Books and proceedings (2)
1. Daniel P. Friedman, William E. Byrd, and Oleg Kiselyov. The Reasoned Schemer. MIT Press, Cambridge, MA, 2005.
@book{trs05,
author = {Daniel P. Friedman and William E. Byrd and Oleg Kiselyov},
title = {The Reasoned Schemer},
year = {2005},
isbn = {0262562146},
publisher = {MIT Press},
}


2. A. Lumsdaine, D. Musser, S. Schupp, and Jeremy Siek, editors. Proceedings of the First International Workshop on Library-Centric Software Design (LCSD '05), 2005.
@proceedings{lumsdaine05:_LCSD,
title = {Proceedings of the First International Workshop on Library-Centric Software Design (LCSD '05)},
editor = {A. Lumsdaine and D. Musser and S. Schupp and Jeremy Siek},
year = 2005
}


 Thesis (1)
1. Jeremy G. Siek. A Language for Generic Programming. PhD thesis, Indiana University, August 2005.
 Annotation: The past decade of software library construction has demonstrated that the discipline of generic programming is an effective approach to the design and implementation of large-scale software libraries. At the heart of generic programming is a semi-formal interface specification language for generic components. Many programming languages have features for describing interfaces, but none of them match the generic programming specification language, and none are as suitable for specifying generic components. This lack of language support impedes the current practice of generic programming. In this dissertation I present and evaluate the design of a new programming language, named G (for generic), that integrates the generic programming specification language with the type system and features of a full programming language. The design of G is based on my experiences, and those of colleagues, in the construction of generic libraries over the past decade. The design space for programming languages is large, thus this experience is vital in guiding choices among the many tradeoffs. The design of G emphasizes modularity because generic programming is inherently about composing separately developed components. In this dissertation I demonstrate that the design is implementable by constructing a compiler for G (translating to C++) and show the suitability of G for generic programming with prototypes of the Standard Template Library and the Boost Graph Library in G. I formalize the essential features of G in a small language and prove type soundness.

@PhdThesis{siek05:_thesis,
author = {Jeremy G. Siek},
title = {A Language for Generic Programming},
school = {Indiana University},
year = 2005,
month = {August},
annote = {The past decade of software library construction has demonstrated that the discipline of generic programming is an effective approach to the design and implementation of large-scale software libraries. At the heart of generic programming is a semi-formal interface specification language for generic components. Many programming languages have features for describing interfaces, but none of them match the generic programming specification language, and none are as suitable for specifying generic components. This lack of language support impedes the current practice of generic programming. In this dissertation I present and evaluate the design of a new programming language, named G (for generic), that integrates the generic programming specification language with the type system and features of a full programming language. The design of G is based on my experiences, and those of colleagues, in the construction of generic libraries over the past decade. The design space for programming languages is large, thus this experience is vital in guiding choices among the many tradeoffs. The design of G emphasizes modularity because generic programming is inherently about composing separately developed components. In this dissertation I demonstrate that the design is implementable by constructing a compiler for G (translating to C++) and show the suitability of G for generic programming with prototypes of the Standard Template Library and the Boost Graph Library in G. I formalize the essential features of G in a small language and prove type soundness.}
}


1. T. Hoefler, R. Janisch, and W. Rehm. Improving the parallel scaling of ABINIT, pages 551-559. CINECA Conzorzio Interuniversitario, 12 2005.
@inbook{hoefler-hpce05,
author={T. Hoefler and R. Janisch and W. Rehm},
title={{Improving the parallel scaling of ABINIT}},
institution={CINECA Consorzio Interuniversitario},
year={2005},
month={12},
pages={551-559},
booktitle={Science and Supercomputing in Europe - Report 2005},
location={Caseleccio di Reno, Italy},
publisher={CINECA Conzorzio Interuniversitario},
isbn={88-86037-17-1},
url={http://www.unixer.de/~htor/publications/},

}


2. T. Hoefler, R. Janisch, and W. Rehm. A Performance Analysis of ABINIT on a Cluster System, pages 37-51. Springer, Lecture Notes in Computational Science and Engineering, 12 2005.
@inbook{hoefler-sfb05,
author={T. Hoefler and R. Janisch and W. Rehm},
title={{A Performance Analysis of ABINIT on a Cluster System}},
institution={TU Chemnitz},
year={2005},
month={12},
pages={37-51},
booktitle={Parallel Algorithms and Cluster Computing},
location={Chemnitz, Germany},
publisher={Springer, Lecture Notes in Computational Science and Engineering},
isbn={3-540-33539-0},
url={./img/hoefler-sfb05.pdf},
url={http://www.unixer.de/~htor/publications/},

}


3. A. Hanemann, J. Boote, E. Boyd, J. Durand, L. Kudarimoti, R. Lapacz, M. Swany, S. Trocha, and J. Zurawski. Perfsonar: A Service Oriented Architecture for Multi-Domain Network Monitoring. In Proceedings of the Third International Conference on Service Oriented Computing (ICSOC 2005), pp 241-254, December 2005.
@article{swany_article_ICSOC_2005,
Author = {A. Hanemann and J. Boote and E. Boyd and J. Durand and L. Kudarimoti and R. Lapacz and M. Swany and S. Trocha and J. Zurawski },
Date-Modified = {2016-06-10 15:59:46 +0000},
Editor = {ACM Sigsoft and Sigweb},
Journal = {In Proceedings of the Third International Conference on Service Oriented Computing (ICSOC 2005)},
Month = {December},
Pages = {241-254},
Title = {Perfsonar: A Service Oriented Architecture for Multi-Domain Network Monitoring },
Year = {2005}
}


