Friday, August 19, 2016

Summer REU Projects in Data Intensive Scientific Computing

We recently wrapped up the first edition of the summer REU in Data Intensive Scientific Computing at the University of Notre Dame.  Ten undergraduate students came to ND from around the country and worked on projects encompassing physics, astronomy, bioinformatics, network sciences, molecular dynamics, and data visualization with faculty at Notre Dame.

To learn more, see these videos and posters produced by the students:


Wednesday, August 10, 2016

Simulation of HP24stab with AWE and Work Queue

The villin headpiece subdomain "HP24stab" is a recently discovered 24-residue stable supersecondary structure that consists of two helices joined by a turn. Simulating 1μs of motion for HP24stab can take days or weeks depending on the available hardware, and folding events take place on a scale of hundreds of nanoseconds to microseconds.  Using the Accelerated Weighted Ensemble (AWE), a total of 19us of trajectory data were simulated over the course of two months using the OpenMM simulation package. These trajectories were then clustered and sampled to create an AWE system of 1000 states and 10 models per state. A Work Queue master dispatched 10,000 simulations to a peak of 1000 connected 4-core workers, for a total of 250ns of concurrent simulation time and 2.5μs per AWE iteration. As of August 8, 2016, the system has run continuously for 18 days and completed 71 iterations, for a total of 177.5μs of simulation time. The data gathered from these simulations will be used to report the mean first passage time, or average time to fold, for HP24stab, as well as the major folding pathways.  - Jeff Kinnison and Jesús Izaguirre, University of Notre Dame

ND Leads DOE Grant on Virtual Clusters for Scientific Computing

Prof. Douglas Thain is leading a new $2.2M DOE-funded project titled "VC3: Virtual Clusters for Community Computation" in an effort to make our national supercomputing facilities more effective for collaborative scientific computing.  The project team brings together researchers from the University of Notre Dame, the University of Chicago, and Brookhaven National Lab.

Our current NSF and DOE supercomputers are very powerful, but they each have different operating systems and software configurations, which makes it difficult and time consuming for new users to deploy their codes and share results.  The new service will create virtual clusters on the existing machines that have the custom software and other services needed to easily run advanced scientific codes from fields such as high energy physics, bioinformatics, and astrophysics.  If successful, users of this service will be able to easily move applications between university and national supercomputing facilities.