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cclpapers.bib
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%% This file was generated automatically from the CCL web page:
%% http://www.cse.nd.edu/~ccl/research/papers/bibtex.php
@inproceedings {
vc3-pearc-2018,
author = "Lincoln Bryant and Jeremy Van and Benedikt Riedel and Robert Gardner and Jose Caballero and John Hover and Ben Tovar and Douglas Thain",
title = "{VC3: A Virtual Cluster Service for Community Computation}",
booktitle = "{PEARC: Practice and Experience in Advanced Research Computing}",
pages = "1-8",
year = 2018,
cclpaperid = "949"
}
@inproceedings {
batch-sciencecloud-2018,
author = "Kyle Sweeney and Douglas Thain",
title = "{Early Experience Using Amazon Batch for Scientific Workflows}",
booktitle = "{ScienceCloud Workshop at HPDC }",
year = 2018,
cclpaperid = "950"
}
@inproceedings {
containers-sciencecloud-2018,
author = "Kyle Sweeney and Douglas Thain",
title = "{Efficient Integration of Containers into Scientific Workflows}",
booktitle = "{Science Cloud Workshop at HPDC}",
year = 2018,
cclpaperid = "951"
}
@inproceedings {
tovar-ic2e-2018,
author = "Benjamin Tovar and Nicholas Hazekamp and Nathaniel Kremer-Herman and Douglas Thain",
title = "{Automatic Dependency Management for Scientific Applications on Clusters}",
booktitle = "{IEEE International Conference on Cloud Engineering (IC2E) }",
year = 2018,
cclpaperid = "945"
}
@inproceedings {
maker-service-ic2e2018,
author = "Nicholas Hazekamp and Upendra Kumar Devisetty and Nirav Merchant and Douglas Thain",
title = "{MAKER as a Service: Moving HPC applications to Jetstream Cloud}",
booktitle = "{IEEE International Conference on Cloud Engineering}",
pages = "6",
year = 2018,
cclpaperid = "946"
}
@inproceedings {
shadho-wacv-2018,
author = "Jeffrey Kinnison and Nathaniel Kremer-Herman and Douglas Thain and Walter Scheirer",
title = "{SHADHO: Massively Scalable Hardware-Aware Distributed Hyperparameter Optimization}",
booktitle = "{IEEE Winter Conference on Applications of Computer Vision}",
pages = "1-10",
year = 2018,
cclpaperid = "947"
}
@article {
tovar-tpds-2017,
author = "Benjamin Tovar and Rafael Ferreira da Silva and Gideon Juve and Ewa Deelman and William Allcock and Douglas Thain and Miron Livny",
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,
cclpaperid = "941"
}
@article {
mf-storage-tpds17,
author = "Nicholas Hazekamp and Nathaniel Kremer-Herman and Benjamin Tovar and Haiyan Meng and Olivia Choudhury and Scott Emrich and Douglas Thain",
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,
cclpaperid = "942"
}
@article {
gpu-ijmf,
author = "James Sweet and David Richter and Douglas Thain",
title = "{GPU acceleration of Eulerian–Lagrangian particle-laden turbulent flow simulations}",
journal = "{International Journal of Multiphase Flow}",
volume = "99",
pages = "437-435",
year = 2018,
cclpaperid = "944"
}
@inproceedings {
wharf-sc17,
author = "Chao Zheng and Lukas Rupprecht and Vasily Tarasov and Mohamed Mohamed and Dimitrios Skourtis and Amit S. Warke and Dean Hildebrand Douglas Thain",
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"
}
@inproceedings {
metafs-pdsw-2017,
author = "Tim Shaffer and Douglas Thain",
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,
cclpaperid = "948"
}
@inproceedings {
PAPER937,
author = "Haiyan Meng and Douglas Thain",
title = "{Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications}",
booktitle = "{The 17th International Conference on Computational Science (ICCS)}",
year = 2017,
cclpaperid = "937"
}
@inproceedings {
social-icdcs17,
