Publications

2025

1. 

   xGFabric: Coupling Sensor Networks and HPC Facilities with Private 5G Wireless Networks for Real-Time Digital Agriculture

   Liubov Kurafeeva, Alan Subedi, Ryan Hartung, Michael Fay, Avhishek Biswas, Shantenu Jha, Ozgur O. Kilic, Chandra Krintz, Andre Merzky, Douglas Thain, Mehmet C. Vuran, and Rich Wolski

   In Workshop on Extreme-Scale Experiment-in-the-Loop Computing (XLOOP) at Supercomputing, 2025

   Bib PDF

   @inproceedings{xgfabric-xloop-2025,
     author = {Kurafeeva, Liubov and Subedi, Alan and Hartung, Ryan and Fay, Michael and Biswas, Avhishek and Jha, Shantenu and Kilic, Ozgur O. and Krintz, Chandra and Merzky, Andre and Thain, Douglas and Vuran, Mehmet C. and Wolski, Rich},
     title = {{xGFabric: Coupling Sensor Networks and HPC Facilities with Private 5G Wireless Networks for Real-Time Digital Agriculture}},
     booktitle = {{Workshop on Extreme-Scale Experiment-in-the-Loop Computing (XLOOP) at Supercomputing}},
     year = {2025},
     cclpaperid = {1005},
     keywords = {xgfabric},
   }

2. 

   Backpacks for Notebooks: Enabling Containerized Notebook Workflows in Distributed Environments

   Md Saiful Islam, Talha Azaz, Raza Ahmad, A D M Shahadat Hossain, Furqan Baig, Shaowen Wang, Kevin Lannon, Tanu Malik, and Douglas Thain

   In IEEE Conference on eScience, 2025

   Bib PDF

   @inproceedings{floability-escience-2025,
     author = {Islam, Md Saiful and Azaz, Talha and Ahmad, Raza and Hossain, A D M Shahadat and Baig, Furqan and Wang, Shaowen and Lannon, Kevin and Malik, Tanu and Thain, Douglas},
     title = {{Backpacks for Notebooks: Enabling Containerized Notebook Workflows in Distributed Environments}},
     booktitle = {{IEEE Conference on eScience}},
     pages = {9},
     year = {2025},
     cclpaperid = {1003},
     keywords = {floability}
   }

3. 

   Liberating the Data Aware Scheduler to Achieve Locality in Layered Scientific Workflow Systems

   Colin Thomas and Douglas Thain

   In IEEE Conference on eScience, 2025

   Bib PDF

   @inproceedings{liberating-escience-2025,
     author = {Thomas, Colin and Thain, Douglas},
     title = {{Liberating the Data Aware Scheduler to Achieve Locality in Layered Scientific Workflow Systems}},
     booktitle = {{IEEE Conference on eScience}},
     pages = {9},
     year = {2025},
     cclpaperid = {1004}
   }

2024

1. 

   Reshaping High Energy Physics Applications for Near-Interactive Execution Using TaskVine

   Barry Sly-Delgado, Ben Tovar, Jin Zhou, and Douglas Thain

   In ACM/IEEE Supercomputing, 2024

   DOI Bib PDF

   @inproceedings{reshaping-sc-2024,
     author = {Sly-Delgado, Barry and Tovar, Ben and Zhou, Jin and Thain, Douglas},
     title = {{Reshaping High Energy Physics Applications for Near-Interactive Execution Using TaskVine}},
     booktitle = {{ACM/IEEE Supercomputing}},
     pages = {1-11},
     year = {2024},
     cclpaperid = {996},
     keywords = {taskvine},
     doi = {10.1109/SC41406.2024.00068}
   }

2. 

   Shepherd: Seamless Integration of Service Workflows into Task-Based Workflows through Log Monitoring

   Saiful Islam and Douglas Thain

   In Workshop on Workflows at ACM Supercomputing, 2024

   Bib PDF

   @inproceedings{shepherd-works-2024,
     author = {Islam, Saiful and Thain, Douglas},
     title = {{Shepherd: Seamless Integration of Service Workflows into Task-Based Workflows through Log Monitoring}},
     booktitle = {{Workshop on Workflows at ACM Supercomputing}},
     pages = {1-8},
     year = {2024},
     cclpaperid = {997},
     keywords = {shepherd},
   }

3. 

   Accelerating Function-Centric Applications by Discovering, Distributing, and Retaining Reusable Context in Workflow Systems

   Thanh Son Phung, Colin Thomas, Logan Ward, Kyle Chard, and Douglas Thain

   In ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC), 2024

   Bib PDF

   @inproceedings{function-context-hpdc-2024,
     author = {Phung, Thanh Son and Thomas, Colin and Ward, Logan and Chard, Kyle and Thain, Douglas},
     title = {{Accelerating Function-Centric Applications by Discovering, Distributing, and Retaining Reusable Context in Workflow Systems}},
     booktitle = {{ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC)}},
     year = {2024},
     cclpaperid = {995},
   }

4. 

   Poster: Leveraging Intermediate Data Management with Parsl/TaskVine

   Colin Thomas and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, 2024

   Bib PDF

   @inproceedings{data-gcasr-2024,
     author = {Thomas, Colin and Thain, Douglas},
     title = {{Poster: Leveraging Intermediate Data Management with Parsl/TaskVine}},
     booktitle = {{Greater Chicago Area Systems Research Workshop}},
     pages = {1},
     year = {2024},
     cclpaperid = {998},
     keywords = {taskvine},
   }

5. 

   Poster: Toward High-Performance Simulation of 1000 Drones

   Md Saiful Islam and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, 2024

   Bib PDF

   @inproceedings{drones-gcasr-2024,
     author = {Islam, Md Saiful and Thain, Douglas},
     title = {{Poster: Toward High-Performance Simulation of 1000 Drones}},
     booktitle = {{Greater Chicago Area Systems Research Workshop}},
     pages = {1},
     year = {2024},
     cclpaperid = {999},
   }

6. 

   Poster: Adaptive Task-Oriented Resource Allocation for Large Dynamic Workflows on Opportunistic Resources

   Thanh Son Phùng and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, 2024

   Bib PDF

   @inproceedings{alloc-gcasr-2024,
     author = {Phùng, Thanh Son and Thain, Douglas},
     title = {{Poster: Adaptive Task-Oriented Resource Allocation for Large Dynamic Workflows on Opportunistic Resources}},
     booktitle = {{Greater Chicago Area Systems Research Workshop}},
     pages = {1},
     year = {2024},
     cclpaperid = {1000},
   }

7. 

   Poster: Import Hoisting for Serverless Libraries

   Jin Zhou and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, 2024

   Bib PDF

   @inproceedings{hoisting-gcasr-2024,
     author = {Zhou, Jin and Thain, Douglas},
     title = {{Poster: Import Hoisting for Serverless Libraries}},
     booktitle = {{Greater Chicago Area Systems Research Workshop}},
     pages = {1},
     year = {2024},
     cclpaperid = {1001},
   }

8. 

   Poster: Reshaping High Energy Physics Applications for Near-Interactive Execution Using TaskVine

   Barry Sly-Delgado and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, 2024

   Bib PDF

   @inproceedings{reshaping-gcasr-2024,
     author = {Sly-Delgado, Barry and Thain, Douglas},
     title = {{Poster: Reshaping High Energy Physics Applications for Near-Interactive Execution Using TaskVine}},
     booktitle = {{Greater Chicago Area Systems Research Workshop}},
     pages = {1},
     year = {2024},
     cclpaperid = {1002},
     keywords = {taskvine},
   }

9. 

   Adaptive Task-Oriented Resource Allocation for Large Dynamic Workflows on Opportunistic Resources

   Thanh Son Phung and Douglas Thain

   In IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2024

   Bib PDF

   @inproceedings{adaptive-ipdps-2024,
     author = {Phung, Thanh Son and Thain, Douglas},
     title = {{Adaptive Task-Oriented Resource Allocation for Large Dynamic Workflows on Opportunistic Resources}},
     booktitle = {{IEEE International Parallel and Distributed Processing Symposium (IPDPS)}},
     pages = {12},
     year = {2024},
     cclpaperid = {994},
   }

2023

1. 

   Maximizing Data Utility for HPC Python Workflow Execution

   Thanh Son Phung, Ben Clifford, Kyle Chard, and Douglas Thain

   In SC23 Workshop: High Performance Python for Science at Scale (HPPSS), 2023

   Bib PDF

   @inproceedings{utility-hppss-2023,
     author = {Phung, Thanh Son and Clifford, Ben and Chard, Kyle and Thain, Douglas},
     title = {{Maximizing Data Utility for HPC Python Workflow Execution}},
     booktitle = {{SC23 Workshop: High Performance Python for Science at Scale (HPPSS)}},
     year = {2023},
     cclpaperid = {990},
   }

2. 

   TaskVine: Managing In-Cluster Storage for High-Throughput Data Intensive Workflows

   Barry Sly-Delgado, Thanh Son Phung, Colin Thomas, David Simonetti, Andrew Hennessee, Ben Tovar, and Douglas Thain

   In 18th Workshop on Workflows in Support of Large-Scale Science, 2023

   Bib PDF

   @inproceedings{taskvine-works-2023,
     author = {Sly-Delgado, Barry and Phung, Thanh Son and Thomas, Colin and Simonetti, David and Hennessee, Andrew and Tovar, Ben and Thain, Douglas},
     title = {{TaskVine: Managing In-Cluster Storage for High-Throughput Data Intensive Workflows}},
     booktitle = {{ 18th Workshop on Workflows in Support of Large-Scale Science}},
     year = {2023},
     cclpaperid = {991},
     keywords = {taskvine},
   }

3. 

   Poster: Minimizing Data Movement Using Distant Futures

   Barry Sly-Delgado and Douglas Thain

   In ACM/IEEE Supercomputing, 2023

   Bib PDF

   @inproceedings{futures-sc-2023,
     author = {Sly-Delgado, Barry and Thain, Douglas},
     title = {{Poster: Minimizing Data Movement Using Distant Futures}},
     booktitle = {{ACM/IEEE Supercomputing}},
     year = {2023},
     cclpaperid = {993},
   }

4. 

   Poster: TaskVine: A User-Level Framework for Data Intensive Scientific Applications

   Douglas Thain

   In CSSI PI Meeting, 2023

   Bib PDF

   @inproceedings{taskvine-cssi-2023,
     author = {Thain, Douglas},
     title = {{Poster: TaskVine: A User-Level Framework for Data Intensive Scientific Applications}},
     booktitle = {{CSSI PI Meeting}},
     year = {2023},
     cclpaperid = {989},
     keywords = {taskvine},
   }

5. 

   Poster: Mixed Modality Workflows in TaskVine

   David Simonetti, Ben Tovar, and Douglas Thain

   In ACM High Performance Distributed Computing, 2023

   Bib PDF

   @inproceedings{mixed-hpdc-2023,
     author = {Simonetti, David and Tovar, Ben and Thain, Douglas},
     title = {{Poster: Mixed Modality Workflows in TaskVine}},
     booktitle = {{ACM High Performance Distributed Computing}},
     pages = {331-332},
     year = {2023},
     cclpaperid = {988},
     keywords = {taskvine},
   }

6. LANDLORD: Coordinating Dynamic Software Environments to Reduce Container Sprawl

   Tim Shaffer, Thanh Son Phung, Kyle Chard, and Douglas Thain

   IEEE Transactions on Parallel and Distributed Systems, 2023

   doi: 10.1109/TPDS.2023.3241598

   Bib

   @article{landlord-tpds-2023,
     author = {Shaffer, Tim and Phung, Thanh Son and Chard, Kyle and Thain, Douglas},
     title = {{LANDLORD: Coordinating Dynamic Software Environments to Reduce Container Sprawl}},
     journal = {{IEEE Transactions on Parallel and Distributed Systems}},
     volume = {34},
     number = {5},
     pages = {1376-1389},
     year = {2023},
     note = {{doi: 10.1109/TPDS.2023.3241598}},
     cclpaperid = {985}
   }

2022

1. 

   Poster: Robust Meta-Workflow Management with Mufasa

   Ben Lyons and Douglas Thain

   In IEEE International Conference on eScience, 2022

   Bib PDF

   @inproceedings{mufasa-escience-2022,
     author = {Lyons, Ben and Thain, Douglas},
     title = {{Poster: Robust Meta-Workflow Management with Mufasa}},
     booktitle = {{IEEE International Conference on eScience}},
     year = {2022},
     cclpaperid = {983},
   }

2. Dynamic Task Shaping for High Throughput Data Analysis Applications in High Energy Physics

   Ben Tovar, Ben Lyons, Kelci Mohrman, Barry Sly-Delgado, Kevin Lannon, and Douglas Thain

   In IEEE International Parallel and Distributed Processing Symposium, 2022

   doi: 10.1109/IPDPS53621.2022.00041

   Bib

   @inproceedings{topeft-ipdps-2022,
     author = {Tovar, Ben and Lyons, Ben and Mohrman, Kelci and Sly-Delgado, Barry and Lannon, Kevin and Thain, Douglas},
     title = {{Dynamic Task Shaping for High Throughput Data Analysis Applications in High Energy Physics}},
     booktitle = {{IEEE International Parallel and Distributed Processing Symposium}},
     year = {2022},
     note = {{doi: 10.1109/IPDPS53621.2022.00041}},
     cclpaperid = {979},
     keywords = {workqueue}
   }

3. 

   PONCHO: Dynamic Package Synthesis for Distributed and Serverless Python Applications

   Barry Sly-Delgado, Nick Locascio, David Simonetti, Brett Wiseman, Ben Tovar, and Douglas Thain

   In Workshop on High Performance Serverless Computing, 2022

   doi: 10.1145/3526060.3535459

   Bib PDF

   @inproceedings{poncho-hips-2022,
     author = {Sly-Delgado, Barry and Locascio, Nick and Simonetti, David and Wiseman, Brett and Tovar, Ben and Thain, Douglas},
     title = {{PONCHO: Dynamic Package Synthesis for Distributed and Serverless Python Applications}},
     booktitle = {{Workshop on High Performance Serverless Computing}},
     year = {2022},
     note = {{doi: 10.1145/3526060.3535459}},
     cclpaperid = {982},
   }

4. Analysis Cyberinfrastructure: Challenges and Opportunities

   Kevin Lannon, Paul Brenner, Michael Hildreth, Kenya Hurtado Anampa, Alan Malta, Rodrigues, Kelci Mohrman, Douglas Thain, and Ben Tovar

   In Snowmass, 2022

   Bib

   @inproceedings{analysis-snowmass-2022,
     author = {Lannon, Kevin and Brenner, Paul and Hildreth, Michael and Anampa, Kenya Hurtado and Malta, Alan and Rodrigues and Mohrman, Kelci and Thain, Douglas and Tovar, Ben},
     title = {{Analysis Cyberinfrastructure: Challenges and Opportunities}},
     booktitle = {{Snowmass}},
     pages = {1-14},
     year = {2022},
     cclpaperid = {986}
   }

5. 

