Papers

2026

1. 

   GROWFLOW: Low-latency Computational Fluid Dynamics at the Edge for Real-time Agricultural Decision Support

   Liubov Kurafeeva, Benjamin Carter, Ryan Hartung, Alan Subedi, Avhishek Biswas, Michael Fay, Shantenu Jha, Chandra Krintz, Andre Merzky, Douglas Thain, Mehmet Can Vuran, and Rich Wolski

   In IEEE SCSETech, 2026

   Bib PDF

   @inproceedings{growflow-2026,
     author = {Kurafeeva, Liubov and Carter, Benjamin and Hartung, Ryan and Subedi, Alan and Biswas, Avhishek and Fay, Michael and Jha, Shantenu and Krintz, Chandra and Merzky, Andre and Thain, Douglas and Vuran, Mehmet Can and Wolski, Rich},
     title = {{GROWFLOW: Low-latency Computational Fluid Dynamics at the Edge for Real-time Agricultural Decision Support}},
     booktitle = {{IEEE SCSETech}},
     pages = {6},
     year = {2026},
     cclpaperid = {1012}
   }

2. 

   Hybrid Workflow Composition for Extreme-Scale Data Processing: A Case Study on the HL-LHC

   Alan Malta Rodrigues and Douglas Thain

   In IEEE Conference on eScience, 2026

   Bib PDF

   @inproceedings{hl-lhc-escience-2026,
     author = {Rodrigues, Alan Malta and Thain, Douglas},
     title = {{Hybrid Workflow Composition for Extreme-Scale Data Processing: A Case Study on the HL-LHC}},
     booktitle = {{IEEE Conference on eScience}},
     pages = {10},
     year = {2026},
     cclpaperid = {1011},
     keywords = {Directed Acyclic Graphs (DAGs), Discrete-Event Simulation, High-Throughput Computing, Performance Modeling, Resource Optimization, Scientific Workflows, Workflow Management Systems}
   }

3. 

   Fusion and Reshaping of Hidden Task Graphs for High Energy Physics Applications

   Barry Sly-Delgado and Douglas Thain

   In IEEE Conference on eScience, 2026

   Bib PDF

   @inproceedings{reshaping-escience-2026,
     author = {Sly-Delgado, Barry and Thain, Douglas},
     title = {{Fusion and Reshaping of Hidden Task Graphs for High Energy Physics Applications}},
     booktitle = {{IEEE Conference on eScience}},
     pages = {7},
     year = {2026},
     cclpaperid = {1010},
     keywords = {taskvine, hep, dask}
   }

4. 

   Declare, Resolve, Reuse: A Portable Data Layer for Notebook Workflows Across HPC Systems

   Md Saiful Islam, Reyer Band, Jin Zhou, Tanu Malik, Kevin Lannon, and Douglas Thain

   In IEEE Conference on eScience, 2026

   Bib PDF

   @inproceedings{floability-escience-2026,
     author = {Islam, Md Saiful and Band, Reyer and Zhou, Jin and Malik, Tanu and Lannon, Kevin and Thain, Douglas},
     title = {{Declare, Resolve, Reuse: A Portable Data Layer for Notebook Workflows Across HPC Systems}},
     booktitle = {{IEEE Conference on eScience}},
     pages = {9},
     year = {2026},
     cclpaperid = {1009},
     keywords = {floability}
   }

5. 

   X-Bucket: A Family of Algorithms for Adaptive Resource Allocation in Dynamic Workflows

   Thanh Son Phung and Douglas Thain

   IEEE Transactions on Parallel & Distributed Systems, 2026

   doi: 10.1109/TPDS.2026.3707191

   DOI Bib PDF

   @article{x-bucket-tpds26,
     author = {Phung, Thanh Son and Thain, Douglas},
     title = {X-Bucket: A Family of Algorithms for Adaptive Resource Allocation in Dynamic Workflows},
     journal = {IEEE Transactions on Parallel \& Distributed Systems},
     keywords = {Resource management, Algorithms, Memory, Timing, Radio access networks, Regional area networks, Schedules, Scheduling, Costing, Costs},
     year = {2026},
     volume = {},
     number = {01},
     issn = {1558-2183},
     pages = {1-15},
     note = {{doi: 10.1109/TPDS.2026.3707191}},
     cclpaperid = {1008},
     doi = {10.1109/TPDS.2026.3707191}
   }

6. 

