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They're simply hardlinks so the files shouldn't actually even be deleted.

What options do I have? It even seems to take quite some load. I don't see how deleting 30.000 hard-links should take more than a minute, let alone a full hour.

I use rsnapshot, centos and an ext3 file system.

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I am also a rsnapshot user and deletes can take a looong time. – cstamas Jun 19 '11 at 17:28
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It may be that the dir_index feature is not enabled for the filesystem. Using debugfs will allow you to verify if enabled and set it if not.

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tune2fs may be a more appropriate tool for end-users than debugfs. – Steven Monday Jun 19 '11 at 17:54
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In order to delete all those files it must traverse the directory tree, and go down into the whole lot, deleting each files & directory one by one. This can take a while.

Sometimes the choice of filesystem can matter. Some filesystems can take a long time to delete lots of little files, some are good at this.

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