Hi Zhiliang, Firstly, I suggest that you run mpiBlast with the default parameters, only use it with -p -i -d and -o. If the default parameter works fine, you should check the system environments: is there any memory limitation? write access? etc. If the default parameter can not work either, I think you should check: 1. How many segements did you format the database? Is the number 12? Make sure you run mpiBlast with two more processes. 2. Can every nodes read in the input sequences? 3. Check your ~/.ncbirc, make sure each node has ~/.ncbirc and each node can access the directorys written in ~/.ncbirc. Regards, XU Zhao