   SciWIND: Effectively Exploiting Node-Local Storage for Data-Intensive High-Energy Physics Workflows

   Jin Zhou, Colin Thomas, Barry Sly-Delgado, Connor Moore, Benjamin Tovar, Kevin Lannon, and Douglas Thain

   In IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2026

   doi: 10.1109/IPDPS65963.2026.00050

   DOI Bib PDF

   @inproceedings{sciwind-ipdps-2026,
     author = {Zhou, Jin and Thomas, Colin and Sly-Delgado, Barry and Moore, Connor and Tovar, Benjamin and Lannon, Kevin and Thain, Douglas},
     title = {{SciWIND: Effectively Exploiting Node-Local Storage for Data-Intensive High-Energy Physics Workflows}},
     booktitle = {{IEEE International Parallel and Distributed Processing Symposium (IPDPS)}},
     year = {2026},
     cclpaperid = {1007},
     note = {{doi: 10.1109/IPDPS65963.2026.00050}},
     doi = {10.1109/IPDPS65963.2026.00050}
   }

7. 

   SADE-SIM: A Scalable Simulation Platform for Validating City-Scale Multi-sUAS Missions

   Laxminarayana Vadnala, Lucas Parzianello, Bohan Zhang, Michael Murphy, Ankit Agrawal, and Douglas Thain

   In Workshop on Software Engineering for Engineering Simulations, and Simulation Engineering for Engineering Software (SE4ES) 2026, 2026

   doi: 10.1145/3803437.3805540

   DOI Bib PDF

   @inproceedings{sade-sim-2026,
     author = {Vadnala, Laxminarayana and Parzianello, Lucas and Zhang, Bohan and Murphy, Michael and Agrawal, Ankit and Thain, Douglas},
     title = {{SADE-SIM: A Scalable Simulation Platform for Validating City-Scale Multi-sUAS Missions}},
     booktitle = {{Workshop on Software Engineering for Engineering Simulations, and Simulation Engineering for Engineering Software (SE4ES) 2026}},
     pages = {8},
     year = {2026},
     cclpaperid = {1006},
     keywords = {sade},
     note = {{doi: 10.1145/3803437.3805540}},
     doi = {10.1145/3803437.3805540}
   }

8. 

   A terminology for scientific workflow systems

   Frédéric Suter, Tainã Coleman, İlkay Altintaş, Rosa M. Badia, Bartosz Balis, Kyle Chard, Iacopo Colonnelli, Ewa Deelman, Paolo Di Tommaso, Thomas Fahringer, Carole Goble, Shantenu Jha, Daniel S. Katz, Johannes Köster, Ulf Leser, Kshitij Mehta, Hilary Oliver, J.-Luc Peterson, Giovanni Pizzi, Loïc Pottier, Raül Sirvent, Eric Suchyta, Douglas Thain, Sean R. Wilkinson, Justin M. Wozniak, and Rafael Ferreira Silva

   Future Generation Computing Systems, Jan 2026

   doi: 10.1016/j.future.2025.107974

   DOI Bib PDF

   @article{terms-fgcs-2025,
     author = {Suter, Frédéric and Coleman, Tainã and Altintaş, İlkay and Badia, Rosa M. and Balis, Bartosz and Chard, Kyle and Colonnelli, Iacopo and Deelman, Ewa and Tommaso, Paolo Di and Fahringer, Thomas and Goble, Carole and Jha, Shantenu and Katz, Daniel S. and Köster, Johannes and Leser, Ulf and Mehta, Kshitij and Oliver, Hilary and Peterson, J.-Luc and Pizzi, Giovanni and Pottier, Loïc and Sirvent, Raül and Suchyta, Eric and Thain, Douglas and Wilkinson, Sean R. and Wozniak, Justin M. and da Silva, Rafael Ferreira},
     title = {A terminology for scientific workflow systems},
     journal = {Future Generation Computing Systems},
     year = {2026},
     volume = {17},
     month = jan,
     number = {107974},
     note = {{doi: 10.1016/j.future.2025.107974}},
     doi = {10.1016/j.future.2025.107974}
   }

2025

1. 