author = "Daniel (Yue) Zhang and Charles (Chao) Zheng and Dong Wang and Doug Thain and Chao Huang and Xin Mu and Greg Madey",
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,
cclpaperid = "938"
}
@inproceedings {
makeflow-mesos-ccgrid17.pdf,
author = "Charles (Chao) Zheng and Ben Tovar and Douglas Thain",
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,
cclpaperid = "939"
}
@thesis {
meng-thesis,
author = "Haiyan Meng",
title = "{Improving the Reproducibility of Scientific Applications with Execution Environment Specifications}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2017,
cclpaperid = "940"
}
@article {
tuning-tcc-2015,
author = "Dinesh Rajan and Douglas Thain",
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,
cclpaperid = "909"
}
@inproceedings {
prune-escience-2016,
author = "Peter Ivie and Douglas Thain",
title = "{PRUNE: A Preserving Run Environment for Reproducible Computing}",
booktitle = "{IEEE Conference on e-Science}",
year = 2016,
cclpaperid = "930"
}
@inproceedings {
umbrella-escience-2016,
author = "Haiyan Meng and Douglas Thain and Alexander Vyushkov and Matthias Wolf and Anna Woodard",
title = "{Conducting Reproducible Research with Umbrella: Tracking, Creating, and Preserving Execution Environments}",
booktitle = "{IEEE Conference on e-Science}",
year = 2016,
cclpaperid = "931"
}
@techreport {
repro-tr-2016,
author = "Peter Ivie and Charles (Chao) Zheng and Douglas Thain",
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"
}
@inproceedings {
oppo-chep2016,
author = "Matthias Wolf and Anna Woodard and Wenzhao Li and Kenyi Hurtado Anampa and Yannakopoulos and Benjamin Tovar and Patrick Donnelly and Paul Brenner and Kevin Lannon and Mike Hildreth and Douglas Thain",
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,
cclpaperid = "934"
}
@inproceedings {
scaling-chep2016,
author = "Matthias Wolf and Anna Woodard and Wenzhao Li and Kenyi Hurtado Anampa and Benjamin Tovar and Paul Brenner and Kevin Lannon and Mike Hildreth and Douglas Thain",
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,
cclpaperid = "935"
}
@inproceedings {
PAPER936,
author = "Peter Ivie and Charles (Chao) Zheng and Douglas Thain",
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,
cclpaperid = "936"
}
@inproceedings {
distia-ase-2016,
author = "Haipeng Cai and Douglas thain",
title = "{DistIA: A Cost-Effective Dynamic Impact Analysis for Distributed Prorgams}",
booktitle = "{IEEE/ACM International Conference on Automated Software Engineering}",
year = 2016,
cclpaperid = "932"
}
@article {
diapro-tosem-2016,
author = "Haipeng Cai and Raul Santelices and Douglas Thain",
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,
cclpaperid = "927"
}
@article {
ccpe-confuga,
author = "Patrick Donnelly and Douglas Thain",
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,
cclpaperid = "929"
}
@thesis {
pdonnelly-thesis,
author = "Patrick Donnelly",
title = "{Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2016,
cclpaperid = "928"
}
@inproceedings {
tauroast-chep-2015,
author = "Haiyan Meng and Matthias Wolf and Peter Ivie and Anna Woodard and Michael Hildreth and Douglas Thain",
title = "{A Case Study in Preserving a High Energy Physics Application with Parrot}",
booktitle = "{Journal of Physics: Conference Series (CHEP 2015)}",
year = 2015,
cclpaperid = "925"
}
@article {
globalfs-cise-2015,
author = "Jakob Blomer and Predrag Buncic and Rene Meusel and Gerardo Ganis and Igor Sfiligoi and Douglas Thain",
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,
cclpaperid = "926"
}
@inproceedings {
techniques-ipres-2015,
author = "Douglas Thain and Peter Ivie and Haiyan Meng",
