You searched for subject:(Parallel Computing).
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1.
Zulian, Patrick.
Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective.
Degree: 2017, Università della Svizzera italiana
URL: http://doc.rero.ch/record/304964 
► In finite element simulations, the handling of geometrical objects and their discrete representation is a critical aspect in both serial and parallel scientific software environments.…
(more)
▼ In finite element simulations, the handling of
geometrical objects and their discrete representation is a critical
aspect in both serial and
parallel scientific software
environments. The development of codes targeting such envinronments
is
subject to great development effort and man-hours invested. In
this thesis we approach these issues from three fronts. First,
stable and efficient techniques for the transfer of discrete fields
between non matching volume or surface meshes are an essential
ingredient for the discretization and numerical solution of coupled
multi-physics and multi-scale problems. In particular
L2-projections allows for the transfer of discrete fields between
unstructured meshes, both in the volume and on the surface. We
present an algorithm for parallelizing the assembly of the
L2-transfer operator for unstructured meshes which are arbitrarily
distributed among different processes. The algorithm requires no a
priori information on the geometrical relationship between the
different meshes. Second, the geometric representation is often a
limiting factor which imposes a trade-off between how accurately
the shape is described, and what methods can be employed for
solving a system of differential equations. Parametric
finite-elements and bijective mappings between polygons or
polyhedra allow us to flexibly construct finite element
discretizations with arbitrary resolutions without sacrificing the
accuracy of the shape description. Such flexibility allows
employing state-of-the-art techniques, such as geometric multigrid
methods, on meshes with almost any shape.t, the way numerical
techniques are represented in software libraries and approached
from a development perspective, affect both usability and
maintainability of such libraries. Completely separating the intent
of high-level routines from the actual implementation and
technologies allows for portable and maintainable performance. We
provide an overview on current trends in the development of
scientific software and showcase our open-source library
utopia.
Advisors/Committee Members: Rolf (Dir.).
Subjects/Keywords: Parallel computing
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APA (6th Edition):
Zulian, P. (2017). Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective. (Thesis). Università della Svizzera italiana. Retrieved from http://doc.rero.ch/record/304964
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zulian, Patrick. “Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective.” 2017. Thesis, Università della Svizzera italiana. Accessed February 17, 2020.
http://doc.rero.ch/record/304964.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zulian, Patrick. “Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective.” 2017. Web. 17 Feb 2020.
Vancouver:
Zulian P. Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective. [Internet] [Thesis]. Università della Svizzera italiana; 2017. [cited 2020 Feb 17].
Available from: http://doc.rero.ch/record/304964.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zulian P. Geometry–aware finite element framework for multi–physics
simulations: an algorithmic and software-centric
perspective. [Thesis]. Università della Svizzera italiana; 2017. Available from: http://doc.rero.ch/record/304964
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Texas A&M University
2.
Hoxha, Dielli.
Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework.
Degree: MS, Computer Engineering, 2016, Texas A&M University
URL: http://hdl.handle.net/1969.1/157157
► Applications of matrices are found in most scienti?c ?elds, such as physics, computer graphics, numerical analysis, etc. The high applicability of matrix algorithms and representations…
(more)
▼ Applications of matrices are found in most scienti?c ?elds, such as physics, computer graphics, numerical analysis, etc. The high applicability of matrix algorithms and representations make them an important component in any
parallel programming language, therefore matrix frameworks are a continuous research e?ort in high performance
computing. This work focuses on a generic matrix framework in the STAPL library. First, we extend the STAPL library by adding a sparse matrix container. Second we implement SUMMA, the
parallel matrix-multiplication algorithm, for ?ne grained computations. Then, implement
parallel matrix-matrix algorithms for the sparse matrix container. Finally, we conduct experimental studies for each of the components we have implemented and discuss the ?ndings. Experiments are conducted on a Cray XE6m cluster. Experimental studies consist of multiple matrix and data inputs that showcase and stress the matrix models implemented. We ?nd that the sparse matrix container outperforms its dense counterpart in sparse in-puts, and vice versa. Both containers, and the matrix summa implementation show scalability up to 512 cores.
Advisors/Committee Members: Amato, Nancy M. (advisor), Rauchwerger, Lawrence (advisor), Ragusa, Jean (committee member).
Subjects/Keywords: Parallel Computing; Sparse Matrix
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APA (6th Edition):
Hoxha, D. (2016). Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/157157
Chicago Manual of Style (16th Edition):
Hoxha, Dielli. “Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework.” 2016. Masters Thesis, Texas A&M University. Accessed February 17, 2020.
http://hdl.handle.net/1969.1/157157.
MLA Handbook (7th Edition):
Hoxha, Dielli. “Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework.” 2016. Web. 17 Feb 2020.
Vancouver:
Hoxha D. Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework. [Internet] [Masters thesis]. Texas A&M University; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/1969.1/157157.
Council of Science Editors:
Hoxha D. Sparse Matrices and Summa Matrix Multiplication Algorithm in STAPL Matrix Framework. [Masters Thesis]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/157157
University of Ontario Institute of Technology
3.
Dubitski, Alexander.
A parallel adaptive method for pseudo-arclength continuation.
Degree: 2011, University of Ontario Institute of Technology
URL: http://hdl.handle.net/10155/196
► We parallelize the pseudo-arclength continuation method for solving nonlinear systems of equations. Pseudo-arclength continuation is a predictor-corrector method where the correction step consists of solving…
(more)
▼ We parallelize the pseudo-arclength continuation method for solving nonlinear systems
of equations. Pseudo-arclength continuation is a predictor-corrector method where the
correction step consists of solving a linear system of algebraic equations. Our algorithm
parallelizes adaptive step-length selection and inexact prediction. Prior attempts to parallelize
pseudo-arclength continuation are typically based on parallelization of the linear
solver which leads to completely solver-dependent software. In contrast, our method is
completely independent of the internal solver and therefore applicable to a large domain
of problems. Our software is easy to use and does not require the user to have extensive
prior experience with High Performance
Computing; all the user needs to provide is the
implementation of the corrector step. When corrector steps are costly or continuation
curves are complicated, we observe up to sixty percent speed up with moderate numbers
of processors. We present results for a synthetic problem and a problem in turbulence.
Advisors/Committee Members: Van Veen, Lennaert.
Subjects/Keywords: HPC; Arclength; Parallel; Computing
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APA (6th Edition):
Dubitski, A. (2011). A parallel adaptive method for pseudo-arclength continuation. (Thesis). University of Ontario Institute of Technology. Retrieved from http://hdl.handle.net/10155/196
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Dubitski, Alexander. “A parallel adaptive method for pseudo-arclength continuation.” 2011. Thesis, University of Ontario Institute of Technology. Accessed February 17, 2020.
http://hdl.handle.net/10155/196.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Dubitski, Alexander. “A parallel adaptive method for pseudo-arclength continuation.” 2011. Web. 17 Feb 2020.
