Let's assume that I have an application X. I only track system calls that X issues. For example in systems like "CS-STILo". The system detects anomalous sequences of system calls to detect code reuse attacks.

If I want to prevent the attack when I detect the attack, what should I do? Can I stop the system calls before it is executed using Stackable Filesystems (e.g., Wrapfs)? If not, is there another way?

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There are SELinux and AppArmor (called MAC - mandatory access control).
AFAIK RedHat, CentOS uses SELinux.
SuSe, Debian, Ubuntu uses AppArmour by default.

In a nutshell with SELinux or AppArmor enabled you need to give permissions which application/daemon is allowed to access which resources (ports, sockets, filesystem ).

For example you need to allow tomcat daemon to access the mysql database on port 3306 or apache webserver to access the filesystem /var/www.

Whenever a systemcall is blocked ie. selinux blocks tomcat accessing mysql, it's logged to /var/log/audit.log or similar depending on your linux flavor.

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