We have heard this in many places from our clients saying, custom status scripts (Like status2k) shows our mysql server is down, though in real it is working fine. The main reason of having this is, we use caching system for mysql databases. For having Cachers mysql connection via tcp port is not legitimate or valid in most of the cases. To connect to mysql server you have to go through the socket file while cacher is enabled. As most of the custom status script uses tcp port to connect and verify mysql server status, thats why it shows the mysql server is down, though its working without any problem in the server.
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