Vancouver:
Dubitski A. A parallel adaptive method for pseudo-arclength continuation. [Internet] [Thesis]. University of Ontario Institute of Technology; 2011. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10155/196.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Dubitski A. A parallel adaptive method for pseudo-arclength continuation. [Thesis]. University of Ontario Institute of Technology; 2011. Available from: http://hdl.handle.net/10155/196
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
4.
Hamsapriya T.
Certain investigations on parallel Computing for
engineering Applications;.
Degree: Certain investigations on parallel Computing for
engineering Applications, 2014, Anna University
URL: http://shodhganga.inflibnet.ac.in/handle/10603/29893
► The need for faster computers is driven by the demands of both newlineComputation intensive applications in science and engineering and dataintensive newlineapplications in commerce The…
(more)
▼ The need for faster computers is driven by the
demands of both newlineComputation intensive applications in
science and engineering and dataintensive newlineapplications in
commerce The main motivation of parallelization of newlineany
sequential algorithm is the desire to reduce the total execution
time of the newlinealgorithm Parallel computing provides a way to
reduce the time taken to newlineexecute a task by dividing the task
between multiple computers that can work newlinesimultaneously to
complete the job As the cost of dedicated parallel machines
newlineis high computing on a cluster of workstations is a viable
alternative for a newlinewide range of engineering applications The
thesis aims at finding cost newlineeffective parallel
implementation of algorithms on a cluster to solve complex
newlineapplications The first part of the thesis addresses the
issues that arise in the newlineparallel implementations The major
issues of concern are load balancing, a newlinewidely used
technique to balance the workload among multiple processors
newlineand fault tolerance the ability to tolerate failures The
proposed load newlinebalancing approach is based on a central
scheduler with hybrid genetic newlinealgorithms and genetic local
search methods Replication approach has been newlineproposed to
improve the performance and fault tolerance of a multiprocessor
newlinesystem newline newline
appendix p215-217, reference
p218-228.
Advisors/Committee Members: Sumathi S.
Subjects/Keywords: Dataintensive applications; Parallel computing
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Manager
APA (6th Edition):
T, H. (2014). Certain investigations on parallel Computing for
engineering Applications;. (Thesis). Anna University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/29893
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
T, Hamsapriya. “Certain investigations on parallel Computing for
engineering Applications;.” 2014. Thesis, Anna University. Accessed February 17, 2020.
http://shodhganga.inflibnet.ac.in/handle/10603/29893.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
T, Hamsapriya. “Certain investigations on parallel Computing for
engineering Applications;.” 2014. Web. 17 Feb 2020.
Vancouver:
T H. Certain investigations on parallel Computing for
engineering Applications;. [Internet] [Thesis]. Anna University; 2014. [cited 2020 Feb 17].
Available from: http://shodhganga.inflibnet.ac.in/handle/10603/29893.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
T H. Certain investigations on parallel Computing for
engineering Applications;. [Thesis]. Anna University; 2014. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/29893
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Saskatchewan
5.
Coutu, Jason Dean.
Reduction of co-simulation runtime through parallel processing.
Degree: 2009, University of Saskatchewan
URL: http://hdl.handle.net/10388/etd-09082009-140047
► During the design phase of modern digital and mixed signal devices, simulations are run to determine the fitness of the proposed design. Some of these…
(more)
▼ During the design phase of modern digital and mixed signal devices, simulations are run to determine the fitness of the proposed design. Some of these simulations can take large amounts of time, thus slowing down the time to manufacture of the system prototype. One of the typical simulations that is done is an integration simulation that simulates the hardware and software at the same time. Most simulators used in this task are monolithic simulators. Some simulators do have the ability to have external libraries and simulators interface with it, but the setup can be a tedious task. This thesis proposes, implements and evaluates a distributed simulator called PDQScS, that allows for speed up of the simulation to reduce this bottleneck in the design cycle without the tedious separation and linking by the user. Using multiple processes and SMP machines a simulation run time reduction was found.
Advisors/Committee Members: Makaroff, Dwight, Bolton, Ron, Eager, Derek, Spiteri, Raymond.
Subjects/Keywords: HW/SW simulation; Parallel computing
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APA (6th Edition):
Coutu, J. D. (2009). Reduction of co-simulation runtime through parallel processing. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/etd-09082009-140047
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Coutu, Jason Dean. “Reduction of co-simulation runtime through parallel processing.” 2009. Thesis, University of Saskatchewan. Accessed February 17, 2020.
http://hdl.handle.net/10388/etd-09082009-140047.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Coutu, Jason Dean. “Reduction of co-simulation runtime through parallel processing.” 2009. Web. 17 Feb 2020.
Vancouver:
Coutu JD. Reduction of co-simulation runtime through parallel processing. [Internet] [Thesis]. University of Saskatchewan; 2009. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10388/etd-09082009-140047.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Coutu JD. Reduction of co-simulation runtime through parallel processing. [Thesis]. University of Saskatchewan; 2009. Available from: http://hdl.handle.net/10388/etd-09082009-140047
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Ontario Institute of Technology
6.
Hazari, Shihab Shahriar.
Design and development of a parallel Proof of Work for permissionless blockchain systems.
Degree: 2019, University of Ontario Institute of Technology
URL: http://hdl.handle.net/10155/1037
► Blockchain, which is the underlying technology for the Bitcoin cryptocurrency, is a distributed ledger forming a decentralized consensus in a peer-to-peer network. A large number…
(more)
▼ Blockchain, which is the underlying technology for the Bitcoin cryptocurrency, is a distributed ledger forming a decentralized consensus in a peer-to-peer network. A large number of the current cryptocurrencies use blockchain technology to maintain the network and the peers use a consensus mechanism called Proof of Work to verify and confirm the transactions. However, the transaction speed in this process is significantly slower than traditional digital transaction systems such as credit cards or PayPal. In this thesis, a
parallel Proof of Work model is proposed in order to increase the scalability of the processing of the transactions. The goal of this model is to ensure that, no two or more miners put the same effort into solving the same block. This model differs from traditional Proof of Work or the Bitcoin pool mining in many aspects, such as the responsibilities of the manager, contribution of active miners, and the reward system. A proof of concept prototype of the proposed model has been constructed based on the attributes of Bitcoin. The prototype has been tested in a local as well as in a cloud environment and results show the feasibility of the proposed model.
Advisors/Committee Members: Mahmoud, Qusay.
Subjects/Keywords: Blockchain; Parallel computing; Scalability; Bitcoin
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APA ·
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Manager
APA (6th Edition):
Hazari, S. S. (2019). Design and development of a parallel Proof of Work for permissionless blockchain systems. (Thesis). University of Ontario Institute of Technology. Retrieved from http://hdl.handle.net/10155/1037
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hazari, Shihab Shahriar. “Design and development of a parallel Proof of Work for permissionless blockchain systems.” 2019. Thesis, University of Ontario Institute of Technology. Accessed February 17, 2020.
http://hdl.handle.net/10155/1037.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hazari, Shihab Shahriar. “Design and development of a parallel Proof of Work for permissionless blockchain systems.” 2019. Web. 17 Feb 2020.