title = "{Techniques for Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness?}",
booktitle = "{12th International Conference on Digital Preservation (iPres)}",
year = 2015,
cclpaperid = "921"
}
@inproceedings {
dagviz-vpa-2015,
author = "An Huynh and Douglas Thain and Miquel Pericas and Kenjiro Taura",
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"
}
@inproceedings {
lobster-cluster-2015,
author = "Anna Woodard and Matthias Wolf and Charles Mueller and Nil Valls and Ben Tovar and Patrick Donnelly and Peter Ivie and Kenyi Hurtado Anampa and Paul Brenner and Douglas Thain and Kevin Lannon and Michael Hildreth",
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"
}
@article {
collab-cise-2015,
author = "Peter Sempolinski and Daniel Wei and Ahsan Kareem and Douglas Thain",
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,
cclpaperid = "916"
}
@inproceedings {
balancing-cluster-2015,
author = "Olivia Choudhury and Dinesh Rajan and Nicholas Hazekamp and Sandra Gesing and Douglas Thain and Scott Emrich",
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"
}
@inproceedings {
monitoring-hpcmaspa-2015,
author = "Gideon Juve and Benjamin Tovar and Rafael Ferreira da Silva and Dariusz Krol and Douglas Thain and Ewa Deelman and William Allcock and Miron Livny",
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"
}
@article {
crowdsourcing-plosone-2015,
author = "Matthew Staffelbach and Peter Sempolinski and Tracy Kijewski-Correa and Douglas Thain and Daniel Wei and Ahsan Kareem and Gregory Madey",
title = "{Lessons Learned from Crowdsourcing Complex Engineering Tasks}",
journal = "{PLOS One}",
volume = "10",
number = "9",
year = 2015,
cclpaperid = "923"
}
@inproceedings {
scaling-escience-2015,
author = "Nicholas Hazekamp and Joseph Sarro and Olivia Choudhury and Sandra Gesing and Scott Emrich and Douglas Thain",
title = "{Scaling Up Bioinformatics Workflows with Dynamic Job Expansion}",
booktitle = "{IEEE International Conference on e-Science}",
year = 2015,
cclpaperid = "920"
}
@article {
invariant-jocs-2015,
author = "Haiyan Meng and Rupa Kommineni and Quan Pham and Robert Gardner and Tanu Malik and Douglas Thain",
title = "{An Invariant Framework for Conducting Reproducible Computational Science}",
journal = "{Journal of Computational Science}",
volume = "9",
pages = "137-142",
year = 2015,
cclpaperid = "914"
}
@inproceedings {
wq-docker-vtdc15,
author = "Charles (Chao) Zheng and Douglas Thain",
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,
cclpaperid = "910"
}
@inproceedings {
umbrella-vtdc15,
author = "Haiyan Meng and Douglas Thain",
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,
cclpaperid = "912"
}
@inproceedings {
confuga-ccgrid2015,
author = "Patrick Donnelly and Nicholas Hazekamp and Douglas Thain",
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,
cclpaperid = "908"
}
@thesis {
dpandiar-dissertation,
author = "Dinesh Rajan",
title = "{Principles for the Design and Operation of Elastic Scientific Applications on Distributed Systems}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2015,
cclpaperid = "913"
}
@techreport {
software-nsf-2014,
author = "Beth Plale and Matt Jones and Douglas Thain",
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"
}
@inproceedings {
casestudy-poster-chep-2015,
author = "Haiyan Meng and Matthias Wolf and Anna Woodard and Peter Ivie and Michael Hildreth and Douglas Thain",
title = "{A Case Study in Preserving a High Energy Physics Application}",
booktitle = "{Computing in High Energy Physics}",
year = 2015,
cclpaperid = "917"
}
@inproceedings {
