XSEDE14 is hosted by

XSEDE, Extreme Science and Engineering Discovery Environment, xsede.org.

In cooperation with

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XSEDE is supported by the 
National Science Foundation

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The XSEDE14 proceedings are available through ACM at http://dl.acm.org/citation.cfm?id=2616498.


Education, Outreach, and Training (EOT)

Tuesday AM: Introducing Computational Science into the Curriculum

A Three-Semester, Interdisciplinary Approach to Parallel Programming in a Liberal Arts University Setting
Karl Frinkle and Mike Morris

Minimum Time, Maximum Effect: Introducing Parallel Computing in CS0 and STEM Outreach Activities Using Scratch
Russell Feldhausen, Scott Bell and Daniel Andresen

Clash of the Timelines: Lessons Learned from the Front Lines of CS Education
Diane Baxter and Beth Simon

DNA Subway: Making Genome Analysis Egalitarian
David Micklos, Cornel Ghiban, Mohammed Khalfan, Jason Williams, Uwe Hilgert, Sheldon McKay and Eun-Sook Jeong

Tuesday PM: Technology and Materials to Bridge into High Performance Computing

LittleFe as a successful on-ramp to HPC
Ivan Babic, Aaron Weeden, Mobeen Ludin, Skylar Thompson, Charles Peck, Kristin Muterspaw, Andrew Fitz Gibbon, Jennifer Houchins and Tom Murphy

XSEDE Campus Bridging Pilot Case Study
Barbara Hallock, Richard Knepper, James Ferguson and Craig Stewart

Architecting an autograder for parallel code
Razvan Carbunescu, Aditya Devarakonda, James Demmel, Steven Gordon, Jay Alameda and Susan Mehringer

An Introductory Course on Modeling and Simulation
David Toth and Jeffrey Solka

Wednesday PM: Integrating Tools in Computational Science Instruction

Revision control system in computational sciences and engineering curriculum
Gowtham S-Michigan Technological University

Integrating Performance Measurement and Program Evaluation to Promote Understanding
Lorna Rivera and Lizanne Destefano



Tuesday AM: Accounting and monitoring

An Analysis of Node Sharing on HPC Clusters using XDMoD/TACC_Stats
Joseph P. White, Robert L. Deleon, Thomas R. Furlani, Steven M. Gallo, Matthew D. Jones, Amin Ghadersohi, Cynthia D. Cornelius, Abani K. Patra, James C. Browne, William L. Barth and John Hammond

Descriptive Data Analysis of File Transfer Data
Sudarshan Srinivasan, Victor Hazlewood and Gregory Peterson

Building an Information System for a Distributed Testbed
Warren Smith and Shava Smallen

pbsacct: A Workload Analysis System for PBS-Based HPC Systems
Troy Baer and Doug Johnson


Tuesday PM: Benchmarking and performance

Benchmarking SSD-Based Lustre File System Configurations
Rick Mohr and Paul Peltz Jr.

SR-IOV: Performance Benefits for Virtualized Interconnects
Glenn K. Lockwood, Mahidhar Tatineni and Rick Wagner

Evaluating Distributed Platforms for Protein-Guided Scientific Workflow
Natasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Campbell, Harkamal Walia and Jitender S. Deogun

Performance of Applications using Dual-Rail InfiniBand 3D Torus network on the Gordon Supercomputer
Dong Ju Choi, Glenn Lockwood, Robert Sinkovits and Mahidhar Tatineni


Wednesday AM: New systems and capabilities

A leap forward with UTK's Cray XC30
Mark Fahey

The OneOklahoma Friction Free Network: Towards a Multi-Institutional Science DMZ in an EPSCoR State
Henry Neeman, David Akin, Joshua Alexander, Dana Brunson, S. Patrick Calhoun, James Deaton, Franklin Fondjo Fotou, Brandon George, Debi Gentis, Zane Gray, Eddie Huebsch, George Louthan, Matt Runion, Joel Snow and Brett Zimmerman

The Oklahoma PetaStore: A Business Model for Big Data on a Small Budget
Patrick Calhoun, David Akin, Joshua Alexander, Brett Zimmerman, Fred Keller, Brandon George and Henry Neeman

Gateways to Discovery: Cyberinfrastructure for the Long Tail of Science
Richard Moore, Chaitan Baru, Diane Baxter, Geoffrey Fox, Amit Majumdar, Phillip Papadopoulos, Wayne Pfeiffer, Robert Sinkovits, Shawn Strande, Mahidhar Tatineni, Richard Wagner, Nancy Wilkins-Diehr and Michael Norman


Wednesday PM: Tools for HPC

PGDB: A Debugger for MPI Applications
Nikoli Dryden

Runtime Pipeline Scheduling System for Heterogeneous Architecture
Julio Olaya and Rodrigo Romero

Thursday AM Session #1: Administration and practices

Best Practices for Administering a Medium Sized Cluster with Intel Xeon Phi Coprocessors
Troy Baer, Paul Peltz Jr.

