It's a hard problem to get right. As well as the Safe module the other comment refers to, you may want to look into OS-level permissions.
Assuming Linux, you may be interested in:
- chroot;
- running as a sandbox user-id which owns no files (and is a member of no other groups). (Clear out that user's home dir before each run);
- ulimit and friends to control resource usage
And in this day and age, another good option is to do all this inside a hosted virtual machine. In particular, I know vmware allows you to have a disk which isn't persistent, i.e. all changes are reset on each boot.
Lastly, you said you need to allow users: "to input a perl expression or program and have it run over string."
That's a really unusual requirement. Is there any chance you could tell us why you need to do that? It's possible someone could think of an alternative approach which isn't as risky.
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