1. A method of responding to a timeout of a message in a parallel computer, the parallel computer including a plurality of compute nodes operatively coupled for data communications over one or more data communications networks, each compute node including one or more tasks, the method comprising: sending, by a first task of a first node, a message to a second task on a second node; in response to a timeout of the message, sending to a partition manager daemon (PMD) located in to the second node, by the first task, a command via a parallel operating environment (POE) located on a third node, the command instructing the second node to perform a timeout motivated operation; receiving from the first task, by the PMD on the second node, the command; and in response to receiving the command, performing, by the PMD, the timeout motivated operation, whereby the timeout motivated operation is used to diagnose the timeout occurrence.