Three key factors exert big influence upon the application′s I/O performance, including the I/O programming interface, the performance characteristic of I/O sub-system( both architecture and system software), and the I/O configuration parameters at user-level. From the user′s perspective, this paper discussed the user-level parallel I/O configuration optimize space toward large scale cluster. Besides, we proposed a method of testing and analyzing the I/O characteristic of large scale cluster. Based on this method, the I/O performance portrait of a domestic super computer was built up and several user-level parallel I/O optimize suggestions were put forward. With these carefully selected I/O configuration parameters, the time of restart data write operation was cut down by 15 percent under 8192 processes in a real application environment, while the program′s initial time is shortened from 10 minutes to 5 seconds at the scale of 4096 processes.