Event will highlight DiaGrid hub's ability to make research computing easier, faster
September 9, 2013
Purdue Professors Bruce Hamaker and Osvaldo Campanella are exploring ideas for using natural starch and protein molecules as delivery vehicles with potential uses ranging from making more tasty gluten-free bread to making chemotherapy easier on patients.
The molecular dynamics simulations the research involves present a challenge, however. The simulations track movements and interactions of numerous molecular particles over significant time scales. On lab computers, one simulation of small molecules forming complexes with amylose, a starch component, required 10 days just to simulate a 2- to 10-nanosecond period.
Enter DiaGrid, a computing system operated by ITaP Research Computing (RCAC) and open for use by Purdue researchers from any field and their students. DiaGrid can make thousands of processors available for tasks able to take advantage of a large processor pool, including Monte Carlo simulations and parameter sweeps.
DiaGrid also offers a growing array of Software as a Service (SaaS) tools — all available at no cost to Purdue users — on the DiaGrid hub Web portal at diagrid.org. ITaP staff will host a DiaGrid informational seminar from 1 to 2 p.m. Tuesday, Sept. 24, in Stewart Center, Room 311.
The seminar will offer an overview of DiaGrid and an introduction to the software tools on the hub. Coffee, tea and cookies will be available. To register, go to: https://diagrid.org/explore/events/details/11. For more information email: firstname.lastname@example.org.
With adequate computing power, including DiaGrid, Hamaker, a Purdue food scientist and director of the Whistler Center for Carbohydrate Research, and Campanella, a Purdue agricultural and biological engineering professor, have been able to run simulations capturing hundreds of nanoseconds — along with details that wouldn’t have shown up in shorter runs.
“It changes the way that I am thinking about these kinds of projects,” Hamaker says.
The DiaGrid hub currently offers BLASTer, a version of the popular bioinformatics tool BLAST; SubmitR, for the R statistical computing environment; Gromacs, a molecular dynamics simulator; and SWATShare, incorporating the Soil and Water Assessment Tool and input model sharing.
A Single Particle Cryo-EM 3-D Reconstruction tool for studying viruses, protein complexes and nanoparticles also is on the hub. ITaP partnered with biology Professor Wen Jiang to make the application available online.
Also in the works are a Community Earth System Model (CESM) tool for global climate modeling, and iData, a tool for managing and publishing spreadsheets, files and geospatial vector and image data.
Whatever the tool, the idea is the same: put a graphical front end on research software traditionally run by typing command lines, with the power of DiaGrid and its thousands of processors on the back end. That combination makes it easier and faster for Purdue researchers to get results, says Carol Song, the senior research scientist who leads the Scientific Solutions Group for ITaP Research Computing (RCAC).
The DiaGrid hub is built on Purdue’s HUBzero platform, hubzero.org. Developed by ITaP, HUBzero is designed to make high-level computational research software and access to high-performance and cloud computing about as easy as using a Web browser.