The issue started after installing the latest mongo server, where the service of mongo has changed from mongod to mongodb, and the service was installed via /usr/lib/systemd and not under /etc/init.

The problem is that the systemd service does not use the limits defined in /etc/security/limits.conf, and mongo starts with 1024 max open files, and easily crashes as it runs out of open files.

Also generally systemd does not check /etc/security/limits.conf and you need to add LimitNOFILES to the service.