Many large-scale scientific simulations generate large, structured multi-dimensional datasets. Data is stored at various intervals on high performance I/O storage systems for checkpointing, post-processing, and visualization. Data storage is very I/O intensive and can dominate the overall running time of an application, depending on the characteristics of the I/O access pattern. Our NCIO benchmark determines how I/O characteristics greatly affect performance (up to 2 orders of magnitude) and provides scientific application developers with guidelines for improvement. In this paper, we examine the impact of various I/O parameters and methods when using the MPI-IO interface to store structured scientific data in an optimized parallel file system.