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SC17 Preview: Molecular Simulation at the Mesoscale

SC17 will continue its HPC Matters Plenary session series this year a talk on Molecular Simulation at the Mesoscale. “We are developing new capabilities for multi-scale dynamic simulations that cross spatial scales from the molecular (angstrom) to cellular ultrastructure (near micron), and temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of organelles and cells (milliseconds to seconds).”

HPC Connects: The Search for Elusive Proteins that perform Gene Editing

In this video from the SC17 HPC Connects series, David Paez-Espino from the Joint Genome Institute describes how researchers are using supercomputing to search for elusive proteins that perform gene editing. “This revolutionary work requires petaflops of computing power to sift through billions of DNA sequences in the JGI data portals to identify proteins like Cas9 that, combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), can “edit” a genome.”

Podcast: Optimizing Cosmos Code on Intel Xeon Phi

In this TACC podcast, Cosmos code developer Chris Fragile joins host Jorge Salazar for a discussion on how researchers are using supercomputers to simulate the inner workings of Black holes. “For this simulation, the manycore architecture of KNL presents new challenges for researchers trying to get the best compute performance. This is a computer chip that has lots of cores compared to some of the other chips one might have interacted with on other systems,” McDougall explained. “More attention needs to be paid to the design of software to run effectively on those types of chips.”

Visualizing with Software Rendering with Intel Xeon Phi

There are two main categories or uses where rendering on the Intel Xeon Phi processors should be investigated. The first is what could be called “Professional rendering” and the second, “Scientific visualization.” “Software based visualization, whether for photo-realistic rendering or scientific visualization can be accelerated with a software only approach. This allows for new algorithms to be implemented faster than waiting for the next generation of hardware systems to appear. As the number of computing elements increases, performance can increase as well.”

SC17 Session Preview: “Taking the Nanoscale to the Exascale”

Brian Ban continues his series of SC17 Session Previews with a look at an invited talk on nanotechnology. “This talk will focus on the challenges that computational chemistry faces in taking the equations that model the very small (molecules and the reactions they undergo) to efficient and scalable implementations on the very large computers of today and tomorrow.”

Video: Evolution of MATLAB

Cleve Moler from MathWorks gave this talk at the 2017 Argonne Training Program on Extreme-Scale Computing. “MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. Typical uses include: Data analysis, exploration, and visualization.”

Searching for Human Brain Memory Molecules with the Piz Daint Supercomputer

Scientists at the University of Basel are using the Piz Daint supercomputer at CSCS to discover interrelationships in the human genome that might simplify the search for “memory molecules” and eventually lead to more effective medical treatment for people with diseases that are accompanied by memory disturbance. “Until now, searching for genes related to memory capacity has been comparable to seeking out the proverbial needle in a haystack.”

HPC Connects: Mapping Global Ocean Currents

In this video from the SC17 HPC Connects series, Dimitris Menemenlis from NASA JPL/Caltech describes how supercomputing enables scientists to accurately map global ocean currents. The ocean is vast and there are still a lot of unknowns. We still can’t represent all the conditions and are pushing the boundaries of current supercomputer power,” said Menemenlis. “This is an exciting time to be an oceanographer who can use satellite observations and numerical simulations to push our understanding of ocean circulation forward.”

Visualization in Software using Intel Xeon Phi processors

“Intel has been at the forefront of working with software partners to develop solutions for visualization of data that will scale in the future as many core systems such as the Intel Xeon Phi processor scale. The Intel Xeon Phi processor is extremely capable of producing visualizations that allow scientists and engineers to interactively view massive amounts of data.”

How Manufacturing will Leap Forward with Exascale Computing

In this special guest feature, Jeremy Thomas from Lawrence Livermore National Lab writes that exascale computing will be a vital boost to the U.S. manufacturing industry. “This is much bigger than any one company or any one industry. If you consider any industry, exascale is truly going to have a sizeable impact, and if a country like ours is going to be a leader in industrial design, engineering and manufacturing, we need exascale to keep the innovation edge.”