Programming interface operations in a driver in communication with a port for reinitialization of storage controller elements

A driver of a host bus adapter of a storage controller performs hardware resets of buses and other logic to which an embedded port of the host bus adapter is connected, in a first period of quiescing of I/O operations in the embedded port. The driver transmits one or more commands to the embedded port to resume selected I/O operations in the embedded port. A reinitialization of the driver is performed during a second period of quiescing of I/O operations in the embedded port, prior to sending a command to allow normal I/O operations in the embedded port.