Derick Rethans has a new post with his own suggestion about using the right debugging tools to help track down a problem (based on some of his own experience debugging the MongoDB PHP extension).
A while ago, we updated the MongoDB PHP driver's embedded C library to a new version. The C library handles most of the connection management and other low level tasks that the PHP driver needs to successfully talk to MongoDB deployments, especially in replicated environments where servers might disappear for maintenance or hardware failures.
After upgrading a related library, he ended up with a failing test related to Atlas connectivity. He walks through the process he took to try and debug the issue using GDB to see where the execution was failing using various techniques. This included looking through the backtrace and, not noticing anything out of the ordinary, going for a walk. Upon returning he noticed an odd line in the backtrace that, after some additional tracking using a GDB helper, showed the problem to be with how the query options are defined and not reset in a loop.