Vancouver:
Hazari SS. Design and development of a parallel Proof of Work for permissionless blockchain systems. [Internet] [Thesis]. University of Ontario Institute of Technology; 2019. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10155/1037.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hazari SS. Design and development of a parallel Proof of Work for permissionless blockchain systems. [Thesis]. University of Ontario Institute of Technology; 2019. Available from: http://hdl.handle.net/10155/1037
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of New South Wales
7.
Ke, Jing.
Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing.
Degree: Computer Science & Engineering, 2018, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/59793
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:49745/SOURCE02?view=true
► Remote sensing is the acquisition of physical response from an object without touch or contact, often collected by remote sensors mounted on satellites or aircraft.…
(more)
▼ Remote sensing is the acquisition of physical response from an object without touch or contact, often collected by remote sensors mounted on satellites or aircraft. Such datasets have been used for many decades in a wide range of applications. With advances in sensor technology, earth imaging is now possible at an unprecedented level of detail, and the amount of data acquired by imaging sensors has been growing rapidly in recent years. Many procedures for processing remotely sensed information are characterised by massively
parallel data processing, intensive computation and complex processing algorithms. These characteristics make real-time processing of large datasets very crucial. Graphical Processing Unit (GPU) is a typical
parallel computing and multicore architecture, designed to perform computations on large amounts of independent data. In recent years, GPU has become dominant for high performance
computing and its massive computational capability is well suited to analyse large-scale remotely sensed information.The thesis studies the
computing architecture and memory hierarchy of GPUs accelerators, and discusses the main performance issues in scientific and
parallel computing.
Parallel computing frameworks, parallelisation strategies, performance optimisation and acceleration algorithms for remotely sensed image processing are provided. Effective and efficient solutions are provided to dynamic programming based NP-hard optimisation problems and pixel-classification based hyperspectral imaging unmixing procedures. Verification methods are desgined to evaluate performance in terms of accuracy and speedup. The proposed methods assume spatial smoothness in remotely sensed images, which distinguishes them from artificial arts or natural photos. The benchmark tests show good performance accelerations compared with both sequential and
parallel implementations in the literature on NVIDIA GPU accelerators. An analysis of performance profile results is presented and can be referred as a guide to similar parallelisation strategies for other
computing platforms.
Advisors/Committee Members: Sowmya, Arcot, Computer Science & Engineering, Faculty of Engineering, UNSW, Bednarz, Tomasz, Art, Faculty of Art & Design, UNSW.
Subjects/Keywords: Parallel computing; GPGPU; Remote sensing
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APA (6th Edition):
Ke, J. (2018). Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/59793 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:49745/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Ke, Jing. “Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing.” 2018. Doctoral Dissertation, University of New South Wales. Accessed February 17, 2020.
http://handle.unsw.edu.au/1959.4/59793 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:49745/SOURCE02?view=true.
MLA Handbook (7th Edition):
Ke, Jing. “Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing.” 2018. Web. 17 Feb 2020.
Vancouver:
Ke J. Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing. [Internet] [Doctoral dissertation]. University of New South Wales; 2018. [cited 2020 Feb 17].
Available from: http://handle.unsw.edu.au/1959.4/59793 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:49745/SOURCE02?view=true.
Council of Science Editors:
Ke J. Parallel Computing and Performance Optimisation in Remotely Sensed Image Processing. [Doctoral Dissertation]. University of New South Wales; 2018. Available from: http://handle.unsw.edu.au/1959.4/59793 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:49745/SOURCE02?view=true
University of Illinois – Urbana-Champaign
8.
Manikandan, Gowthami Jayashri.
Comprehensive evaluation of error correction methods for high-throughput sequencing data.
Degree: MS, Electrical & Computer Engr, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/97787
► The advent of DNA and RNA sequencing has significantly revolutionized the study of genomics and molecular biology. Development of high-throughput sequencing technologies have brought about…
(more)
▼ The advent of DNA and RNA sequencing has significantly revolutionized the study of genomics and molecular biology. Development of high-throughput sequencing technologies have brought about a quick and cheaper way to sequence genomes. Different technologies use different underlying methods for sequencing and are prone to different error rates. Though many tools exist for error correction in high-throughput sequencing data, no standard technology-independent method is available yet to evaluate the accuracy and effectiveness of these error correction tools. In order to supply a standard way to evaluate error correction methods for DNA and RNA sequencing, this thesis presents a Software Package for Error Correction Tool Assessment on nuCLEic acid sequences (SPECTACLE). SPECTACLE can evaluate corrected DNA and RNA reads from many underlying sequencing technologies and differentiate heterozygous alleles from sequencing errors. The work provides some key insights on many factors that stress the challenges in error correction by compiling high-throughput sequencing read sets from technologies like Illumina, PacBio and ONT. The performances of 23 different error correction tools have been analyzed using SPECTACLE and the compiled datasets. This thesis also provides unique and helpful insights into the strengths and weaknesses of various error correction tools and aims to establish a standard platform for evaluating error correction tools in the future.
Advisors/Committee Members: Chen, Deming (advisor).
Subjects/Keywords: Computational genomics; Algorithms; Parallel computing
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APA (6th Edition):
Manikandan, G. J. (2017). Comprehensive evaluation of error correction methods for high-throughput sequencing data. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/97787
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Manikandan, Gowthami Jayashri. “Comprehensive evaluation of error correction methods for high-throughput sequencing data.” 2017. Thesis, University of Illinois – Urbana-Champaign. Accessed February 17, 2020.
http://hdl.handle.net/2142/97787.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Manikandan, Gowthami Jayashri. “Comprehensive evaluation of error correction methods for high-throughput sequencing data.” 2017. Web. 17 Feb 2020.
Vancouver:
Manikandan GJ. Comprehensive evaluation of error correction methods for high-throughput sequencing data. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2017. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/2142/97787.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Manikandan GJ. Comprehensive evaluation of error correction methods for high-throughput sequencing data. [Thesis]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/97787
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Georgia Tech
9.
Schieber, Matthew Cole.
Optimizing computational kernels in quantum chemistry.
Degree: MS, Computational Science and Engineering, 2018, Georgia Tech
URL: http://hdl.handle.net/1853/59949
► Density fitting is a rank reduction technique popularly used in quantum chemistry in order to reduce the computational cost of evaluating, transforming, and processing the…
(more)
▼ Density fitting is a rank reduction technique popularly used in quantum chemistry in
order to reduce the computational cost of evaluating, transforming, and processing the
4-center electron repulsion integrals (ERIs). By utilizing the resolution of the identity technique, density fitting reduces the 4-center ERIs into a 3-center form. Doing so not only alleviates the high storage cost of the ERIs, but it also reduces the computational cost of operations involving them. Still, these operations can remain as computational bottlenecks which commonly plague quantum chemistry procedures. The goal of this thesis is to investigate various optimizations for density-fitted version of computational kernels used ubiquitously throughout quantum chemistry. First, we detail the spatial sparsity available to the 3-center integrals and the application of such sparsity to various operations, including integral computation, metric contractions, and integral transformations. Next, we investigate sparse memory layouts and their implication on the performance of the integral transformation kernel. Next, we analyze two transformation algorithms and how their performance will vary depending on the context in which they are used. Then, we propose two sparse memory layouts and the resulting performance of Coulomb and exchange evaluations. Since the memory required for these tensors grows rapidly, we frame these discussions in the context of their in-core and disk performance. We implement these methods in the P SI 4 electronic structure package and reveal the optimal algorithm for the kernel should vary depending on whether a disk-based implementation must be used.