   VisDict: A Visual Dictionary in a Science Gateway

   Sanda Gesing, Ewa Deelman, Rafael Ferreira Silva, Michael Hildreth, Mary Ann McDowell, Natalie K. Meyers, and Douglas Thain

   In Gateways, 2022

   Bib PDF

   @inproceedings{visdict-gateways-2022,
     author = {Gesing, Sanda and Deelman, Ewa and da Silva, Rafael Ferreira and Hildreth, Michael and McDowell, Mary Ann and Meyers, Natalie K. and Thain, Douglas},
     title = {{VisDict: A Visual Dictionary in a Science Gateway}},
     booktitle = {{Gateways}},
     year = {2022},
     cclpaperid = {987},
   }

2021

1. 

   Not All Tasks Are Created Equal: Adaptive Resource Allocation for Heterogeneous Tasks in Dynamic Workflows

   Thanh Son Phung, Logan Ward, Kyle Chard, and Douglas Thain

   In WORKS Workshop on Workflows at Supercomputing, 2021

   Bib PDF

   @inproceedings{tasks-works-2021,
     author = {Phung, Thanh Son and Ward, Logan and Chard, Kyle and Thain, Douglas},
     title = {{Not All Tasks Are Created Equal: Adaptive Resource Allocation for Heterogeneous Tasks in Dynamic Workflows}},
     booktitle = {{WORKS Workshop on Workflows at Supercomputing}},
     year = {2021},
     cclpaperid = {978},
   }

2. 

   Regulating Traffic in Crowded Cache

   Kevin Gao, Tim Shaffer, and Kyle Chard

   In Student Poster Session at Supercomputing, 2021

   Bib PDF

   @inproceedings{regulating-sc-2021,
     author = {Gao, Kevin and Shaffer, Tim and Chard, Kyle},
     title = {{Regulating Traffic in Crowded Cache}},
     booktitle = {{Student Poster Session at Supercomputing}},
     year = {2021},
     cclpaperid = {981},
   }

3. 

   An Empirical Study of Package Dependencies and Lifetimes in Binder Python Containers

   Tim Shaffer, Kyle Chard, and Douglas Thain

   In IEEE International Conference on e-Science, 2021

   Bib PDF

   @inproceedings{binder-escience-2021,
     author = {Shaffer, Tim and Chard, Kyle and Thain, Douglas},
     title = {{An Empirical Study of Package Dependencies and Lifetimes in Binder Python Containers}},
     booktitle = {{IEEE International Conference on e-Science}},
     year = {2021},
     cclpaperid = {977},
   }

4. Binder Software Environments

   Tim Shaffer, Kyle Chard, and Douglas Thain

   2021

   doi: 10.5281/zenodo.4891790

   Bib

   @misc{binder-dataset,
     author = {Shaffer, Tim and Chard, Kyle and Thain, Douglas},
     title = {{Binder Software Environments}},
     year = {2021},
     note = {{doi: 10.5281/zenodo.4891790}},
     cclpaperid = {976}
   }

5. Lightweight Function Monitors for Fine-Grained Management in Large Scale Python Applications

   Tim Shaffer, Zhuozhao Li, Ben Tovar, Yadu Babuji, TJ Dasso, Zoe Surma, Kyle Chard, Ian Foster, and Douglas Thain

   In IEEE International Parallel and Distributed Processing Symposium, 2021

   doi: 10.1109/IPDPS49936.2021.00088

   Bib

   @inproceedings{lfm-ipdps-2021,
     author = {Shaffer, Tim and Li, Zhuozhao and Tovar, Ben and Babuji, Yadu and Dasso, TJ and Surma, Zoe and Chard, Kyle and Foster, Ian and Thain, Douglas},
     title = {{Lightweight Function Monitors for Fine-Grained Management in Large Scale Python Applications}},
     booktitle = {{IEEE International Parallel and Distributed Processing Symposium}},
     year = {2021},
     note = {{doi: 10.1109/IPDPS49936.2021.00088}},
     cclpaperid = {968}
   }

6. Harnessing HPC resources for CMS jobs using a Virtual Private Network

   Benjamin Tovar, Brian Bockelman, Michael Hildreth, Kevin Lannon, and Douglas Thain

   In 25th International Conference on Computing in High Energy and Nuclear Physics (CHEP), 2021

   doi: 10.1051/epjconf/202125102032

   Bib

   @inproceedings{vpn-chep-2021,
     author = {Tovar, Benjamin and Bockelman, Brian and Hildreth, Michael and Lannon, Kevin and Thain, Douglas},
     title = {{Harnessing HPC resources for CMS jobs using a Virtual Private Network}},
     booktitle = {{25th International Conference on Computing in High Energy and Nuclear Physics (CHEP)}},
     year = {2021},
     note = {{doi: 10.1051/epjconf/202125102032}},
     cclpaperid = {973}
   }

7. 

   Log Discovery, Log Custody, and the Web Inspired Approach for Open Distributed Systems Troubleshooting

   Nathaniel Kremer-Herman

   2021

   Bib PDF

   @thesis{nkremerh-dissertation,
     author = {Kremer-Herman, Nathaniel},
     title = {{Log Discovery, Log Custody, and the Web Inspired Approach for Open Distributed Systems Troubleshooting}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2021},
     cclpaperid = {971},
   }

8. A Community Roadmap for Scientific Workflows Research and Development

   R. F. al.

   In IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 2021

   doi: 10.1109/WORKS54523.2021.00016

   Bib

   @inproceedings{roadmap-works-2021,
     author = {da Silva et al., R. F.},
     title = {{A Community Roadmap for Scientific Workflows Research and Development}},
     booktitle = {{IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)}},
     pages = {81-90},
     year = {2021},
     note = {{doi: 10.1109/WORKS54523.2021.00016}},
     cclpaperid = {984}
   }

2020

1. 

   Autoscaling High Throughput Workloads on Container Orchestrators

   Chao Zheng, Nathaniel Kremer-Herman, Tim Shaffer, and Douglas Thain

   In IEEE Conference on Cluster Computing, 2020

   doi: 10.1109/CLUSTER49012.2020.00024

   Bib PDF

   @inproceedings{autoscaling-cluster-2020,
     author = {Zheng, Chao and Kremer-Herman, Nathaniel and Shaffer, Tim and Thain, Douglas},
     title = {{Autoscaling High Throughput Workloads on Container Orchestrators }},
     booktitle = {{IEEE Conference on Cluster Computing}},
     pages = {1-10},
     year = {2020},
     note = {{doi: 10.1109/CLUSTER49012.2020.00024}},
     cclpaperid = {967},
   }

2. 

   Log Discovery for Troubleshooting Open Distributed Systems with TLQ

   Nathaniel Kremer-Herman and Douglas Thain

   In Practice and Experience of Advanced Research Computing (PEARC), 2020

   doi: 10.1145/3311790.3396633

   Bib PDF

   @inproceedings{tlq-pearc-2020,
     author = {Kremer-Herman, Nathaniel and Thain, Douglas},
     title = {{Log Discovery for Troubleshooting Open Distributed Systems with TLQ}},
     booktitle = {{Practice and Experience of Advanced Research Computing (PEARC)}},
     year = {2020},
     note = {{doi: 10.1145/3311790.3396633}},
     cclpaperid = {966},
   }

3. Solving the Container Explosion Problem for Distributed High Throughput Computing

   Tim Shaffer, Nicholas Hazekamp, Jakob Blomer, and Douglas Thain

   In International Parallel and Distributed Processing Symposium, 2020

   doi: 10.1109/IPDPS47924.2020.00048

   Bib

   @inproceedings{explosion-ipdps-2020,
     author = {Shaffer, Tim and Hazekamp, Nicholas and Blomer, Jakob and Thain, Douglas},
     title = {{Solving the Container Explosion Problem for Distributed High Throughput Computing}},
     booktitle = {{International Parallel and Distributed Processing Symposium}},
     year = {2020},
     note = {{doi: 10.1109/IPDPS47924.2020.00048}},
     cclpaperid = {964}
   }

2019

1. 

   Methods Enabling Portability of Scientific Workflows

   Nicholas Hazekamp

   2019

   Bib PDF

   @thesis{hazekamp-dissertation,
     author = {Hazekamp, Nicholas},
     title = {{Methods Enabling Portability of Scientific Workflows}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2019},
     cclpaperid = {970},
   }

2. 

   The Challenges of Scaling Up High-Throughput Workflow with Container Technologies

   Chao Zheng

   2019

   Bib PDF

   @thesis{czheng-dissertation,
     author = {Zheng, Chao},
     title = {{The Challenges of Scaling Up High-Throughput Workflow with Container Technologies}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2019},
     cclpaperid = {963},
   }

3. 

   Dynamic Sizing of Continuously Divisible Jobs for Heterogeneous Resources

   Nick Hazekamp, Ben Tovar, and Douglas Thain

   In IEEE International Conference on e-Science, 2019

   doi: 10.1109/eScience.2019.00026

   Bib PDF

   @inproceedings{sizing-escience-2019,
     author = {Hazekamp, Nick and Tovar, Ben and Thain, Douglas},
     title = {{Dynamic Sizing of Continuously Divisible Jobs for Heterogeneous Resources}},
     booktitle = {{IEEE International Conference on e-Science}},
     year = {2019},
     note = {{doi: 10.1109/eScience.2019.00026}},
     cclpaperid = {962},
   }

4. Flexible Partitioning of Scientific Workflows Using the JX Workflow Language

   Tim Shaffer, Nathaniel Kremer-Herman, and Douglas Thain

   In Practice and Experience in Advanced Research Computing (PEARC), 2019

   doi: 10.1145/3332186.3338100

   Bib

   @inproceedings{jx-pearc19,
     author = {Shaffer, Tim and Kremer-Herman, Nathaniel and Thain, Douglas},
     title = {{Flexible Partitioning of Scientific Workflows Using the JX Workflow Language}},
     booktitle = {{Practice and Experience in Advanced Research Computing (PEARC)}},
     year = {2019},
     note = {{doi: 10.1145/3332186.3338100}},
     cclpaperid = {961},
     keywords = {makeflow}
   }

2018

1. A Lightweight Model for Right-Sizing Master-Worker Applications

   Nathaniel Kremer-Herman, Benjamin Tovar, and Douglas Thain

   In ACM/IEEE Supercomputing (SC), 2018

   doi: 10.1109/SC.2018.00042

   Bib

   @inproceedings{capacity-sc18,
     author = {Kremer-Herman, Nathaniel and Tovar, Benjamin and Thain, Douglas},
     title = {{A Lightweight Model for Right-Sizing Master-Worker Applications}},
     booktitle = {{ACM/IEEE Supercomputing (SC)}},
     year = {2018},
     note = {{doi: 10.1109/SC.2018.00042}},
     cclpaperid = {955}
   }

2. 

   Reduction of Workflow Resource Consumption Using a Density-based Clustering Model

   Qimin Zhang, Ben Tovar, Nate Kremer-Herman, and Douglas Thain

   In WORKS Workshop at Supercomputing, 2018

   Bib PDF

   @inproceedings{clustering-works-2018,
     author = {Zhang, Qimin and Tovar, Ben and Kremer-Herman, Nate and Thain, Douglas},
     title = {{Reduction of Workflow Resource Consumption Using a Density-based Clustering Model}},
     booktitle = {{WORKS Workshop at Supercomputing}},
     year = {2018},
     cclpaperid = {956},
   }

3. An Algebra for Robust Workflow Transformations

   Nicholas Hazekamp and Douglas Thain

   In IEEE International Conference on e-Science, 2018

   doi: 10.1109/eScience.2018.00031

   Bib

   @inproceedings{transformation-escience-2018,
     author = {Hazekamp, Nicholas and Thain, Douglas},
     title = {{An Algebra for Robust Workflow Transformations}},
     booktitle = {{IEEE International Conference on e-Science}},
     pages = {12},
     year = {2018},
     note = {{doi: 10.1109/eScience.2018.00031}},
     cclpaperid = {953}
   }

4. Poster: A First Look at the JX Workflow Language

   Tim Shaffer, Kyle M.D. Sweeney, Nathaniel Kremer-Herman, and Douglas Thain

   In IEEE International Conference on e-Science, 2018

   doi: 10.1109/eScience.2018.00094

   Bib

   @inproceedings{jx-escience18,
     author = {Shaffer, Tim and Sweeney, Kyle M.D. and Kremer-Herman, Nathaniel and Thain, Douglas},
     title = {{Poster: A First Look at the JX Workflow Language}},
     booktitle = {{IEEE International Conference on e-Science}},
     year = {2018},
     note = {{doi: 10.1109/eScience.2018.00094}},
     cclpaperid = {954}
   }

5. 

   Wharf: Sharing Docker Images in a Distributed File System

   Chao Zheng, Lukas Rupprecht, Vasily Tarasov, Douglas Thain, Mohamed Mohamed, Dimitrios Skourtis, Amit S. Warke, and Dean Hildrebarnd

   In ACM Symposium on Cloud Computing, 2018

   doi: 10.1145/3267809.3267836

   Bib PDF

   @inproceedings{wharf-socc-2018,
     author = {Zheng, Chao and Rupprecht, Lukas and Tarasov, Vasily and Thain, Douglas and Mohamed, Mohamed and Skourtis, Dimitrios and Warke, Amit S. and Hildrebarnd, Dean},
     title = {{Wharf: Sharing Docker Images in a Distributed File System}},
     booktitle = {{ACM Symposium on Cloud Computing}},
     pages = {12},
     year = {2018},
     note = {{doi: 10.1145/3267809.3267836}},
     cclpaperid = {957},
   }

6. 

   VC3: A Virtual Cluster Service for Community Computation

   Lincoln Bryant, Jeremy Van, Benedikt Riedel, Robert Gardner, Jose Caballero, John Hover, Ben Tovar, and Douglas Thain

   In PEARC: Practice and Experience in Advanced Research Computing, 2018

   doi: 10.1145/3219104.3219125

   Bib PDF

   @inproceedings{vc3-pearc-2018,
     author = {Bryant, Lincoln and Van, Jeremy and Riedel, Benedikt and Gardner, Robert and Caballero, Jose and Hover, John and Tovar, Ben and Thain, Douglas},
     title = {{VC3: A Virtual Cluster Service for Community Computation}},
     booktitle = {{PEARC: Practice and Experience in Advanced Research Computing}},
     pages = {1-8},
     year = {2018},
     note = {{doi: 10.1145/3219104.3219125}},
     cclpaperid = {949},
   }

7. 