4. Sriram Sankaran, Jeffrey M. Squyres, Brian Barrett, Andrew Lumsdaine, Jason Duell, Paul Hargrove, and Eric Roman. The LAM/MPI Checkpoint/Restart Framework: System-Initiated Checkpointing. International Journal of High Performance Computing Applications, 19(4):479--493, December 2005.
Keywords: MPI, checkpoint/restart, rollback-recovery.
@Article{sankaran05:_lam_mpi_check_restar_framew,
author = {Sriram Sankaran and Jeffrey M. Squyres and Brian Barrett and Andrew Lumsdaine and Jason Duell and Paul Hargrove and Eric Roman},
title = {The {LAM/MPI} Checkpoint/Restart Framework: System-Initiated Checkpointing},
journal = {International Journal of High Performance Computing Applications},
year = 2005,
volume = 19,
number = 4,
pages = {479--493},
month = {December},
keywords = {MPI, checkpoint/restart, rollback-recovery},
thanks = {This work was supported by a grant from the Lilly Endowment, by National Science Foundation grant 0116050, and by the U.S. Department of Energy under Contract No. DE-AC03-76SF00098. Brian Barrett was supported by a Department of Energy High Performance Computer Science fellowship.},

}


5. M. Murray, S. Smallen, O. Khalili, and M. Swany. Comparison of End-to-end Bandwidth Measurement Tools on the 10GigE TeraGrid Backbone. 6th International Workshop on Grid Computing (Grid2005) -Poster Session, November 2005.
@article{swany_article_TeraGrid_Backbone,
Author = {M. Murray and S. Smallen and O. Khalili and M. Swany},
Date-Modified = {2016-06-10 15:45:07 +0000},
Journal = {6th International Workshop on Grid Computing (Grid2005) -Poster Session},
Month = {November},
Title = {Comparison of End-to-end Bandwidth Measurement Tools on the 10GigE TeraGrid Backbone},
Year = {2005}
}


6. Debasis Dan, Chris Mueller, Kun Chen, and James A. Glazier. Solving the advection-diffusion equations in biological contexts using the cellular Potts model. Phys. Rev. E, 72(041909), October 2005.
@Article{mueller_physreve05,
author = { Debasis Dan and Chris Mueller and Kun Chen and James A. Glazier},
title = {Solving the advection-diffusion equations in biological contexts using the cellular Potts model },
journal = {Phys. Rev. E},
month = {October},
year = {2005},
volume = {72},
number = {041909},
doi = { 10.1103/PhysRevE.72.041909 }
}


7. J. Atlas, K. Decker, and M. Swany. Flexible Grid Workflows Using TAEMS. Workshop on Exploring Planning and Scheduling for Web Services, Grid and Autonomic Computing (with AAAI-05), July 2005.
@article{swany_article_TAEMS,
Author = {J. Atlas and K. Decker and M. Swany},
Date-Modified = {2016-06-10 15:39:18 +0000},
Journal = {Workshop on Exploring Planning and Scheduling for Web Services, Grid and Autonomic Computing (with AAAI-05)},
Month = {July},
Title = {Flexible Grid Workflows Using TAEMS},
Year = {2005}
}


8. Douglas Gregor, Jaakko Järvi, Mayuresh Kulkarni, Andrew Lumsdaine, David Musser, and Sibylle Schupp. Generic Programming and High-Performance Libraries. International Journal of Parallel Programming, 33(2), June 2005.
 Annotation: Generic programming is an especially attractive paradigm for developing libraries for high-performance computing because it simultaneously emphasizes generality and efficiency. In the generic programming approach, interfaces are based on sets of specified requirements on types, rather than on any particular types, allowing algorithms to inter-operate with any data types meeting the necessary requirements. These sets of requirements, known as concepts, can specify syntactic as well as semantic requirements. Besides providing a powerful means of describing interfaces to maximize software reuse, concepts provide a uniform mechanism for more closely coupling libraries with compilers and for effecting domain-specific library-based compiler extensions. To realize this goal however, programming languages and their associated tools must support concepts as first-class constructs. In this paper we advocate better syntactic and semantic support to make concepts first-class and present results demonstrating the kinds of improvements that are possible with static checking, compiler optimization, and algorithm correctness proofs for generic libraries based on concepts.

@Article{GregorEtAl:IJPP:05,
author = {Douglas Gregor and Jaakko J\"arvi and Mayuresh Kulkarni and Andrew Lumsdaine and David Musser and Sibylle Schupp},
title = {Generic Programming and High-Performance Libraries},
journal = {International Journal of Parallel Programming},
volume = 33,
number = 2,
month = {June},
year = 2005,
annote = {Generic programming is an especially attractive paradigm for developing libraries for high-performance computing because it simultaneously emphasizes generality and efficiency. In the generic programming approach, interfaces are based on sets of specified requirements on types, rather than on any particular types, allowing algorithms to inter-operate with any data types meeting the necessary requirements. These sets of requirements, known as concepts, can specify syntactic as well as semantic requirements. Besides providing a powerful means of describing interfaces to maximize software reuse, concepts provide a uniform mechanism for more closely coupling libraries with compilers and for effecting domain-specific library-based compiler extensions. To realize this goal however, programming languages and their associated tools must support concepts as first-class constructs. In this paper we advocate better syntactic and semantic support to make concepts first-class and present results demonstrating the kinds of improvements that are possible with static checking, compiler optimization, and algorithm correctness proofs for generic libraries based on concepts. },
thanks = {NSF grant EIA-0131354 and by a grant from the Lilly Endowment}
}


