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Nothing wrong with using aggressive limiting, we just need to get it to the point that it doesn't affect non-abusive image downloads and browsing of the site. As I've mentioned previously, for years I've only used a maximum of 1 connection per download (no multi-part), and a maximum of 3 (rarely 4) downloads globally. Pool zips I've never downloaded more than one at a time, even before you set the limits.

Even with this new adjusted limit, I'm still seeing intermittent problems attempting to load pages with Firefox 11 (no error). The server appears to occasionally throttle page loading to an extent that the site takes 2-4 minutes to fully load, or just time-outs. I just woke up so I haven't had a chance to test other aspects of your recent limit adjustment, but since these limits still seem to be occasionally breaking normal browsing of the site with Firefox 11, something must not be configured correctly.

Something still looks a bit strange with your Munin graphs. Ever since your RAID scrub completed, CPU usage dropped significantly compared to before the scrub, inode table use increased, and there appear to be daily spikes of 300Mbps & 100% disk utilization for a couple hours daily.