diff --git a/scripts/prepare_instrumentation.sh b/scripts/prepare_instrumentation.sh
index bbf401dd4052ef75beafed5991b47eeecef649ba..c4e4a3a17f5050df739f3255fdac2cb9023beb64 100755
--- a/scripts/prepare_instrumentation.sh
+++ b/scripts/prepare_instrumentation.sh
@@ -134,5 +134,9 @@ fi
 sed -i.bak -e "s/\/\*[[:space:]]*\(#define[[:space:]]*WMOPS\)[[:space:]]*\*\//\1/g" $targetdir/lib_com/options.h
 sed -i.bak -e "s/\/\/[[:space:]]*\(#define[[:space:]]*WMOPS\)/\1/g"        $targetdir/lib_com/options.h
 
+# disable treating warnings as errors, since clang's -Wdollar-in-identifier-extension is not compatible with the instrumentation macros
+sed -i.bak -e "s/-Werror[[:space:]]/ /g" $targetdir/Makefile
+sed -i.bak -e "s/-Werror[[:space:]]/ /g" $targetdir/CMakeLists.txt
+
 # return to start dir
 cd "$currdir"