   Scaling Up Throughput-oriented LLM Inference Applications on Heterogeneous Opportunistic GPU Clusters with Pervasive Context Management

   Thanh Son Phung and Douglas Thain

   Jan 2025

   doi: 10.48550/arXiv.2509.13201

   DOI Bib PDF

   @misc{phung2025scalingthroughputorientedllminference,
     title = {Scaling Up Throughput-oriented LLM Inference Applications on Heterogeneous Opportunistic GPU Clusters with Pervasive Context Management},
     author = {Phung, Thanh Son and Thain, Douglas},
     year = {2025},
     eprint = {2509.13201},
     archiveprefix = {arXiv},
     primaryclass = {cs.DC},
     url = {https://arxiv.org/abs/2509.13201},
     keywords = {taskvine, llm, gpu},
     note = {{doi: 10.48550/arXiv.2509.13201}},
     doi = {10.48550/arXiv.2509.13201}
   }

2. 

   Reshaping Analysis for Fast Turnaround: Leveraging Concurrency to Reduce Latency in Late-Stage LHC Analysis Workflows

   Kevin Lannon, Connor Moore, Barry Sly-Delgado, Benjamin Tovar, Austin Townsend, and Jin Zhou

   In 27th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2024), Jan 2025

   doi: 10.1051/epjconf/202533701283

   DOI Bib PDF

   @inproceedings{reshaping-chep-2025,
     author = {Lannon, Kevin and Moore, Connor and Sly-Delgado, Barry and Tovar, Benjamin and Townsend, Austin and Zhou, Jin},
     title = {Reshaping Analysis for Fast Turnaround: Leveraging Concurrency to Reduce Latency in Late-Stage LHC Analysis Workflows},
     booktitle = {{27th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2024)}},
     year = {2025},
     keywords = {taskvine, hep},
     note = {{doi: 10.1051/epjconf/202533701283}},
     doi = {10.1051/epjconf/202533701283}
   }

3. 

   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, Jan 2025

   doi: 10.1145/3731599.3767589

   DOI 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},
     note = {{doi: 10.1145/3731599.3767589}},
     doi = {10.1145/3731599.3767589}
   }

4. 

   Backpacks for Notebooks: Enabling Containerized Notebook Workflows in Distributed Environments

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

   In IEEE Conference on eScience, Jan 2025

   doi: 10.1109/eScience65000.2025.00028

   DOI Bib PDF

   @inproceedings{floability-escience-2025,
     author = {Islam, Md Saiful and Azaz, Talha and Ahmad, Raza and Hossain, A S 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},
     note = {{doi: 10.1109/eScience65000.2025.00028}},
     doi = {10.1109/eScience65000.2025.00028}
   }

5. 

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

   Colin Thomas and Douglas Thain

   In IEEE Conference on eScience, Jan 2025

   doi: 10.1109/eScience65000.2025.00029

   DOI 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},
     note = {{doi: 10.1109/eScience65000.2025.00029}},
     doi = {10.1109/eScience65000.2025.00029}
   }

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, Jan 2024

   doi: 10.1109/SC41406.2024.00068

   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, hep},
     note = {{doi: 10.1109/SC41406.2024.00068}},
     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, Jan 2024

   doi: 10.1109/SCW63240.2024.00260

   DOI 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},
     note = {{doi: 10.1109/SCW63240.2024.00260}},
     doi = {10.1109/SCW63240.2024.00260}
   }

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), Jan 2024

   doi: 10.1145/3625549.3658663

   DOI 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},
     keywords = {taskvine},
     note = {{doi: 10.1145/3625549.3658663}},
     doi = {10.1145/3625549.3658663}
   }

4. 

   Poster: Leveraging Intermediate Data Management with Parsl/TaskVine

   Colin Thomas and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, Jan 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, Jan 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, Jan 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},
     keywords = {taskvine},
   }

7. 

   Poster: Import Hoisting for Serverless Libraries

   Jin Zhou and Douglas Thain

   In Greater Chicago Area Systems Research Workshop, Jan 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, Jan 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), Jan 2024

   doi: 10.1109/IPDPS57955.2024.00034

   DOI 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},
     note = {{doi: 10.1109/IPDPS57955.2024.00034}},
     doi = {10.1109/IPDPS57955.2024.00034}
   }

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), Jan 2023

   doi: 10.1145/3624062.3624136

   DOI 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},
     keywords = {taskvine},
     note = {{doi: 10.1145/3624062.3624136}},
     doi = {10.1145/3624062.3624136}
   }

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, Jan 2023

   doi: 10.1145/3624062.3624277

   DOI 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},
     note = {{doi: 10.1145/3624062.3624277}},
     doi = {10.1145/3624062.3624277}
   }

3. 

