ECSS Symposium

June 18, 2013

Atomistic Characterization of Stable and Metastable Alumina Surfaces

Presenter: Sudhakar Pamidighantam, (NCSA)
Principal Investigator: Douglas Spearot, Co-pi: shawn Coleman (University of Arkansas)

[Presentation Slides]

This presentation is to describe work in progress for the extended collaborative support requested to assist the PIs, with (1) improving the parallel scalability of the virtual diffraction algorithm implemented as a "compute" in LAMMPS and (2) creating a workflow that automates the data transfer of the atomistic simulation results from TACC Stampede to SDSC Gordon in order to perform the virtual diffraction analysis and (3) visualization. Before the virtual diffraction algorithm is made publically available and incorporated into the main distribution of LAMMPS, the performance of the code must scale to larger atomic models. Currently the algorithm is memory-bound, likely due to the simple MPI parallelization used. Strategies and implementation of scaling methods in Compute will be described. Visualization using VisIT system with various configuration protocols is being implemented. Integration into GridChem science gateway and user interactions will be discussed. A plan for the workflow implementation will be presented. Sudhakar.

April 16, 2013

Data Analysis on Massive Online Game Logs

Presenter: Dora Cai (NCSA)

Principal Investigator: Marshall Scott Poole (UIUC)

Presentation Slides

This presentation will talk about the work with Professor Marshall Scott Poole entitled "Some Assembly Required: Using High Performance Computing to Understand the Emergence of Teams and Ecosystems of Teams". Massively Multiplayer Online Games (MMOGs) provide unique opportunities to investigate large social networks. This project is a multidisciplinary Social Sciences project dedicated to the study of communication-related behaviors using data from MMOGs. A twenty-person team of scholars from four universities is engaged in the study. The project has performed systematic studies on many research areas, such as social network analysis, gamer behavior studies, and virtual world simulation. The Gordon supercomputer has provided great support on this project. This talk will provide an overview of the project, describe my involvement as an ECSS consultant in this project, and present the recent progress on developing a tool to visualize the social networks in MMOGs

Development of Novel Quantum Chemical Molecular Dynamics for Materials Science Modeling

Presenter: Jacek Jakowski (NICS)

Co-Principal Investigators: Jacek Jakowski (NICS), Sophya Garashchuk, (U. of South Carolina), Steve Stuart (Clemson University), Predrag Krstic (University of Tennessee& ORNL), Stephan Irle (Nagoya University)

I will present my work on the project titled: "Modeling of nano-scale carbon and metalized carbon materials for the 'EPSCoR Desktop to TeraGrid EcoSystems project'". with CO-PI: Sophya Garashchuk, (U. of South Carolina), Steve Stuart (Clemson University), Predrag Krstic (University of Tennessee& ORNL), Stephan Irle (Nagoya University). This project contains several subprojects that focus on development and application of various molecular dynamics approaches to material science problems. I will particularly discuss development and parallelization of Bohmian dynamics for modeling quantum nuclear effects of selected nuclei. Implementation and scaling on Kraken at NICS and science problems illustration will be presented.

March 19, 2013

Visualization of Volcanic Eruption Simulations (CFDLib)

Presenter: Amit Chourasia (SDSC)

Principal Investigator: Darcy Ogden (SIO, UCSD)

Presentation Slides

Eruptive conduits feeding volcanic jets and plumes are connected to the atmosphere through volcanic vents that, depending on their size and 3D shape, can alter the dynamics and structure of these eruptions. The host rock comprising the vent, in turn, can collapse, fracture, and erode in response to the eruptive flow field. This project uses visualization to illustrate and analyze results from fully coupled numerical simulations of high speed, multiphase volcanic mixtures erupting through erodible, visco-plastic host rocks. This work explores the influence of different host rock rheologies and eruptive conditions on the development of simulated volcanic jets. The visualizations shows the dependence of lithic segregation in the plume on eruption pressure.

Using Hybrid MPI+OpenMP Approach to Improve the Scalability of a Phase-Field-Crystal Code

Presenter: Reuben Budiardja (NICS)

Principal Investigator: Katsuyo Thornton (University of Michigan)

Presentation Slides

Phase-Field-Crystal (PFC) model is a recent development in the computational modeling of nanostructured materials that addresses the challenges for understanding of complex processes in nanostructure growth and self-assembly. A PFC-based code requires good scalability and time-to-solution to perform calculations with sufficient resolutions on the dynamics of metals. In this talk we will describe the work in improving the scalability of a PFC code. At the heart of the code is the solving of multiple indefinite Helmholtz equations. We will discuss the hybrid OpenMP + MPI approach to improve the time-to-solution by exploiting different parallelisms that exist in the code.

February 19, 2013

I/O Analysis for the Community Multiscale Air Quality (CMAQ) Simulation

Presenter: Kwai Wong (University of tennessee)

Principal Investigator: Joshua Fu (University of Tennessee)

Presentation Slides

The Community Multiscale Air Quality (CMAQ) Model is commonly used by many researches to simulate ozone, particulate matter (PM), toxics, visibility, and acidic and nutrient pollutant? throughout the troposphere. The scale of the model ranges from urban (few km) to regional (hundreds of kilometers) to inter-continental (thousands of kilometers) transport. Depending on the time and length scales of a simulation, the amount of IO will affect the overall performance of the simulation. In this presentation, we will examine the steps and results of the IO procedures used in the code.

Improving the performance and efficiency of an inverse stiffness mapping problem

Presenter: Carlos Rosales (TACC)

Principal Investigator: Lorraine Olson (Rose-Hulman Institute of Technology)

Presentation Slides

In this talk we will discuss the improvement to a legacy Fortran code used by the PI to investigate early stage breast cancer detection by using an inverse stiffness mapping approach. The talk will describe the basic methodology, the original naive attempts at improving its performance, and the computational trick used to substitute the original solver with a a more effective MUMPS and BLAS combination.

January 15, 2013

Graph Analytics: An XSEDE Introduction

Presenter: Nick Nystrom (PSC)

Novel and Innovative Projects

Presentation Slides

Effectively analyzing "big data" is increasingly essential to problems of scientific and societal importance. That analysis can take on various forms, depending on the nature of both the data and the intended results. In particular, researchers often seek to discover relationships in complex networks of data that can be represented as sets of nodes and edges, i.e. graphs. Graphs can represent unstructured data in a very general and extensible way, with nodes and edges representing concepts and relationships that need not be defined in a priori schema. Complex networks are readily expressed as graphs include, for example, social networks, protein interaction and gene expression networks, epidemiology, security, citation and authorship networks, supply chains, and datasets for machine learning. The mathematical analysis of graphs is a well-developed field, and standards, software, and even purpose-built computers now support multiple approaches to computational graph analytics. In many cases the graphs of interest are not partitionable; that is, they cannot be divided into subgraphs that can be tackled separately and efficiently. This makes graph analytics a particularly challenging aspect of dealing with big data.

This XSEDE Symposium will cover the following topics:

• an introduction to graph analytics, to establish motivation and terminology,
• several important W3C standards and community software technologies, e.g. RDF, SPARQL, and GraphLab, that offer powerful capability for working with large graphs, and
• XSEDE and other NSF-funded computational resources, namely Blacklight and Sherlock, that are well-suited to large-scale graph analytics.

(Videos not listed above, from prior years, can be found here)