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Quickly deleting thousands of files

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I'm working with a backup system put in place by somebody else, and I'm having trouble removing old backups in a reasonable amount of time. Here's what they setup: - Connected a 2TB USB2 drive to a Windows 7 PC, formatted NTFS - use cygwin and rsync to connect to a linux server and pull down nearly the entire file system (/etc, /usr, /home) - rsync is configured to use the previous day's backup as a "link-dest" so new backups will be complete by only contain hard-links to existing, unmodified files instead of a completely new copy. - a new backup is created every day So eventually the 2TB drive filled up and stopped backing up. Now I have ~100 days of backups, each folder contains serval thousand hard-links in hundreds of folders. Trying to remove a backup folder normally takes hours (I never let it complete fully). Trying to use "rm -rvf" in cygwin at least gives me some feedback, but still takes about 10 hours per folder. Is there anything I'm missing to speeding this up? Is there a better way to store the backups in the future such that it won't take so long to delete them? Thanks! -- University of Southern California - Fight On!

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