Bumped my server up to a 4 cpu machine. Very rewarding to see BLAST running significantly faster. But for a complex BLAST job, sometimes the longest part of the job is waiting for SequenceServer to process the results! I’ve watched TOP and verified that SequenceServer only runs on one CPU - and it can often take 10 minutes to process a very complex job. Is there any way I can make SequenceServer support multiple processors?
Right, for complex searches formatting the results can be the
bottleneck. I am sorry, you can't set an option to enable multi-core
usage for that yet. SS would have to change heavily to be able to
take advantage of multiple CPUs. I feel there is a room to improve
SS' performance without resorting to threads though, and they should be
explored first.
-- Priyam