Advisors/Committee Members: Sherrill, Charles D. (advisor), Chow, Edmond (committee member), McDaniel, Jesse (committee member).
Subjects/Keywords: Quantum chemistry; Parallel computing; High performance computing
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APA (6th Edition):
Schieber, M. C. (2018). Optimizing computational kernels in quantum chemistry. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/59949
Chicago Manual of Style (16th Edition):
Schieber, Matthew Cole. “Optimizing computational kernels in quantum chemistry.” 2018. Masters Thesis, Georgia Tech. Accessed February 17, 2020.
http://hdl.handle.net/1853/59949.
MLA Handbook (7th Edition):
Schieber, Matthew Cole. “Optimizing computational kernels in quantum chemistry.” 2018. Web. 17 Feb 2020.
Vancouver:
Schieber MC. Optimizing computational kernels in quantum chemistry. [Internet] [Masters thesis]. Georgia Tech; 2018. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/1853/59949.
Council of Science Editors:
Schieber MC. Optimizing computational kernels in quantum chemistry. [Masters Thesis]. Georgia Tech; 2018. Available from: http://hdl.handle.net/1853/59949
Louisiana State University
10.
Yang, Shuangyang.
A Persistent Storage Model for Extreme Computing.
Degree: PhD, Computer Sciences, 2014, Louisiana State University
URL: etd-10312014-133428
;
https://digitalcommons.lsu.edu/gradschool_dissertations/2910
► The continuing technological progress resulted in a dramatic growth in aggregate computational performance of the largest supercomputing systems. Unfortunately, these advances did not translate to…
(more)
▼ The continuing technological progress resulted in a dramatic growth in aggregate computational performance of the largest supercomputing systems. Unfortunately, these advances did not translate to the required extent into accompanying I/O systems and little more in terms of architecture or effective access latency. New classes of algorithms developed for massively parallel applications, that gracefully handle the challenges of asynchrony, heavily multi-threaded distributed codes, and message-driven computation, must be matched by similar advances in I/O methods and algorithms to produce a well performing and balanced supercomputing system. This dissertation proposes PXFS, a storage model for persistent objects inspired by the ParalleX model of execution that addresses many of these challenges. The PXFS model is designed to be asynchronous in nature to comply with ParalleX model and proposes an active TupleSpace concept to hold all kinds of metadata/meta-object for either storage objects or runtime objects. The new active TupleSpace can also register ParalleX actions to be triggered under certain tuple operations. An first implementation of PXFS utilizing a well-known Orange parallel file system as its back-end via asynchronous I/O layer and the implementation of TupleSpace component in HPX, the implementation of ParalleX. These details are also described along with the preliminary performance data. A house-made micro benchmark is developed to measure the disk I/O throughput of the PXFS asynchronous interface. The results show perfect scalability and 3x to 20x times speedup of I/O throughput performance comparing to OrangeFS synchronous user interface. Use cases of TupleSpace components are discussed for real-world applications including micro check-pointing. By utilizing TupleSpace in HPX applications for I/O, global barrier can be replaced with fine-grained parallelism to overlap more computation with communication and greatly boost the performance and efficiency. Also the dissertation showcases the distributed directory service in Orange file system which process directory entries in parallel and effectively improves the directory metada operations.
Subjects/Keywords: parallel computing; parallel file system; parallel runtime system
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APA (6th Edition):
Yang, S. (2014). A Persistent Storage Model for Extreme Computing. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-10312014-133428 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2910
Chicago Manual of Style (16th Edition):
Yang, Shuangyang. “A Persistent Storage Model for Extreme Computing.” 2014. Doctoral Dissertation, Louisiana State University. Accessed February 17, 2020.
etd-10312014-133428 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2910.
MLA Handbook (7th Edition):
Yang, Shuangyang. “A Persistent Storage Model for Extreme Computing.” 2014. Web. 17 Feb 2020.
Vancouver:
Yang S. A Persistent Storage Model for Extreme Computing. [Internet] [Doctoral dissertation]. Louisiana State University; 2014. [cited 2020 Feb 17].
Available from: etd-10312014-133428 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2910.
Council of Science Editors:
Yang S. A Persistent Storage Model for Extreme Computing. [Doctoral Dissertation]. Louisiana State University; 2014. Available from: etd-10312014-133428 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2910
University of Tasmania
11.
Atkinson, AK.
Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment.
Degree: 2010, University of Tasmania
URL: https://eprints.utas.edu.au/9996/1/Alistair_Atkinson_PhD_Thesis.pdf
► This thesis describes Tupleware, an implementation of a distributed tuple space which acts as a scalable and efficient cluster middleware for computationally intensive numerical and…
(more)
▼ This thesis describes Tupleware, an implementation of a distributed tuple space which acts as a scalable and efficient cluster middleware for computationally intensive numerical and scientific applications. Tupleware is based on the Linda coordination language (Gelernter 1985), and incorporates additional techniques such as peer-to-peer communications and exploitation of data locality in order to address problems such as scalability and performance, which are commonly encountered by traditional centralised tuple space implementations.
Tupleware is implemented in such as way that, whilepr ocessing is taking place, all communication between cluster nodes is decentralised in a peer-to-peer fashion. Communication events are initiated by a node requesting a tuple which is located on a remote node, and in order to make tuple retrieval as efficient as possible, a tuple
search algorithm is used to minimise the number of communication instances required to retrieve a remote tuple. This algorithm is based on the locality of a remote
tuple and the success of previous remote tuple requests. As Tupleware is targetted at numerical applications which generally involve the partitioning and processing of 1-D or 2-D arrays, the locality of a remote tuple can generally be determined as being located on one of a small number nodes which are processing neighbouring partitions of the array.
Furthermore, unlike some other distributed tuple space implementations, Tupleware does not burden the programmer with any additional complexity due to this distribution. At the application level, the Tupleware middleware behaves exactly like a centralised tuple space, and provides much greater flexibility with regards to where components of a system are executed.
The design and implementation of Tupleware is described, and placed in the context of other distributed tuple space implementations, along with the specific requirements of the applications that the system caters for. Finally, Tupleware is evaluated using several numerical and/or scientific applications, which show it to provide a sufficient level of scalability for a broad range tasks.
The main contribution of this work is the identification of techniques which enable a tuple space to be efficiently and transparently distributed across the nodes in a cluster. Central to this is the use of an algorithm for tuple retrieval which minimises the number of communication instances which occur during system execution. Distribution transparency is ensured by the provision of a simple interface to the underlying system, so that the distributed tuple space appears to the programmer as a single unified resource.
It is hoped that this research in some way furthers the adoption of the tuple space programming model for distributed computing, by enhancing its ability to
provide improved performance, scalability, flexibility and simplicity for a range of applications not traditionally suited to tuple space based systems.