lobster-poster-chep-2015,
author = "Anna Woodard and Matthias Wolf and Charles Nicholas Mueller and Ben Tovar and Patrick Donnelly and Kenyi Hurtado Anampa and Paul Brenner and Kevin Lannon and Michael Hildreth",
title = "{Exploiting Volatile Opportunistic Computing Resources with Lobster}",
booktitle = "{Computing in High Energy Physics}",
year = 2015,
cclpaperid = "918"
}
@article {
awe-jcim-2014,
author = "Badi Abdul-Wahid and Haoyun Feng and Dinesh Rajan and Ronan Costaouec and Eric Darve and Douglas Thain and Jesus A. Izaguirre",
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,
cclpaperid = "907"
}
@article {
maker-wq-ijbra,
author = "Andrew Thrasher and Zachary Musgrave and Brian Kachmark and Douglas Thain and Scott Emrich",
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,
cclpaperid = "904"
}
@inproceedings {
pivie-deltadb-2014,
author = "Peter Ivie and Douglas Thain",
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,
cclpaperid = "906"
}
@inproceedings {
oppo-ccgrid14,
author = "Dillon Skeehan and Paul Brenner and Ben Tovar and Douglas Thain and Nil Valls and Anna Woodard and Matthew Wolf and Tessa Pearson and Sean Lynch and Kevin Lannon",
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,
cclpaperid = "902"
}
@inproceedings {
bio-partition-c4bio-grid14,
author = "Olivia Choudhury and Nicholas L. Hazekamp and Douglas Thain and Scott Emrich",
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"
}
@inproceedings {
abstract-mechturk,
author = "Matthew Staffelbach and Peter Sempolinski and David Hachen and Ahsan Kareem and Tracy Kijewski-Correa and Douglas Thain and Daniel Wei and Gregory Madey",
title = "{Lessons Learned from an Experiment in Crowdsourcing Complex Citizen Engineering Tasks with Amazon Mechanical Turk}",
booktitle = "{Collective Intelligence}",
year = 2014,
cclpaperid = "905"
}
@inproceedings {
workflow-expand-grid14,
author = "Nicholas Hazekamp and Olivia Choudhury and Sandra Gesing and Scott Emrich and Douglas Thain",
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,
cclpaperid = "901"
}
@inproceedings {
automated-packaging-works13,
author = "Casey Robinson and Douglas Thain",
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,
cclpaperid = "899"
}
@inproceedings {
confuga-discs2013,
author = "Patrick Donnelly and Douglas Thain",
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,
cclpaperid = "900"
}
@inproceedings {
wqh-cluster13,
author = "Michael Albrecht and Dinesh Rajan and Douglas Thain",
title = "{Making Work Queue Cluster-Friendly for Data Intensive Scientific Applications}",
booktitle = "{IEEE International Conference on Cluster Computing}",
year = 2013,
cclpaperid = "898"
}
@thesis {
PAPER896,
author = "Li Yu",
title = "{Right-sizing Resource Allocations for Scientific Applications in Clusters, Grids, and Clouds}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2013,
cclpaperid = "896"
}
@inproceedings {
casestudies-ccgrid13,
author = "Dinesh Rajan and Andrew Thrasher and Badi Abdul-Wahid and Jesus A Izaguirre and Scott Emrich and Douglas Thain",
title = "{Case Studies in Designing Elastic Applications}",
booktitle = "{ 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)}",
year = 2013,
cclpaperid = "893"
}
@techreport {
search-tr,
author = "Brenden Kokoszka and Patrick Donnelly and Douglas Thain",
title = "{Search Should be a System Call}",
institution = "{University of Notre Dame, Computer Science and Engineering Department}",
number = "2013-03",
year = 2013,
cclpaperid = "894"
}
@article {
assembly-tpds,
author = "Christopher Moretti and Andrew Thrasher and Li Yu and Michael Olson and Scott Emrich and Douglas Thain",
