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Towards frameworks for large scale ensemble-based execution patterns

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TitleInfo
Title
Towards frameworks for large scale ensemble-based execution patterns
Name (type = personal)
NamePart (type = family)
Balasubramanian
NamePart (type = given)
Vivekanandan
NamePart (type = date)
1991-
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Vivekanandan Balasubramanian
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Jha
NamePart (type = given)
Shantenu
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Shantenu Jha
Affiliation
Advisory Committee
Role
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chair
Name (type = personal)
NamePart (type = family)
Javanmard
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Mehdi
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Mehdi Javanmard
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Advisory Committee
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internal member
Name (type = personal)
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Gajic
NamePart (type = given)
Zoran
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Zoran Gajic
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
York
NamePart (type = given)
Darrin M
DisplayForm
Darrin M York
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm (authority = RULIB)
school
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Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2015
DateOther (qualifier = exact); (type = degree)
2015-05
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2015
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Towards Frameworks for Large Scale Ensemble-based Execution Patterns by Vivekanandan Balasubramanian Thesis Director: Dr. Shantenu Jha A major challenge in the field of chemical sciences is to bridge the gap between the ability to study matter at an atomic scale and to predict how these details behave and impact at a macroscopic scale. Molecular Dynamics (MD) simulations are a powerful tool for the study of macromolecular systems as they provide the ability to compute thermodynamic and kinetic parameters accurately. In order for MD simulations to be effective, they must adequately sample, e.g., effi- ciently and accurately sample all conformational space for a molecule. A long standing debate in the MD community has been around approaches to effective sampling: for a given amount of compute time, which is likely to guarantee better sampling: a single long-running simulation or multiple smaller simulations? In this project, we provide support for the scenario when multiple small simulations are to be used. Another important requirement faced by MD community is the need for iterative simulation and analysis stages, from which data can be extracted and, based on prob- ability densities and weights, new set of trajectories can be generated. These scenarios result in the following computational challenges: (i) Executing large number of tasks concurrently, (ii) Support for heterogeneous resource, (iii) Effective data movement that is correlated with stage transitions. iiTo address these requirements, we developed the Ensemble MD Toolkit (EnMDTK). The EnMDTK has three primary design features: (1) Fundamental support for multiple concurrent simulations, (2) Support for different ensemble-based execution patterns, and (3) Execution Plugins which abstract, from the user the challenges /difficulties of managing the execution of these patterns on heterogeneous systems. The toolkit enables scientists to easily and scalably develop their own applications using pre-determined patterns supported by the EnMDTK. Our contribution to this project is the development, testing and documentation of the specific iterative Simulation-Analysis pattern of EnMDTK. The development re- quired extensive study and testing of the underlying RADICAL-Pilot framework in order to use it in the most effective form. Knowledge of the individual kernels, work- ing and their specific dependencies were required for their deployment on the various resources. Testing revealed certain optimizations that could be done with the data movement. Performance characterization of the final toolkit was also done.
Subject (authority = RUETD)
Topic
Electrical and Computer Engineering
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_6405
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (ix, 42 p. : ill.)
Note (type = degree)
M.S.
Note (type = bibliography)
Includes bibliographical references
Subject (authority = ETD-LCSH)
Topic
Molecular dynamics--Computer simulation
Subject (authority = ETD-LCSH)
Topic
Macromolecular Systems
Note (type = statement of responsibility)
by Vivekanandan Balasubramanian
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
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NjNbRU
Identifier (type = doi)
doi:10.7282/T39Z96QV
Genre (authority = ExL-Esploro)
ETD graduate
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Balasubramanian
GivenName
Vivekanandan
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2015-04-15 13:16:28
AssociatedEntity
Name
Vivekanandan Balasubramanian
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
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Copyright protected
Availability
Status
Open
Reason
Permission or license
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RULTechMD (ID = TECHNICAL1)
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ETD
OperatingSystem (VERSION = 5.1)
windows xp
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