The file sharing protocols available on Lion Server are native to different operating systems, though Lion Server and all other Macs have the ability to use all these protocols. You can use multiple file-sharing protocols at the same time to support different client operating systems:
Apple Filing Protocol (AFP): AFP is the native file-sharing protocol for Macs. It’s been used in the Mac OS for years, so even your most ancient, pre-OS X Macs use it. AFP should be your first-choice file-sharing protocol for Mac clients. It can be faster than SMB, and your Mac clients will have fewer file-sharing glitches.
AFP also provides Mac users with special features that the other protocols don’t support, such as the ability to search server folders with Spotlight. AFP also supports Kerberos authentication, access control lists, and the extended attributes of some Mac files.
AFP also provides Automatic Reconnect: When a Mac client goes into sleep mode, Mac OS X Server disconnects its AFP session. AFP can automatically reconnect to Mac clients after they wake, enabling users to resume working on open files from where they left off.
Clients that wake up within a 24-hour period can reconnect automatically after waking. If the client Mac wakes after 24 hours, the user will need to log in.
Windows clients don’t use AFP.
Server Message Block (SMB): SMB is the native protocol that Windows clients use to access file servers. Many Linux and Unix clients also use SMB. Mac clients running Mac OS X 10.6 or later can also access files using SMB in Lion Server, but they get better results with AFP.
When Mac OS X Server runs these protocols, the user can’t tell that the shared files are on a Mac. To Windows clients, SMB share points hosted by Lion Server behave just as they do on a Windows server.
web-Based Distributed Authoring and Versioning (webDAV): Lion Server uses webDAV for file sharing with iPads running Apple’s Pages and Numbers word-processing and spreadsheet programs, and in Apple’s Keynote presentation software for iPad. It’s possible that developers of other iPad apps could also make use of webDAV as time goes on. webDAV is based on the Hypertext Transfer Protocol (HTTP) used for the web.
Network File System (NFS): Lion Server has the ability to use NFS to host home directories, typically for Linux and Unix clients. However, you won’t see anything about NFS in any of the administration tools. That’s because Apple removed NFS from Server Admin and didn’t include it in the Server app.
Apple did, however, retain the actual server software. Lion Server uses NFS, behind the scenes, with the Podcast Producer and NetBoot services. If you know Unix commands, you can configure NFS with Terminal, share files, and create NFS home folders. For more information, see Apple’s Mac OS X Command Line Administration.
File Transfer Protocol (FTP): As with NFS, Apple removed the graphics user interface for FTP that was present in previous versions of Mac OS X Server. In Lion Server, FTP is available only through the command line. Unlike NFS, none of Lion Server’s services uses FTP.
FTP is a different animal from AFP, SMB, and NFS. FTP volumes don’t mount on a user’s machine, and you can’t open a document while it resides on an FTP server. A benefit of FTP is that any computer operating system can download files from an FTP server with a web browser. FTP is often used to serve files across the Internet, but it isn’t secure.
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Source:http://www.dummies.com/how-to/content/lion-server-filesharing-protocols-101.html
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