   Reproducibility in Scientific Computing

   Peter Ivie and Douglas Thain

   ACM Computing Surveys, 2018

   doi: 10.1145/3186266

   Bib PDF

   @article{repro-survey,
     author = {Ivie, Peter and Thain, Douglas},
     title = {{Reproducibility in Scientific Computing}},
     journal = {{ACM Computing Surveys}},
     volume = {51},
     number = {3},
     year = {2018},
     note = {{doi: 10.1145/3186266}},
     cclpaperid = {952},
   }

8. 

   Early Experience Using Amazon Batch for Scientific Workflows

   Kyle Sweeney and Douglas Thain

   In ScienceCloud Workshop at HPDC , 2018

   doi: 10.1145/3217880.3217885

   Bib PDF

   @inproceedings{batch-sciencecloud-2018,
     author = {Sweeney, Kyle and Thain, Douglas},
     title = {{Early Experience Using Amazon Batch for Scientific Workflows}},
     booktitle = {{ScienceCloud Workshop at HPDC }},
     year = {2018},
     note = {{doi: 10.1145/3217880.3217885}},
     cclpaperid = {950},
   }

9. 

   Efficient Integration of Containers into Scientific Workflows

   Kyle Sweeney and Douglas Thain

   In Science Cloud Workshop at HPDC, 2018

   doi: 10.1145/3217880.3217887

   Bib PDF

   @inproceedings{containers-sciencecloud-2018,
     author = {Sweeney, Kyle and Thain, Douglas},
     title = {{Efficient Integration of Containers into Scientific Workflows}},
     booktitle = {{Science Cloud Workshop at HPDC}},
     year = {2018},
     note = {{doi: 10.1145/3217880.3217887}},
     cclpaperid = {951},
   }

10. Automatic Dependency Management for Scientific Applications on Clusters

    Benjamin Tovar, Nicholas Hazekamp, Nathaniel Kremer-Herman, and Douglas Thain

    In IEEE International Conference on Cloud Engineering (IC2E) , 2018

    doi: 10.1109/IC2E.2018.00026

    Bib

    @inproceedings{tovar-ic2e-2018,
      author = {Tovar, Benjamin and Hazekamp, Nicholas and Kremer-Herman, Nathaniel and Thain, Douglas},
      title = {{Automatic Dependency Management for Scientific Applications on Clusters}},
      booktitle = {{IEEE International Conference on Cloud Engineering (IC2E) }},
      year = {2018},
      note = {{doi: 10.1109/IC2E.2018.00026}},
      cclpaperid = {945}
    }

11. 

    MAKER as a Service: Moving HPC applications to Jetstream Cloud

    Nicholas Hazekamp, Upendra Kumar Devisetty, Nirav Merchant, and Douglas Thain

    In IEEE International Conference on Cloud Engineering, 2018

    doi: 10.1109/IC2E.2018.00029

    Bib PDF

    @inproceedings{maker-service-ic2e2018,
      author = {Hazekamp, Nicholas and Devisetty, Upendra Kumar and Merchant, Nirav and Thain, Douglas},
      title = {{MAKER as a Service: Moving HPC applications to Jetstream Cloud}},
      booktitle = {{IEEE International Conference on Cloud Engineering}},
      pages = {6},
      year = {2018},
      note = {{doi: 10.1109/IC2E.2018.00029}},
      cclpaperid = {946},
    }

12. A Workflow Management System to Facilitate Reproducibility of Scientific Computing Applications

    Peter Ivie

    2018

    Bib

    @thesis{ivie-thesis,
      author = {Ivie, Peter},
      title = {{A Workflow Management System to Facilitate Reproducibility of Scientific Computing Applications}},
      editor = {Thesis, Ph.D.},
      booktitle = {{University of Notre Dame}},
      year = {2018},
      cclpaperid = {960}
    }

13. 

    SHADHO: Massively Scalable Hardware-Aware Distributed Hyperparameter Optimization

    Jeffrey Kinnison, Nathaniel Kremer-Herman, Douglas Thain, and Walter Scheirer

    In IEEE Winter Conference on Applications of Computer Vision, 2018

    doi: 10.1109/WACV.2018.00086

    Bib PDF

    @inproceedings{shadho-wacv-2018,
      author = {Kinnison, Jeffrey and Kremer-Herman, Nathaniel and Thain, Douglas and Scheirer, Walter},
      title = {{SHADHO: Massively Scalable Hardware-Aware Distributed Hyperparameter Optimization}},
      booktitle = {{IEEE Winter Conference on Applications of Computer Vision}},
      pages = {1-10},
      year = {2018},
      note = {{doi: 10.1109/WACV.2018.00086}},
      cclpaperid = {947},
    }

14. A Job Sizing Strategy for High-Throughput Scientific Workflows

    Benjamin Tovar, Rafael Ferreira Silva, Gideon Juve, Ewa Deelman, William Allcock, Douglas Thain, and Miron Livny

    IEEE Transactions on Parallel and Distributed Systems, 2018

    doi: 10.1109/TPDS.2017.2762310

    Bib

    @article{tovar-tpds-2017,
      author = {Tovar, Benjamin and da Silva, Rafael Ferreira and Juve, Gideon and Deelman, Ewa and Allcock, William and Thain, Douglas and Livny, Miron},
      title = {{A Job Sizing Strategy for High-Throughput Scientific Workflows}},
      journal = {{IEEE Transactions on Parallel and Distributed Systems}},
      volume = {29},
      number = {2},
      pages = {240-253},
      year = {2018},
      note = {{doi: 10.1109/TPDS.2017.2762310}},
      cclpaperid = {941}
    }

15. 

    Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows

    Nicholas Hazekamp, Nathaniel Kremer-Herman, Benjamin Tovar, Haiyan Meng, Olivia Choudhury, Scott Emrich, and Douglas Thain

    IEEE Transactions on Parallel and Distributed Systems, 2018

    doi: 10.1109/TPDS.2017.2764897

    Bib PDF

    @article{mf-storage-tpds17,
      author = {Hazekamp, Nicholas and Kremer-Herman, Nathaniel and Tovar, Benjamin and Meng, Haiyan and Choudhury, Olivia and Emrich, Scott and Thain, Douglas},
      title = {{Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows}},
      journal = {{IEEE Transactions on Parallel and Distributed Systems}},
      volume = {29},
      number = {2},
      pages = {338-350},
      year = {2018},
      note = {{doi: 10.1109/TPDS.2017.2764897}},
      cclpaperid = {942},
    }

16. 

    GPU acceleration of Eulerian–Lagrangian particle-laden turbulent flow simulations

    James Sweet, David Richter, and Douglas Thain

    International Journal of Multiphase Flow, 2018

    doi: 10.1016/j.ijmultiphaseflow.2017.11.010

    Bib PDF

    @article{gpu-ijmf,
      author = {Sweet, James and Richter, David and Thain, Douglas},
      title = {{GPU acceleration of Eulerian–Lagrangian particle-laden turbulent flow simulations}},
      journal = {{International Journal of Multiphase Flow}},
      volume = {99},
      pages = {437-435},
      year = {2018},
      note = {{doi: 10.1016/j.ijmultiphaseflow.2017.11.010}},
      cclpaperid = {944},
    }

2017

1. Poster: Wharf: Sharing Docker Images across Hosts from a Distributed Filesystem

   Chao Zheng, Lukas Rupprecht, Vasily Tarasov, Mohamed Mohamed, Dimitrios Skourtis, Amit S. Warke, and Dean Hildebrand Douglas Thain

   In IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, 2017

   Bib

   @inproceedings{wharf-sc17,
     author = {Zheng, Chao and Rupprecht, Lukas and Tarasov, Vasily and Mohamed, Mohamed and Skourtis, Dimitrios and Warke, Amit S. and Thain, Dean Hildebrand Douglas},
     title = {{Poster: Wharf: Sharing Docker Images across Hosts from a Distributed Filesystem}},
     booktitle = {{IEEE International Conference for High Performance Computing, Networking, Storage and Analysis}},
     year = {2017},
     cclpaperid = {943}
   }

2. 

   Taming Metadata Storms in Parallel Filesystems with MetaFS

   Tim Shaffer and Douglas Thain

   In Workshop on Parallel Data Storage and Data Intensive Scalable Computing Systems, 2017

   doi: 10.1145/3149393.3149401

   Bib PDF

   @inproceedings{metafs-pdsw-2017,
     author = {Shaffer, Tim and Thain, Douglas},
     title = {{Taming Metadata Storms in Parallel Filesystems with MetaFS}},
     booktitle = {{Workshop on Parallel Data Storage and Data Intensive Scalable Computing Systems}},
     pages = {25-30},
     year = {2017},
     note = {{doi: 10.1145/3149393.3149401}},
     cclpaperid = {948},
   }

3. Enabling Implementation and Optimization of Scientific Algorithms via Graphics Processing Units

   James Sweet

   2017

   Bib

   @thesis{sweet-thesis,
     author = {Sweet, James},
     title = {{Enabling Implementation and Optimization of Scientific Algorithms via Graphics Processing Units}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2017},
     cclpaperid = {959}
   }

4. Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications

   Haiyan Meng and Douglas Thain

   In The 17th International Conference on Computational Science (ICCS), 2017

   doi: 10.1016/j.procs.2017.05.116

   Bib

   @inproceedings{PAPER937,
     author = {Meng, Haiyan and Thain, Douglas},
     title = {{Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications}},
     booktitle = {{The 17th International Conference on Computational Science (ICCS)}},
     year = {2017},
     note = {{doi: 10.1016/j.procs.2017.05.116}},
     cclpaperid = {937}
   }

5. 

   Towards Scalable and Dynamic Social Sensing Using A Distributed Computing Framework

   Daniel (Yue) Zhang, Charles (Chao) Zheng, Dong Wang, Doug Thain, Chao Huang, Xin Mu, and Greg Madey

   In The 37th IEEE International Conference on Distributed Computing Systems (ICDCS 2017), 2017

   doi: 10.1109/ICDCS.2017.196

   Bib PDF

   @inproceedings{social-icdcs-2017,
     author = {Zhang, Daniel (Yue) and Zheng, Charles (Chao) and Wang, Dong and Thain, Doug and Huang, Chao and Mu, Xin and Madey, Greg},
     title = {{Towards Scalable and Dynamic Social Sensing Using A Distributed Computing Framework}},
     booktitle = {{The 37th IEEE International Conference on Distributed Computing Systems (ICDCS 2017)}},
     year = {2017},
     note = {{doi: 10.1109/ICDCS.2017.196}},
     cclpaperid = {938},
   }

6. Deploying High Throughput Scientific Workflows on Container Schedulers with Makeflow and Mesos

   Charles (Chao) Zheng, Ben Tovar, and Douglas Thain

   In 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2017), 2017

   doi: 10.1109/CCGRID.2017.9

   Bib

   @inproceedings{makeflow-mesos-ccgrid17.pdf,
     author = {Zheng, Charles (Chao) and Tovar, Ben and Thain, Douglas},
     title = {{Deploying High Throughput Scientific Workflows on Container Schedulers with Makeflow and Mesos}},
     booktitle = {{17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2017)}},
     year = {2017},
     note = {{doi: 10.1109/CCGRID.2017.9}},
     cclpaperid = {939}
   }

7. 

   Improving the Reproducibility of Scientific Applications with Execution Environment Specifications

   Haiyan Meng

   2017

   Bib PDF

   @thesis{meng-thesis,
     author = {Meng, Haiyan},
     title = {{Improving the Reproducibility of Scientific Applications with Execution Environment Specifications}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2017},
     cclpaperid = {940},
   }

8. 

   Designing Self-Tuning Split-Map-Merge Applications for High Cost-Efficiency in the Cloud

   Dinesh Rajan and Douglas Thain

   IEEE Transactions on Cloud Computing, 2017

   doi: 10.1109/TCC.2015.2415780

   Bib PDF

   @article{tuning-tcc-2015,
     author = {Rajan, Dinesh and Thain, Douglas},
     title = {{Designing Self-Tuning Split-Map-Merge Applications for High Cost-Efficiency in the Cloud}},
     journal = {{IEEE Transactions on Cloud Computing}},
     volume = {5},
     number = {2},
     pages = {303-316},
     year = {2017},
     note = {{doi: 10.1109/TCC.2015.2415780}},
     cclpaperid = {909},
   }

2016

1. 

   PRUNE: A Preserving Run Environment for Reproducible Computing

   Peter Ivie and Douglas Thain

   In IEEE Conference on e-Science, 2016

   doi: 10.1109/eScience.2016.7870886

   Bib PDF

   @inproceedings{prune-escience-2016,
     author = {Ivie, Peter and Thain, Douglas},
     title = {{PRUNE: A Preserving Run Environment for Reproducible Computing}},
     booktitle = {{IEEE Conference on e-Science}},
     year = {2016},
     note = {{doi: 10.1109/eScience.2016.7870886}},
     cclpaperid = {930},
   }

2. 

   Conducting Reproducible Research with Umbrella: Tracking, Creating, and Preserving Execution Environments

   Haiyan Meng, Douglas Thain, Alexander Vyushkov, Matthias Wolf, and Anna Woodard

   In IEEE Conference on e-Science, 2016

   doi: 10.1109/eScience.2016.7870889

   Bib PDF

   @inproceedings{umbrella-escience-2016,
     author = {Meng, Haiyan and Thain, Douglas and Vyushkov, Alexander and Wolf, Matthias and Woodard, Anna},
     title = {{Conducting Reproducible Research with Umbrella: Tracking, Creating, and Preserving Execution Environments}},
     booktitle = {{IEEE Conference on e-Science}},
     year = {2016},
     note = {{doi: 10.1109/eScience.2016.7870889}},
     cclpaperid = {931},
   }

3. 

   A First Look at Reproducibility and Non-Determinism in CMS Codes and ROOT Data

   Peter Ivie, Charles (Chao) Zheng, and Douglas Thain

   2016

   Bib PDF

   @techreport{repro-tr-2016,
     author = {Ivie, Peter and Zheng, Charles (Chao) and Thain, Douglas},
     title = {{A First Look at Reproducibility and Non-Determinism in CMS Codes and ROOT Data}},
     institution = {{University of Notre Dame, Computer Science and Engineering Department}},
     number = {2016-01},
     year = {2016},
     cclpaperid = {933},
   }

4. 

