All data eventually gets stored on some kind of block device. NAS servers use block devices to store their data. Both file level and block level operations are used. That is the reason I've analyzed storage networks as being composed of wiring, storing and filing functions.
- Data tends to be managed at the filing level
- Storage trends to be managed at the storing level
- Networks and buses are managed at the wiring level
There are differences between file access and block access - what is instantiated in products as NAS and SAN. The vendors there can make their claims for superiority. Data structure can be a key element. Network Appliance has built their business around the WAFL (write anywhere file layout) file system. I would agree with them and tell you that data structure makes a big difference for their product.
As to the question about data structure on block devices, the data structure is determined primarily by the file system (but not entirely, storage devices have their say in the matter). The type of data you have maps more effectively to a block-size for the FS. Often it makes a big difference what the block size is.
Microsoft will tell you there are huge advantages to using NTFS over FAT data structures. These differences have little to do with block sizes and much more to do with the disk layout.
Yes, data structures matter a great deal.
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