Hi Everyone: We have a 16-node Xserve cluster, with 2GB memory on each node and dual processors. I was able to install mpiBLAST on it, along with LAM/MPI. However, the performance that I saw with some test runs has not been that good and quite confusing. Here is what I did: 1.) I formatted the nt database: mpiformatdb -N 16 -i nt 2.) I ran the mpiblast on one, two, five, ten, twenty, and more sequences (about 500bp each) and with the command: time mpirun N mpiblast -p blastn -d nt -i single.fa -o blast_results. Here are the numbers: Single: 1m39.054s Two: 0m11.009s Five: 0m16.021s Ten: 0m46.591s twenty: 3m7.541s .. I am all confused. First of all, the performance is not that impressive. Secondly, the numbers are very confusing to me. Why is that a single sequence query takes so much more time than a two (BTW, I reran the query of a single sequence right after the query of two and got similar results)? And query of five takes only 5 seconds more than the query of two and so on.. I am afraid that I have done something wrong and would really appreciate any thoughts. Thanks Xiaowu