You need to contact your hosting provider to resolve the issue. Your mysql server turned off. 

i'm using cloudflare is that reason ? 

I'm sorry I can't give you the exact reason, why that happened. What did you do before that happened?

nup nothing happend before 

Well, I don't know what was the reason. Anyway, contact your hosting provider support to resolve the issue. 

but this problem is not happening in case of subdomains ??

probably, the software installed in the root, send some query, and the connection was closed, there are a lot of reasons that could happen. do the search on google. 

ok 

get your hosting to restart sql server 

thanks @tammy 

As Ross said you should contact you hosting provider, there are many reasons may cause this, or you can check your php settings to see if it turned off

but i didn't change it myself ..  / by the way what is the .php file location and which command ?  thanks