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the system currently have a directory with all the invalid files. how bad is it to move a single file to a directory containing 3 million files already?

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What are you doing with so many invalid files? – soandos Jul 25 '11 at 20:12
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Bad enough to relegate you to the 5 ring of hell. At least. – music2myear Jul 25 '11 at 20:14
What is the filesystem format for that volume? ReiserFS? ext? umsdos? … – JdeBP Jul 26 '11 at 12:39

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It would depend upon the filesystem, but probably pretty bad. Few filesystems are designed to handle folders of that size.

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which filesystem do you suggest for such operations? – Tusker Jul 28 '11 at 5:14
I'd recommend XFS myself, but in any filesystem what you're trying to do is going to be a nightmare. This might be of some help though. – Darth Android Jul 28 '11 at 14:12
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If dir_index is enabled for the filesystem, not too bad. Otherwise, look out. In either case, reading from that directory will be painful regardless.

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Is it enabled for mac os hfs? How to enable that? – Tusker Jul 28 '11 at 5:15
It does not exist for HFS/HFS+; it is found on ext3/ext4. – Ignacio Vazquez-Abrams Jul 28 '11 at 7:02

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