How to store big amount files to disk?



I'd like to save 1 000 000 files to disk.
What is better:

A. To save all files (one milion) in same directory.

B. To create 1000 directories and in each of them then save 1000 files. (1000 x 1000 = 1 000 000)

Is B soluton better regarding performance?
Is there any better solution?
Where is the limit how much files can contain single folder?


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