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Each solution uses its native protocol for I/O. NAS uses Ethernet, and SAN uses SCSI over Fibre Channel. The end nodes are responsible for tracking the receipt of frames or blocks. Taking SAN as an example, using an enterprise class storage array, each I/O from the host is acknowledged as received in the array as soon as it hits the cache of the storage array.
File access over IP uses standard Ethernet handshaking.
Read Randy Kerns' answer to this question.
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