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==Permissions & Access Control Issues==
===SPARQL SELECT COUNT(*) queries are slow===

Counting is inherently slow. Even more so when you need to read the stuff you 
count from disk. If you need faster disk access I recommend using more 
disks and spread them on different SATA buses (if you've SATA disk) and 
tell Virtuoso to use stripes. This way you'll have more Disk I/O 
bandwidth and parallelization.