I don't think run3 can be used in a threaded environment. Looking at the module code, it makes the redirects, then does system() i.e. fork/exec. A thread-safe version would open the streams; fork(); redirect i/o; exec().

The second problem is waiting upon the processes. You'll need a mechanism to catch child notifications and forward them to the interested threads (via Thread::Queue probably).

In the end, it might be smarter to implement a separate job-controller thread to launch and reap the external jobs.

Update. On a second thought, if your workers only ever wait on a single process at a time, you can get away with just the waitpid($pid, 0); and no job control is necessary...