Towards Large-scale Genomics, Transcriptomics, and Metagenomics for All

Presenter(s): Philip Blood (PSC)

Principal Investigator(s): Noushin Ghaffari (Texas A&M) Ping Ma (U. Georgia) James Taylor (Johns Hopkins)

Presentation Slides

Although increasing numbers of researchers in genomics and related disciplines are utilizing advanced cyberinfrastructure for their work, these still represent a relatively small fraction of the biologists who could benefit from access to the latest genomics tools backed by large-scale computing resources. Rapid advances in these fields have caused an explosion of tools and algorithms that present a dizzying array of constantly changing options. Hence, even for scientists who are adept at using advanced computing infrastructure, it is challenging to determine the optimal mix of tools and employ these effectively to analyze large genomic data sets. In this talk I will highlight several XSEDE ECSS projects aimed at tackling aspects of these problems, both through formal ECSS collaborations and the "Novel and Innovative Projects" (NIP) arm of ECSS. These projects include the development of a pipeline for high-quality transcriptome analysis based on well-characterized RNA Sequencing Quality Control (SEQC) datasets, making memory-hungry sequence assembly tools available through the Galaxy XSEDE Gateway (usegalaxy.org), enabling large-scale analysis of human microbiome data, and facilitating the Critical Assessment of Metagenome Interpretation (CAMI: http://www.cami-challenge.org/).

Petascale DNS Using the Fast Poisson Solver PSH3D

Presenter(s): Darren Adams (NCSA)

Principal Investigator(s): Antonio Ferrante (U Wash)

Presentation Slides

Direct numerical simulation (DNS) of high Reynolds number (Re = O(105)) turbulent flows requires computational meshes of O(1012) grid points. Thus, DNS requires the use of petascale supercomputers. DNS often requires the solution of a Helmholtz (or Poisson) equation for pressure, which constitutes the bottleneck of the solver. We have developed and implemented a parallel solver of the Helmholtz equation in 3D called petascale Helmholtz 3D (PSH3D). The numerical method underlying PSH3D combines a parallel 2D Fast Fourier transform (P2DFFT) and a parallel linear solver (PLS). Our numerical results show that PSH3D scales up to at least 262,144 cores. PSH3D has a peak performance 6× faster than 3D FFT-based methods (e.g., P3DFFT) when used with the partial-global optimization. We have verified that the use of PSH3D with the partial-global optimization in our DNS solver does not reduce the accuracy of the numerical solution when tested for the Taylor-Green vortex flow.