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1. Fast uncovering of graph communities on a chip: Toward scalable community detection on multicore and manycore platforms
by Kalyanaraman, Ananth and Halappanavar, Mahantesh and Chavarría-Miranda, Daniel and Lu, Hao and Duraisamy, Karthi and Pande, Partha Pratim
Foundations and Trends in Electronic Design Automation, ISSN 1551-3939, 2016, Volume 10, Issue 3, pp. 145 - 247
Graph representations are pervasive in scientific and social computing. They serve as vital tools to model the interplay among different interacting entities.... 
Networks | Architecture | Computation | Communities | Organizations | Graphs | Graphical representations | Trends
Journal Article
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2. Full Text Algorithms for Balanced Graph Colorings with Applications in Parallel Computing
by Hao Lu and Halappanavar, Mahantesh and Chavarria-Miranda, Daniel and Gebremedhin, Assefaw H and Panyala, Ajay and Kalyanaraman, Ananth
IEEE Transactions on Parallel and Distributed Systems, ISSN 1045-9219, 05/2017, Volume 28, Issue 5, pp. 1240 - 1256
Graph coloring-in a generic sense-is used to identify subsets of independent tasks in parallel scientific computing applications. Traditional coloring... 
Context | Tilera manycore architecture | Color | Standards | partial distance-2 coloring | Balanced coloring | Image color analysis | Processor scheduling | distance-1 coloring | parallel graph coloring | Bipartite graph | community detection | graph algorithms | COMPUTER SCIENCE, THEORY & METHODS | HEURISTICS | ENGINEERING, ELECTRICAL & ELECTRONIC | Image coding | Research | Multiprocessing | Methods | Algorithms | Parallel processing | Graph coloring | Computation | Heuristic
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3. Full Text Exploring performance and energy tradeoffs for irregular applications: A case study on the Tilera many-core architecture
by Panyala, Ajay and Chavarría-Miranda, Daniel and Manzano, Joseph B and Tumeo, Antonino and Halappanavar, Mahantesh and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Journal of Parallel and Distributed Computing, ISSN 0743-7315, 06/2017, Volume 104, pp. 234 - 251
High performance, parallel applications with irregular data accesses are becoming a critical workload class for modern systems. In particular, the execution of... 
Sparse conjugate gradient | Auto tuning | Data layouts | Community detection | Many-core processors | Irregular applications | Energy optimization | COMPUTER SCIENCE, THEORY & METHODS | Case studies | Data mining | Energy conservation | Machine learning | irregular applications | energy optimization | sparse conjugate gradient | auto tuning | community detection
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4. Full Text Scaling graph community detection on the Tilera many-core architecture
by Chavarria-Miranda, Daniel and Halappanavar, Mahantesh and Kalyanaraman, Ananth
2014 21st International Conference on High Performance Computing (HiPC), ISSN 1094-7256, 12/2014, pp. 1 - 11
In an era when power constraints and data movement are proving to be significant barriers for the application of high-end computing, the Tilera many-core... 
Image color analysis | Multicore processing | Communities | Layout | parallel | many-core | Resource management | Tilera | community detection | Convergence | graph algorithms
Conference Proceeding
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5. Full Text Global transformations for legacy parallel applications via structural analysis and rewriting
by Chavarría-Miranda, Daniel and Panyala, Ajay and Ma, Wenjing and Prantl, Adrian and Krishnamoorthy, Sriram
Parallel Computing, ISSN 0167-8191, 03/2015, Volume 43, pp. 1 - 26
Performance and scalability optimization of large HPC applications is currently a labor-intensive, manual process with very low productivity. Major... 
Term rewriting | Legacy parallel applications | Source-to-source transformations | Semantic patches | LANGUAGE | PERFORMANCE | MPI | DATA-FLOW | COMPUTER SCIENCE, THEORY & METHODS | COMMUNICATION
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6. Technical and economic feasibility of a solar-bio-powered waste utilization and treatment system in Central America
by Ronald Esteban Aguilar Alvarez and Mauricio Bustamante Roman and Dana Kirk and Jose Alberto Miranda Chavarria and Daniel Baudrit and Jose Francisco Aguilar Pereira and Werner Rodriguez Montero and Dawn Reinhold and Wei Liao
Journal of Environmental Management, ISSN 0301-4797, 12/2016, Volume 184, p. 371
  The purpose of this study was to implement and evaluate a pilot-scale and closed-loop system that synergistically combines solar thermal collector, anaerobic... 
Waste materials | Photovoltaic cells | Alternative energy | Artificial wetlands | Fertilizers
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7. Full Text On eliminating synchronous communication in molecular simulations to improve scalability
by Straatsma, T.P and Chavarría-Miranda, Daniel G
Computer Physics Communications, ISSN 0010-4655, 12/2013, Volume 184, Issue 12, pp. 2634 - 2640
Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular... 