   Poster: Minimizing Data Movement Using Distant Futures

   Barry Sly-Delgado and Douglas Thain

   In ACM/IEEE Supercomputing, Jan 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},
     keywords = {taskvine},
   }

4. 

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

   Douglas Thain

   In CSSI PI Meeting, Jan 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, Jan 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, Jan 2023

   doi: 10.1109/TPDS.2023.3241598

   DOI Bib PDF

   @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},
     doi = {10.1109/TPDS.2023.3241598}
   }

2022

1. 

   Poster: Robust Meta-Workflow Management with Mufasa

   Ben Lyons and Douglas Thain

   In IEEE International Conference on eScience, Jan 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, Jan 2022

   doi: 10.1109/IPDPS53621.2022.00041

   DOI Bib PDF

   @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}},
     doi = {10.1109/IPDPS53621.2022.00041},
     cclpaperid = {979},
     keywords = {workqueue, hep},
   }

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, Jan 2022

   doi: 10.1145/3526060.3535459

   DOI 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}},
     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, Jan 2022

   Bib PDF

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

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, Jan 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, Jan 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},
     keywords = {workqueue, resource_monitor},
   }

2. 

   Regulating Traffic in Crowded Cache

   Kevin Gao, Tim Shaffer, and Kyle Chard

   In Student Poster Session at Supercomputing, Jan 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, Jan 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

   Jan 2021

   doi: 10.5281/zenodo.4891790

   DOI Bib PDF

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

   doi: 10.1109/IPDPS49936.2021.00088

   DOI Bib PDF

   @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}},
     doi = {10.1109/IPDPS49936.2021.00088},
     cclpaperid = {968},
     keywords = {workqueue, resource_monitor},
   }

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), Jan 2021

   doi: 10.1051/epjconf/202125102032

   DOI Bib PDF

   @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}},
     doi = {10.1051/epjconf/202125102032},
     cclpaperid = {973},
     keywords = {workqueue},
   }

7. 

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

   Nathaniel Kremer-Herman

   Jan 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), Jan 2021

   doi: 10.1109/WORKS54523.2021.00016

   DOI Bib PDF

   @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}},
     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, Jan 2020

   doi: 10.1109/CLUSTER49012.2020.00024

   DOI 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}},
     doi = {10.1109/CLUSTER49012.2020.00024},
     cclpaperid = {967},
     keywords = {workqueue},
   }

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), Jan 2020

   doi: 10.1145/3311790.3396633

   DOI 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}},
     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, Jan 2020

   doi: 10.1109/IPDPS47924.2020.00048

   DOI Bib PDF

   @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}},
     doi = {10.1109/IPDPS47924.2020.00048},
     cclpaperid = {964},
   }

2019

1. 

   Methods Enabling Portability of Scientific Workflows

   Nicholas Hazekamp

   Jan 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

   Jan 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, Jan 2019

   doi: 10.1109/eScience.2019.00026

   DOI 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}},
     doi = {10.1109/eScience.2019.00026},
     cclpaperid = {962},
     keywords = {workqueue},
   }

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), Jan 2019

   doi: 10.1145/3332186.3338100

   DOI Bib PDF

   @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}},
     doi = {10.1145/3332186.3338100},
     cclpaperid = {961},
     keywords = {makeflow, jx},
   }

2018

1. 

   A Lightweight Model for Right-Sizing Master-Worker Applications

   Nathaniel Kremer-Herman, Benjamin Tovar, and Douglas Thain

   In ACM/IEEE Supercomputing (SC), Jan 2018

   doi: 10.1109/SC.2018.00042

   DOI Bib PDF

   @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}},
     doi = {10.1109/SC.2018.00042},
     cclpaperid = {955},
     keywords = {workqueue},
   }

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, Jan 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},
     keywords = {makeflow, resource_monitor},
   }

3. 

