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I've used rsync to copy an entire hard disk from one to another which was just newly formatted. It's about 640GB of data, but the destination hard drive has 750MB more that shows up under the 'df' output of Used. How can this be? The source is ext4 and the destination is ext3, would that make a difference? Thanks!

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df counts the used space in a file system as the number of free inodes multiplied by the default inode size. If the two file systems have different inode sizes, then the number of bytes wasted by not filling up the last inode used by each file will almost certainly be different. (There are other differences between different instances of filesystems, for instance the number of blocks reserved for the super user in case of space emergency, but this one is the most probable culprit.)

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