Obtain a suitable batch-processing engine for your environment, and arrange for the web-page to “submit a job.”   Provide, in the web-site (or in web software already supplied with the batch package), the means for users to monitor the jobs, to cancel them (maybe), and to retrieve their output.

httpd is no place to do heavy-lifting processing.   That’s never been its job.   A web-page is a user interface.

Do not expect that you’re going to have to “roll your own” batch processing system.   There are many dozen available for Windows, and even more for Unix/Linux.   If you find yourself grabbing for a piece of paper and doodling some big system design, stop.