It must be the disk</sarcasm>
Seriously though, we have had some major throughput problems with out deduplication setup.
To begin with we had a primary deduplicated copy via two MediaAgents (each with 2 x 3GHz Intel and 8GB RAM) to two separate Sun 6140 SAN sporting around 45TB total. We then ran into problems auxiliary copying data to tape, with ridiculous speeds between 30 to 60GB/hr in some cases.
After enough cries from support about hardware not being up to spec, I replaced the lot. The CS is now a dual X5660 Nehalem, with a 4 spindle SAS2 RAID10 for database, and a 4 spindle SAS2 RAID10 for the index cache too. The DDB manager is a dedicated dual X5660, with 24GB of RAM, and 2 x 4 spindle SAS2 RAID0 for the DDB's. The datamovers are still Dell PE2900's with dual 3.0GHz Intel CPU's, each sporting 4 x 4GB FC HBA's, two dedicated to tape library, two for magnetic.
At some point (forgive me, this is all a bit blurry!) we decided to try a secondary magnetic copy. We put in a dual X5660 with 24GB of RAM and 114TB of raw direct attached near line SAS (over 4 trays with SAS2 controllers). Copy performance isn't much (or any?) better on that either. No disk queue, low atime during auxiliary copy, but CV takes 2 minutes to read a chunk (or so I'm told..)
So, six months (or more) down the track, we're back to "It must be the disk"... And V9 will be much less read intensive...
Frustrating to say the least.