Molecular dynamics | One-sided communication | Global arrays | DYNAMICS SIMULATIONS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | NWCHEM | PHYSICS, MATHEMATICAL | Analysis | Algorithms | Synchronous | Computer simulation | Computation | Synchronism | Synchronization | Arrays | Dynamical systems
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8. HiPCNA-PG'11
: proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid : November 13, 2011, Seattle, Washington, USA
by Chavarría-Miranda, Daniel and Akyol, Bora and Sigarch and Pacific Northwest National Laboratory (U.S.)
2011, ISBN 9781450310611
High performance computing | Data processing | Electric power systems
Web Resource
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9. HiPCNA-PG'11
: proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid : November 13, 2011, Seattle, Washington, USA
by Chavarría-Miranda, Daniel and Akyol, Bora and Sigarch and Pacific Northwest National Laboratory (U.S.)
2011, ISBN 9781450310611
High performance computing | Data processing | Electric power systems
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10. Full Text Aho-Corasick String Matching on Shared and Distributed-Memory Parallel Architectures
by Tumeo, A and Villa, O and Chavarria-Miranda, D. G
IEEE Transactions on Parallel and Distributed Systems, ISSN 1045-9219, 03/2012, Volume 23, Issue 3, pp. 436 - 443
String matching requires a combination of (sometimes all) the following characteristics: high and/or predictable performance, support for large data sets and... 
Algorithm design and analysis | Dictionaries | Cray XMT | Instruction sets | Aho-Corasick | multithreaded architectures | Computer architecture | Doped fiber amplifiers | string matching | GPGPU | high-performance computing | Graphics processing unit | High-performance computing | String matching | Multithreaded architectures | COMPUTER SCIENCE, THEORY & METHODS | ENGINEERING, ELECTRICAL & ELECTRONIC | Technology application | Usage | Collective memory | Data security | Innovations | Distributed processing (Computers) | Mathematical optimization
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11. Full Text Technical and economic feasibility of a solar-bio-powered waste utilization and treatment system in Central America
by Aguilar Alvarez, Ronald Esteban and Bustamante Roman, Mauricio and Kirk, Dana and Miranda Chavarria, Jose Alberto and Baudrit, Daniel and Aguilar Pereira, Jose Francisco and Rodriguez Montero, Werner and Reinhold, Dawn and Liao, Wei
Journal of Environmental Management, ISSN 0301-4797, 12/2016, Volume 184, Issue Pt 2, pp. 371 - 379
The purpose of this study was to implement and evaluate a pilot-scale and closed-loop system that synergistically combines solar thermal collector, anaerobic... 
Methane | Solar thermal collector | Reclaimed water | Constructed treatment wetland | Anaerobic digestion | ENVIRONMENTAL SCIENCES | EFFLUENT | THERMOPHILIC-ANAEROBIC-DIGESTION | MANURE | BATCH | Anaerobiosis | Central America | Manure | Phosphorus | Nitrogen | Solar Energy - economics | Waste Management - methods | Costa Rica | Fertilizers | Wetlands | Waste Management - instrumentation | Pilot Projects | Animals | Bioreactors | Waste Management - economics | Renewable Energy | Water Purification - methods | Food | Alternative energy sources | School facilities | Refuse and refuse disposal | Education parks | Waste management
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12. Critical points based register-concurrency autotuning for GPUs
by Li, Ang and Song, Shuaiwen Leon and Kumar, Akash and Zhang, Eddy Z and Chavarria-Miranda, Daniel and Corporaal, Henk
The Institute of Electrical and Electronics Engineers, Inc. (IEEE) Conference Proceedings, 03/2016, pp. 1273 - 1278
The unprecedented prevalence of GPGPU is largely attributed to its abundant on-chip register resources, which allow massively concurrent threads and extremely... 
Design engineering | Automation | Electronics | Performance enhancement | Registers | Expansion | Tuning | Optimization
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13. Full Text Critical points based register-concurrency autotuning for GPUs
by Ang Li and Song, Shuaiwen Leon and Kumar, Akash and Zhang, Eddy Z and Chavarria-Miranda, Daniel and Corporaal, Henk
2016 Design, Automation & Test in Europe Conference & Exhibition (DATE), 03/2016, pp. 1273 - 1278
The unprecedented prevalence of GPGPU is largely attributed to its abundant on-chip register resources, which allow massively concurrent threads and extremely... 
