The NCBI offers their web-based BLAST search service publicly, so they need to set priorities and limits. One limit they set is the amount of time any one job is allowed to run. Currently, this is about one hour of joint CPU time, as outlined on the NCBI website here:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#sigxcpu

If you see the error "CPU usage limit exceeded" when you run a BLAST search at the NCBI, you have exceeded this limit.

Limits and priority settings at the NCBI are not something that we control.