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Presentations
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
Technology
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