   Opportunistic Computing with Lobster: Lessons Learned from Scaling up to 25K Non-Dedicated Cores

   Matthias Wolf, Anna Woodard, Wenzhao Li, Kenyi Hurtado Anampa, Yannakopoulos, Benjamin Tovar, Patrick Donnelly, Paul Brenner, Kevin Lannon, Mike Hildreth, and Douglas Thain

   In International Conference on Computing in High Energy Physics, 2016

   doi: 10.1088/1742-6596/898/5/052036

   Bib PDF

   @inproceedings{oppo-chep2016,
     author = {Wolf, Matthias and Woodard, Anna and Li, Wenzhao and Anampa, Kenyi Hurtado and Yannakopoulos and Tovar, Benjamin and Donnelly, Patrick and Brenner, Paul and Lannon, Kevin and Hildreth, Mike and Thain, Douglas},
     title = {{Opportunistic Computing with Lobster: Lessons Learned from Scaling up to 25K Non-Dedicated Cores}},
     booktitle = {{International Conference on Computing in High Energy Physics}},
     year = {2016},
     note = {{doi: 10.1088/1742-6596/898/5/052036}},
     cclpaperid = {934},
   }

5. 

   Scaling Up a CMS Tier-3 Site with Campus Resources and a 100Gb/s Network Connection: What Could Go Wrong?

   Matthias Wolf, Anna Woodard, Wenzhao Li, Kenyi Hurtado Anampa, Benjamin Tovar, Paul Brenner, Kevin Lannon, Mike Hildreth, and Douglas Thain

   In International Conference on Computing in High Energy Physics, 2016

   doi: 10.1088/1742-6596/898/8/082041

   Bib PDF

   @inproceedings{scaling-chep2016,
     author = {Wolf, Matthias and Woodard, Anna and Li, Wenzhao and Anampa, Kenyi Hurtado and Tovar, Benjamin and Brenner, Paul and Lannon, Kevin and Hildreth, Mike and Thain, Douglas},
     title = {{Scaling Up a CMS Tier-3 Site with Campus Resources and a 100Gb/s Network Connection: What Could Go Wrong?}},
     booktitle = {{International Conference on Computing in High Energy Physics}},
     year = {2016},
     note = {{doi: 10.1088/1742-6596/898/8/082041}},
     cclpaperid = {935},
   }

6. An Analysis of Reproducibility and Non-Determinism in HEP Software and ROOT Data

   Peter Ivie, Charles (Chao) Zheng, and Douglas Thain

   In International Conference on Computing in High Energy and Nuclear Physics, 2016

   doi: 10.1088/1742-6596/898/10/102007

   Bib

   @inproceedings{PAPER936,
     author = {Ivie, Peter and Zheng, Charles (Chao) and Thain, Douglas},
     title = {{An Analysis of Reproducibility and Non-Determinism in HEP Software and ROOT Data}},
     booktitle = {{International Conference on Computing in High Energy and Nuclear Physics}},
     year = {2016},
     note = {{doi: 10.1088/1742-6596/898/10/102007}},
     cclpaperid = {936}
   }

7. DistIA: A Cost-Effective Dynamic Impact Analysis for Distributed Prorgams

   Haipeng Cai and Douglas thain

   In IEEE/ACM International Conference on Automated Software Engineering, 2016

   doi: 10.1145/2970276.2970352

   Bib

   @inproceedings{distia-ase-2016,
     author = {Cai, Haipeng and thain, Douglas},
     title = {{DistIA: A Cost-Effective Dynamic Impact Analysis for Distributed Prorgams}},
     booktitle = {{IEEE/ACM International Conference on Automated Software Engineering}},
     year = {2016},
     note = {{doi: 10.1145/2970276.2970352}},
     cclpaperid = {932}
   }

8. 

   DIAPRO: Unifying Dynamic Impact Analyses for Improved and Variable Cost-Effectiveness

   Haipeng Cai, Raul Santelices, and Douglas Thain

   ACM Transactions on Software Engineering and Methodology, 2016

   doi: 10.1145/2894751

   Bib PDF

   @article{diapro-tosem-2016,
     author = {Cai, Haipeng and Santelices, Raul and Thain, Douglas},
     title = {{DIAPRO: Unifying Dynamic Impact Analyses for Improved and Variable Cost-Effectiveness}},
     journal = {{ACM Transactions on Software Engineering and Methodology}},
     volume = {25},
     number = {2},
     year = {2016},
     note = {{doi: 10.1145/2894751}},
     cclpaperid = {927},
   }

9. Balancing push and pull in Confuga, an active storage cluster file system for scientific workflows

   Patrick Donnelly and Douglas Thain

   Concurrency and Computation: Practice and Experience, 2016

   doi: 10.1002/cpe.3834

   Bib

   @article{ccpe-confuga,
     author = {Donnelly, Patrick and Thain, Douglas},
     title = {{Balancing push and pull in Confuga, an active storage cluster file system for scientific workflows}},
     journal = {{Concurrency and Computation: Practice and Experience}},
     volume = {29},
     number = {4},
     year = {2016},
     note = {{doi: 10.1002/cpe.3834}},
     cclpaperid = {929}
   }

10. 

    Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows

    Patrick Donnelly

    2016

    Bib PDF

    @thesis{pdonnelly-thesis,
      author = {Donnelly, Patrick},
      title = {{Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows}},
      editor = {Thesis, Ph.D.},
      booktitle = {{University of Notre Dame}},
      year = {2016},
      cclpaperid = {928},
    }

2015

1. A Case Study in Preserving a High Energy Physics Application with Parrot

   Haiyan Meng, Matthias Wolf, Peter Ivie, Anna Woodard, Michael Hildreth, and Douglas Thain

   In Journal of Physics: Conference Series (CHEP 2015), 2015

   doi: 10.1088/1742-6596/664/3/032022

   Bib

   @inproceedings{tauroast-chep-2015,
     author = {Meng, Haiyan and Wolf, Matthias and Ivie, Peter and Woodard, Anna and Hildreth, Michael and Thain, Douglas},
     title = {{A Case Study in Preserving a High Energy Physics Application with Parrot}},
     booktitle = {{Journal of Physics: Conference Series (CHEP 2015)}},
     year = {2015},
     note = {{doi: 10.1088/1742-6596/664/3/032022}},
     cclpaperid = {925}
   }

2. 

   The Evolution of Global Scale Filesystems for Scientific Software Distribution

   Jakob Blomer, Predrag Buncic, Rene Meusel, Gerardo Ganis, Igor Sfiligoi, and Douglas Thain

   IEEE/AIP Computing in Science and Engineering, 2015

   doi: 10.1109/MCSE.2015.111

   Bib PDF

   @article{globalfs-cise-2015,
     author = {Blomer, Jakob and Buncic, Predrag and Meusel, Rene and Ganis, Gerardo and Sfiligoi, Igor and Thain, Douglas},
     title = {{The Evolution of Global Scale Filesystems for Scientific Software Distribution}},
     journal = {{IEEE/AIP Computing in Science and Engineering}},
     volume = {17},
     number = {6},
     pages = {61-71},
     year = {2015},
     note = {{doi: 10.1109/MCSE.2015.111}},
     cclpaperid = {926},
   }

3. 

   Techniques for Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness?

   Douglas Thain, Peter Ivie, and Haiyan Meng

   In 12th International Conference on Digital Preservation (iPres), 2015

   doi: 10.7274/R0CZ353M

   Bib PDF

   @inproceedings{techniques-ipres-2015,
     author = {Thain, Douglas and Ivie, Peter and Meng, Haiyan},
     title = {{Techniques for Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness?}},
     booktitle = {{12th International Conference on Digital Preservation (iPres)}},
     year = {2015},
     note = {{doi: 10.7274/R0CZ353M}},
     cclpaperid = {921},
   }

4. 

   DAGViz: A DAG Visualization Tool for Analzying Task Parallel Program Traces

   An Huynh, Douglas Thain, Miquel Pericas, and Kenjiro Taura

   In Workshop on Visual Performance Analysis (VPA) at ACM Supercomputing (SC), 2015

   Bib PDF

   @inproceedings{dagviz-vpa-2015,
     author = {Huynh, An and Thain, Douglas and Pericas, Miquel and Taura, Kenjiro},
     title = {{DAGViz: A DAG Visualization Tool for Analzying Task Parallel Program Traces}},
     booktitle = {{Workshop on Visual Performance Analysis (VPA) at ACM Supercomputing (SC)}},
     year = {2015},
     cclpaperid = {924},
   }

5. 

   Scaling Data Intensive Physics Applications to 10k Cores on Non-Dedicated Clusters with Lobster

   Anna Woodard, Matthias Wolf, Charles Mueller, Nil Valls, Ben Tovar, Patrick Donnelly, Peter Ivie, Kenyi Hurtado Anampa, Paul Brenner, Douglas Thain, Kevin Lannon, and Michael Hildreth

   In IEEE Conference on Cluster Computing, 2015

   Bib PDF

   @inproceedings{lobster-cluster-2015,
     author = {Woodard, Anna and Wolf, Matthias and Mueller, Charles and Valls, Nil and Tovar, Ben and Donnelly, Patrick and Ivie, Peter and Anampa, Kenyi Hurtado and Brenner, Paul and Thain, Douglas and Lannon, Kevin and Hildreth, Michael},
     title = {{Scaling Data Intensive Physics Applications to 10k Cores on Non-Dedicated Clusters with Lobster}},
     booktitle = {{IEEE Conference on Cluster Computing}},
     year = {2015},
     cclpaperid = {915},
   }

6. Adapting Collaborative Software Development Techniques to Structural Engineering

   Peter Sempolinski, Daniel Wei, Ahsan Kareem, and Douglas Thain

   IEEE/AIP Computing in Science and Engineering, 2015

   doi: 10.1109/MCSE.2015.88

   Bib

   @article{collab-cise-2015,
     author = {Sempolinski, Peter and Wei, Daniel and Kareem, Ahsan and Thain, Douglas},
     title = {{Adapting Collaborative Software Development Techniques to Structural Engineering}},
     journal = {{IEEE/AIP Computing in Science and Engineering}},
     volume = {17},
     number = {51},
     pages = {27-34},
     year = {2015},
     note = {{doi: 10.1109/MCSE.2015.88}},
     cclpaperid = {916}
   }

7. 

   Balancing Thread-level and Task-level Parallelism for Data-Intensive Workloads on Clusters and Clouds

   Olivia Choudhury, Dinesh Rajan, Nicholas Hazekamp, Sandra Gesing, Douglas Thain, and Scott Emrich

   In IEEE Conference on Cluster Computing, 2015

   Bib PDF

   @inproceedings{balancing-cluster-2015,
     author = {Choudhury, Olivia and Rajan, Dinesh and Hazekamp, Nicholas and Gesing, Sandra and Thain, Douglas and Emrich, Scott},
     title = {{Balancing Thread-level and Task-level Parallelism for Data-Intensive Workloads on Clusters and Clouds}},
     booktitle = {{IEEE Conference on Cluster Computing}},
     year = {2015},
     cclpaperid = {919},
   }

8. 

   Practical Resource Monitoring for Robust High Throughput Computing

   Gideon Juve, Benjamin Tovar, Rafael Ferreira Silva, Dariusz Krol, Douglas Thain, Ewa Deelman, William Allcock, and Miron Livny

   In Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications at IEEE Cluster Computing, 2015

   Bib PDF

   @inproceedings{monitoring-hpcmaspa-2015,
     author = {Juve, Gideon and Tovar, Benjamin and da Silva, Rafael Ferreira and Krol, Dariusz and Thain, Douglas and Deelman, Ewa and Allcock, William and Livny, Miron},
     title = {{Practical Resource Monitoring for Robust High Throughput Computing}},
     booktitle = {{Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications at IEEE Cluster Computing}},
     year = {2015},
     cclpaperid = {922},
   }

9. Lessons Learned from Crowdsourcing Complex Engineering Tasks

   Matthew Staffelbach, Peter Sempolinski, Tracy Kijewski-Correa, Douglas Thain, Daniel Wei, Ahsan Kareem, and Gregory Madey

   PLOS One, 2015

   doi: 10.1371/journal.pone.0134978

   Bib

   @article{crowdsourcing-plosone-2015,
     author = {Staffelbach, Matthew and Sempolinski, Peter and Kijewski-Correa, Tracy and Thain, Douglas and Wei, Daniel and Kareem, Ahsan and Madey, Gregory},
     title = {{Lessons Learned from Crowdsourcing Complex Engineering Tasks}},
     journal = {{PLOS One}},
     volume = {10},
     number = {9},
     year = {2015},
     note = {{doi: 10.1371/journal.pone.0134978}},
     cclpaperid = {923}
   }

10. 

    Scaling Up Bioinformatics Workflows with Dynamic Job Expansion

    Nicholas Hazekamp, Joseph Sarro, Olivia Choudhury, Sandra Gesing, Scott Emrich, and Douglas Thain

    In IEEE International Conference on e-Science, 2015

    Bib PDF

    @inproceedings{scaling-escience-2015,
      author = {Hazekamp, Nicholas and Sarro, Joseph and Choudhury, Olivia and Gesing, Sandra and Emrich, Scott and Thain, Douglas},
      title = {{Scaling Up Bioinformatics Workflows with Dynamic Job Expansion}},
      booktitle = {{IEEE International Conference on e-Science}},
      year = {2015},
      cclpaperid = {920},
    }

11. 

    An Invariant Framework for Conducting Reproducible Computational Science

    Haiyan Meng, Rupa Kommineni, Quan Pham, Robert Gardner, Tanu Malik, and Douglas Thain

    Journal of Computational Science, 2015

    doi: 10.1016/j.jocs.2015.04.012

    Bib PDF

    @article{invariant-jocs-2015,
      author = {Meng, Haiyan and Kommineni, Rupa and Pham, Quan and Gardner, Robert and Malik, Tanu and Thain, Douglas},
      title = {{An Invariant Framework for Conducting Reproducible Computational Science}},
      journal = {{Journal of Computational Science}},
      volume = {9},
      pages = {137-142},
      year = {2015},
      note = {{doi: 10.1016/j.jocs.2015.04.012}},
      cclpaperid = {914},
    }

12. 

    Integrating Containers into Workflows: A Case Study Using Makeflow, Work Queue, and Docker

    Charles (Chao) Zheng and Douglas Thain

    In Workshop on Virtualization Technologies in Distributed Computing (VTDC), 2015

    doi: 10.1145/2755979.2755984

    Bib PDF

    @inproceedings{wq-docker-vtdc15,
      author = {Zheng, Charles (Chao) and Thain, Douglas},
      title = {{Integrating Containers into Workflows: A Case Study Using Makeflow, Work Queue, and Docker}},
      booktitle = {{Workshop on Virtualization Technologies in Distributed Computing (VTDC)}},
      year = {2015},
      note = {{doi: 10.1145/2755979.2755984}},
      cclpaperid = {910},
    }

13. 

    Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids

    Haiyan Meng and Douglas Thain

    In Workshop on Virtualization Technologies in Distributed Computing (VTDC) at HPDC, 2015

    doi: 10.1145/2755979.2755982

    Bib PDF

    @inproceedings{umbrella-vtdc15,
      author = {Meng, Haiyan and Thain, Douglas},
      title = {{Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids}},
      booktitle = {{Workshop on Virtualization Technologies in Distributed Computing (VTDC) at HPDC}},
      year = {2015},
      note = {{doi: 10.1145/2755979.2755982}},
      cclpaperid = {912},
    }

14. 

    Confuga: Scalable Data Intensive Computing for POSIX Workflows

    Patrick Donnelly, Nicholas Hazekamp, and Douglas Thain

    In IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 2015

    doi: 10.1109/CCGrid.2015.95

    Bib PDF

    @inproceedings{confuga-ccgrid2015,
      author = {Donnelly, Patrick and Hazekamp, Nicholas and Thain, Douglas},
      title = {{Confuga: Scalable Data Intensive Computing for POSIX Workflows}},
      booktitle = {{IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing}},
      pages = {392-401},
      year = {2015},
      note = {{doi: 10.1109/CCGrid.2015.95}},
      cclpaperid = {908},
    }

15. 

    Principles for the Design and Operation of Elastic Scientific Applications on Distributed Systems

    Dinesh Rajan

    2015

    Bib PDF

    @thesis{dpandiar-dissertation,
      author = {Rajan, Dinesh},
      title = {{Principles for the Design and Operation of Elastic Scientific Applications on Distributed Systems}},
      editor = {Thesis, Ph.D.},
      booktitle = {{University of Notre Dame}},
      year = {2015},
      cclpaperid = {913},
    }

16. 

    Software in Science: a Report of Outcomes of the 2014 National Science Foundation Software Infrastructure for Sustained Innovation (SI2) Meeting

    Beth Plale, Matt Jones, and Douglas Thain

    2015

    Bib PDF

    @techreport{software-nsf-2014,
      author = {Plale, Beth and Jones, Matt and Thain, Douglas},
      title = {{Software in Science: a Report of Outcomes of the 2014 National Science Foundation Software Infrastructure for Sustained Innovation (SI2) Meeting}},
      year = {2015},
      cclpaperid = {911},
    }

17. 

    A Case Study in Preserving a High Energy Physics Application

    Haiyan Meng, Matthias Wolf, Anna Woodard, Peter Ivie, Michael Hildreth, and Douglas Thain

    In Computing in High Energy Physics, 2015

    Bib PDF

    @inproceedings{casestudy-poster-chep-2015,
      author = {Meng, Haiyan and Wolf, Matthias and Woodard, Anna and Ivie, Peter and Hildreth, Michael and Thain, Douglas},
      title = {{A Case Study in Preserving a High Energy Physics Application}},
      booktitle = {{Computing in High Energy Physics}},
      year = {2015},
      cclpaperid = {917},
    }

18. 

    Exploiting Volatile Opportunistic Computing Resources with Lobster

    Anna Woodard, Matthias Wolf, Charles Nicholas Mueller, Ben Tovar, Patrick Donnelly, Kenyi Hurtado Anampa, Paul Brenner, Kevin Lannon, and Michael Hildreth

    In Computing in High Energy Physics, 2015

    Bib PDF

    @inproceedings{lobster-poster-chep-2015,
      author = {Woodard, Anna and Wolf, Matthias and Mueller, Charles Nicholas and Tovar, Ben and Donnelly, Patrick and Anampa, Kenyi Hurtado and Brenner, Paul and Lannon, Kevin and Hildreth, Michael},
      title = {{Exploiting Volatile Opportunistic Computing Resources with Lobster}},
      booktitle = {{Computing in High Energy Physics}},
      year = {2015},
      cclpaperid = {918},
    }

2014

1. 

   AWE-WQ: Fast-Forwarding Molecular Dynamics using the Accelerated Weighted Ensemble

   Badi Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain, and Jesus A. Izaguirre

   Journal of Chemical Information and Modeling, 2014

   doi: 10.1021/ci500321g

   Bib PDF

   @article{awe-jcim-2014,
     author = {Abdul-Wahid, Badi and Feng, Haoyun and Rajan, Dinesh and Costaouec, Ronan and Darve, Eric and Thain, Douglas and Izaguirre, Jesus A.},
     title = {{AWE-WQ: Fast-Forwarding Molecular Dynamics using the Accelerated Weighted Ensemble}},
     journal = {{Journal of Chemical Information and Modeling}},
     volume = {54},
     number = {10},
     pages = {3033-3043},
     year = {2014},
     note = {{doi: 10.1021/ci500321g}},
     cclpaperid = {907},
   }

2. 

   Scaling Up Genome Annotation with MAKER and Work Queue

   Andrew Thrasher, Zachary Musgrave, Brian Kachmark, Douglas Thain, and Scott Emrich

   International Journal of Bioinformatics Research and Applications, 2014

   doi: 10.1504/IJBRA.2014.062994

   Bib PDF

   @article{maker-wq-ijbra,
     author = {Thrasher, Andrew and Musgrave, Zachary and Kachmark, Brian and Thain, Douglas and Emrich, Scott},
     title = {{Scaling Up Genome Annotation with MAKER and Work Queue}},
     journal = {{International Journal of Bioinformatics Research and Applications}},
     volume = {10},
     number = {4-5},
     pages = {447-460},
     year = {2014},
     note = {{doi: 10.1504/IJBRA.2014.062994}},
     cclpaperid = {904},
   }

3. 

   DeltaDB: A Scalable Database Design for Time-Varying Schema-Free Data

   Peter Ivie and Douglas Thain

   In IEEE International Congress on Big Data (BigData 2014), 2014

   doi: 10.1109/BigData.Congress.2014.24

   Bib PDF

   @inproceedings{pivie-deltadb-2014,
     author = {Ivie, Peter and Thain, Douglas},
     title = {{DeltaDB: A Scalable Database Design for Time-Varying Schema-Free Data}},
     booktitle = {{IEEE International Congress on Big Data (BigData 2014)}},
     pages = {104-111},
     year = {2014},
     note = {{doi: 10.1109/BigData.Congress.2014.24 }},
     cclpaperid = {906},
   }

4. 

   Opportunistic High Energy Physics Computing in User Space with Parrot

   Dillon Skeehan, Paul Brenner, Ben Tovar, Douglas Thain, Nil Valls, Anna Woodard, Matthew Wolf, Tessa Pearson, Sean Lynch, and Kevin Lannon

   In IEEE Symposium on Cluster, Cloud, and Grid Computing (CCGrid), 2014

   doi: 10.1109/CCGrid.2014.34

   Bib PDF

   @inproceedings{oppo-ccgrid14,
     author = {Skeehan, Dillon and Brenner, Paul and Tovar, Ben and Thain, Douglas and Valls, Nil and Woodard, Anna and Wolf, Matthew and Pearson, Tessa and Lynch, Sean and Lannon, Kevin},
     title = {{Opportunistic High Energy Physics Computing in User Space with Parrot}},
     booktitle = {{IEEE Symposium on Cluster, Cloud, and Grid Computing (CCGrid)}},
     pages = {170-175},
     year = {2014},
     note = {{doi: 10.1109/CCGrid.2014.34}},
     cclpaperid = {902},
   }

5. 

   Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning

   Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, and Scott Emrich

   In C4BIO Workshop at IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), 2014

   Bib PDF

   @inproceedings{bio-partition-c4bio-grid14,
     author = {Choudhury, Olivia and Hazekamp, Nicholas L. and Thain, Douglas and Emrich, Scott},
     title = {{Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning}},
     booktitle = {{C4BIO Workshop at IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID)}},
     year = {2014},
     cclpaperid = {903},
   }

6. 

   Lessons Learned from an Experiment in Crowdsourcing Complex Citizen Engineering Tasks with Amazon Mechanical Turk

   Matthew Staffelbach, Peter Sempolinski, David Hachen, Ahsan Kareem, Tracy Kijewski-Correa, Douglas Thain, Daniel Wei, and Gregory Madey

   In Collective Intelligence, 2014

   Bib PDF

   @inproceedings{abstract-mechturk,
     author = {Staffelbach, Matthew and Sempolinski, Peter and Hachen, David and Kareem, Ahsan and Kijewski-Correa, Tracy and Thain, Douglas and Wei, Daniel and Madey, Gregory},
     title = {{Lessons Learned from an Experiment in Crowdsourcing Complex Citizen Engineering Tasks with Amazon Mechanical Turk}},
     booktitle = {{Collective Intelligence}},
     year = {2014},
     cclpaperid = {905},
   }

7. 

   Poster: Expanding Tasks of Logical Workflows into Independent Workflows for Improved Scalability

   Nicholas Hazekamp, Olivia Choudhury, Sandra Gesing, Scott Emrich, and Douglas Thain

   In IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 2014

   doi: 10.1109/CCGrid.2014.84

   Bib PDF

   @inproceedings{workflow-expand-grid14,
     author = {Hazekamp, Nicholas and Choudhury, Olivia and Gesing, Sandra and Emrich, Scott and Thain, Douglas},
     title = {{Poster: Expanding Tasks of Logical Workflows into Independent Workflows for Improved Scalability}},
     booktitle = {{IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing}},
     pages = {548-549},
     year = {2014},
     note = {{doi: 10.1109/CCGrid.2014.84}},
     cclpaperid = {901},
   }

2013

1. 

   Automated Packaging of Bioinformatics Workflows for Portability and Durability Using Makeflow

   Casey Robinson and Douglas Thain

   In Workshop on Workflows in Support of Large-Scale Science (WORKS), 2013

   doi: 10.1145/2534248.2534258

   Bib PDF

   @inproceedings{automated-packaging-works13,
     author = {Robinson, Casey and Thain, Douglas},
     title = {{Automated Packaging of Bioinformatics Workflows for Portability and Durability Using Makeflow}},
     booktitle = {{Workshop on Workflows in Support of Large-Scale Science (WORKS)}},
     year = {2013},
     note = {{doi: 10.1145/2534248.2534258}},
     cclpaperid = {899},
   }

2. Design of an Active Storage Cluster File System for DAG Workflows

   Patrick Donnelly and Douglas Thain

   In International Workshop on Data-Intensive Scalable Computing Systems, 2013

   doi: 10.1145/2534645.2534656

   Bib

   @inproceedings{confuga-discs2013,
     author = {Donnelly, Patrick and Thain, Douglas},
     title = {{Design of an Active Storage Cluster File System for DAG Workflows}},
     booktitle = {{International Workshop on Data-Intensive Scalable Computing Systems}},
     pages = {37-42},
     year = {2013},
     note = {{doi: 10.1145/2534645.2534656}},
     cclpaperid = {900}
   }

3. 

   Toward Fine Grained Online Task Chracteristics Estimation in Scientific Workflows

   Rafael Ferreira Silva, Gideon Juve, Ewa Deelman, Tristan Glatard, Frederic Desprez, Douglas Thain, Benjamin Tovar, and Miron Livny

   In Workshop on Workflows in Support of Large Scale Science (WORKS), 2013

   doi: 10.1145/2534248.2534254

   Bib PDF

   @inproceedings{tasks-works-2013,
     author = {da Silva, Rafael Ferreira and Juve, Gideon and Deelman, Ewa and Glatard, Tristan and Desprez, Frederic and Thain, Douglas and Tovar, Benjamin and Livny, Miron},
     title = {{Toward Fine Grained Online Task Chracteristics Estimation in Scientific Workflows}},
     booktitle = {{Workshop on Workflows in Support of Large Scale Science (WORKS)}},
     pages = {58-67},
     year = {2013},
     note = {{doi: 10.1145/2534248.2534254}},
     cclpaperid = {980},
   }

4. 

   Making Work Queue Cluster-Friendly for Data Intensive Scientific Applications

   Michael Albrecht, Dinesh Rajan, and Douglas Thain

   In IEEE International Conference on Cluster Computing, 2013

   doi: 10.1109/CLUSTER.2013.6702628

   Bib PDF

   @inproceedings{wqh-cluster13,
     author = {Albrecht, Michael and Rajan, Dinesh and Thain, Douglas},
     title = {{Making Work Queue Cluster-Friendly for Data Intensive Scientific Applications}},
     booktitle = {{IEEE International Conference on Cluster Computing}},
     year = {2013},
     note = {{doi: 10.1109/CLUSTER.2013.6702628}},
     cclpaperid = {898},
   }

5. Right-sizing Resource Allocations for Scientific Applications in Clusters, Grids, and Clouds

   Li Yu

   2013

   Bib

   @thesis{PAPER896,
     author = {Yu, Li},
     title = {{Right-sizing Resource Allocations for Scientific Applications in Clusters, Grids, and Clouds}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2013},
     cclpaperid = {896}
   }

6. 

   Case Studies in Designing Elastic Applications

   Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesus A Izaguirre, Scott Emrich, and Douglas Thain

   In 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), 2013

   doi: 0.1109/CCGrid.2013.46

   Bib PDF

   @inproceedings{casestudies-ccgrid13,
     author = {Rajan, Dinesh and Thrasher, Andrew and Abdul-Wahid, Badi and Izaguirre, Jesus A and Emrich, Scott and Thain, Douglas},
     title = {{Case Studies in Designing Elastic Applications}},
     booktitle = {{ 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)}},
     year = {2013},
     note = {{doi: 0.1109/CCGrid.2013.46}},
     cclpaperid = {893},
   }

7. 

   Search Should be a System Call

   Brenden Kokoszka, Patrick Donnelly, and Douglas Thain

   2013

   Bib PDF

   @techreport{search-tr,
     author = {Kokoszka, Brenden and Donnelly, Patrick and Thain, Douglas},
     title = {{Search Should be a System Call}},
     institution = {{University of Notre Dame, Computer Science and Engineering Department}},
     number = {2013-03},
     year = {2013},
     cclpaperid = {894},
   }

2012

1. A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids

   Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich, and Douglas Thain

   IEEE Transactions on Parallel and Distributed Systems, 2012

   doi: 10.1109/TPDS.2012.80

   Bib

   @article{assembly-tpds,
     author = {Moretti, Christopher and Thrasher, Andrew and Yu, Li and Olson, Michael and Emrich, Scott and Thain, Douglas},
     title = {{A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids}},
     journal = {{IEEE Transactions on Parallel and Distributed Systems}},
     volume = {23},
     number = {12},
     year = {2012},
     note = {{doi: 10.1109/TPDS.2012.80}},
     cclpaperid = {100}
   }

2. 

