ECSS experience with non-traditional HPC users

Presenter(s): Junqi Yin (NICS)

Principal Investigator(s): Annette Engel (U. Tenn) Yong Zeng (UMKC)

Mothur is an open source bioinformatics pipeline used for biological sequence analysis that has gained increasing attention in the microbial ecology community. Because a large set of functionalities in Mothur are memory bound, it is well suited for shared memory architectures. I will discuss performance results for several commands in Mothur that are popular in the operational taxonomic unit analysis, and show that pipeline processes can be accelerated by orders of magnitude faster.

Real-time Bayesian estimation for financial ultra-high frequency data is plagued with the curse of high dimensionality. Methods have been developed to manage this problem through the use of MPI. By porting to CUDA, I'll show that an adequately equipped GPU workstation can rise to the task, producing reasonably real-time results with actual data from financial markets.

P3DFFT: a scalable open-source solution for Fourier Transforms and other algorithms in three dimensions

Presenter(s): Dmitry Pekurovsky (SDSC)

P3DFFT is an open-source package developed at SDSC. It implements three-dimensional Fourier Transforms and other algorithms, in a highly scalable and efficient way. P3DFFT achieves good scaling on hundreds of thousands of compute cores. It has received much interest and use from scientists in diverse fields such as DNS turbulence simulations, astrophysics, oceanography and material science. Recently it has been the subject of an internal ECSS project, aimed at making it XSEDE community software. It has been ported, tested and documented on the largest computational systems at XSEDE. Additional features have been added to help widen the impact in the community. In this presentation I will go over the main features of P3DFFT, including the recently added, and review how users of XSEDE can access it on XSEDE platforms.