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When creating a new NTFS partition one is asked to choose a cluster size. The default size is 4k but one can choose a smaller sizes, too. 512 bytes is the smallest.

The smaller size leads to wasted space reduction. Each file occupies 1 or more clusters depending on file size. If the file size can be divided by the cluster size then no space is wasted by default. Otherwise only some part of the last cluster will store file data and remaining space will be wasted. On average it's about half of the cluster size per file. Considering that a typical partition stores tens of thousands of files 265 vs. 2k per file sounds like a big deal for me.

I always choose 512 bytes to reduce the amount of wasted space but I believe that there might be some negative effects of using smaller clusters. Otherwise 512 bytes would be used by default. What are those drawbacks?

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up vote 2 down vote accepted

Smaller cluser size means that a file will be distributed between more clusters (obvious). This means potentially more fragmentation and possibly more lookups to find the clusters. It is the usual speed vs size optimisation. As the hard disks are cheap, I would go for larger cluster sizes, but anyway, you will probably not see that much difference ...

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An additional point to this is that NTFS only has so much room for the directory data reserved. With 512 clusters versus 4k, you may wind up needing 8 times the records to track larger files that grow in small increments. When working with 1TB and larger disks and growing files (logs, DBs), you can exhaust that resource and wind up not being able to create new files! I've had to reformat a 4TB partition since regular defraggers can't fix NTFS meta-data issues. – Mark Jun 12 '15 at 18:03

NTFS is extent based (like xfs, ext4 and more on the *nix side) so the slowdown you get from non-extent based filesystems (eg fat, ext3) is reduced.

There's still an overhead though, and where it starts to hurt is fragmentation. Windows is HORRIBLE about fragmentation, try running defraggler to see how even sequentially written files (eg from program installation) can end up in 30+ fragments.

I'd generally suggest 4k as a good size, although if a drive is to be used for large media files 64k or larger can help.

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One reason to go for a 512 byte sector size is if you are planning to use Microsoft Windows Backup on a server. Amazingly if you use Windows 2008 (I do not know whether this has been fixed in Windows 2012 or later versions) but the backup will fail if you use the default 4k sector size on an off-the-shelf usb external hard drive! I recently purchased a new Seagate drive after speaking with Seagate's tech support to confirm that this was possible and I could reformat the 4k sector size back to 512 bytes and my backup worked. It is strange that neither Seagate's nor Microsoft's support website point this out.

The earlier external drives do not allow you to reformat the drive with a sector size of 512 bytes; the minimum is 4k.

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This is a reason why they should use 512 but not a reason why they shouldn't. It isn't an answer to the question, but just part of the discussion. It might be better to write this as a comment to the question rather than clutter the answer section with non-answers. – Mark Jun 12 '15 at 17:57

I wouldn't change from the default cluster size, unless you really know what you are doing.

Yes, smaller cluster sizes do mean less slack space and thus less wasted space. However, smaller cluster sizes also mean that less data is being transferred from the disk in each read operation and thus you may get a drop in read performance. It is also likely that there will be less fragmentation with a larger cluster size, as the data is more likely to be stored either in one cluster, or contiguously.

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