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How to best partition USB sticks and SD cards?

The article in a nutshell:
On weakly-managed flash-based storage (i.e. with direct addressing of the flash cells) you have to take extra care when setting up the filesystem to take into account the physical layout of the flash cells.
The key is here first and foremost to have your logical block device ("partition") aligned with the physical blocks, and to offset the FS metadata in such a way, that it will not cause mis-alignment on the FS level. You can also occasionally tune the FS to be more aware of certain flash-caused limitations, such as setting a minimum block size that is close to an erase-block, or even by using a flash-specific FS which implements wear leveling in software.

On the other hand, it doesn't matter much, when you're not writing to the disk very often, i.e. the OS disk for a NAS box would not benefit significantly from jumping through those hoops, if you're only installing critical updates.
 
TLDNR:

When your USB/SD flash storage is new, immediately identify it's partition offset and file cluster size. Partition offset can be read using msinfo32 or AS SSD Benchmark. File cluster size can be seen when running chkdsk. Whenever you delete partitions, clear the file table, or reformat use the same partition offset and file cluster size.

HOWEVER:

I have benchmarked performance for different file clusters and partition offsets. Read performance is unaffected. Write performance was only a concern for very few when Window's write cache is turned off for the device.

SD cards/USB are so cheap. 32GB for $8 is a typical holiday blowout sale. I wouldn't worry about it. In fact for most SD cards being used in smartphones/digital cameras, I recommend using the device to format the card.
 
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