9. Lie-Quan Lee and Andrew Lumsdaine. Generic Programming for High Performance Scientific Applications. Concurrency and Computation: Practice & Experience, 17(7-8):941--965, June/july 2005.
@Article{lee03:_ccpe,
author = {Lie-Quan Lee and Andrew Lumsdaine},
title = {Generic Programming for High Performance Scientific Applications},
journal = {Concurrency and Computation: Practice {\&} Experience},
year = 2003,
pages = {941--965},
volume = 17,
number = {7-8},
month = {June/July},
year = 2005,
thanks = {NSF ACI-9982205}
}


10. Jeffrey M. Squyres. Doing More With Less. ClusterWorld Magazine, MPI Mechanic Column, 3(6):32--34,50, June 2005.
Keywords: MPI.
@Article{squyres05:_doing_more_with_less,
author = {Jeffrey M. Squyres},
title = {Doing More With Less},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {32--34,50},
year = 2005,
volume = 3,
number = 6,
month = {June},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


11. Jeremiah Willcock, Andrew Lumsdaine, and Arch Robison. Using MPI with C# and the Common Language Infrastructure. Concurrency and Computation: Practice & Experience, 17(7-8):895--917, June/july 2005.
@Article{willcock03:_ccpe,
author = {Jeremiah Willcock and Andrew Lumsdaine and Arch Robison},
title = {Using {MPI} with {C\#} and the {C}ommon {L}anguage {I}nfrastructure},
journal = {Concurrency and Computation: Practice {\&} Experience},
year = 2005,
volume = 17,
number = {7-8},
month = {June/July},
pages = {895--917},
thanks = {NSF ACI-9982205, Lilly Endowment}
}


12. Jeffrey M. Squyres. Progress is the Opposite of Congress. ClusterWorld Magazine, MPI Mechanic Column, 3(5):32--35, May 2005.
Keywords: MPI.
@Article{squyres05:_progr_oppos_congr,
author = {Jeffrey M. Squyres},
title = {"Progress" is the Opposite of "Congress"},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {32--35},
year = 2005,
volume = 3,
number = 5,
month = {May},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


13. Jeffrey M. Squyres. Why Are There So Many MPI Implementations?. ClusterWorld Magazine, MPI Mechanic Column, 3(4):32--35, April 2005.
Keywords: MPI.
@Article{squyres05:_why_are_there_so_many_mpi_implem,
author = {Jeffrey M. Squyres},
title = {Why Are There So Many MPI Implementations?},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {32--35},
year = 2005,
volume = 3,
number = 4,
month = {April},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


14. Jeffrey M. Squyres. Is Your Application Spawnworthy?. ClusterWorld Magazine, MPI Mechanic Column, 3(3):32--33,46--47, March 2005.
Keywords: MPI.
@Article{squyres05:_is_your_applic_spawn,
author = {Jeffrey M. Squyres},
title = {Is Your Application {\em Spawnworthy}?},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {32--33,46--47},
year = 2005,
volume = 3,
number = 3,
month = {March},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


15. Jeffrey M. Squyres. The Spawn of MPI. ClusterWorld Magazine, MPI Mechanic Column, 3(2):40--43, February 2005.
Keywords: MPI.
@Article{squyres05:_spawn_mpi,
author = {Jeffrey M. Squyres},
title = {The Spawn of {MPI}},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {40--43},
year = 2005,
volume = 3,
number = 2,
month = {February},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


16. J. Dantzer, C. Moad, R. Heiland, and S.D. Mooney. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Research, 33(2):W311--W314, 2005.
@article{mooney05:_NAR05,
author = {J. Dantzer and C. Moad and R. Heiland and S.D. Mooney},
title = {MutDB services: interactive structural analysis of mutation data},
year = 2005,
journal = {Nucleic Acids Research},
volume = 33,
number = 2,
pages = {W311--W314},
url = {http://nar.oxfordjournals.org/content/33/suppl_2/W311.full},

}


17. Jesse Davis, Douglas Stark, and Nicholas Edmonds. Method of Interaction in a Modular Architecture for Sensor Systems (MASS). International Journal of Software Engineering and Knowledge Engineering, 5(2), 2005.
@Article{edmonds05:MASS_JSEKE,
author = {Jesse Davis and Douglas Stark and Nicholas Edmonds},
title = {Method of Interaction in a Modular Architecture for Sensor Systems ({MASS})},
journal = {International Journal of Software Engineering and Knowledge Engineering},
volume = {5},
number = {2},
year = {2005},

}


18. Ronald Garcia and Andrew Lumsdaine. MultiArray: a C++ library for generic programming with arrays.. Softw., Pract. Exper., 35(2):159--188, 2005.
@article{DBLP:journals/spe/GarciaL05,
author = {Ronald Garcia and Andrew Lumsdaine},
title = {MultiArray: a C++ library for generic programming with arrays.},
journal = {Softw., Pract. Exper.},
volume = {35},
number = {2},
year = {2005},
pages = {159--188},
ee = {http://dx.doi.org/10.1002/spe.630},
bibsource = {DBLP, http://dblp.uni-trier.de},
thanks = {Lilly Endowment, NSF ACI-0219884 and NSF EIA-0131354}
}


19. Ralf Müller, Peter Gottschling, and Martin Gaber. Water Concentration and Diffusivity in Silicates Obtained by Vacuum Extraction. Glass Science and Technology, 78:76--89, 2005.
@ARTICLE{pg_extraction,
author = {Ralf M{\"{u}}ller and Peter Gottschling and Martin Gaber},
title = {Water Concentration and Diffusivity in Silicates Obtained by Vacuum Extraction},
journal = {Glass Science and Technology},
year = {2005},
volume = {78},
pages = {76--89}
}


