Ok, I have a 1 TB 7200 rpm system drive and two 1.5 TB 5400 rpm storage drives(all samsung drives). About a week after my fresh ubuntu install, I noticed that file transfers to my two 5400 rpm drives were getting slower and slower. Reads were fine, but whenever I had to write to the drive (however small) the whole system would slow down, or lock up, and the transfers would eventually slow to close to 3 MB/s. I expected them to be slower than the 7200 rpm drive, but not that bad.

Initially I focused the brunt of my anger at the drives themselves, but after looking, I couldn't find any reference online to these drives behaving that slowly(they have universally stellar reviews, part of the reason I went with them), so I started to dig a little bit deeper.

I swapped drive locations, sata cables, power cables, and I was even exploring the possibility of a different distribution, but in the end, the problem was in the bios.

The sata mode of the drives was set to "Auto" which should under normal circumstances work just fine, but apparently linux kernel 2.6 will default to the slowest allowed mode on all non system drives. This is obviously a problem, so I just told it the only mode available was UDMA 6 (newest/fastest mode). This may not work on all drives, so you may need to try UDMA 5 first, but my drives are all brand new so it was a pretty safe bet that it would work just fine.

Now writes to the 5400 rpm drives are 60 + MB/s, and to the 7200 rpm drive it's 85 + MB/s. all is well.

To make it even better, I have found that writes to a buddy's USB hdd was hovering around 50 MB/s which is the fastest that I have ever seen from a drive running on USB. Mind you it slowed down considerably with multiple reads/writes going on at the same time. Still though, fairly impressive.