Subjects/Keywords: Distributed computing; parallel computing; concurrency; high-performance computing; tuple space.
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APA (6th Edition):
Atkinson, A. (2010). Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment. (Thesis). University of Tasmania. Retrieved from https://eprints.utas.edu.au/9996/1/Alistair_Atkinson_PhD_Thesis.pdf
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Atkinson, AK. “Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment.” 2010. Thesis, University of Tasmania. Accessed February 17, 2020.
https://eprints.utas.edu.au/9996/1/Alistair_Atkinson_PhD_Thesis.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Atkinson, AK. “Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment.” 2010. Web. 17 Feb 2020.
Vancouver:
Atkinson A. Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment. [Internet] [Thesis]. University of Tasmania; 2010. [cited 2020 Feb 17].
Available from: https://eprints.utas.edu.au/9996/1/Alistair_Atkinson_PhD_Thesis.pdf.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Atkinson A. Tupleware: a distributed tuple space for the development and execution of array-based applications in a cluster computing environment. [Thesis]. University of Tasmania; 2010. Available from: https://eprints.utas.edu.au/9996/1/Alistair_Atkinson_PhD_Thesis.pdf
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Vanderbilt University
12.
Varshneya, Pooja.
Distributed and Adaptive Parallel Computing for Computational Finance Applications.
Degree: MS, Computer Science, 2010, Vanderbilt University
URL: http://etd.library.vanderbilt.edu/available/etd-06082010-053600/
;
► Analysts, scientist, engineers, and multimedia professionals require massive processing power to analyze financial trends, create test simulations, model climate, compile code, render video, decode genomes…
(more)
▼ Analysts, scientist, engineers, and multimedia professionals require massive processing power to analyze financial trends, create test simulations, model climate, compile code, render video, decode genomes and other complex tasks. These group of applications can greatly benefit from the use of adaptive,
parallel computing middleware that can enable quick parallelization of existing applications and improve application performance by porting these applications on
parallel computing platforms like HPC clusters, clouds and multi-core machines.
This work focuses on benchmarking the performance of currently available
parallel computing frameworks: OpenMPI and Zircon middleware software, using computation-intensive financial computation applications like binomial option pricing and heston calibrations for option pricing and also compares and contrasts the pros and cons of the two frameworks.
Advisors/Committee Members: Dr. Aniruddha Gokhale (committee member), Dr. Douglas C. Schmidt (chair).
Subjects/Keywords: distributed adaptive computing; MPI; parallel computing; high performance computing
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APA (6th Edition):
Varshneya, P. (2010). Distributed and Adaptive Parallel Computing for Computational Finance Applications. (Masters Thesis). Vanderbilt University. Retrieved from http://etd.library.vanderbilt.edu/available/etd-06082010-053600/ ;
Chicago Manual of Style (16th Edition):
Varshneya, Pooja. “Distributed and Adaptive Parallel Computing for Computational Finance Applications.” 2010. Masters Thesis, Vanderbilt University. Accessed February 17, 2020.
http://etd.library.vanderbilt.edu/available/etd-06082010-053600/ ;.
MLA Handbook (7th Edition):
Varshneya, Pooja. “Distributed and Adaptive Parallel Computing for Computational Finance Applications.” 2010. Web. 17 Feb 2020.
Vancouver:
Varshneya P. Distributed and Adaptive Parallel Computing for Computational Finance Applications. [Internet] [Masters thesis]. Vanderbilt University; 2010. [cited 2020 Feb 17].
Available from: http://etd.library.vanderbilt.edu/available/etd-06082010-053600/ ;.
Council of Science Editors:
Varshneya P. Distributed and Adaptive Parallel Computing for Computational Finance Applications. [Masters Thesis]. Vanderbilt University; 2010. Available from: http://etd.library.vanderbilt.edu/available/etd-06082010-053600/ ;
Northeastern University
13.
Sun, Enqiang.
Cross-platform heterogeneous runtime environment.
Degree: PhD, Department of Electrical and Computer Engineering, 2016, Northeastern University
URL: http://hdl.handle.net/2047/D20213163
► Heterogeneous platforms are becoming widely adopted thanks for the support from new languages and programming models. Among these languages/models, OpenCL is an industry standard for…
(more)
▼ Heterogeneous platforms are becoming widely adopted thanks for the support from new languages and programming models. Among these languages/models, OpenCL is an industry standard for parallel programming on heterogeneous devices. With OpenCL, compute-intensive portions of an application can be offloaded to a variety of processing units within a system. OpenCL is one of the first standards that focuses on portability, allowing programs to be written once and run unmodified on multiple heterogeneous devices, regardless of vendor.; While OpenCL has been widely adopted, there still remains a lack of support for automatic workload balancing and data consistency when multiple devices are present in the system. To address this need, we have designed a cross-platform heterogeneous runtime environment which provides a high-level, unified execution model that is coupled with an intelligent resource management facility. The main motivation for developing this runtime environment is to provide OpenCL programmers with a convenient programming paradigm to fully utilize all possible devices in a system and incorporate flexible workload balancing schemes without compromising the user's ability to assign tasks according to the data affinity. Our work removes much of the cumbersome initialization of the platform, and now devices and related OpenCL objects are hidden under the hood.; Equipped with this new runtime environment and associated programming interface, the programmer can focus on designing the application and worry less about customization to the target platform. Further, the programmer can now take advantage of multiple devices using a dynamic workload balancing algorithm to reap the benefits of task-level parallelism.; To demonstrate the value of this cross-platform heterogeneous runtime environment, we have evaluated it running both micro benchmarks and popular OpenCL benchmark applications. With minimal overhead of managing data objects across devices, the experimental results show a scalable performance speedup with increasing number of computing devices, without any changes of program source code.
Subjects/Keywords: parallel computing; runtime; Heterogeneous computing; Parallel programming (Computer science); Parallel processing (Electronic computers); Parallel computers; Electronic data processing; Distributed processing
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APA (6th Edition):
Sun, E. (2016). Cross-platform heterogeneous runtime environment. (Doctoral Dissertation). Northeastern University. Retrieved from http://hdl.handle.net/2047/D20213163
Chicago Manual of Style (16th Edition):
Sun, Enqiang. “Cross-platform heterogeneous runtime environment.” 2016. Doctoral Dissertation, Northeastern University. Accessed February 17, 2020.
http://hdl.handle.net/2047/D20213163.
MLA Handbook (7th Edition):
Sun, Enqiang. “Cross-platform heterogeneous runtime environment.” 2016. Web. 17 Feb 2020.
Vancouver:
Sun E. Cross-platform heterogeneous runtime environment. [Internet] [Doctoral dissertation]. Northeastern University; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/2047/D20213163.
Council of Science Editors:
Sun E. Cross-platform heterogeneous runtime environment. [Doctoral Dissertation]. Northeastern University; 2016. Available from: http://hdl.handle.net/2047/D20213163
University of Utah
14.
Hunsaker, Isaac L.
Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations.