   An Algebra for Robust Workflow Transformations

   Nicholas Hazekamp and Douglas Thain

   In IEEE International Conference on e-Science, Jan 2018

   doi: 10.1109/eScience.2018.00031

   DOI Bib PDF

   @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}},
     doi = {10.1109/eScience.2018.00031},
     cclpaperid = {953},
     keywords = {makeflow},
   }

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, Jan 2018

   doi: 10.1109/eScience.2018.00094

   DOI Bib PDF

   @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}},
     doi = {10.1109/eScience.2018.00094},
     cclpaperid = {954},
     keywords = {makeflow, jx},
   }

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, Jan 2018

   doi: 10.1145/3267809.3267836

   DOI 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}},
     doi = {10.1145/3267809.3267836},
     cclpaperid = {957},
     keywords = {filesystems, career, gridfs},
   }

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, Jan 2018

   doi: 10.1145/3219104.3219125

   DOI 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}},
     doi = {10.1145/3219104.3219125},
     cclpaperid = {949},
     keywords = {vc3},
   }

7. 

   Reproducibility in Scientific Computing

   Peter Ivie and Douglas Thain

   ACM Computing Surveys, Jan 2018

   doi: 10.1145/3186266

   DOI 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}},
     doi = {10.1145/3186266},
     cclpaperid = {952},
     keywords = {daspos},
   }

8. 

   Early Experience Using Amazon Batch for Scientific Workflows

   Kyle Sweeney and Douglas Thain

   In ScienceCloud Workshop at HPDC , Jan 2018

   doi: 10.1145/3217880.3217885

   DOI 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}},
     doi = {10.1145/3217880.3217885},
     cclpaperid = {950},
     keywords = {makeflow},
   }

9. 

   Efficient Integration of Containers into Scientific Workflows

   Kyle Sweeney and Douglas Thain

   In Science Cloud Workshop at HPDC, Jan 2018

   doi: 10.1145/3217880.3217887

   DOI 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}},
     doi = {10.1145/3217880.3217887},
     cclpaperid = {951},
     keywords = {makeflow},
   }

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) , Jan 2018

    doi: 10.1109/IC2E.2018.00026

    DOI Bib PDF

    @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}},
      doi = {10.1109/IC2E.2018.00026},
      cclpaperid = {945},
      keywords = {vc3},
    }

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, Jan 2018

    doi: 10.1109/IC2E.2018.00029

    DOI 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}},
      doi = {10.1109/IC2E.2018.00029},
      cclpaperid = {946},
      keywords = {workqueue},
    }

12. 

    A Workflow Management System to Facilitate Reproducibility of Scientific Computing Applications

    Peter Ivie

    Jan 2018

    Bib PDF

    @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, Jan 2018

    doi: 10.1109/WACV.2018.00086

    DOI 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}},
      doi = {10.1109/WACV.2018.00086},
      cclpaperid = {947},
      keywords = {workqueue},
    }

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, Jan 2018

    doi: 10.1109/TPDS.2017.2762310

    DOI Bib PDF

    @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}},
      doi = {10.1109/TPDS.2017.2762310},
      cclpaperid = {941},
      keywords = {workqueue, resource_monitor},
    }

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, Jan 2018

    doi: 10.1109/TPDS.2017.2764897

    DOI 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}},
      doi = {10.1109/TPDS.2017.2764897},
      cclpaperid = {942},
      keywords = {makeflow},
    }

16. 

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

    James Sweet, David Richter, and Douglas Thain

    International Journal of Multiphase Flow, Jan 2018

    doi: 10.1016/j.ijmultiphaseflow.2017.11.010

    DOI 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}},
      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, Jan 2017

   Bib PDF

   @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, Jan 2017

   doi: 10.1145/3149393.3149401

   DOI 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}},
     doi = {10.1145/3149393.3149401},
     cclpaperid = {948},
     keywords = {filesystems, career, gridfs},
   }

3. 

   Enabling Implementation and Optimization of Scientific Algorithms via Graphics Processing Units

   James Sweet

   Jan 2017

   Bib PDF

   @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), Jan 2017

   doi: 10.1016/j.procs.2017.05.116

   DOI Bib PDF

   @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}},
     doi = {10.1016/j.procs.2017.05.116},
     cclpaperid = {937},
     keywords = {makeflow, umbrella},
   }

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), Jan 2017

   doi: 10.1109/ICDCS.2017.196

   DOI 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}},
     doi = {10.1109/ICDCS.2017.196},
     cclpaperid = {938},
     keywords = {workqueue},
   }

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), Jan 2017

   doi: 10.1109/CCGRID.2017.9

   DOI Bib PDF

   @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}},
     doi = {10.1109/CCGRID.2017.9},
     cclpaperid = {939},
     keywords = {makeflow},
   }

7. 