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,
cclpaperid = "100"
}
@inproceedings {
folding-escience12,
author = "Badi Abdul-Wahid and Li Yu and Dinesh Rajan and Haoyun Feng and Eric Darve and Douglas Thain and Jesus A. Izaguirre",
title = "{Folding Proteins at 500 ns/hour with Work Queue}",
booktitle = "{8th IEEE International Conference on eScience (eScience 2012)}",
year = 2012,
cclpaperid = "891"
}
@inproceedings {
psempoli-escience12,
author = "Peter Sempolinski and Daniel Wei and Douglas Thain and Ahsan Kareem",
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,
cclpaperid = "892"
}
@article {
roars-pddb-2012,
author = "Hoang Bui and Peter Bui and Patrick Flynn and Douglas Thain",
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,
cclpaperid = "890"
}
@thesis {
pbui-dissertation.pdf,
author = "Peter Bui",
title = "{A Compiler Toolchain For Data Intensive Scientific Workflows}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2012,
cclpaperid = "889"
}
@inproceedings {
chirp-tickets-ccgrid12,
author = "Patrick Donnelly and Douglas Thain",
title = "{Fine-Grained Access Control in the Chirp Distributed File System}",
booktitle = "{IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing}",
year = 2012,
cclpaperid = "101"
}
@inproceedings {
makeflow-sweet12,
author = "Michael Albrecht and Patrick Donnelly and Peter Bui and Douglas Thain",
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,
cclpaperid = "104"
}
@thesis {
hbui-dissertation,
author = "Hoang Bui",
title = "{A Rich Metadata Filesystem for Scientific Data}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2012,
cclpaperid = "105"
}
@inproceedings {
maker-iccabs12,
author = "Andrew Thrasher and Zachary Musgrave and Douglas Thain and Scott Emrich",
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"
}
@incollection {
chirp-didc-chapter,
author = "Douglas Thain and Michael Albrecht and Hoang Bui and Peter Bui and Rory Carmichael and Scott Emrich and Patrick Flynn",
title = "{Data Intensive Computing with Clustered Chirp Servers}",
editor = "Tevfik Kosar",
booktitle = "{Data Intensive Distributed Computing: Challenges and Solutions for Large Scale Information Management}",
pages = "140-154",
publisher = "IGI",
year = 2012,
cclpaperid = "99"
}
@article {
biocompute-ccpe,
author = "Rory Carmichael and Patrick Braga-Henebry and Douglas Thain and Scott Emrich",
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,
cclpaperid = "96"
}
@inproceedings {
elasticrepex-cloudcom11,
author = "Dinesh Rajan and Anthony Canino and Jesus A Izaguirre and Douglas Thain",
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"
}
@inproceedings {
wq-python-pyhpc2011,
author = "Peter Bui and Dinesh Rajan and Badi Abdul-Wahid and Jesus Izaguirre and Douglas Thain",
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"
}
@article {
weaver-ccpe,
author = "Peter Bui and Li Yu and Andrew Thrasher and Rory Carmichael and Irena Lanc and Patrick Donnelly and Douglas Thain",
title = "{Scripting distributed scientific workflows using Weaver}",
journal = "{Concurrency and Computation: Practice and Experience}",
volume = "24",
number = "15",
year = 2011,
cclpaperid = "98"
}
@inproceedings {
adapting-ecmls11,
author = "Irena Lanc and Peter Bui and Douglas Thain and Scott Emrich",
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,
cclpaperid = "94"
}
@incollection {
cloud-chapter,
author = "Peter Sempolinski and Douglas Thain",
title = "{An Introduction to Open-Source IaaS Cloud Middleware}",
editor = "Boualem Benatallah",
booktitle = "{Cloud Computing: Methodology, Systems, and Applications}",