Degree: PhD, Chemical Engineering, 2015, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/4020/rec/1795
► Radiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the…
(more)
▼ Radiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the associated combustion chemistry. The radiative properties are in turn affected by the turbulent flow field. This bi-directional coupling of radiation turbulence interactions poses a major challenge in creating parallel-capable, high-fidelity combustion simulations. In this work, a new model was developed in which reciprocal monte carlo radiation was coupled with a turbulent, large-eddy simulation combustion model. A technique wherein domain patches are stitched together was implemented to allow for scalable parallelism. The combustion model runs in parallel on a decomposed domain. The radiation model runs in parallel on a recomposed domain. The recomposed domain is stored on each processor after information sharing of the decomposed domain is handled via the message passing interface. Verification and validation testing of the new radiation model were favorable. Strong scaling analyses were performed on the Ember cluster and the Titan cluster for the CPU-radiation model and GPU-radiation model, respectively. The model demonstrated strong scaling to over 1,700 and 16,000 processing cores on Ember and Titan, respectively.
Subjects/Keywords: combustion; parallel computing; radiation; ray tracing
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APA (6th Edition):
Hunsaker, I. L. (2015). Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/4020/rec/1795
Chicago Manual of Style (16th Edition):
Hunsaker, Isaac L. “Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations.” 2015. Doctoral Dissertation, University of Utah. Accessed February 17, 2020.
http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/4020/rec/1795.
MLA Handbook (7th Edition):
Hunsaker, Isaac L. “Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations.” 2015. Web. 17 Feb 2020.
Vancouver:
Hunsaker IL. Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations. [Internet] [Doctoral dissertation]. University of Utah; 2015. [cited 2020 Feb 17].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/4020/rec/1795.
Council of Science Editors:
Hunsaker IL. Parallel distributed, reciprocal monte carlo radiation in coupled, large eddy combustion simulations. [Doctoral Dissertation]. University of Utah; 2015. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/4020/rec/1795
University of Newcastle Upon Tyne
15.
Chen, Xian.
Automatic parallelisation for a class of URE problems.
Degree: PhD, 1995, University of Newcastle Upon Tyne
URL: http://hdl.handle.net/10443/1974
► This thesis deals with the methodology and software of automatic parallelisation for numerical supercomputing and supercomputers. Basically, we focus on the problem of Uniform Recurrence…
(more)
▼ This thesis deals with the methodology and software of automatic parallelisation for numerical supercomputing and supercomputers. Basically, we focus on the problem of Uniform Recurrence Equations (URE) which exists widely in numerical computations. vVepropose a complete methodology of automatic generation of parallel programs for regular array designs. The methodology starts with an introduction of a set of canonical dependencies which generates a general modelling of the various URE problems. Based on these canonical dependencies, partitioning and mapping methods are developed which gives the foundation of the universal design process. Using the theoretical results we propose the structures of parallel programs and eventually generate automatically parallel codes which run correctly and efficiently on transputer array. The achievements presented in this thesis can be regarded as a significant progress in the area of automatic generation of parallel codes and regular (systolic) array design. This methodology is integrated and self-contained, and may be the only practical working package in this area.
Subjects/Keywords: 005; Parallel computing
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APA (6th Edition):
Chen, X. (1995). Automatic parallelisation for a class of URE problems. (Doctoral Dissertation). University of Newcastle Upon Tyne. Retrieved from http://hdl.handle.net/10443/1974
Chicago Manual of Style (16th Edition):
Chen, Xian. “Automatic parallelisation for a class of URE problems.” 1995. Doctoral Dissertation, University of Newcastle Upon Tyne. Accessed February 17, 2020.
http://hdl.handle.net/10443/1974.
MLA Handbook (7th Edition):
Chen, Xian. “Automatic parallelisation for a class of URE problems.” 1995. Web. 17 Feb 2020.
Vancouver:
Chen X. Automatic parallelisation for a class of URE problems. [Internet] [Doctoral dissertation]. University of Newcastle Upon Tyne; 1995. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10443/1974.
Council of Science Editors:
Chen X. Automatic parallelisation for a class of URE problems. [Doctoral Dissertation]. University of Newcastle Upon Tyne; 1995. Available from: http://hdl.handle.net/10443/1974
The Ohio State University
16.
Maddipati, Sai Ratna Kiran.
Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer.
Degree: MS, Computer Science and Engineering, 2016, The Ohio State University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1461334523
► In a thermodynamically unstable environment, the Boltzman-Transport Equation (BTE) defines the behavior of heat transfer-rate at each location in the environment, the direction of heat…
(more)
▼ In a thermodynamically unstable environment, the
Boltzman-Transport Equation (BTE) defines the behavior of heat
transfer-rate at each location in the environment, the direction of
heat transfer by the particles of the environment and the final
equilibrium temperature conditions of the environment. The BTE is a
very computationally intensive application and there is a need for
efficient parallelization. Parallelization implementation of this
application is explained along with brief details about several
techniques that have been used by others in past work. The
implementation involves several code-iterations of the BTE
application with distinct changes in order to compare and analyze
the performance and identify the reason for the performance
improvement or deterioration. Then, experimental results are
presented to show the resulting performance of the
implementation.
Advisors/Committee Members: Sadayappan, P (Advisor).
Subjects/Keywords: Computer Science; Parallel Computing, OpenMP, MPI
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APA (6th Edition):
Maddipati, S. R. K. (2016). Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer. (Masters Thesis). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1461334523
Chicago Manual of Style (16th Edition):
Maddipati, Sai Ratna Kiran. “Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer.” 2016. Masters Thesis, The Ohio State University. Accessed February 17, 2020.
http://rave.ohiolink.edu/etdc/view?acc_num=osu1461334523.
MLA Handbook (7th Edition):
Maddipati, Sai Ratna Kiran. “Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer.” 2016. Web. 17 Feb 2020.
Vancouver:
Maddipati SRK. Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer. [Internet] [Masters thesis]. The Ohio State University; 2016. [cited 2020 Feb 17].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1461334523.
Council of Science Editors:
Maddipati SRK. Improving the Parallel Performance of Boltzman-Transport
Equation for Heat Transfer. [Masters Thesis]. The Ohio State University; 2016. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1461334523
Université de Montréal
17.
Kemerchou, Nabil.
Logiciel de génération de nombres aléatoires dans OpenCL
.