20. Jeffrey M. Squyres. Debugging in Parallel (in Parallel). ClusterWorld Magazine, MPI Mechanic Column, 3(1):34--37, January 2005.
Keywords: MPI.
@Article{squyres05:_debug_paral_paral,
author = {Jeffrey M. Squyres},
title = {Debugging in Parallel (in Parallel)},
journal = {ClusterWorld Magazine, {MPI} Mechanic Column},
pages = {34--37},
year = 2005,
volume = 3,
number = 1,
month = {January},
url = {http://cw.squyres.com/},
keywords = {MPI}
}


 Conference articles (26)
1. T. Hoefler. The Cell Processor. In 22C3 Proceedings, pages 286-292, 12 2005.
@inproceedings{hoefler-22c3-05,
author={T. Hoefler},
title={{The Cell Processor}},
journal={22. Chaos Communication Congress},
year={2005},
month={12},
pages={286-292},
booktitle={22C3 Proceedings},
location={Berlin, Germany},
isbn={ 3-934636-04-7},
url={http://events.ccc.de/congress/2005/fahrplan/attachments/545-Paper_TheCellProcessor.pdf},
url={http://www.unixer.de/~htor/publications/},

}


2. A. Danalis, K. Kim, L. Pollock, and M. Swany. Transformations to Parrallel Codes for Communication-Computation Overlap. In , November 2005.
@Inproceedings{swany_Inproceedings_SC2005,
Author = {A. Danalis and K. Kim and L. Pollock and M. Swany},
Date-Modified = {2016-06-10 15:54:40 +0000},
Journal = {In Proceedings of IEEE/ACM Conference on High Performance Computing and Networking 2005 (SC2005)},
Month = {November},
Title = {Transformations to Parrallel Codes for Communication-Computation Overlap},
Year = {2005}
}


3. Torsten Hoefler, Jeffrey M. Squyres, Torsten Mehlan, Frank Mietke, and Wolfgang Rehm. Implementing a Hardware-Based Barrier in Open MPI. In Proceedings of KiCC'05, Chemnitzer Informatik Berichte, November 2005.
@inproceedings{hoeflerkicc05,
author = {Torsten Hoefler and Jeffrey M. Squyres and Torsten Mehlan and Frank Mietke and Wolfgang Rehm},
title = {Implementing a Hardware-Based Barrier in {O}pen {MPI}},
booktitle = {Proceedings of KiCC'05, Chemnitzer Informatik Berichte},
year = 2005,
month = {November},
isbn = {0-7659-2381-1},
location = {Chemnitz, Germany},

}


4. Douglas Gregor and Andrew Lumsdaine. Lifting Sequential Graph Algorithms for Distributed-Memory Parallel Computation. In Proceedings of the 2005 ACM SIGPLAN conference on Object-oriented programming, systems, languages, and applications (OOPSLA '05), pages 423--437, October 2005.
 Annotation: This paper describes the process used to extend the Boost Graph Library (BGL) for parallel operation with distributed memory. The BGL is a library of generic graph algorithms and supporting data structures written in C++, but it was not originally designed with parallelism in mind. The generic programming process of lifting is illustrated using one of the core algorithms in the BGL--breadth-first search--abstracting away the implicit requirements of sequential execution and a single, shared address space. The resulting generic algorithm is completely unchanged from the sequential algorithm, requiring only the introduction of external (distributed) data structures for parallelization. More importantly, the generic implementation retains its interface and semantics, such that other distributed algorithms can be built upon it with no loss of efficiency. By characterizing these extensions as well as the extension process, we develop general principles and patterns for using (and reusing) generic high-performance parallel software libraries. We demonstrate that the resulting algorithm implementations are both efficient and scalable with performance results for several algorithms.

@InProceedings{Gregor:OOPSLA:2005,
author = {Douglas Gregor and Andrew Lumsdaine},
title = {Lifting Sequential Graph Algorithms for Distributed-Memory Parallel Computation},
booktitle = {Proceedings of the 2005 {ACM} {SIGPLAN} conference on {O}bject-oriented programming, systems, languages, and applications ({OOPSLA} '05)},
year = 2005,
pages = {423--437},
month = {October},
pages = {423--437},
thanks = {NSF grant EIA-0131354 and by a grant from the Lilly Endowment},
annote = {This paper describes the process used to extend the Boost Graph Library (BGL) for parallel operation with distributed memory. The BGL is a library of generic graph algorithms and supporting data structures written in C++, but it was not originally designed with parallelism in mind. The generic programming process of lifting is illustrated using one of the core algorithms in the BGL--breadth-first search--abstracting away the implicit requirements of sequential execution and a single, shared address space. The resulting generic algorithm is completely unchanged from the sequential algorithm, requiring only the introduction of external (distributed) data structures for parallelization. More importantly, the generic implementation retains its interface and semantics, such that other distributed algorithms can be built upon it with no loss of efficiency. By characterizing these extensions as well as the extension process, we develop general principles and patterns for using (and reusing) generic high-performance parallel software libraries. We demonstrate that the resulting algorithm implementations are both efficient and scalable with performance results for several algorithms.},
thanks = {NSF grant EIA-0131354 and by a grant from the Lilly Endowment, AVIDD cluster used in the experiments was funded in part by NSF Grant CDA-9601632}
}


5. B. Barrett, J. M. Squyres, A. Lumsdaine, R. L. Graham, and G. Bosilca. Analysis of the Component Architecture Overhead in Open MPI. In Proceedings, 12th European PVM/MPI Users' Group Meeting, Sorrento, Italy, September 2005.
@InProceedings{barrett05:_analy_compon_archit_overh_open_mpi,
thanks = {Lilly Endowment and NSF 0116050},
author = {B. Barrett and J. M. Squyres and A. Lumsdaine and R. L. Graham and G. Bosilca},
title = {Analysis of the Component Architecture Overhead in Open MPI},
booktitle = {Proceedings, 12th European PVM/MPI Users' Group Meeting},
year = 2005,
month = {September},