   Improving the Reproducibility of Scientific Applications with Execution Environment Specifications

   Haiyan Meng

   Jan 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, Jan 2017

   doi: 10.1109/TCC.2015.2415780

   DOI 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}},
     doi = {10.1109/TCC.2015.2415780},
     cclpaperid = {909},
     keywords = {makeflow, workqueue, hecura},
   }

2016

1. 

   PRUNE: A Preserving Run Environment for Reproducible Computing

   Peter Ivie and Douglas Thain

   In IEEE Conference on e-Science, Jan 2016

   doi: 10.1109/eScience.2016.7870886

   DOI 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}},
     doi = {10.1109/eScience.2016.7870886},
     cclpaperid = {930},
     keywords = {workqueue, prune, daspos},
   }

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, Jan 2016

   doi: 10.1109/eScience.2016.7870889

   DOI 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}},
     doi = {10.1109/eScience.2016.7870889},
     cclpaperid = {931},
     keywords = {parrot, umbrella, daspos},
   }

3. 

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

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

   Jan 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},
     keywords = {daspos},
   }

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, Jan 2016

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

   DOI 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}},
     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, Jan 2016

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

   DOI 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}},
     doi = {10.1088/1742-6596/898/8/082041},
     cclpaperid = {935},
     keywords = {workqueue},
   }

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, Jan 2016

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

   DOI Bib PDF

   @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}},
     doi = {10.1088/1742-6596/898/10/102007},
     cclpaperid = {936},
     keywords = {daspos},
   }

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, Jan 2016

   doi: 10.1145/2970276.2970352

   DOI Bib PDF

   @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}},
     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, Jan 2016

   doi: 10.1145/2894751

   DOI 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}},
     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, Jan 2016

   doi: 10.1002/cpe.3834

   DOI Bib PDF

   @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}},
     doi = {10.1002/cpe.3834},
     cclpaperid = {929},
     keywords = {makeflow, chirp, confuga},
   }

10. 

    Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows

    Patrick Donnelly

    Jan 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},
      keywords = {makeflow, chirp, confuga},
    }

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), Jan 2015

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

   DOI Bib PDF

   @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}},
     doi = {10.1088/1742-6596/664/3/032022},
     cclpaperid = {925},
     keywords = {parrot, daspos},
   }

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, Jan 2015

   doi: 10.1109/MCSE.2015.111

   DOI 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}},
     doi = {10.1109/MCSE.2015.111},
     cclpaperid = {926},
     keywords = {parrot, filesystems, career, gridfs},
   }

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), Jan 2015

   doi: 10.7274/R0CZ353M

   DOI 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}},
     doi = {10.7274/R0CZ353M},
     cclpaperid = {921},
     keywords = {parrot, prune, umbrella, daspos},
   }

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), Jan 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, Jan 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},
     keywords = {workqueue, hep},
   }

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, Jan 2015

   doi: 10.1109/MCSE.2015.88

   DOI Bib PDF

   @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}},
     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, Jan 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, Jan 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},
     keywords = {resource_monitor},
   }

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, Jan 2015

   doi: 10.1371/journal.pone.0134978

   DOI Bib PDF

   @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}},
     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, Jan 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},
      keywords = {makeflow},
    }

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, Jan 2015

    doi: 10.1016/j.jocs.2015.04.012

    DOI 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}},
      doi = {10.1016/j.jocs.2015.04.012},
      cclpaperid = {914},
      keywords = {parrot},
    }

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), Jan 2015

    doi: 10.1145/2755979.2755984

    DOI 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}},
      doi = {10.1145/2755979.2755984},
      cclpaperid = {910},
      keywords = {makeflow, workqueue},
    }

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, Jan 2015

    doi: 10.1145/2755979.2755982

    DOI 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}},
      doi = {10.1145/2755979.2755982},
      cclpaperid = {912},
      keywords = {parrot, umbrella},
    }

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, Jan 2015

    doi: 10.1109/CCGrid.2015.95

    DOI 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}},
      doi = {10.1109/CCGrid.2015.95},
      cclpaperid = {908},
      keywords = {makeflow, chirp, confuga},
    }

15. 