Degree: 2016, Université de Montréal
URL: http://hdl.handle.net/1866/13473
► clRNG et clProbdist sont deux interfaces de programmation (APIs) que nous avons développées pour la génération de nombres aléatoires uniformes et non uniformes sur des…
(more)
▼ clRNG et clProbdist sont deux interfaces de programmation (APIs) que nous avons développées pour la génération de nombres aléatoires uniformes et non uniformes sur des dispositifs de calculs parallèles en utilisant l’environnement OpenCL. La première interface permet de créer au niveau d’un ordinateur central (hôte) des objets de type stream considérés comme des générateurs virtuels parallèles qui peuvent être utilisés aussi bien sur l’hôte que sur les dispositifs parallèles (unités de traitement graphique, CPU multinoyaux, etc.) pour la génération de séquences de nombres aléatoires. La seconde interface permet aussi de générer au niveau de ces unités des variables aléatoires selon
différentes lois de probabilité continues et discrètes. Dans ce mémoire, nous allons rappeler des notions de base sur les générateurs de nombres aléatoires, décrire les systèmes hétérogènes ainsi que les techniques de génération parallèle de nombres aléatoires. Nous présenterons aussi les différents modèles composant l’architecture de l’environnement OpenCL et détaillerons les structures des APIs développées. Nous distinguons pour clRNG les fonctions qui permettent la création des streams, les fonctions qui génèrent les variables aléatoires uniformes ainsi que celles qui manipulent les états des streams. clProbDist contient les fonctions de génération de variables aléatoires non uniformes selon la technique d’inversion ainsi que les fonctions qui permettent de retourner différentes statistiques des lois de distribution implémentées. Nous évaluerons ces interfaces de programmation avec deux simulations qui implémentent un exemple simplifié d’un modèle d’inventaire et un exemple d’une option financière. Enfin, nous fournirons les résultats d’expérimentation sur les performances des générateurs implémentés.
Advisors/Committee Members: L'Écuyer, Pierre (advisor).
Subjects/Keywords: Rng;
Parallélisme;
OpenCL;
Gpu;
Parallel computing
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APA (6th Edition):
Kemerchou, N. (2016). Logiciel de génération de nombres aléatoires dans OpenCL
. (Thesis). Université de Montréal. Retrieved from http://hdl.handle.net/1866/13473
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Kemerchou, Nabil. “Logiciel de génération de nombres aléatoires dans OpenCL
.” 2016. Thesis, Université de Montréal. Accessed February 17, 2020.
http://hdl.handle.net/1866/13473.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kemerchou, Nabil. “Logiciel de génération de nombres aléatoires dans OpenCL
.” 2016. Web. 17 Feb 2020.
Vancouver:
Kemerchou N. Logiciel de génération de nombres aléatoires dans OpenCL
. [Internet] [Thesis]. Université de Montréal; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/1866/13473.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kemerchou N. Logiciel de génération de nombres aléatoires dans OpenCL
. [Thesis]. Université de Montréal; 2016. Available from: http://hdl.handle.net/1866/13473
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Berkeley
18.
Rhoden, Barret.
Operating System Support for Parallel Processes.
Degree: Computer Science, 2014, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/8gt545mj
► High-performance, parallel programs want uninterrupted access to physical resources. This characterization is true not only for traditional scientific computing, but also for high-priority data center…
(more)
▼ High-performance, parallel programs want uninterrupted access to physical resources. This characterization is true not only for traditional scientific computing, but also for high-priority data center applications that run on parallel processors. These applications require high, predictable performance and low latency, and they are important enough to warrant engineering effort at all levels of the software stack. Given the recent resurgence of interest in parallel computing as well as the increasing importance of data center applications, what changes can we make to operating system abstractions to support parallel programs?Akaros is a research operating system designed for single-node, large-scale SMP and many-core architectures. The primary feature of Akaros is a new process abstraction called the "Many-Core Process" (MCP) that embodies transparency, application control of physical resources, and performance isolation. The MCP is built on the idea of separating cores from threads: the operating system grants spatially partitioned cores to the MCP, and the application schedules its threads on those cores. Data centers typically have a mix of high-priority applications and background batch jobs, where the demands of the high-priority application can change over time. For this reason, an important part of Akaros is the provisioning, allocation, and preemption of resources, and the MCP must be able to handle having a resource revoked at any moment.In this work, I describe the MCP abstraction and the salient details of Akaros. I discuss how the kernel and user-level libraries work together to give an application control over its physical resources and to adapt to the revocation of cores at any time - even when the code is holding locks. I show an order of magnitude less interference for the MCP compared to Linux, more resilience to the loss of cores for an HPC application, and how a customized user-level scheduler can increase the performance of a simple webserver.
Subjects/Keywords: Computer science; Operating Systems; Parallel Computing
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APA (6th Edition):
Rhoden, B. (2014). Operating System Support for Parallel Processes. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/8gt545mj
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Rhoden, Barret. “Operating System Support for Parallel Processes.” 2014. Thesis, University of California – Berkeley. Accessed February 17, 2020.
http://www.escholarship.org/uc/item/8gt545mj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Rhoden, Barret. “Operating System Support for Parallel Processes.” 2014. Web. 17 Feb 2020.
Vancouver:
Rhoden B. Operating System Support for Parallel Processes. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2020 Feb 17].
Available from: http://www.escholarship.org/uc/item/8gt545mj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Rhoden B. Operating System Support for Parallel Processes. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/8gt545mj
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Southern California
19.
Peng, Liu.
Parallelization framework for scientific application kernels
on multi-core/many-core platforms.
Degree: PhD, Computer Science, 2011, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/624895/rec/4910
► The advent of multi-core/many-core paradigm has provided unprecedented computing power, and it is of great significance to develop a parallelization framework for various scientific applications…
(more)
▼ The advent of multi-core/many-core paradigm has
provided unprecedented
computing power, and it is of great
significance to develop a parallelization framework for various
scientific applications to harvest the
computing power. However, it
is a great challenge to design an efficient parallelization
framework that continues to scale on future architectures due to
the complexity of real-world applications and the variety of
multi-core/many-core platforms. ❧ To address this challenge, I
propose a hierarchical optimization framework that maps
applications to hardware by exploiting multiple levels of
parallelization: (1) Inter-node level parallelism via spatial
decomposition; (2) inter-core level parallelism via cellular
decomposition; and (3) single-instruction multiple-data (SIMD)
parallelization. The framework includes application-based SIMD
analysis and optimization, which allows application scientists to
determine whether their applications are viable for SIMDization and
provide various code transformation techniques to enhance the SIMD
efficiency as well as simple recipes when compiler
auto-vectorization fails. I also propose a suite of optimization
strategies to achieve ideal on-chip inter-core strong scalability
on emerging many-core architectures: (1) A divide-and-conquer
algorithm adaptive to local memory; (2) a novel data layout to
improve data locality; (3) on-chip locality-aware
parallel
algorithms to enhance data reuse; and (4) a pipeline algorithm
using data transfer agent to orchestrate computation and memory
operations to hide latency to shared memory. ❧ I have applied the
framework to three scientific applications, which represent most of
the numerical classes in the seven dwarfs (which are known to cover
most high performance
computing applications): (1) Stencil
computation, specifically lattice Boltzmann method (LBM)for fluid
flow simulation; (2) molecular dynamics (MD) simulation; and (3)
molecular fragment analysis via connected component detection. ❧ I
have achieved high inter-node, inter-core (multithreading), and
SIMD efficiency on various
computing platforms: (1) For LBM,
inter-node
parallel efficiency 0.978 on 131,072 BlueGene/P
processors, multithreading efficiency 0.882 on 6 cores of a Cell
BE, and SIMD efficiency 0.780 using 4-element vector registers of a
Cell BE; (2) for MD simulation, inter-node
parallel efficiency
0.985 on 106,496 BlueGene/L processors, and inter-core
multithreading
parallel efficiency 0.99 on the 64-core Godson-T
many-core architecture; (3) for molecular fragment analysis, nearly
linear inter-node strong scalability up to 50 million vertices
molecular graph on 32
computing nodes, and over 13-fold inter-core
speedup on 16 cores. In addition, a simple performance model based
on hierarchical parallelization is derived, which suggests that the
optimization scheme is likely to scale well toward exascale.
