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This is the story of how a company with nearly $400 million in assets went bankrupt in 45-minutes because of a failed deployment.
The first course of business was to regain control of the server. Every service on the machine was unresponsive, including SSH. The only thing to do was perform a remote restart and wait for things to come back online.
Service started well with the init file, but stop or restart didn't. In the end the cause was a different path to the pid file in the nginx.conf and the init script. Make sure they both point to the same location.