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

    Dinesh Rajan

    Jan 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

    Jan 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, Jan 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, Jan 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},
      keywords = {workqueue},
    }

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, Jan 2014

   doi: 10.1021/ci500321g

   DOI 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}},
     doi = {10.1021/ci500321g},
     cclpaperid = {907},
     keywords = {workqueue, awe},
   }

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, Jan 2014

   doi: 10.1504/IJBRA.2014.062994

   DOI 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}},
     doi = {10.1504/IJBRA.2014.062994},
     cclpaperid = {904},
     keywords = {workqueue},
   }

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), Jan 2014

   doi: 10.1109/BigData.Congress.2014.24

   DOI 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 }},
     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), Jan 2014

   doi: 10.1109/CCGrid.2014.34

   DOI 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}},
     doi = {10.1109/CCGrid.2014.34},
     cclpaperid = {902},
     keywords = {parrot},
   }

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), Jan 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},
     keywords = {makeflow, workqueue},
   }

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, Jan 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, Jan 2014

   doi: 10.1109/CCGrid.2014.84

   DOI 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}},
     doi = {10.1109/CCGrid.2014.84},
     cclpaperid = {901},
     keywords = {makeflow},
   }

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), Jan 2013

   doi: 10.1145/2534248.2534258

   DOI 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}},
     doi = {10.1145/2534248.2534258},
     cclpaperid = {899},
     keywords = {makeflow},
   }

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, Jan 2013

   doi: 10.1145/2534645.2534656

   DOI Bib PDF

   @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}},
     doi = {10.1145/2534645.2534656},
     cclpaperid = {900},
     keywords = {chirp, confuga},
   }

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), Jan 2013

   doi: 10.1145/2534248.2534254

   DOI 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}},
     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, Jan 2013

   doi: 10.1109/CLUSTER.2013.6702628

   DOI 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}},
     doi = {10.1109/CLUSTER.2013.6702628},
     cclpaperid = {898},
     keywords = {workqueue, awe},
   }

5. 

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

   Li Yu

   Jan 2013

   Bib PDF

   @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), Jan 2013

   doi: 0.1109/CCGrid.2013.46

   DOI 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}},
     doi = {0.1109/CCGrid.2013.46},
     cclpaperid = {893},
     keywords = {workqueue},
   }

7. 

   Search Should be a System Call

   Brenden Kokoszka, Patrick Donnelly, and Douglas Thain

   Jan 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, Jan 2012

   doi: 10.1109/TPDS.2012.80

   DOI Bib PDF

   @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}},
     doi = {10.1109/TPDS.2012.80},
     cclpaperid = {100},
     keywords = {workqueue, sand},
   }

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), Jan 2012

   doi: 10.1109/eScience.2012.6404429

   DOI 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}},
     doi = {10.1109/eScience.2012.6404429},
     cclpaperid = {891},
     keywords = {workqueue, awe},
   }

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, Jan 2012

   doi: 10.1109/eScience.2012.6404433

   DOI Bib PDF

   @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 }},
     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, Jan 2012

   doi: 10.1007/s10619-012-7103-5

   DOI 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}},
     doi = {10.1007/s10619-012-7103-5},
     cclpaperid = {890},
     keywords = {chirp},
   }

5. 

   A Compiler Toolchain For Data Intensive Scientific Workflows

   Peter Bui

   Jan 2012

   Bib PDF

   @thesis{pbui-dissertation,
     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},
     keywords = {makeflow, hecura},
   }

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, Jan 2012

   doi: 10.1109/CCGrid.2012.128

   DOI Bib PDF

   @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}},
     doi = {10.1109/CCGrid.2012.128},
     cclpaperid = {101},
     keywords = {parrot, chirp, filesystems, career, gridfs},
   }

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, Jan 2012

   doi: 10.1145/2443416.2443417

   DOI Bib PDF

   @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}},
     doi = {10.1145/2443416.2443417},
     cclpaperid = {104},
     keywords = {makeflow, hecura},
   }

8. 