pages = "133-149",
publisher = "CRC Press",
year = 2011,
cclpaperid = "895"
}
@inproceedings {
survey-cloudCom2010,
author = "Peter Sempolinski and Douglas Thain",
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,
cclpaperid = "89"
}
@inproceedings {
chirp+parrot+hdfs,
author = "Patrick Donnelly and Peter Bui and Douglas Thain",
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,
cclpaperid = "90"
}
@inproceedings {
taming-works10.pdf,
author = "Andrew Thrasher and Rory Carmichael and Peter Bui and Li Yu and Douglas Thain and Scott Emrich",
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,
cclpaperid = "92"
}
@article {
abstr-jcc,
author = "Li Yu and Christopher Moretti and Andrew Thrasher and Scott Emrich and Kenneth Judd and Douglas Thain",
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,
cclpaperid = "83"
}
@inproceedings {
eoc-green,
author = "Paul Brenner and Ryan Jansen and David Go and Douglas Thain",
title = "{Environmentally Opportunistic Computing: Transforming the Data Center for Economic and Environmental Sustainability}",
booktitle = "{IEEE Green Computing Conference}",
pages = "383-388",
year = 2010,
cclpaperid = "97"
}
@incollection {
abstr-cloudbook,
author = "Douglas Thain and Christopher Moretti",
title = "{Abstractions for Cloud Computing with Condor}",
editor = "Syed Ahson and Mohammad Ilyas",
booktitle = "{Cloud Computing and Software Services: Theory and Techniques}",
pages = "153-171",
publisher = "CRC Press",
year = 2010,
cclpaperid = "78"
}
@inproceedings {
roars-didc10,
author = "Hoang Bui and Peter Bui and Patrick Flynn and Douglas Thain",
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,
cclpaperid = "85"
}
@inproceedings {
weaver-clade10,
author = "Peter Bui and Li Yu and Douglas Thain",
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,
cclpaperid = "86"
}
@inproceedings {
quality-didc10,
author = "Hoang Bui and Diane Wright and Clarence Helm and Rachel Witty and Patrick Flynn and Douglas Thain",
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,
cclpaperid = "87"
}
@thesis {
moretti-dissertation,
author = "Christopher Moretti",
title = "{Abstractions for Scientific Computing on Campus Grids}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2010,
cclpaperid = "88"
}
@inproceedings {
biocompute-ecmls,
author = "Rory Carmichael and Patrick Braga-Henebry and Douglas Thain and Scott Emrich",
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,
cclpaperid = "91"
}
@article {
allpairs-tpds,
author = "Christopher Moretti and Hoang Bui and Karen Hollingsworth and Brandon Rich and Patrick Flynn and Douglas Thain",
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,
cclpaperid = "12"
}
@article {
threadscope-ccpe09,
author = "Kyle Wheeler and Douglas Thain",
title = "{Visualizing Massively Multithreaded Applications with ThreadScope}",
journal = "{Concurrency and Computation: Practice and Experience}",
volume = "22",
number = "1",
pages = "45-67",
year = 2010,
cclpaperid = "59"
}
@incollection {
raicu-manytask-chapter,
author = "Ioan Raicu and Ian Foster and Yong Zhao and Alex Szalay and Philip Little and Christopher Moretti and Amitabh Chaudhary and Douglas Thain",
title = "{Towards Data Intensive Many Task Computing}",
editor = "Tevfik Kosar",
booktitle = "{Data Intensive Distributed Computing: Challenges and Solutions for Large-Scale Information Management}",
publisher = "IGI",
year = 2009,
cclpaperid = "80"
}
@thesis {
wheeler-thesis,
author = "Kyle Wheeler",
title = "{Exploiting Locality with QThreads for Portable Parallel Performance}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2009,