Concurrent computing | Instruction sets | Graphics processing units | Registers | System-on-chip | Kernel | Message systems
Conference Proceeding
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14. Full Text BioGraphE: High-performance bionetwork analysis using the Biological Graph Environment
by Chin Jr, George Chin and Chavarria, Daniel G and Nakamura, Grant C and Sofia, Heidi J
BMC Bioinformatics, ISSN 1471-2105, 05/2008, Volume 9, Issue 6, pp. S6 - S6
Background: Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and... 
ALGORITHMS | SEARCH | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BLAST | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Computer Graphics | Algorithms | Models, Biological | Computer Simulation | Signal Transduction - physiology | Software | Proteome - metabolism
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15. Full Text Responses of anaerobic microorganisms to different culture conditions and corresponding effects on biogas production and solid digestate quality
by Chen, Rui and Roos, Mariana Murillo and Zhong, Yuan and Marsh, Terence and Roman, Mauricio Bustamante and Hernandez Ascencio, Walter and Uribe, Lidieth and Uribe Lorio, Lorena and Kirk, Dana and Reinhold, Dawn Marie and Miranda Chavarria, Jose Alberto and Baudrit Ruiz, Daniel and Pereira, Jose Francisco Aguilar and Montero, Werner Rodriguez and Srivastava, Ajit and Liao, Wei
Biomass and Bioenergy, ISSN 0961-9534, 02/2016, Volume 85, pp. 84 - 93
Microbial communities of anaerobic digestion have been intensively investigated in the past decades. Majority of these studies focused on correlating microbial... 
Biorefining feedstock | Biogas | Anaerobic microbes | Solid digestate | Co-digestion | PHYLOGENETIC DIVERSITY | WASTE-WATER TREATMENT | FOOD WASTE | ENERGY & FUELS | ENZYMATIC-HYDROLYSIS | SP NOV | MICROBIAL COMMUNITY | GREEN NONSULFUR BACTERIA | AGRICULTURAL ENGINEERING | TEMPERATURE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GRANULAR SLUDGES | Microorganisms | Molecular genetics | Biomass energy | Analysis | Yuan (China)
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16. Full Text On the use of term rewriting for performance ooptimization of legacy HPC applications
by Panyala, Ajay and Chavarría-Miranda, Daniel and Krishnamoorthy, Sriram
Proceedings of the International Conference on Parallel Processing, ISSN 0190-3918, 2012, pp. 399 - 409
load balancing | term rewriting | TASCEL | Global Arrays
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17. Full Text On the Use of Term Rewriting for Performance Optimization of Legacy HPC Applications
by Panyala, A and Chavarria-Miranda, D and Krishnamoorthy, S
2012 41st International Conference on Parallel Processing, ISSN 0190-3918, 09/2012, pp. 399 - 409
Preparing codes for next generation supercomputer systems is anticipated to require significant changes to the optimization strategies employed in established... 
term rewriting | load balancing | Tiles | Heuristic algorithms | Semantics | TASCEL | Abstracts | Syntactics | Benchmark testing | Kernel | Global Arrays
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18. Full Text High-performance computing (HPC): Application & use in the power grid
by Chavarria-Miranda, D and Zhenyu Huang and Yousu Chen
2012 IEEE Power and Energy Society General Meeting, ISSN 1932-5517, 07/2012, pp. 1 - 7
The intent of this paper is to present a tutorial overview of high-performance computing (HPC) and its application to solving power system problems. The... 
Computers | High Performance Computing | State Estimation | Instruction sets | Parallel Computing | Hardware | Libraries | Power Engineering | Arrays | Sparse matrices | Contingency Analysis
Conference Proceeding
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19. Full Text Performance evaluation of counter-based dynamic load balancing schemes for massive contingency analysis with different computing environments
by Yousu Chen and Zhenyu Huang and Chavarria-Miranda, D
IEEE PES General Meeting, ISSN 1932-5517, 07/2010, pp. 1 - 6
Contingency analysis is a key function in the Energy Management System (EMS) to assess the impact of various combinations of power system component failures... 
and Dynamic Load Balancing | Program processors | Ethernet networks | Radiation detectors | Computational modeling | Power system dynamics | Parallel Computing | Load management | Power grids | Contingency Analysis | Energy Management System | Parallel computing | Contingency analysis | Dynamic load balancing | Energy management system
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20. Full Text Design and implementation of a high‐performance CCA event service
by Gorton, Ian and Chavarria, Daniel and Nieplocha, Jarek
Concurrency and Computation: Practice and Experience, ISSN 1532-0626, 06/2009, Volume 21, Issue 9, pp. 1159 - 1179
Event services based on publish–subscribe architectures are well‐established components of distributed computing applications. Recently, an event service has... 
common component architecture | components | event service | Components | Common component architecture | Event service | COMPUTER SCIENCE, SOFTWARE ENGINEERING | COMPUTER SCIENCE, THEORY & METHODS | MODEL
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