   A Rich Metadata Filesystem for Scientific Data

   Hoang Bui

   Jan 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},
     keywords = {filesystems, career, gridfs},
   }

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, Jan 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},
     keywords = {workqueue},
   }

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, Jan 2012

    isbn: 9781615209712

    DOI 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}},
      doi = {10.4018/978-1-61520-971-2.ch009},
      cclpaperid = {99},
      keywords = {chirp, filesystems, career, gridfs}
    }

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, Jan 2011

   doi: 10.1002/cpe.1782

   DOI 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}},
     doi = {10.1002/cpe.1782},
     cclpaperid = {96},
     keywords = {makeflow},
   }

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), Jan 2011

   Bib PDF

   @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},
     keywords = {workqueue},
   }

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) , Jan 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},
     keywords = {workqueue, awe},
   }

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, Jan 2011

   doi: 10.1002/cpe.1871

   DOI 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}},
     doi = {10.1002/cpe.1871},
     cclpaperid = {98},
     keywords = {makeflow},
   }

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, Jan 2011

   doi: 10.1145/1996023.1996025

   DOI 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}},
     doi = {10.1145/1996023.1996025},
     cclpaperid = {94},
     keywords = {workqueue},
   }

6. 

   An Introduction to Open-Source IaaS Cloud Middleware

   Peter Sempolinski and Douglas Thain

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

   isbn: 978-1-4398-5641-3

   DOI 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}},
     doi = {10.1201/b11149-7},
     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, Jan 2010

   doi: 10.1109/CloudCom.2010.42

   DOI Bib PDF

   @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}},
     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, Jan 2010

   doi: 10.1109/CloudCom.2010.74

   DOI 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}},
     doi = {10.1109/CloudCom.2010.74},
     cclpaperid = {90},
     keywords = {parrot, chirp, filesystems, career, gridfs},
   }

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, Jan 2010

   doi: 10.1109/WORKS.2010.5671858

   DOI Bib PDF

   @inproceedings{taming-works10,
     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}},
     doi = {10.1109/WORKS.2010.5671858},
     cclpaperid = {92},
     keywords = {makeflow},
   }

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, Jan 2010

   doi: 10.1007/s10586-010-0134-7

   DOI 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}},
     doi = {10.1007/s10586-010-0134-7},
     cclpaperid = {83},
     keywords = {makeflow, workqueue, allpairs, wavefront, hecura},
   }

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, Jan 2010

   doi: 10.1109/GREENCOMP.2010.5598289

   DOI Bib PDF

   @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  }},
     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, Jan 2010

   isbn: 9781439803158

   Bib PDF

   @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},
     keywords = {workqueue, wavefront, hecura},
   }

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, Jan 2010

   doi: 10.1145/1851476.1851587

   DOI Bib PDF

   @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}},
     doi = {10.1145/1851476.1851587},
     cclpaperid = {85},
     keywords = {chirp, filesystems, career, hecura, gridfs},
   }

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, Jan 2010

   doi: 10.1145/1851476.1851570

   DOI Bib PDF

   @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}},
     doi = {10.1145/1851476.1851570},
     cclpaperid = {86},
     keywords = {workqueue, hecura},
   }

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, Jan 2010

   doi: 10.1145/1851476.1851559

   DOI Bib PDF

   @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}},
     doi = {10.1145/1851476.1851559},
     cclpaperid = {87},
   }

10. 

    Abstractions for Scientific Computing on Campus Grids

    Christopher Moretti

    Jan 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},
      keywords = {hecura},
    }

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, Jan 2010

    doi: 10.1145/1851476.1851547

    DOI Bib PDF

    @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}},
      doi = {10.1145/1851476.1851547},
      cclpaperid = {91},
      keywords = {chirp},
    }

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, Jan 2010

    doi: 10.1109/TPDS.2009.49

    DOI Bib PDF

    @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}},
      doi = {10.1109/TPDS.2009.49},
      cclpaperid = {12},
      keywords = {allpairs, hecura},
    }

13. 

    Visualizing Massively Multithreaded Applications with ThreadScope

    Kyle Wheeler and Douglas Thain

    Concurrency and Computation: Practice and Experience, Jan 2010

    doi: 10.1002/cpe.1469

    DOI Bib PDF

    @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}},
      doi = {10.1002/cpe.1469},
      cclpaperid = {59},
    }