]; then
+  $SUDO cp $HPC_STACK_ROOT/modulefiles/stack/hpc/hpc.lua \
+           $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua
+  # Replace #PREFIX# from template with $PREFIX,
+  # sed does not like delimiter (/) to be a part of replacement string, do magic!
+  cd $PREFIX/modulefiles/stack/hpc
+  repl=$(echo ${PREFIX} | sed -e "s#/#\\\/#g")
+  $SUDO sed -i -e "s/#HPC_OPT#/${repl}/g" $PREFIX/modulefiles/stack/hpc/$HPC_STACK_VERSION.lua
+  [[ -f $HPC_STACK_VERSION.lua-e ]] && $SUDO rm -f "$HPC_STACK_VERSION.lua-e"
+fi
 
 #===============================================================================