}


6. R. H. Castain, T. S. Woodall, D. J. Daniel, J. M. Squyres, B. Barrett, and G .E. Fagg. The Open Run-Time Environment (OpenRTE): A Transparent Multi-Cluster Environment for High-Performance Computing. In Proceedings, 12th European PVM/MPI Users' Group Meeting, Sorrento, Italy, September 2005.
@InProceedings{castain05:_open_rte,
thanks = {Lilly Endowment and NSF 0116050},
author = {R. H. Castain and T. S. Woodall and D. J. Daniel and J. M. Squyres and B. Barrett and G .E. Fagg},
title = {The Open Run-Time Environment (OpenRTE): A Transparent Multi-Cluster Environment for High-Performance Computing},
booktitle = {Proceedings, 12th European PVM/MPI Users' Group Meeting},
year = 2005,
month = {September},

}


7. L. Fishgold, A. Danalis, L. Pollock, and M. Swany. An Automated Approach to Improve Communication-Computation Overlap in Clusters. In , September 2005.
@Inproceedings{swany_Inproceedings_ParCo,
Author = {L. Fishgold and A. Danalis and L. Pollock and M. Swany},
Date-Modified = {2016-06-10 15:41:58 +0000},
Journal = {Proceedings of Parallel Computing Conference (ParCo) 2005},
Month = {September},
Title = {An Automated Approach to Improve Communication-Computation Overlap in Clusters},
Year = {2005}
}


8. Ronald Garcia and Andrew Lumsdaine. Type Classes Without Types. In 2005 Workshop on Scheme and Functional Programming, September 2005.
@inproceedings{garcia05:_type_class,
author = "Ronald Garcia and Andrew Lumsdaine",
title = "Type Classes Without Types",
booktitle = "2005 Workshop on Scheme and Functional Programming",
month = "September",
year = 2005,

}


9. Richard L. Graham, Timothy S. Woodall, and Jeffrey M. Squyres. Open MPI: A Flexible High Performance MPI. In Proceedings, 6th Annual International Conference on Parallel Processing and Applied Mathematics, Poznan, Poland, September 2005.
@InProceedings{graham05:_open_mpi,
author = {Richard L. Graham and Timothy S. Woodall and Jeffrey M. Squyres},
title = {Open {MPI}: A Flexible High Performance {MPI}},
booktitle = {Proceedings, 6th Annual International Conference on Parallel Processing and Applied Mathematics},
year = 2005,
month = {September}
}


10. Craig E. Rasmussen and Jeffrey M. Squyres. A Case for New MPI Fortran Bindings. In Proceedings, 12th European PVM/MPI Users' Group Meeting, Sorrento, Italy, September 2005.
@InProceedings{rasmussen05:_case_new_mpi_fortran_bindings,
thanks = {Lilly Endowment and NSF 0116050},
author = {Craig E. Rasmussen and Jeffrey M. Squyres},
title = {A Case for New MPI Fortran Bindings},
booktitle = {Proceedings, 12th European PVM/MPI Users' Group Meeting},
year = 2005,
month = {September},

}


11. Jeremy Siek and Andrew Lumsdaine. Language Requirements for Large-Scale Generic Libraries. In GPCE '05: Proceedings of the fourth international conference on Generative Programming and Component Engineering, September 2005.
Note: Accepted for publication.
 Annotation: The past decade of experience has demonstrated that the generic programming methodology is highly effective for the design, implementation, and use of large-scale software libraries. The fundamental principle of generic programming is the realization of interfaces for entire sets of components, based on their essential syntactic and semantic requirements, rather than for any particular components. Many programming languages have features for describing interfaces between software components, but none completely support the approach used in generic programming. We have recently developed G, a language designed to provide first-class language support for generic programming and large-scale libraries. In this paper, we present an overview of G and analyze the interdependence between language features and libraries design in light of a complete implementation of the Standard Template Library using G. In addition, we discuss important issues related to modularity and encapsulation in large-scale libraries and how language support for validation of components in isolation can prevent many common problems in component integration.

@InProceedings{siek05:_g_stl,
author = {Jeremy Siek and Andrew Lumsdaine},
title = {Language Requirements for Large-Scale Generic Libraries},
booktitle = {{GPCE} '05: Proceedings of the fourth international conference on {Generative} {Programming} and {Component} {Engineering}},
year = 2005,
month = {September},
note = {accepted for publication},
annote = {The past decade of experience has demonstrated that the generic programming methodology is highly effective for the design, implementation, and use of large-scale software libraries. The fundamental principle of generic programming is the realization of interfaces for entire sets of components, based on their essential syntactic and semantic requirements, rather than for any particular components. Many programming languages have features for describing interfaces between software components, but none completely support the approach used in generic programming. We have recently developed G, a language designed to provide first-class language support for generic programming and large-scale libraries. In this paper, we present an overview of G and analyze the interdependence between language features and libraries design in light of a complete implementation of the Standard Template Library using G. In addition, we discuss important issues related to modularity and encapsulation in large-scale libraries and how language support for validation of components in isolation can prevent many common problems in component integration.}
}