On Automating XSEDE User Ticket Classification
Victor Hazlewood, Gregory Peterson, Gwang Son

Workload Aware Utilization Optimization for a Petaflop Supercomputer
Fei Xing, Haihang You

Data Management Practices on Large-Scale Lustre Scratch File Systems
Jesse Hanley, Richard Mohr, Gary Rogers


Software and Software Environments (Gateways, Bridging, and Application Developers)

Tuesday AM: Middleware and performance

HPC Simulation Workflows for Engineering Innovation
Mark Shephard and Cameron Smith

Statistical Performance Analysis for Scientific Applications
Fei Xing, Haihang You and Charng-Da Lu

UNICORE in XSEDE: Through Development, Integration, Deployment and beyond
Tabitha Samuel, Shahbaz Memon, Bernd Schuller and Shava Smallen

Performance Improvement and Workflow Development of Virtual Diffraction Calculations
Shawn Coleman, Sudhakar Pamidighantam, Mark Van Moer, Yang Wang, Lars Koesterke and Douglas Spearot


Tuesday PM: Science gateways

Integrating Science Gateways with XSEDE Security: A Survey of Credential Management Approaches
Jim Basney, Rion Dooley, Jeff Gaynor, Thejaka Amila Kanewala, Suresh Marru, Marlon Pierce and Joe Stubbs

Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave
Rion Dooley and Joe Stubbs

XRAS: Allocations software as a service in XSEDE
David Hart, Amy Schuele, Ester Soriano, Maytal Dahan and Matthew Hanlon

Incorporating Job Predictions into the SEAGrid Science Gateway
Ye Fan, Sudhakar Pamidighantam and Warren Smith

Leveraging XSEDE HPC resources to address computational challenges with high-resolution topography data
Choonhan Youn, Viswanath Nandigam, Minh Phan, David Tarboton, Nancy Wilkins-Diehr, Chaitanya Baru, Christopher Crosby, Anand Padmanabhan and Shaowen Wang

Wednesday AM: Community software and services

TextRWeb: Large-Scale Text Analytics with R on the Web
Guangchen Ruan-Indiana University; Hui Zhang-Indiana University Pervasive Technology Institute; Beth Plale-Indiana University; Eric Wernert-Indiana University Pervasive Technology Institute

A Tool for Interactive Parallelization
Ritu Arora, Julio Olaya and Madhav Gupta

Once you SCOOP, no need to fork
Yannick Hold-Geoffroy, Olivier Gagnon and Marc Parizeau

Accessible Parallelization for the Open Modeling Interface
Tom Bulatewicz and Daniel Andresen


Accelerating Discovery in Scholarly Research

Tuesday AM:  Impacts of ECSS

Advanced Application Support for Improved GPU Utilization on Keeneland
Jeffrey Young, M. Graham Lopez, Mitch Horton, Dick Glassbrook and Jeffrey Vetter

Accelerating TauDEM as a Scalable Hydrological Terrain Analysis Service on XSEDE
Ye Fan, Yan Liu, Shaowen Wang, David Tarboton, Ahmet Yildirim and Nancy Wilkins-Diehr

ECSS Experience: Particle Tracing Reinvented
Carlos Rosales-Fernandez and Robert McLay

XSEDE Support: Revolutionizing the Next-Generation Therapeutic Drug Discovery
Bhanu Rekepalli and Yuri Peterson


Tuesday PM: Bioinformatics

Using SAGA and the Open Science Grid to Search for Aptamers
Kevin Shieh, Pilib Ó Broin, David Rhee, Matthew Levy and Aaron Golden

Porting Mothur to Nautilus
Junqi Yin, Bhanu Rekepalli, Pragneshkumar Patel, Chanda Drennen and Annette Engel

