2016 Presentations

Jan 27, 2016

Title: High performance computing and molecular simulations for designing materials for biomedical and energy applications (Jayaraman Research Group)

Location: Faculty Commons (116 Pearson Hall)

Time: 10 a.m. to noon

Post-presentation materials:

Prof. Arthi Jayaraman and her research group members will present an overview of how they use high performance computing and molecular simulations to design polymers used in materials tailored for energy applications (e.g. solar cells), commonly used nanocomposites (e.g. tires), and biomedical applications (e.g. DNA delivery for therapy). They will present how each of the three representative projects the group has worked on have different supercomputing needs. They will also briefly go over their use of GPU computing, particularly in their work on polymer nanocomposites.

Presenters: Prof. Arthi Jayaraman, Mr. Tyler Martin, 5th year graduate student, and Dr. Ahmad Ghobadi and Dr. Francesca Stanzione, both postdoctoral researchers.

Feb 24, 2016

Title: UD-IT HPC Team

Location: Faculty Commons (116 Pearson Hall)

Time: 10 a.m. to noon

The IT HPC team plans to lead discussions on the following topics:

  • Mills end-of-life policy, including how jobs will be affected by the implementation of the spillover queue starting Mon, Feb. 29;
  • benchmarking jobs;
  • specifying resources such as memory, standby and exclusive; and
  • Lustre

Those interested can request other topics to be added to the agenda when registering.

This symposium session is intended to be a working session. Researchers should bring their laptops to work with IT HPC staff to resolve issues or discuss other topics.

For more information about this symposium see “Mills: Job Scheduling Change”, “Benchmarking jobs: Computational models for running Matlab on a shared cluster“, “Getting started with Farber” and the blog post.

Jun 8, 2016

Title: Quantifying dynamic, complex social communication in freely interacting mice

Location: Faculty Commons (116 Pearson Hall)

Time: 10 a.m. to noon

Post-presentation materials:

In the animal kingdom, innate social behaviors play a crucial role in survival and reproduction. For mice, these complex and dynamic behaviors are accompanied by ultrasonic vocalizations.  Although recent work has shown that male and female mice vocally interact during courtship, the role these auditory sensory signals play in shaping social behavior remains a mystery. To elucidate the impact communication has on the development of mouse social behavior, our lab simultaneously records audio and video data of freely socializing mice for extended periods of time. The data in each of these recordings can exceed half-a-terabyte, which makes manually finding social information unfeasible; therefore, our lab has created a high throughput data analysis pipeline that rapidly extracts information crucial for quantifying social interactions. I will describe the tools we need to interpret social behavior and how we setup our data analysis pipeline on the University of Delaware’s high performance computer cluster (Farber).  Finally, I will reveal some of our lab’s preliminary results that emerged from our data analysis pipeline, which lays the groundwork for a mechanistic dissection of communication during social behavior.

Presenters: The Neunuebel Neuroscience Lab (Neural Basis of Social Behavior)

Sep 28, 2016

Title: Using parallel programming models for migrating legacy code to today’s platforms

Location: Faculty Commons (116 Pearson Hall)

Time: 10 a.m. to noon

Post-Presentation Materials:

Prof. Chandrasekaran and her research group will present an overview of how they are using parallel programming models such as OpenMP and OpenACC to migrate legacy scientific code to HPC platforms. They will present on how the computing challenges differ from application to application and what are the tools and techniques used to gather profiling and performance data of applications. They will also discuss some of the recent results gathered on using NVIDIA K80 GPU using an emerging programming model, OpenACC.

Presenters: Prof. Sunita Chandrasekaran, Sergio Pino (third year graduate student) and Collin Clark (undergraduate student).


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