Hi, I'm the administrator the bioinformatics laboratory at Université du Québec à Montréal. I have a room filled with dual P4 3GHz workstations. The boxen are dual booted with Windows and GNU/Linux but they spend most of their time on GNU/Linux. Each box have 2Gb of RAM so I expected decent performance with local BLAST jobs but the sad truth is that my jobs are run about 4 times slower with blast2 than with blastcl3 with the same parameters. The hard drive is IDE so I suspect a bottle neck here. Strangely if I set the number of threads to 2 or 3 with -a my jobs run slower. Do you think there is a way to like those machines together in order to get better performance ? I think that I can't use something like mpiBlast because there is always a risk that a node be rebooted under windows making a part of the database suddenly unavailable. -- Yannick Gingras