Large-scale sequencing and assembly of cereal genomes using Blacklight
Philip Blood, Shoshana Marcus and Michael Schatz

An Integrated Analytic Pipeline for Identifying and Predicting Genetic Interactions based on Perturbation Data from High Content Double RNAi Screening
Zheng Yin, Fuhai Li and Stephen Wong

Accelerating Sparse Canonical Correlation Analysis for Large Brain Imaging Genetics Data
Jingwen Yan, Hui Zhang, Lei Du, Eric Wernert, Andrew Saykin and Li Shen


Wednesday PM: Education and broadening impact towards accelerating discovery

XSEDE OpenACC workshop enables Blue Waters Researchers to Accelerate Key Algorithms
Galen Arnold, Manisha Gajbe, Seid Koric and John Urbanic

Introducing MPI in Diverse Curricula
Steve Spicklemire

Exploring the Performance of a Minimalistic Simulator on Massive Parallel Systems – improve ||
Rong Rong, Hao Jiang and Jason Liu

Towards a Scientific Impact Measuring Framework for Large Computing Facilities - a Case Study on XSEDE
Gregor von Laszewski, Fugang Wang, Geoffrey C. Fox, Thomas Furlani, Robert Deleon and Steven Gallo


Wednesday PM Session #1:  HPC simulations supporting large scale instruments

Highly Energetic Collisions of Xe with Fullerene Clusters
Dulma Nugawela, Steven Stuart and Jacek Jakowski

Photoionization of Ne+8
M Pindzola, Sh. Adel-Naby and Connor Balance


Wednesday PM Session #2: Biomolecular simulation

Prediction of micellar properties from molecular simulation
Peter Koenig

Molecular dynamics simulation of nucleic acids: Convergence, reproducibility, assessment/validation, and data dissemination enabled by XSEDE and Blue Waters.
Thomas Cheatham


Thursday AM Session #1: Big data analysis and dissemination

FeatureSelector: an XSEDE-Enabled Tool for Massive Game Log Analysis
Y. Dora Cai, Bettina Riedl, Rabindra Ratan, Cuihua Shen and Arnold Picot

Applying Lessons from e-Discovery to Process Big Data using HPC
Sukrit Sondhi and Ritu Arora

Academic Torrents: A Community-Maintained Distributed Repository
Joseph Paul Cohen and Henry Lo

MOVIE: Large Scale Automated Analysis of MOVing ImagEs
Virginia Kuhn, Luigi Marini, Michael Simeone, Alan Craig, Liana Diesendruck, Sandeep Puthanveetil Satheesan and David Bock


Thursday AM Session #2: Quantum and fluids grab bag

Accelerating Ab Initio Nucleon Structure Calculations with All-Mode-Averaging on Gordon
Meifeng Lin-Brookhaven National Laboratory; Yasumichi Aoki-Nagoya University; Thomas Blum-University of Connecticut; Taku Izubuchi-Brookhaven National Laboratory; Chulwoo Jung-Brookhaven National Laboratory; Shigemi Ohta-KEK; Eigo Shintani-University of Mainz; Takeshi Yamazaki-Nagoya University; Shoichi Sasaki-Tohoku University

The hybrid Quantum Trajectory/Electronic Structure DFTB-based approach to Molecular Dynamics
Lei Wang, James Mazzuca, Sophya Garashchuk and Jacek Jakowski

Towards Efficient Direct Semiclassical Molecular Dynamics for Complex Molecular Systems
Yu Zhuang, Michele Ceotto and Bill Hase

Detailed computational modeling of laminar and turbulent sooting flames
Adhiraj Dasgupta, Somesh Roy and Daniel C Haworth


Thursday AM Session #3: Hybrid || and accelerators

Challenges in particle tracking in turbulence on a massive scale
Dhawal Buaria and Pui-Keun Yeung

A SIMD Solution for the Quadratic Assignment Problem with GPU Acceleration
Abhilash Chaparala, Clara Novoa and Apan Qasem

Brownian Dynamics Simulations with Hydrodynamic Interactions on GPUs
Graham Lopez, Mitch Horton and Edmond Chow

Efficient 3D Movement-Based Kernel Density Estimator and Application to Wildlife Ecology
Jeff Tracey, James Sheppard, Glenn Lockwood, Amit Chourasia, Mahidhar Tatineni, Robert Fisher and Robert Sinkovits