12. Douglas Gregor and Andrew Lumsdaine. The Parallel BGL: A Generic Library for Distributed Graph Computations. In Parallel Object-Oriented Scientific Computing (POOSC), July 2005.
@InProceedings{Gregor:POOSC:2005,
author = {Douglas Gregor and Andrew Lumsdaine},
title = {The {Parallel} {BGL}: {A} Generic Library for Distributed Graph Computations},
booktitle = {Parallel Object-Oriented Scientific Computing (POOSC)},
year = 2005,
month = {July},
thanks = {NSF grant EIA-0131354 and by a grant from the Lilly Endowment}
}


13. T. Hoefler, L. Cerquetti, T. Mehlan, F. Mietke, and W. Rehm. A practical approach to the rating of barrier algorithms using the LogP model and Open-MPI. In Proceedings of the 2005 International Conference on Parallel Processing Workshops, pages 562--569, 06 2005.
@inproceedings{hoefler-icpp-05,
author={T. Hoefler and L. Cerquetti and T. Mehlan and F. Mietke and W. Rehm},
title={{A practical approach to the rating of barrier algorithms using the LogP model and Open-MPI}},
year={2005},
month={06},
pages={562--569},
booktitle={Proceedings of the 2005 International Conference on Parallel Processing Workshops},
location={Oslo, Norway},
isbn={0-7659-2381-1},
url={img/hoefler-icpp05.pdf},
url={http://www.unixer.de/~htor/publications/},

}


14. T. Hoefler and W. Rehm. A Communication Model for Small Messages with InfiniBand. In PARS Mitteilungen, pages 32-41, 06 2005. PARS.
Note: (Awarded with the PARS Junior Researcher Prize).
@inproceedings{hoefler-pars-05,
author={T. Hoefler and W. Rehm},
title={{A Communication Model for Small Messages with InfiniBand}},
institution={PARS},
year={2005},
month={06},
pages={32-41},
booktitle={PARS Mitteilungen},
location={Luebeck, Germany},
publisher={PARS},
issn={0177-0454},
note={(Awarded with the PARS Junior Researcher Prize)},
url={./img/hoefler-pars05.pdf},
url={http://www.unixer.de/~htor/publications/},

}


15. F. Mietke, M. Steiger, T. Mehlan, T. Hoefler, and W. Rehm. SHIBA Shared Memory Support for InfiniBand MPICH2 Device. In PARS Mitteilungen 2005, pages 14-23, 6 2005.
@inproceedings{mietke-pars-05,
author={F. Mietke and M. Steiger and T. Mehlan and T. Hoefler and W. Rehm},
title={{SHIBA Shared Memory Support for InfiniBand MPICH2 Device}},
year={2005},
month={6},
pages={14-23},
booktitle={PARS Mitteilungen 2005},
location={Luebeck, Germany},
issn={0177-0454},
url={http://www.unixer.de/~htor/publications/},

}


16. Jeremy G. Siek and Andrew Lumsdaine. Essential Language Support for Generic Programming. In PLDI '05: Proceedings of the ACM SIGPLAN 2005 Conference on Programming Language Design and Implementation, pages 73--84, June 2005. ACM Press.
 Annotation: Concepts'' are an essential language feature needed to support generic programming in the large. Concepts allow for succinct expression of bounds on type parameters of generic algorithms, enable systematic organization of problem domain abstractions, and make generic algorithms easier to use. In this paper we present the design of a type system and semantics for concepts that is suitable for non-type-inferencing languages. Our design shares much in common with the type classes of Haskell, though our primary influence is from best practices in the \C pp{} community, where concepts are used to document type requirements for templates in generic libraries. Concepts include a novel combination of associated types and same-type constraints that do not appear in type classes, but that are similar to nested types and type sharing in ML.

@inproceedings{Siek:2005mf,
Annote = {Concepts'' are an essential language feature needed to support generic programming in the large. Concepts allow for succinct expression of bounds on type parameters of generic algorithms, enable systematic organization of problem domain abstractions, and make generic algorithms easier to use. In this paper we present the design of a type system and semantics for concepts that is suitable for non-type-inferencing languages. Our design shares much in common with the type classes of Haskell, though our primary influence is from best practices in the \Cpp{} community, where concepts are used to document type requirements for templates in generic libraries. Concepts include a novel combination of associated types and same-type constraints that do not appear in type classes, but that are similar to nested types and type sharing in ML.},
Author = {Jeremy G. Siek and Andrew Lumsdaine},
Booktitle = {{PLDI} '05: Proceedings of the {ACM} {SIGPLAN} 2005 Conference on Programming Language Design and Implementation},
Date-Modified = {2010-12-17 10:23:11 -0700},
Isbn = {1-59593-056-6},
Month = {June},
Pages = {73--84},
Publisher = {{ACM} Press},
Title = {Essential Language Support for Generic Programming},
Year = 2005
}


17. S. Wei, J. Mirkovic, and M. Swany. Distributed Worm Simulation with a Realistic Internet Model. In , June 2005.
@Inproceedings{swany_Inproceedings_worm_simulation,
Author = {S. Wei and J. Mirkovic and M. Swany},
Date-Modified = {2016-06-10 16:05:55 +0000},
Journal = {Proceedings of Symposium on Measurement, Modeling and Simulation of Malware, in conjunction with the Conference on Parallel and Distributed Simulation},
Month = {June},
Title = {Distributed Worm Simulation with a Realistic Internet Model},
Year = {2005}
}


18. Jesse Davis, Doug Stark, and Nicholas Edmonds. Method for Module Interaction in a Modular Architecture for Sensor Systems (MASS). In International Embedded and Hybrid Systems Conference, Singapore, May 2005.
@InProceedings{edmonds05:IEHSC,
author = {Jesse Davis and Doug Stark and Nicholas Edmonds},
title = {Method for Module Interaction in a Modular Architecture for Sensor Systems ({MASS})},
booktitle = {International Embedded and Hybrid Systems Conference},
year = 2005,
month = {May},
}