   Folding Proteins at 500 ns/hour with Work Queue

   Badi Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, and Jesus A. Izaguirre

   In 8th IEEE International Conference on eScience (eScience 2012), 2012

   doi: 10.1109/eScience.2012.6404429

   Bib PDF

   @inproceedings{folding-escience12,
     author = {Abdul-Wahid, Badi and Yu, Li and Rajan, Dinesh and Feng, Haoyun and Darve, Eric and Thain, Douglas and Izaguirre, Jesus A.},
     title = {{Folding Proteins at 500 ns/hour with Work Queue}},
     booktitle = {{8th IEEE International Conference on eScience (eScience 2012)}},
     year = {2012},
     note = {{doi: 10.1109/eScience.2012.6404429}},
     cclpaperid = {891},
   }

3. A System for Management of Computational Fluid Dynamics Simulations for Civil Engineering

   Peter Sempolinski, Daniel Wei, Douglas Thain, and Ahsan Kareem

   In 8th IEEE International Conference on eScience, 2012

   doi: 10.1109/eScience.2012.6404433

   Bib

   @inproceedings{psempoli-escience12,
     author = {Sempolinski, Peter and Wei, Daniel and Thain, Douglas and Kareem, Ahsan},
     title = {{A System for Management of Computational Fluid Dynamics Simulations for Civil Engineering}},
     booktitle = {{8th IEEE International Conference on eScience}},
     pages = {1-8},
     year = {2012},
     note = {{doi: 10.1109/eScience.2012.6404433 }},
     cclpaperid = {892}
   }

4. 

   ROARS: A Robust Object Archival System for Data Intensive Scientific Computing

   Hoang Bui, Peter Bui, Patrick Flynn, and Douglas Thain

   Distributed and Parallel Databases, 2012

   doi: 10.1007/s10619-012-7103-5

   Bib PDF

   @article{roars-pddb-2012,
     author = {Bui, Hoang and Bui, Peter and Flynn, Patrick and Thain, Douglas},
     title = {{ROARS: A Robust Object Archival System for Data Intensive Scientific Computing}},
     journal = {{Distributed and Parallel Databases}},
     volume = {30},
     number = {5-6},
     publisher = {Springer},
     year = {2012},
     note = {{doi: 10.1007/s10619-012-7103-5}},
     cclpaperid = {890},
   }

5. A Compiler Toolchain For Data Intensive Scientific Workflows

   Peter Bui

   2012

   Bib

   @thesis{pbui-dissertation.pdf,
     author = {Bui, Peter},
     title = {{A Compiler Toolchain For Data Intensive Scientific Workflows}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2012},
     cclpaperid = {889}
   }

6. Fine-Grained Access Control in the Chirp Distributed File System

   Patrick Donnelly and Douglas Thain

   In IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, 2012

   doi: 10.1109/CCGrid.2012.128

   Bib

   @inproceedings{chirp-tickets-ccgrid12,
     author = {Donnelly, Patrick and Thain, Douglas},
     title = {{Fine-Grained Access Control in the Chirp Distributed File System}},
     booktitle = {{IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing}},
     year = {2012},
     note = {{doi: 10.1109/CCGrid.2012.128}},
     cclpaperid = {101}
   }

7. Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters, Clouds, and Grids

   Michael Albrecht, Patrick Donnelly, Peter Bui, and Douglas Thain

   In Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET) at ACM SIGMOD, 2012

   doi: 10.1145/2443416.2443417

   Bib

   @inproceedings{makeflow-sweet12,
     author = {Albrecht, Michael and Donnelly, Patrick and Bui, Peter and Thain, Douglas},
     title = {{Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters, Clouds, and Grids}},
     booktitle = {{Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET) at ACM SIGMOD}},
     year = {2012},
     note = {{doi: 10.1145/2443416.2443417}},
     cclpaperid = {104}
   }

8. 

   A Rich Metadata Filesystem for Scientific Data

   Hoang Bui

   2012

   Bib PDF

   @thesis{hbui-dissertation,
     author = {Bui, Hoang},
     title = {{A Rich Metadata Filesystem for Scientific Data}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2012},
     cclpaperid = {105},
   }

9. 

   Shifting the Bioinformatics Computing Paradigm: A Case Study in Parallelizing Genome Annotation Using Maker and Work Queue

   Andrew Thrasher, Zachary Musgrave, Douglas Thain, and Scott Emrich

   In IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2012

   Bib PDF

   @inproceedings{maker-iccabs12,
     author = {Thrasher, Andrew and Musgrave, Zachary and Thain, Douglas and Emrich, Scott},
     title = {{Shifting the Bioinformatics Computing Paradigm: A Case Study in  Parallelizing Genome Annotation Using Maker and Work Queue}},
     booktitle = {{IEEE International Conference on Computational Advances in Bio and Medical Sciences}},
     year = {2012},
     cclpaperid = {102},
   }

10. Data Intensive Computing with Clustered Chirp Servers

    Douglas Thain, Michael Albrecht, Hoang Bui, Peter Bui, Rory Carmichael, Scott Emrich, and Patrick Flynn

    In Data Intensive Distributed Computing: Challenges and Solutions for Large Scale Information Management, 2012

    isbn: 9781615209712

    Bib

    @incollection{chirp-didc-chapter,
      author = {Thain, Douglas and Albrecht, Michael and Bui, Hoang and Bui, Peter and Carmichael, Rory and Emrich, Scott and Flynn, Patrick},
      title = {{Data Intensive Computing with Clustered Chirp Servers}},
      editor = {Kosar, Tevfik},
      booktitle = {{Data Intensive Distributed Computing: Challenges and Solutions for Large Scale Information Management}},
      pages = {140-154},
      publisher = {IGI},
      year = {2012},
      note = {{isbn: 9781615209712}},
      cclpaperid = {99}
    }

2011

1. 

   Biocompute 2.0: An Improved Collaborative Workspace for Data Intensive Bio-Science.

   Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, and Scott Emrich

   Concurrency and Computation: Practice and Experience, 2011

   doi: 10.1002/cpe.1782

   Bib PDF

   @article{biocompute-ccpe,
     author = {Carmichael, Rory and Braga-Henebry, Patrick and Thain, Douglas and Emrich, Scott},
     title = {{Biocompute 2.0: An Improved Collaborative Workspace for Data Intensive Bio-Science.}},
     journal = {{Concurrency and Computation: Practice and Experience}},
     volume = {23},
     number = {17},
     pages = {2305-2314},
     year = {2011},
     note = {{doi: 10.1002/cpe.1782}},
     cclpaperid = {96},
   }

2. Converting a High Performance Application to an Elastic Cloud Application

   Dinesh Rajan, Anthony Canino, Jesus A Izaguirre, and Douglas Thain

   In The 3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011), 2011

   Bib

   @inproceedings{elasticrepex-cloudcom11,
     author = {Rajan, Dinesh and Canino, Anthony and Izaguirre, Jesus A and Thain, Douglas},
     title = {{Converting a High Performance Application to an Elastic Cloud Application}},
     booktitle = {{The 3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011)}},
     year = {2011},
     cclpaperid = {93}
   }

3. 

   Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications

   Peter Bui, Dinesh Rajan, Badi Abdul-Wahid, Jesus Izaguirre, and Douglas Thain

   In Workshop on Python for High Performance and Scientific Computing (PyHPC) at the ACM/IEEE International Conference for High Performance Computing, Networking, Storage, and Analysis (Supercomputing) , 2011

   Bib PDF

   @inproceedings{wq-python-pyhpc2011,
     author = {Bui, Peter and Rajan, Dinesh and Abdul-Wahid, Badi and Izaguirre, Jesus and Thain, Douglas},
     title = {{Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications}},
     booktitle = {{Workshop on Python for High Performance and Scientific Computing (PyHPC) at the ACM/IEEE International Conference for High Performance Computing, Networking, Storage, and Analysis (Supercomputing) }},
     year = {2011},
     cclpaperid = {95},
   }

4. 

   Scripting distributed scientific workflows using Weaver

   Peter Bui, Li Yu, Andrew Thrasher, Rory Carmichael, Irena Lanc, Patrick Donnelly, and Douglas Thain

   Concurrency and Computation: Practice and Experience, 2011

   doi: 10.1002/cpe.1871

   Bib PDF

   @article{weaver-ccpe,
     author = {Bui, Peter and Yu, Li and Thrasher, Andrew and Carmichael, Rory and Lanc, Irena and Donnelly, Patrick and Thain, Douglas},
     title = {{Scripting distributed scientific workflows using Weaver}},
     journal = {{Concurrency and Computation: Practice and Experience}},
     volume = {24},
     number = {15},
     year = {2011},
     note = {{doi: 10.1002/cpe.1871}},
     cclpaperid = {98},
   }

5. 

   Adapting Bioinformatics Applications for Heterogeneous Systems: A Case Study

   Irena Lanc, Peter Bui, Douglas Thain, and Scott Emrich

   In Emerging Computational Methods for the Life Sciences Workshop at ACM HPDC, 2011

   doi: 10.1145/1996023.1996025

   Bib PDF

   @inproceedings{adapting-ecmls11,
     author = {Lanc, Irena and Bui, Peter and Thain, Douglas and Emrich, Scott},
     title = {{Adapting Bioinformatics Applications for Heterogeneous Systems: A Case Study}},
     booktitle = {{Emerging Computational Methods for the Life Sciences Workshop at ACM HPDC}},
     pages = {7-13},
     year = {2011},
     note = {{doi: 10.1145/1996023.1996025}},
     cclpaperid = {94},
   }

6. An Introduction to Open-Source IaaS Cloud Middleware

   Peter Sempolinski and Douglas Thain

   In Cloud Computing: Methodology, Systems, and Applications, 2011

   isbn: 978-1-4398-5641-3

   Bib

   @incollection{cloud-chapter,
     author = {Sempolinski, Peter and Thain, Douglas},
     title = {{An Introduction to Open-Source IaaS Cloud Middleware}},
     editor = {Benatallah, Boualem},
     booktitle = {{Cloud Computing: Methodology, Systems, and Applications}},
     pages = {133-149},
     publisher = {CRC Press},
     year = {2011},
     note = {{isbn: 978-1-4398-5641-3}},
     cclpaperid = {895}
   }

2010

1. A Comparison and Critique of Eucalyptus, OpenNebula and Nimbus

   Peter Sempolinski and Douglas Thain

   In IEEE International Conference on Cloud Computing Technology and Science, 2010

   doi: 10.1109/CloudCom.2010.42

   Bib

   @inproceedings{survey-cloudCom2010,
     author = {Sempolinski, Peter and Thain, Douglas},
     title = {{A Comparison and Critique of Eucalyptus, OpenNebula and Nimbus}},
     booktitle = {{IEEE International Conference on Cloud Computing Technology and Science}},
     pages = {417-426},
     year = {2010},
     note = {{doi: 10.1109/CloudCom.2010.42}},
     cclpaperid = {89}
   }

2. 

   Attaching Cloud Storage to a Campus Grid Using Parrot, Chirp, and Hadoop

   Patrick Donnelly, Peter Bui, and Douglas Thain

   In IEEE International Conference on Cloud Computing Technology and Science, 2010

   doi: 10.1109/CloudCom.2010.74

   Bib PDF

   @inproceedings{chirp+parrot+hdfs,
     author = {Donnelly, Patrick and Bui, Peter and Thain, Douglas},
     title = {{Attaching Cloud Storage to a Campus Grid Using Parrot, Chirp, and Hadoop}},
     booktitle = {{IEEE International Conference on Cloud Computing Technology and Science}},
     pages = {488-495},
     year = {2010},
     note = {{doi: 10.1109/CloudCom.2010.74}},
     cclpaperid = {90},
   }

3. Taming Complex Bioinformatics Workflows with Weaver, Makeflow, and Starch

   Andrew Thrasher, Rory Carmichael, Peter Bui, Li Yu, Douglas Thain, and Scott Emrich

   In Workshop on Workflows in Support of Large Scale Science, 2010

   doi: 10.1109/WORKS.2010.5671858

   Bib

   @inproceedings{taming-works10.pdf,
     author = {Thrasher, Andrew and Carmichael, Rory and Bui, Peter and Yu, Li and Thain, Douglas and Emrich, Scott},
     title = {{Taming Complex Bioinformatics Workflows with Weaver, Makeflow, and Starch}},
     booktitle = {{Workshop on Workflows in Support of Large Scale Science}},
     pages = {1-6},
     year = {2010},
     note = {{doi: 10.1109/WORKS.2010.5671858}},
     cclpaperid = {92}
   }

4. 

   Harnessing Parallelism in Multicore Clusters with the All-Pairs, Wavefront, and Makeflow Abstractions

   Li Yu, Christopher Moretti, Andrew Thrasher, Scott Emrich, Kenneth Judd, and Douglas Thain

   Journal of Cluster Computing, 2010

   doi: 10.1007/s10586-010-0134-7

   Bib PDF

   @article{abstr-jcc,
     author = {Yu, Li and Moretti, Christopher and Thrasher, Andrew and Emrich, Scott and Judd, Kenneth and Thain, Douglas},
     title = {{Harnessing Parallelism in Multicore Clusters with the All-Pairs, Wavefront, and Makeflow Abstractions}},
     journal = {{Journal of Cluster Computing}},
     volume = {13},
     number = {3},
     pages = {243-256},
     year = {2010},
     note = {{doi: 10.1007/s10586-010-0134-7}},
     cclpaperid = {83},
   }

5. Environmentally Opportunistic Computing: Transforming the Data Center for Economic and Environmental Sustainability

   Paul Brenner, Ryan Jansen, David Go, and Douglas Thain

   In IEEE Green Computing Conference, 2010

   doi: 10.1109/GREENCOMP.2010.5598289

   Bib

   @inproceedings{eoc-green,
     author = {Brenner, Paul and Jansen, Ryan and Go, David and Thain, Douglas},
     title = {{Environmentally Opportunistic Computing: Transforming the Data Center for Economic and Environmental Sustainability}},
     booktitle = {{IEEE Green Computing Conference}},
     pages = {383-388},
     year = {2010},
     note = {{doi: 10.1109/GREENCOMP.2010.5598289  }},
     cclpaperid = {97}
   }

6. Abstractions for Cloud Computing with Condor

   Douglas Thain and Christopher Moretti

   In Cloud Computing and Software Services: Theory and Techniques, 2010

   isbn: 9781439803158

   Bib

   @incollection{abstr-cloudbook,
     author = {Thain, Douglas and Moretti, Christopher},
     title = {{Abstractions for Cloud Computing with Condor}},
     editor = {Ahson, Syed and Ilyas, Mohammad},
     booktitle = {{Cloud Computing and Software Services: Theory and Techniques}},
     pages = {153-171},
     publisher = {CRC Press},
     year = {2010},
     note = {{isbn: 9781439803158}},
     cclpaperid = {78}
   }

7. ROARS: A Scalable Repository for Data Intensive Scientific Computing

   Hoang Bui, Peter Bui, Patrick Flynn, and Douglas Thain

   In The Third International Workshop on Data Intensive Distributed Computing at ACM HPDC 2010, 2010

   doi: 10.1145/1851476.1851587

   Bib

   @inproceedings{roars-didc10,
     author = {Bui, Hoang and Bui, Peter and Flynn, Patrick and Thain, Douglas},
     title = {{ROARS: A Scalable Repository for Data Intensive Scientific Computing}},
     booktitle = {{The Third International Workshop on Data Intensive Distributed Computing at ACM HPDC 2010}},
     year = {2010},
     note = {{doi: 10.1145/1851476.1851587}},
     cclpaperid = {85}
   }

8. Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python

   Peter Bui, Li Yu, and Douglas Thain

   In Challenges of Large Applications in Distributed Environments at ACM HPDC 2010, 2010

   doi: 10.1145/1851476.1851570

   Bib

   @inproceedings{weaver-clade10,
     author = {Bui, Peter and Yu, Li and Thain, Douglas},
     title = {{Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python}},
     booktitle = {{Challenges of Large Applications in Distributed Environments at ACM HPDC 2010}},
     year = {2010},
     note = {{doi: 10.1145/1851476.1851570}},
     cclpaperid = {86}
   }

9. Towards Long Term Data Quality in a Large Scale Biometrics Experiment

   Hoang Bui, Diane Wright, Clarence Helm, Rachel Witty, Patrick Flynn, and Douglas Thain

   In Managing Data Quality for Collaborative Science at ACM HPDC 2010, 2010

   doi: 10.1145/1851476.1851559

   Bib

   @inproceedings{quality-didc10,
     author = {Bui, Hoang and Wright, Diane and Helm, Clarence and Witty, Rachel and Flynn, Patrick and Thain, Douglas},
     title = {{Towards Long Term Data Quality in a Large Scale Biometrics Experiment}},
     booktitle = {{Managing Data Quality for Collaborative Science at ACM HPDC 2010}},
     year = {2010},
     note = {{doi: 10.1145/1851476.1851559}},
     cclpaperid = {87}
   }

10. 

