The built-in collaboration features of SharePoint Server 2013 (such as check out, check in, versioning, publishing , single instance storage, expiration information policies, multiple users editing the same file at the same time, metadata based search and so on) is alluring enterprises to move their fileshares to SharePoint document libraries. But file storage is not the same thing as file collaboration and there are multiple scenarios as below where File Servers are the better storage option.
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Any edit of a file needs marginally more space than earlier versions in SharePoint 2013 whereas on the NTFS file system, the space required is the same as the file size. So document storage in SharePoint is more expensive than an NTFS file system. Also costlier SharePoint licenses will be required when maximum content databases is crossed. The maximum number of content databases per farm is 500. With 200 GB in 500 content databases the content that can be stored per farm is approximately 100 TB. This theoretical size is not only for documents but also for versioning, auditing, recycle bins and other SharePoint objects. Details on SharePoint 2013 software boundaries in various scenarios can be found here.
Of course maintaining such a loaded SharePoint Farm will be a nightmare.
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For large document storage (documents over 2 GB) File Servers are preferred. SharePoint best handles documents in the 50-300 MB range. It can handle documents up to 2 GB with configuration changes but that will be a burden on SharePoint and hence performance will be affected.
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There is no hard limit for depth of nested folders in the file shares whereas the recommended total length of a URL in SharePoint is 260 characters. The URL in SharePoint means: URL = protocol + server name + folder or file path + folder or file name+ parameters Internet Explorer URL limitations also need to be kept in mind. Exact limitations can be found here.
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There is a limit in SharePoint for synchronising team sites and personal sites locally. For team sites the limit is 5000 items and for personal sites the limit is 20000 in one library.
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Documents can be secured easily in file shares. Content owners need to know how to secure their documents in SharePoint. The site administrators and site collection administrators need to be monitored.
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Files such as source control of assemblies and code files are better managed in source configuration systems that require a file server.
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Other files such as database files, Outlook files and so on, that do not require SharePoint features, are best stored on a File Server.
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Archive files that will not to be changed in the foreseeable future are best stored on a file server. If there is no collaboration expected on these files and just for applying policies for expiration purposes then SharePoint 2013 will prove costlier than File Servers.
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Systems Management Service (SMS) distribution points for hot fixes, updates and application distribution for files and folders is handled much better from a file server.
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For nightly backup of file shares, group policies can be applied on File Servers. In SharePoint, backup can be done at a granular level, but there is no concept on policy-based backup.
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If files need to be retained for a longer period of time, let's say 7 to 10 years then the NTFS file system is a cheaper option since newer versions of SharePoint will mean migration expenses for the enterprise.
So a blind migration of Files Servers should not be done to be replaced with SharePoint, unless there is a strong business need for a document management system.