What would cause a server to "lose" a file, or function?

My server is pretty straightforward. Centos, PHP, Nginx, Apache, etc. Two days ago I started getting an error in my logs that it could not find a file that was there plain as day. After I deleted, then replaced the file, and restarted Apache things worked.

Today I started getting an error that it couldn’t find a PHP function in a class that extended another class. I renamed both files to old, then uploaded the original file and things started working again.

Permissions do not appear to have been changed and neither has the ownership changed.

These files in question haven’t been update/touched in months.

Looking for ideas as to what might be going on.

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Bobby Iliev
Site Moderator
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February 7, 2024
Accepted Answer


From what you’re describing, it sounds like you’re experiencing a rather peculiar issue. Files and functions “disappearing” or becoming “unrecognized” despite being present and unchanged for months can indeed be baffling. Given the stack you’re working with (CentOS, PHP, Nginx, Apache), there are a few areas we can explore to troubleshoot this issue:

  1. OPcache Issues: OPcache improves PHP performance by storing precompiled script bytecode in shared memory, thus eliminating the need for PHP to load and parse scripts on each request. However, if there are issues with the cache, it could lead to PHP not recognizing changes to files or, in rare cases, functions. Clearing the OPcache (opcache_reset();) or temporarily disabling it could help determine if this is the cause. This might also be related to the available RAM on the server.

  2. Inodes Running Out: If your server is running out of inodes, it could lead to strange filesystem behavior, including the inability to recognize existing files. You can check inode usage with df -i. Here is a guide on how to check your disk usage as well:

  1. Review Logs: Lastly, don’t forget to go through your Apache, Nginx, and PHP error logs around the times the issues occurred. They might offer more specific clues as to what’s happening. Sometimes, the error messages can be misleading or vague, but they are a good starting point for troubleshooting.

Let me know how it goes!



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