    Abstractions for Scientific Computing on Campus Grids

    Christopher Moretti

    2010

    Bib PDF

    @thesis{moretti-dissertation,
      author = {Moretti, Christopher},
      title = {{Abstractions for Scientific Computing on Campus Grids}},
      editor = {Thesis, Ph.D.},
      booktitle = {{University of Notre Dame}},
      year = {2010},
      cclpaperid = {88},
    }

11. Biocompute: Toward a Collaborative Workspace for Data Intensive Bio-Science

    Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, and Scott Emrich

    In Workshop on Emerging Computational Methods for Life Sciences at ACM HPDC 2010, 2010

    doi: 10.1145/1851476.1851547

    Bib

    @inproceedings{biocompute-ecmls,
      author = {Carmichael, Rory and Braga-Henebry, Patrick and Thain, Douglas and Emrich, Scott},
      title = {{Biocompute: Toward a Collaborative Workspace for Data Intensive Bio-Science}},
      booktitle = {{Workshop on Emerging Computational Methods for Life Sciences at ACM HPDC 2010}},
      pages = {489-498},
      year = {2010},
      note = {{doi: 10.1145/1851476.1851547}},
      cclpaperid = {91}
    }

12. All-Pairs: An Abstraction for Data Intensive Computing on Campus Grids

    Christopher Moretti, Hoang Bui, Karen Hollingsworth, Brandon Rich, Patrick Flynn, and Douglas Thain

    IEEE Transactions on Parallel and Distributed Systems, 2010

    doi: 10.1109/TPDS.2009.49

    Bib

    @article{allpairs-tpds,
      author = {Moretti, Christopher and Bui, Hoang and Hollingsworth, Karen and Rich, Brandon and Flynn, Patrick and Thain, Douglas},
      title = {{All-Pairs: An Abstraction for Data Intensive Computing on Campus Grids}},
      journal = {{IEEE Transactions on Parallel and Distributed Systems}},
      volume = {21},
      number = {1},
      pages = {33-46},
      year = {2010},
      note = {{doi: 10.1109/TPDS.2009.49}},
      cclpaperid = {12}
    }

13. Visualizing Massively Multithreaded Applications with ThreadScope

    Kyle Wheeler and Douglas Thain

    Concurrency and Computation: Practice and Experience, 2010

    doi: 10.1002/cpe.1469

    Bib

    @article{threadscope-ccpe09,
      author = {Wheeler, Kyle and Thain, Douglas},
      title = {{Visualizing Massively Multithreaded Applications with ThreadScope}},
      journal = {{Concurrency and Computation: Practice and Experience}},
      volume = {22},
      number = {1},
      pages = {45-67},
      year = {2010},
      note = {{doi: 10.1002/cpe.1469}},
      cclpaperid = {59}
    }

2009

1. Towards Data Intensive Many Task Computing

   Ioan Raicu, Ian Foster, Yong Zhao, Alex Szalay, Philip Little, Christopher Moretti, Amitabh Chaudhary, and Douglas Thain

   In Data Intensive Distributed Computing: Challenges and Solutions for Large-Scale Information Management, 2009

   Bib

   @incollection{raicu-manytask-chapter,
     author = {Raicu, Ioan and Foster, Ian and Zhao, Yong and Szalay, Alex and Little, Philip and Moretti, Christopher and Chaudhary, Amitabh and Thain, Douglas},
     title = {{Towards Data Intensive Many Task Computing}},
     editor = {Kosar, Tevfik},
     booktitle = {{Data Intensive Distributed Computing: Challenges and Solutions for Large-Scale Information Management}},
     publisher = {IGI},
     year = {2009},
     cclpaperid = {80}
   }

2. 

   Exploiting Locality with QThreads for Portable Parallel Performance

   Kyle Wheeler

   2009

   Bib PDF

   @thesis{wheeler-thesis,
     author = {Wheeler, Kyle},
     title = {{Exploiting Locality with QThreads for Portable Parallel Performance}},
     editor = {Thesis, Ph.D.},
     booktitle = {{University of Notre Dame}},
     year = {2009},
     cclpaperid = {81},
   }

3. 

   Highly Scalable Genome Assembly on Campus Grids

   Christopher Moretti, Michael Olson, Scott Emrich, and Douglas Thain

   In Many-Task Computing on Grids and Supercomputers (MTAGS), 2009

   doi: 10.1145/1646468.1646480

   Bib PDF

   @inproceedings{assembly-mtags09,
     author = {Moretti, Christopher and Olson, Michael and Emrich, Scott and Thain, Douglas},
     title = {{Highly Scalable Genome Assembly on Campus Grids}},
     booktitle = {{Many-Task Computing on Grids and Supercomputers (MTAGS)}},
     year = {2009},
     note = {{doi: 10.1145/1646468.1646480}},
     cclpaperid = {82},
   }

4. 

   Reflections on the Virtues of Modularity: A Case Study in Linux Security Modules

   Andrew Blaich, Douglas Thain, and Aaron Striegel

   Software: Practice and Experience, 2009

   doi: 10.1002/spe.933

   Bib PDF

   @article{modularity-spe,
     author = {Blaich, Andrew and Thain, Douglas and Striegel, Aaron},
     title = {{Reflections on the Virtues of Modularity: A Case Study in Linux Security Modules}},
     journal = {{Software: Practice and Experience}},
     volume = {39},
     number = {15},
     pages = {1235-1251},
     year = {2009},
     note = {{doi: 10.1002/spe.933}},
     cclpaperid = {11},
   }

5. Cooperative Localization in GPS-Limited Urban Environments

   Jeffrey Hemmes, Douglas Thain, and Christian Poellabauer

   In ICST AdHocNets, 2009

   Bib

   @inproceedings{teamtrak-adhocnets,
     author = {Hemmes, Jeffrey and Thain, Douglas and Poellabauer, Christian},
     title = {{Cooperative Localization in GPS-Limited Urban Environments}},
     booktitle = {{ICST AdHocNets}},
     year = {2009},
     cclpaperid = {61}
   }

6. 

   Scheduling Grid Workloads on Multicore Clusters to Minimize Energy and Maximize Performance

   Michael Lammie, Douglas Thain, and Paul Brenner

   In IEEE Grid Computing, 2009

   Bib PDF

   @inproceedings{multicore-grid09,
     author = {Lammie, Michael and Thain, Douglas and Brenner, Paul},
     title = {{Scheduling Grid Workloads on Multicore Clusters to Minimize Energy and Maximize Performance}},
     booktitle = {{IEEE Grid Computing}},
     year = {2009},
     cclpaperid = {75},
   }

7. 

   Portable Performance from Workstation to Supercomputer: Distributing Data Structures with Qthreads

   Kyle Wheeler, Douglas Thain, and Rich Murphy

   In Workshop on Programming Models for Emerging Architectures, 2009

   Bib PDF

   @inproceedings{qthreads-pmea09,
     author = {Wheeler, Kyle and Thain, Douglas and Murphy, Rich},
     title = {{Portable Performance from Workstation to Supercomputer: Distributing Data Structures with Qthreads}},
     booktitle = {{Workshop on Programming Models for Emerging Architectures}},
     pages = {1-8},
     year = {2009},
     cclpaperid = {76},
   }

8. Coordination of Access to Large-scale Datasets in Distributed Environments

   T. Kosar, A. Hutanu, J. McLaren, and D. Thain

   In Scientific Data Management: Challenges, Existing Technology, and Deployment, 2009

   isbn: 978-1420069808

   Bib

   @incollection{kosar-databook,
     author = {Kosar, T. and Hutanu, A. and McLaren, J. and Thain, D.},
     title = {{Coordination of Access to Large-scale Datasets in Distributed Environments}},
     editor = {Shoshani, A. and Rotem, D.},
     booktitle = {{Scientific Data Management: Challenges, Existing Technology, and Deployment}},
     publisher = {Chapman and Hall / CRC Press},
     year = {2009},
     note = {{isbn: 978-1420069808}},
     cclpaperid = {8}
   }

9. Scalable Modular Genome Assembly on Campus Grids

   Christopher Moretti, Michael Olson, Scott Emrich, and Douglas Thain

   2009

   Bib

   @techreport{assembly-tr,
     author = {Moretti, Christopher and Olson, Michael and Emrich, Scott and Thain, Douglas},
     title = {{Scalable Modular Genome Assembly on Campus Grids}},
     institution = {{University of Notre Dame, Computer Science and Engineering Department}},
     number = {2009-04},
     year = {2009},
     cclpaperid = {77}
   }

10. 

    Improving Data Availability in Mobile Applications Through Enhanced Cooperative Localization

    Jeffrey Hemmes

    2009

    Bib PDF

    @thesis{jhemmes-thesis,
      author = {Hemmes, Jeffrey},
      title = {{Improving Data Availability in Mobile Applications Through Enhanced Cooperative Localization}},
      editor = {Thesis, Ph.D.},
      booktitle = {{University of Notre Dame}},
      year = {2009},
      cclpaperid = {79},
    }

11. 

    Harnessing Parallelism in Multicore Clusters with the All-Pairs and Wavefront Abstractions

    Li Yu, Christopher Moretti, Scott Emrich, Kenneth Judd, and Douglas Thain

    In IEEE High Performance Distributed Computing, 2009

    doi: 10.1145/1551609.1551613

    Bib PDF

    @inproceedings{abstr-hpdc09,
      author = {Yu, Li and Moretti, Christopher and Emrich, Scott and Judd, Kenneth and Thain, Douglas},
      title = {{Harnessing Parallelism in Multicore Clusters with the All-Pairs and Wavefront Abstractions}},
      booktitle = {{IEEE High Performance Distributed Computing}},
      pages = {1-10},
      year = {2009},
      note = {{doi: 10.1145/1551609.1551613}},
      cclpaperid = {5},
    }

12. 

    Grid Heating Clusters: Transforming Cooling Constraints Into Thermal Benefits

    Paul Brenner, Douglas Thain, and Dewitt Latimer

    In The Uptime Institute Green Enterprise IT Award Paper, 2009

    Bib PDF

    @inproceedings{gheat-uptime09,
      author = {Brenner, Paul and Thain, Douglas and Latimer, Dewitt},
      title = {{Grid Heating Clusters: Transforming Cooling Constraints Into Thermal Benefits}},
      booktitle = {{The Uptime Institute Green Enterprise IT Award Paper}},
      pages = {1-7},
      year = {2009},
      cclpaperid = {60},
    }

13. 

    CDF Software Distribution on the Grid using Parrot

    Gabrielle Compostella, Simone Pagan Griso, Donatella Lucchesi, Igor Sfiligoi, and Douglas Thain

    In Computing in High Energy Physics, 2009

    doi: 10.1088/1742-6596/219/6/062009

    Bib PDF

    @inproceedings{parrot-chep09,
      author = {Compostella, Gabrielle and Griso, Simone Pagan and Lucchesi, Donatella and Sfiligoi, Igor and Thain, Douglas},
      title = {{CDF Software Distribution on the Grid using Parrot}},
      booktitle = {{Computing in High Energy Physics}},
      year = {2009},
      note = {{doi: 10.1088/1742-6596/219/6/062009}},
      cclpaperid = {22},
    }

14. Biocompute: Harnessing Distributed Systems for Bioinformatics

    Patrick Braga-Henebry

    2009

    Bib

    @thesis{pbh-thesis,
      author = {Braga-Henebry, Patrick},
      title = {{Biocompute: Harnessing Distributed Systems for Bioinformatics}},
      editor = {Thesis, B.S. Honors},
      booktitle = {{University of Notre Dame}},
      year = {2009},
      cclpaperid = {64}
    }

15. Experience with BXGrid: A Data Repository and Computing Grid for Biometrics Research

    Hoang Bui, Michael Kelly, Christopher Lyon, Mark Pasquier, Deborah Thomas, Patrick Flynn, and Douglas Thain

    Journal of Cluster Computing, 2009

    doi: 10.1007/s10586-009-0098-7

    Bib

    @article{bxgrid-jcc,
      author = {Bui, Hoang and Kelly, Michael and Lyon, Christopher and Pasquier, Mark and Thomas, Deborah and Flynn, Patrick and Thain, Douglas},
      title = {{Experience with BXGrid: A Data Repository and Computing Grid for Biometrics Research}},
      journal = {{Journal of Cluster Computing}},
      volume = {12},
      number = {4},
      pages = {373},
      year = {2009},
      note = {{doi: 10.1007/s10586-009-0098-7}},
      cclpaperid = {1}
    }

16. 