cclpaperid = "81"
}
@inproceedings {
assembly-mtags09,
author = "Christopher Moretti and Michael Olson and Scott Emrich and Douglas Thain",
title = "{Highly Scalable Genome Assembly on Campus Grids}",
booktitle = "{Many-Task Computing on Grids and Supercomputers (MTAGS)}",
year = 2009,
cclpaperid = "82"
}
@article {
modularity-spe,
author = "Andrew Blaich and Douglas Thain and Aaron Striegel",
title = "{Reflections on the Virtues of Modularity: A Case Study in Linux Security Modules}",
journal = "{Software: Practice and Experience}",
volume = "39",
number = "15",
pages = "1235-1251",
year = 2009,
cclpaperid = "11"
}
@inproceedings {
teamtrak-adhocnets,
author = "Jeffrey Hemmes and Douglas Thain and Christian Poellabauer",
title = "{Cooperative Localization in GPS-Limited Urban Environments}",
booktitle = "{ICST AdHocNets}",
year = 2009,
cclpaperid = "61"
}
@inproceedings {
multicore-grid09,
author = "Michael Lammie and Douglas Thain and Paul Brenner",
title = "{Scheduling Grid Workloads on Multicore Clusters to Minimize Energy and Maximize Performance}",
booktitle = "{IEEE Grid Computing}",
year = 2009,
cclpaperid = "75"
}
@inproceedings {
qthreads-pmea09,
author = "Kyle Wheeler and Douglas Thain and Rich Murphy",
title = "{Portable Performance from Workstation to Supercomputer: Distributing Data Structures with Qthreads}",
booktitle = "{Workshop on Programming Models for Emerging Architectures}",
pages = "1-8",
year = 2009,
cclpaperid = "76"
}
@incollection {
kosar-databook,
author = "T. Kosar and A. Hutanu and J. McLaren and D. Thain",
title = "{Coordination of Access to Large-scale Datasets in Distributed Environments}",
editor = "A. Shoshani and D. Rotem",
booktitle = "{Scientific Data Management: Challenges, Existing Technology, and Deployment}",
publisher = "Chapman and Hall / CRC Press",
year = 2009,
cclpaperid = "8"
}
@techreport {
assembly-tr,
author = "Christopher Moretti and Michael Olson and Scott Emrich and Douglas Thain",
title = "{Scalable Modular Genome Assembly on Campus Grids}",
institution = "{University of Notre Dame, Computer Science and Engineering Department}",
number = "2009-04",
year = 2009,
cclpaperid = "77"
}
@thesis {
jhemmes-thesis,
author = "Jeffrey Hemmes",
title = "{Improving Data Availability in Mobile Applications Through Enhanced Cooperative Localization}",
editor = "Ph.D. Thesis",
booktitle = "{University of Notre Dame}",
year = 2009,
cclpaperid = "79"
}
@inproceedings {
abstr-hpdc09,
author = "Li Yu and Christopher Moretti and Scott Emrich and Kenneth Judd and Douglas Thain",
title = "{Harnessing Parallelism in Multicore Clusters with the All-Pairs and Wavefront Abstractions}",
booktitle = "{IEEE High Performance Distributed Computing}",
pages = "1-10",
year = 2009,
cclpaperid = "5"
}
@inproceedings {
gheat-uptime09,
author = "Paul Brenner and Douglas Thain and Dewitt Latimer",
title = "{Grid Heating Clusters: Transforming Cooling Constraints Into Thermal Benefits}",
booktitle = "{The Uptime Institute Green Enterprise IT Award Paper}",
pages = "1-7",
year = 2009,
cclpaperid = "60"
}
@inproceedings {
parrot-chep09,
author = "Gabrielle Compostella and Simone Pagan Griso and Donatella Lucchesi and Igor Sfiligoi and Douglas Thain",
title = "{CDF Software Distribution on the Grid using Parrot}",
booktitle = "{Computing in High Energy Physics}",
year = 2009,
cclpaperid = "22"
}
@thesis {
pbh-thesis,
author = "Patrick Braga-Henebry",
title = "{Biocompute: Harnessing Distributed Systems for Bioinformatics}",
editor = "B.S. Honors Thesis",
booktitle = "{University of Notre Dame}",
year = 2009,
cclpaperid = "64"
}