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I'm running Ubuntu 11.04 (Natty), with an i5 2500k (not overclocked) and a z68 board.

I'm trying to encode DVD quality VOB files to the iPhone preset in Handbrake, but in mkv format. I'm currently getting about 105 fps average and it takes me somewhere between 15 and 20 minutes to complete. This definitely isn't bad performance, but based on these reviews and benchmarks:

http://www.servethehome.com/Intel-core-i5-2500k-review-sandy-bridge-home-server/

http://www.legitreviews.com/article/1501/14/

I should be getting twice what I see. I tried duplicating their tests as closely as possible, the only exception may be that they're using Windows and I'm using Linux.

Both reviews are using Handbrake for their tests, as am I. Because Handbrake doesn't support QuickSync/GPU encoding, it's of no consequence that there is no QuickSync support in Linux.

Can anyone think of reasons why I'm see "degraded" performance?

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This is an easy answer. Both of those reviews you referenced are using SSD's. I'll bet that you don't have one of those. SSD's virtually eliminate latency (seek times), and have much faster READ / WRITE performance than standard hard drives, which is likely why those reviews appear so much faster than yours -- again, assuming you're using a traditional mechanical drive.

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You're right, I'm not using an SSD. Does that really make THAT much of a difference? Enough to give me < half the performance? My CPU cores are nearly maxed out during the encoding process. I would think that if they were starved for data because of HDD read speeds, they wouldn't be that busy. In lieu of buying an SSD just for encoding, would striping 3 hard drives give me better performance? Maybe not AS good as an SSD, but I already have a few spare hard drives I could use. –  Justin Miller Sep 13 '11 at 17:16
    
I don't think striping hard drives would make much of a difference. The main bottleneck is the latency (or "seek time"), which is the amount of time to find the bits of data to read from, or space to write to. It MIGHT help to increase the amount of RAM in your system. It would certainly help to get a smallish / cheap 64GB or so SSD that you could use as a "scratch disk" and copy the files you need to work on on that disk so encoding read / save operations occur only on the SSD. –  Joshua Sep 14 '11 at 14:34
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