R. Latham, C. Daley, W.-K. Liao, K. Gao, R. Ross, A. Dubey, and A. Choudhary, "A Case Study for Scientific I/O: Improving the FLASH Astrophysics Code," A case study for scientific I/O: improving the FLASH astrophysics code, vol. 5, Computational Science & Discovery, 2011, . Also Preprint ANL/MCS-P1819-0111, January 2011. [pdf]
The FLASH code is a computational science tool for simulating and studying thermonuclear reactions. The program periodically outputs large checkpoint files (to resume a calculation from a particular point in time) and smaller plot files (for visualization and analysis). Initial experiments on BlueGene/P spent excessive time in I/O, making it difficult to do actual science. Our investigation of time spent in I/O revealed several locations in the I/O software stack where we could make improvements. Fixing data corruption in the MPI-IO library allowed us to use collective I/O, yielding an order of magnitude improvement. Restructuring the data layout provided a more efficient I/O access pattern and yielded another doubling of performance, but broke format assumptions made by other tools in the application workflow. Using new nonblocking APIs in the Parallel-NetCDF library allowed us to keep high performance and maintain backward compatibility. While these optimizations required a detailed understanding of both the FLASH application and the I/O system software, this work demonstrates how collaboration between application and computer science groups can magnify each others efforts.