19. Douglas Gregor and Andrew Lumsdaine. The Execution Instance Overloading Pattern. In Workshop on Patterns in High-Performance Computing, May 2005.
@InProceedings{Gregor05:eio_pattern,
author = {Douglas Gregor and Andrew Lumsdaine},
booktitle = {Workshop on Patterns in High-Performance Computing},
month = {May},
year = 2005
}


20. DongInn Kim, Jeffrey M. Squyres, and Andrew Lumsdaine. Revamping the OSCAR database: A Flexible Approach to Cluster Configuration Data Management. In Ilias Kotsireas and Deborah Stacey, editors, 19th International Symposium on High Performance Computing Systems and Applications, Guelph, Ontario, Canada, pages 326-332, May 2005. IEEE Computer Society.
Keywords: OSCAR, high performance computing, cluster.
@InProceedings{kim05:_revam_oscar,
author = {DongInn Kim and Jeffrey M.\ Squyres and Andrew Lumsdaine},
title = {Revamping the {OSCAR} database: A Flexible Approach to Cluster Configuration Data Management},
booktitle = {19th International Symposium on High Performance Computing Systems and Applications},
pages = {326-332},
year = 2005,
editor = {Ilias Kotsireas and Deborah Stacey},
month = {May},
publisher = {IEEE Computer Society},
url = {http://www.csm.ornl.gov/oscar05/},
keywords = "OSCAR, high performance computing, cluster",
thanks = {Lilly Endowment}
}


21. J. Zurawski, M. Swany, M. Beck, and Y. Ding. Logistical Multicast for Data Distribution. In , May 2005.
@Inproceedings{swany_Inproceedings_CCGrid2005,
Author = {J. Zurawski and M. Swany and M. Beck and Y. Ding },
Date-Modified = {2016-06-10 15:11:28 +0000},
Journal = {In Proceedings of Workshop on Grid Advanced Networks, In conjunction with IEEE International Symposium on Cluster Computing and the Grid (CCGrid2005)},
Month = {May},
Title = {Logistical Multicast for Data Distribution },
Year = {2005}
}


22. Nicholas Edmonds, Doug Stark, and Jesse Davis. MASS: Modular Architecture for Sensor Systems. In 4th International Workshop on Information Processing in Sensor Networks, Los Angeles, California, April 2005.
@InProceedings{edmonds05:MASS,
author = {Nicholas Edmonds and Doug Stark and Jesse Davis},
title = {{MASS}: Modular Architecture for Sensor Systems},
booktitle = {4th International Workshop on Information Processing in Sensor Networks},
month = {Apr},
year = 2005
}


23. Christopher Mueller, Mehmet Dalkilic, and Andrew Lumsdaine. High-Performance Direct Pairwise Comparison of Large Genomic Sequences. In Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), April 2005.
@InProceedings{mueller_hicomb05,
author = {Christopher Mueller and Mehmet Dalkilic and Andrew Lumsdaine},
title = {High-Performance Direct Pairwise Comparison of Large Genomic Sequences},
booktitle = {Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005)},
year = 2005,
month = {April},
location = {Denver, CO},
url = "http://www.hicomb.org/papers/HICOMB2005-05.pdf"
}


24. Jaakko Järvi, Jeremiah Willcock, and Andrew Lumsdaine. Associated types and constraint propagation for mainstream object-oriented generics. In OOPSLA '05: Proceedings of the 20th annual ACM SIGPLAN conference on Object-oriented programming systems languages and applications, New York, NY, USA, pages 1--19, 2005. ACM Press.
@inproceedings{jarvi05:oopsla,
author = {Jaakko J\"arvi and Jeremiah Willcock and Andrew Lumsdaine},
title = {Associated types and constraint propagation for mainstream object-oriented generics},
booktitle = {{OOPSLA} '05: Proceedings of the 20th annual {ACM SIGPLAN} conference on Object-oriented programming systems languages and applications},
year = 2005,
isbn = {1-59593-031-0},
pages = {1--19},
location = {San Diego, CA, USA},
doi = {http://doi.acm.org/10.1145/1094811.1094813},
publisher = {ACM Press},
address = {New York, NY, USA},
thanks = {NSF EIA-0131354, Lilly Endowment, DOE HPCSF},

}


25. Todd L. Veldhuizen. Software Libraries and Their Reuse: Entropy, Kolmogorov Complexity, and Zipf's Law. In , 2005.
Note: ArXiv:cs.SE/0508023.
@inproceedings{Veldhuizen:LCSD:2005,
author = {Todd L. Veldhuizen},
title = {Software Libraries and Their Reuse: Entropy, {Kolmogorov} Complexity, and {Zipf's} Law},
conftitle = { OOPSLA 2005 Workshop on Library-Centric Software Design (LCSD'05)},
conflocation = { San Diego, USA },
confdate = { October 16, 2005 },
note = { OOPSLA 2005 Workshop on Library-Centric Software Design (LCSD'05), San Diego, October 16 },
url = { http://arxiv.org/abs/cs.SE/0508023 },
year = { 2005 },
note = { arXiv:cs.SE/0508023 }
}


26. Marcin Zalewski and Sibylle Schupp. Changing Iterators with Confidence. A Case Study of Change Impact Analysis Applied to Conceptual Specifications.. In David Musser and Jeremy Siek, editors, Proc. 1st Int. Workshop on Library-Centric Software Design, 2005.
@inproceedings{zalewski_changing_2005,
title = {Changing Iterators with Confidence. {A} Case Study of Change Impact Analysis Applied to Conceptual Specifications.},
url = {http://www.cs.rpi.edu/research/pdf/06-12.pdf},
booktitle = {Proc. 1st Int. Workshop on {Library-Centric} Software Design},
author = {Marcin Zalewski and Sibylle Schupp},
editor = {David Musser and Jeremy Siek},
year = 2005,

