Robin Harris of Storagemojo pointed to an interesting article about about deduplication and it's impact to the resiliency of your data against data corruption on ACM Queue.

The problem in short: A considerable number of filesystems store important metadata at multiple locations. For example the ZFS rootblock is copied to three locations. Other filesystems have similar provisions to protect their metadata. However you can easily proof, that the rootblock pointer in the uberblock of ZFS for example is pointing to blocks with absolutely equal content in all three locatition (with zdb -uu and zdb -r). It has to be that way, because they are protected by the same checksum. A number of devices offer block level dedup, either as an option or as part of their inner workings. However when you store three identical blocks on them and the devices does block level dedup internally, the device may just deduplicated your redundant metadata to a block stored just once that is stored on the non-voilatile storage. When this block is corrupted, you have essentially three corrupted copies. Three hit with one bullet.

This is indeed an interesting problem: A device doing deduplication doesn't know if a block is important or just a datablock. This is the reason why I like deduplication like it's done in ZFS. It's an integrated part and so important parts don't get deduplicated away. A disk accessed by a block level interface doesn't know anything about the importance of a block. A metadata block is nothing different to it's inner mechanism than a normal data block because there is no way to tell that this is important and that those redundancies aren't allowed to fall prey to some clever deduplication mechanism.

Robin talks about this in regard of the Sandforce disk controllers who use a kind of dedup to reduce some of the nasty effects of writing data to flash, but the problem is much broader. However this is relevant whenever you are using a device with block level deduplication. It's just the point that you have to activate it for most implementation by command, whereas certain devices do this by default or by design and you don't know about it. However I'm not perfectly sure about that ? given that storage administration and server administration are often different groups with different business objectives I would ask your storage guys if they have activated dedup without telling somebody elase on their boxes in order to speak less often with the storage sales rep.

The problem is even more interesting with ZFS. You may use ditto blocks to protect important data to store multiple copies of data in the pool to increase redundancy, even when your pool just consists out of one disk or just a striped set of disk. However when your device is doing dedup internally it may remove your redundancy before it hits the nonvolatile storage. You've won nothing. Just spend your disk quota on the the LUNs in the SAN and you make your disk admin happy because of the good dedup ratio However you can just fall in this specific "deduped ditto block"trap when your pool just consists out of a single device, because ZFS writes ditto blocks on different disks, when there is more than just one disk. Yet another reason why you should spend some extra-thought when putting your zpool on a single LUN, especially when the LUN is sliced and dices out of a large heap of storage devices by a storage controller.

However I have one problem with the articles and their specific mention of ZFS: You can just hit by this problem when you are using the deduplicating device for the pool. However in the specifically mentioned case of SSD this isn't the usecase. Most implementations of SSD in conjunction with ZFS are hybrid storage pools and so rotating rust disk is used as pool and SSD are used as L2ARC/sZIL. And there it simply doesn't matter: When you really have to resort to the sZIL (your system went down, it doesn't matter of one block or several blocks are corrupt, you have to fail back to the last known good transaction group the device. On the other side, when a block in L2ARC is corrupt, you simply read it from the pool and in HSP implementations this is the already mentioned rust.

In conjunction with ZFS this is more interesting when using a storage array, that is capable to do dedup and where you use LUNs for your pool. However as mentioned before, on those devices it's a user made decision to do so, and so it's less probable that you deduplicating your redundancies.

Other filesystems lacking acapability similar to hybrid storage pools are more "haunted" by this problem of SSD using dedup-like mechanisms internally, because those filesystem really store the data on the the SSD instead of using it just as accelerating devices.

However at the end Robin is correct: It's jet another point why protecting your data by creating redundancies by dispersing it several disks (by mirror or parity RAIDs) is really important. No dedup mechanism inside a device can dedup away your redundancy when you write it to a totally different and indepenent device.