    Chirp: A Practical Global Filesystem for Cluster and Grid Computing

    Douglas Thain, Christopher Moretti, and Jeffrey Hemmes

    Journal of Grid Computing, 2009

    doi: 10.1007/s10723-008-9100-5

    Bib PDF

    @article{chirp-jgc,
      author = {Thain, Douglas and Moretti, Christopher and Hemmes, Jeffrey},
      title = {{Chirp: A Practical Global Filesystem for Cluster and Grid Computing}},
      journal = {{Journal of Grid Computing}},
      volume = {7},
      number = {1},
      pages = {51-72},
      year = {2009},
      note = {{doi: 10.1007/s10723-008-9100-5}},
      cclpaperid = {14},
    }

2008

1. Poster: BXGrid: A Data Repository and Workflow Abstraction for Biometrics Research

   Hoang Bui, Deborah Thomas, Michael Kelly, Christopher Lyon, Douglas Thain, and Patrick J. Flynn

   2008

   isbn: 10.1109/eScience.2008.135

   Bib

   @article{bxgrid-escience09,
     author = {Bui, Hoang and Thomas, Deborah and Kelly, Michael and Lyon, Christopher and Thain, Douglas and Flynn, Patrick J.},
     title = {{Poster: BXGrid: A Data Repository and Workflow Abstraction for Biometrics Research}},
     booktitle = {{IEEE International Conference on e-Science}},
     pages = {394-395},
     year = {2008},
     note = {{isbn: 10.1109/eScience.2008.135}},
     cclpaperid = {24}
   }

2. 

   Scaling Up Classifiers to Cloud Computers

   Christopher Moretti, Karsten Steinhaeuser, Douglas Thain, and Nitesh V. Chawla

   In IEEE International Conference on Data Mining (ICDM), 2008

   doi: 10.1109/ICDM.2008.99

   Bib PDF

   @inproceedings{classify-icdm08,
     author = {Moretti, Christopher and Steinhaeuser, Karsten and Thain, Douglas and Chawla, Nitesh V.},
     title = {{Scaling Up Classifiers to Cloud Computers}},
     booktitle = {{IEEE International Conference on Data Mining (ICDM)}},
     pages = {472-481},
     year = {2008},
     note = {{doi: 10.1109/ICDM.2008.99}},
     cclpaperid = {25},
   }

3. Biomolecular Committor Probability Calculation Enabled by Processing in Network Storage

   Paul Brenner, Justin Wozniak, Douglas Thain Aaron Striegel, Jeffrey Peng, and Jesus Izaguirre

   Journal of Parallel Computing, 2008

   doi: 10.1016/j.parco.2008.08.001

   Bib

   @article{pins-jpc,
     author = {Brenner, Paul and Wozniak, Justin and Striegel, Douglas Thain Aaron and Peng, Jeffrey and Izaguirre, Jesus},
     title = {{Biomolecular Committor Probability Calculation Enabled by Processing in Network Storage}},
     journal = {{Journal of Parallel Computing}},
     volume = {34},
     number = {11},
     pages = {652-660},
     year = {2008},
     note = {{doi: 10.1016/j.parco.2008.08.001}},
     cclpaperid = {13}
   }

4. 

   ENAVis: Enterprise Network Activities Visualization

   Qi Liao, Andrew Blaich, Aaron Striegel, and Douglas Thain

   In USENIX Large Installation System Administration (LISA), 2008

   Bib PDF

   @inproceedings{enavis-lisa08,
     author = {Liao, Qi and Blaich, Andrew and Striegel, Aaron and Thain, Douglas},
     title = {{ENAVis: Enterprise Network Activities Visualization}},
     booktitle = {{USENIX Large Installation System Administration (LISA)}},
     pages = {59-74},
     year = {2008},
     cclpaperid = {23},
   }

5. 

   Troubleshooting Thousands of Jobs on Production Grids Using Data Mining Techniques

   David Cieslak, Nitesh Chawla, and Douglas Thain

   In IEEE Grid Computing, 2008

   doi: 10.1109/GRID.2008.4662802

   Bib PDF

   @inproceedings{debug-grid08,
     author = {Cieslak, David and Chawla, Nitesh and Thain, Douglas},
     title = {{Troubleshooting Thousands of Jobs on Production Grids Using Data Mining Techniques}},
     booktitle = {{IEEE Grid Computing}},
     pages = {217-224},
     year = {2008},
     note = {{doi: 10.1109/GRID.2008.4662802}},
     cclpaperid = {26},
   }

6. 

   Poster: DataLab: Transactional Data Parallel Computing on an Active Storage Cloud

   Brandon Rich and Douglas Thain

   In IEEE/ACM High Performance Distributed Computing, 2008

   isbn: 10.1145/1383422.1383461

   Bib PDF

   @inproceedings{datalab-hpdc08,
     author = {Rich, Brandon and Thain, Douglas},
     title = {{Poster: DataLab: Transactional Data Parallel Computing on an Active Storage Cloud}},
     booktitle = {{IEEE/ACM High Performance Distributed Computing}},
     pages = {233-234},
     year = {2008},
     note = {{isbn: 10.1145/1383422.1383461}},
     cclpaperid = {27},
   }

7. 

   All-Pairs: An Abstraction for Data Intensive Cloud Computing

   Christopher Moretti, Jared Bulosan, Douglas Thain, and Patrick Flynn

   In IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2008

   doi: 10.1109/IPDPS.2008.4536311

   Bib PDF

   @inproceedings{allpairs-ipdps08,
     author = {Moretti, Christopher and Bulosan, Jared and Thain, Douglas and Flynn, Patrick},
     title = {{All-Pairs: An Abstraction for Data Intensive Cloud Computing}},
     booktitle = {{IEEE International Parallel and Distributed Processing Symposium (IPDPS)}},
     pages = {1-11},
     year = {2008},
     note = {{doi: 10.1109/IPDPS.2008.4536311 }},
     cclpaperid = {28},
   }

8. 

   QThreads: An API for Programming with Millions of Lightweight Threads

   Kyle Wheeler, Richard Murphy, and Douglas thain

   In Workshop on Multithreaded Architectures and Applications at IEEE IPDPS, 2008

   doi: 10.1109/IPDPS.2008.4536359

   Bib PDF

   @inproceedings{qthreads-mtaap08,
     author = {Wheeler, Kyle and Murphy, Richard and thain, Douglas},
     title = {{QThreads: An API for Programming with Millions of Lightweight Threads}},
     booktitle = {{Workshop on Multithreaded Architectures and Applications at IEEE IPDPS}},
     pages = {1-8},
     year = {2008},
     note = {{doi: 10.1109/IPDPS.2008.4536359}},
     cclpaperid = {29},
   }

9. 

   Towards a Data Analysis Grid for Biometrics Research

   Douglas Thain and Patrick Flynn

   2008

   Bib PDF

   @techreport{bxgrid-tr,
     author = {Thain, Douglas and Flynn, Patrick},
     title = {{Towards a Data Analysis Grid for Biometrics Research}},
     institution = {{University of Notre Dame, Computer Science and Engineering Department}},
     number = {2008-05},
     year = {2008},
     cclpaperid = {62},
   }

10. Making the Best of a Bad Situation: Prioritized Storage Management in GEMS

    Justin Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus Izaguirre

    Future Generation Computing Systems, 2008

    doi: 10.1016/j.future.2007.04.003

    Bib

    @article{priority-fgcs,
      author = {Wozniak, Justin and Brenner, Paul and Thain, Douglas and Striegel, Aaron and Izaguirre, Jesus},
      title = {{Making the Best of a Bad Situation: Prioritized Storage Management in GEMS}},
      journal = {{Future Generation Computing Systems}},
      volume = {24},
      number = {1},
      pages = {10-16},
      year = {2008},
      note = {{doi: 10.1016/j.future.2007.04.003}},
      cclpaperid = {15}
    }

11. Grid Heating: Transforming Cooling Constraints Into Thermal Benefits

    Paul Brenner, Douglas Thain, and Dewitt Latimer

    2008

    Bib

    @techreport{gheat-tr,
      author = {Brenner, Paul and Thain, Douglas and Latimer, Dewitt},
      title = {{Grid Heating: Transforming Cooling Constraints Into Thermal Benefits}},
      institution = {{University of Notre Dame, Computer Science and Engineering Department}},
      number = {2008-09},
      year = {2008},
      cclpaperid = {7}
    }

2007

1. On Demand Transient Storage and Backup in Mobile Systems

   Jeffrey Hemmes, Christian Poellabauer, and Douglas Thain

   In IEEE Military Communications Conference, 2007

   doi: 10.1109/MILCOM.2007.4454917

   Bib

   @inproceedings{teamtrak-milcom07,
     author = {Hemmes, Jeffrey and Poellabauer, Christian and Thain, Douglas},
     title = {{On Demand Transient Storage and Backup in Mobile Systems}},
     booktitle = {{IEEE Military Communications Conference}},
     pages = {1-7},
     year = {2007},
     note = {{doi: 10.1109/MILCOM.2007.4454917}},
     cclpaperid = {30}
   }

2. Lessons Learned Building TeamTrak: An Urban/Outdoor Mobile Testbed

   Jeffrey Hemmes, Douglas Thain, Christian Poellabauer, Christopher Moretti, Phil Snowberger, and Brendan McNutt

   In International Conference on Wireless Architectures Systems and Applications, 2007

   doi: 10.1109/WASA.2007.35

   Bib

   @inproceedings{teamtrak-wasa07,
     author = {Hemmes, Jeffrey and Thain, Douglas and Poellabauer, Christian and Moretti, Christopher and Snowberger, Phil and McNutt, Brendan},
     title = {{Lessons Learned Building TeamTrak: An Urban/Outdoor Mobile Testbed}},
     booktitle = {{International Conference on Wireless Architectures Systems and Applications}},
     pages = {219-224},
     year = {2007},
     note = {{doi: 10.1109/WASA.2007.35}},
     cclpaperid = {33}
   }

3. Work in Progress: Integrating Undergraduate Research and Education via the TeamTrak Mobile Computing Framework

   Jeffrey Hemmes, Douglas Thain, and Christian Poellabauer

   In IEEE Frontiers in Education, 2007

   doi: 10.1109/FIE.2007.4418007

   Bib

   @inproceedings{teamtrak-fie07,
     author = {Hemmes, Jeffrey and Thain, Douglas and Poellabauer, Christian},
     title = {{Work in Progress: Integrating Undergraduate Research and Education via the TeamTrak Mobile Computing Framework}},
     booktitle = {{IEEE Frontiers in Education}},
     pages = {1-2},
     year = {2007},
     note = {{doi: 10.1109/FIE.2007.4418007}},
     cclpaperid = {35}
   }

4. 

   Efficient Access to Many Small Files in a Filesystem for Grid Computing

   Douglas Thain and Christopher Moretti

   In IEEE Grid Computing, 2007

   doi: 10.1109/GRID.2007.4354139

   Bib PDF

   @inproceedings{small-grid07,
     author = {Thain, Douglas and Moretti, Christopher},
     title = {{Efficient Access to Many Small Files in a Filesystem for Grid Computing}},
     booktitle = {{IEEE Grid Computing}},
     pages = {243-250},
     year = {2007},
     note = {{doi: 10.1109/GRID.2007.4354139}},
     cclpaperid = {31},
   }

5. Poster: Lockdown: Distributed Policy Analysis and Enforcement within the Enterprise Network

   Andrew Blaich, Qi Liao, Greg Allan, Aaron Striegel, and Douglas Thain

   In USENIX Security Symposium, 2007

   Bib

   @inproceedings{lockdown-security07,
     author = {Blaich, Andrew and Liao, Qi and Allan, Greg and Striegel, Aaron and Thain, Douglas},
     title = {{Poster: Lockdown: Distributed Policy Analysis and Enforcement within the Enterprise Network}},
     booktitle = {{USENIX Security Symposium}},
     year = {2007},
     cclpaperid = {32}
   }

6. 

   Poster: All-Pairs: An Abstraction for Data Intensive Computing

   Christopher Moretti, Jared Bulosan, Douglas Thain, and Patrick J. Flynn

   In IEEE/ACM Grid Computing, 2007

   Bib PDF

   @inproceedings{allpairs-grid07,
     author = {Moretti, Christopher and Bulosan, Jared and Thain, Douglas and Flynn, Patrick J.},
     title = {{Poster: All-Pairs: An Abstraction for Data Intensive Computing}},
     booktitle = {{IEEE/ACM Grid Computing}},
     year = {2007},
     cclpaperid = {63},
   }

7. 

   Challenges in Executing Data Intensive Biometric Workloads on a Desktop Grid

   Christopher Moretti, Timothy Faltemier, Douglas Thain, and Patrick J. Flynn

   In Workshop on Large Scale and Volatile Desktop Grids at IEEE IPDPS, 2007

   doi: 10.1109/IPDPS.2007.370671

   Bib PDF

   @inproceedings{challenges-pcgrid07,
     author = {Moretti, Christopher and Faltemier, Timothy and Thain, Douglas and Flynn, Patrick J.},
     title = {{Challenges in Executing Data Intensive Biometric Workloads on a Desktop Grid}},
     booktitle = {{Workshop on Large Scale and Volatile Desktop Grids at IEEE IPDPS}},
     pages = {481-489},
     year = {2007},
     note = {{doi: 10.1109/IPDPS.2007.370671}},
     cclpaperid = {34},
   }

8. Biomolecular Path Sampling Enabled by Processing in Network Storage

   Paul Brenner, Justin Wozniak, Douglas Thain, Aaron Striegel, Jeffrey Peng, and Jesus Izaguirre

   In Workshop on High Performance Computational Biology at IEEE IPDPS, 2007

   doi: 10.1109/IPDPS.2007.370446

   Bib

   @inproceedings{pins-bio07,
     author = {Brenner, Paul and Wozniak, Justin and Thain, Douglas and Striegel, Aaron and Peng, Jeffrey and Izaguirre, Jesus},
     title = {{Biomolecular Path Sampling Enabled by Processing in Network Storage}},
     booktitle = {{Workshop on High Performance Computational Biology at IEEE IPDPS}},
     pages = {1-6},
     year = {2007},
     note = {{doi: 10.1109/IPDPS.2007.370446}},
     cclpaperid = {36}
   }

9. Flexible Object Based Filesystems for Scientific Computing

   Christopher Moretti

   2007

   Bib

   @thesis{moretti-ms-thesis,
     author = {Moretti, Christopher},
     title = {{Flexible Object Based Filesystems for Scientific Computing}},
     editor = {Thesis, M.S.},
     booktitle = {{University of Notre Dame}},
     year = {2007},
     cclpaperid = {65}
   }

10. Sub-Identities: A Hierarchical Identity Model for Practical Containment

    Philip Snowberger

    2007

    Bib

    @thesis{snowberger-ms-thesis,
      author = {Snowberger, Philip},
      title = {{Sub-Identities: A Hierarchical Identity Model for Practical Containment}},
      editor = {Thesis, M.S.},
      booktitle = {{University of Notre Dame}},
      year = {2007},
      cclpaperid = {66}
    }