}


 Internal reports (5)
1. Brian W. Barrett, Jeffrey M. Squyres, and Andrew Lumsdaine. Implementation of Open MPI on Red Storm. Technical report LA-UR-05-8307, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, October 2005.
@TechReport{barrett05:_implem_open_mpi_red_storm,
author = {Brian W. Barrett and Jeffrey M. Squyres and Andrew Lumsdaine},
title = {Implementation of Open MPI on Red Storm},
institution = {Los Alamos National Laboratory},
year = 2005,
number = {LA-UR-05-8307},
address = {Los Alamos, New Mexico, USA},
month = {October}
}


2. Douglas Gregor and Jeremy Siek. Implementing Concepts. Technical report N1848=05-0108, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++, August 2005.
@TechReport{gregor05:implementing_concepts,
author = {Douglas Gregor and Jeremy Siek},
title = {Implementing Concepts},
institution = {ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language {C++}},
year = 2005,
number = {N1848=05-0108},
month = {August}
}


3. Douglas Gregor, Jeremy Siek, Jeremiah Willcock, Jaakko Järvi, Ronald Garcia, and Andrew Lumsdaine. Concepts for C++0x (Revision 1). Technical report N1849=05-0109, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++, August 2005.
@TechReport{gregor05:concepts_c++0x,
author = {Douglas Gregor and Jeremy Siek and Jeremiah Willcock and Jaakko J\"{a}rvi and Ronald Garcia and Andrew Lumsdaine},
title = {Concepts for {C++0x} (Revision 1)},
institution = {ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language {C++}},
year = 2005,
number = {N1849=05-0109},
month = {August}
}


4. Douglas Gregor and Jeremy Siek. Explicit model definitions are necessary. Technical report N1798=05-0058, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++, May 2005.
@TechReport{gregor05:explicit_models,
author = {Douglas Gregor and Jeremy Siek},
title = {Explicit model definitions are necessary},
institution = {ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language {C++}},
year = 2005,
month = {May},
number = {N1798=05-0058}
}


5. Jeremy Siek, Douglas Gregor, Ronald Garcia, Jeremiah Willcock, Jaakko Järvi, and Andrew Lumsdaine. Concepts for C++0x. Technical report N1758=05-0018, ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language C++, January 2005.
@TechReport{siek05:_concepts_cpp0x,
author = {Jeremy Siek and Douglas Gregor and Ronald Garcia and Jeremiah Willcock and Jaakko J\"arvi and Andrew Lumsdaine},
title = {Concepts for C++0x},
institution = {ISO/IEC JTC 1, Information Technology, Subcommittee SC 22, Programming Language {C++}},
month = jan,
year = 2005,
url = "http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2005/n1758.pdf",
number = {N1758=05-0018}
}


1. Peter Gottschling. Generic Libraries to Support FEM Applications. Presentation at Extended Finite Element Tutorial, Lausanne, Switzerland, December 2005.
@MISC{gottschling05:xfem_presentation,
author = {Peter Gottschling},
title = {Generic Libraries to Support {FEM} Applications},
howpublished = {Presentation at Extended Finite Element Tutorial, Lausanne, Switzerland},
month = {December},
year = {2005}
}


2. Christopher Mueller and Andrew Lumsdaine. Developing Reliable Complex Software Systems in a Research Environment, September 2005.
Note: Presentation at iLight 2005.
@Misc{mueller_presilight05,
author = {Christopher Mueller and Andrew Lumsdaine},
title = {Developing Reliable Complex Software Systems in a Research Environment},
note = {Presentation at iLight 2005},
month = {September},
year = {2005},
location = {Indianapolis, IN}
}


3. T. Hoefler. Evaluation of publicly available Barrier-Algorithms and Improvement of the Barrier-Operation for large-scale Cluster-Systems with special Attention on InfiniBand Networks, Apr. 2005.
@masterthesis{hoefler-thesis-05,
author={T. Hoefler},
title={{Evaluation of publicly available Barrier-Algorithms and Improvement of the Barrier-Operation for large-scale Cluster-Systems with special Attention on InfiniBand Networks}},
institution={Technical University of Chemnitz},
year={2005},
month={Apr.},
location={Chemnitz, Germany},
url={http://www.unixer.de/~htor/publications/},

}


4. R. Heiland, D. Milsho, and K. Browning. Using Squeak to graphically model symmetries in nature. Poster presentation at the ITAP Teaching and Learning with Technology Conference, West Lafayette, IN, February 2005.
@Misc{heiland05:_itap,
author = {R. Heiland and D. Milsho and K. Browning},
title = {Using Squeak to graphically model symmetries in nature},
howpublished = {Poster presentation at the ITAP Teaching and Learning with Technology Conference, West Lafayette, IN},
month = {Feb},
year = 2005
}


5. Christopher Mueller, Mehmet Dalkilic, and Andrew Lumsdaine. Implementing Data Parallel Algorithms for Bioinformatics, February 2005.
Note: Presentation at SIAM Conference on Computational Science and Engineering, Orlando, FL.
@Misc{mueller_pressiam05,
author = {Christopher Mueller and Mehmet Dalkilic and Andrew Lumsdaine},
title = {Implementing Data Parallel Algorithms for Bioinformatics},
note = {Presentation at SIAM Conference on Computational Science and Engineering, Orlando, FL},
month = {February},
year = {2005}
}


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