Furthermore, I have analyzed the impact of architectural features
on applications' performance to find that certain architectural
features are essential for these…
Advisors/Committee Members: Nakano, Aiichiro (Committee Chair), Prasanna, Viktor K. (Committee Member), Shing, Katherine S. (Committee Member).
Subjects/Keywords: multi/many core; parallel computing; scientific simulation
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APA (6th Edition):
Peng, L. (2011). Parallelization framework for scientific application kernels
on multi-core/many-core platforms. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/624895/rec/4910
Chicago Manual of Style (16th Edition):
Peng, Liu. “Parallelization framework for scientific application kernels
on multi-core/many-core platforms.” 2011. Doctoral Dissertation, University of Southern California. Accessed February 17, 2020.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/624895/rec/4910.
MLA Handbook (7th Edition):
Peng, Liu. “Parallelization framework for scientific application kernels
on multi-core/many-core platforms.” 2011. Web. 17 Feb 2020.
Vancouver:
Peng L. Parallelization framework for scientific application kernels
on multi-core/many-core platforms. [Internet] [Doctoral dissertation]. University of Southern California; 2011. [cited 2020 Feb 17].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/624895/rec/4910.
Council of Science Editors:
Peng L. Parallelization framework for scientific application kernels
on multi-core/many-core platforms. [Doctoral Dissertation]. University of Southern California; 2011. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll127/id/624895/rec/4910
University of Sydney
20.
Pang, Xiaolin.
Scalable Algorithms for Outlier Detection
.
Degree: 2014, University of Sydney
URL: http://hdl.handle.net/2123/11743
► Outlier detection is an important problem for the data mining community as outliers often embody potentially new and valuable information. Nowadays, in the face of…
(more)
▼ Outlier detection is an important problem for the data mining community as outliers often embody potentially new and valuable information. Nowadays, in the face of exponential growth in data generation, extracting outliers from such massive data sets is a non-trivial task and requires the design and implementation of new scalable algorithms which is the main focus of the thesis. More specifically, we make the following contributions:
We propose a new algorithm for detecting emerging outliers in traffic data by extending the Likelihood Ratio Test Statistics (LRT) framework. We also propose a general and efficient pattern mining approach for spatio-temporal outlier detection that is based on our statistical models.
We propose a unified parallel approach for LRT computation in GPGPU, multi-core and cloud cluster environments. We also present new algorithmic techniques for computing the Likelihood Ratio Test (LRT) in parallel for a large spatial data grid by utilizing these distributed architectures.
As a separate contribution, we present novel approaches which simultaneously perform clustering and outlier detection without specifying the number of clusters. These methods are formulated as an integer programming optimisation task.
Subjects/Keywords: scalable algorithms;
outlier detection;
parallel computing
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Manager
APA (6th Edition):
Pang, X. (2014). Scalable Algorithms for Outlier Detection
. (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/11743
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Pang, Xiaolin. “Scalable Algorithms for Outlier Detection
.” 2014. Thesis, University of Sydney. Accessed February 17, 2020.
http://hdl.handle.net/2123/11743.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pang, Xiaolin. “Scalable Algorithms for Outlier Detection
.” 2014. Web. 17 Feb 2020.
Vancouver:
Pang X. Scalable Algorithms for Outlier Detection
. [Internet] [Thesis]. University of Sydney; 2014. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/2123/11743.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pang X. Scalable Algorithms for Outlier Detection
. [Thesis]. University of Sydney; 2014. Available from: http://hdl.handle.net/2123/11743
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
21.
Washington, Ian D.
Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing.
Degree: PhD, 2016, McMaster University
URL: http://hdl.handle.net/11375/19092
► This research focuses on the development of a solution strategy for the optimization of large-scale dynamic systems under uncertainty. Uncertainty resides naturally within the external…
(more)
▼ This research focuses on the development of a solution strategy for the optimization of
large-scale dynamic systems under uncertainty. Uncertainty resides naturally within the
external forces posed to the system or from within the system itself. For example, in chemical
process systems, external inputs include flow rates, temperatures or compositions; while
internal sources include kinetic or mass transport parameters; and empirical parameters
used within thermodynamic correlations and expressions. The goal in devising a dynamic
optimization approach which explicitly accounts for uncertainty is to do so in a manner
which is computationally tractable and is general enough to handle various types and
sources of uncertainty. The approach developed in this thesis follows a so-called multiperiod
technique whereby the infinite dimensional uncertainty space is discretized at numerous
points (known as periods or scenarios) which creates different possible realizations of the
uncertain parameters. The resulting optimization formulation encompasses an approximated
expected value of a chosen objective functional subject to a dynamic model for all the
generated realizations of the uncertain parameters. The dynamic model can be solved,
using an appropriate numerical method, in an embedded manner for which the solution
is used to construct the optimization formulation constraints; or alternatively the model
could be completely discretized over the temporal domain and posed directly as part of the
optimization formulation.
Our approach in this thesis has mainly focused on the embedded model technique for
dynamic optimization which can either follow a single- or multiple-shooting solution method.
The first contribution of the thesis investigates a combined multiperiod multiple-shooting
dynamic optimization approach for the design of dynamic systems using ordinary differential
equation (ODE) or differential-algebraic equation (DAE) process models. A major aspect
of this approach is the analysis of the parallel solution of the embedded model within the
optimization formulation. As part of this analysis, we further consider the application of
the dynamic optimization approach to several design and operation applications. Another
vmajor contribution of the thesis is the development of a nonlinear programming (NLP) solver
based on an approach that combines sequential quadratic programming (SQP) with an
interior-point method (IPM) for the quadratic programming subproblem. A unique aspect of
the approach is that the inherent structure (and parallelism) of the multiperiod formulation
is exploited at the linear algebra level within the SQP-IPM nonlinear programming algorithm
using an explicit Schur-complement decomposition. Our NLP solution approach is further
assessed using several static and dynamic optimization benchmark examples.
Thesis
Doctor of Philosophy (PhD)
Advisors/Committee Members: Swartz, Christopher L.E., Chemical Engineering.
Subjects/Keywords: Dynamic Optimization; DAE process models; Parallel Computing
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APA (6th Edition):
Washington, I. D. (2016). Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/19092
Chicago Manual of Style (16th Edition):
Washington, Ian D. “Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing.” 2016. Doctoral Dissertation, McMaster University. Accessed February 17, 2020.
http://hdl.handle.net/11375/19092.
MLA Handbook (7th Edition):
Washington, Ian D. “Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing.” 2016. Web. 17 Feb 2020.
Vancouver:
Washington ID. Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing. [Internet] [Doctoral dissertation]. McMaster University; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/11375/19092.
Council of Science Editors:
Washington ID. Large-Scale Dynamic Optimization Under Uncertainty using Parallel Computing. [Doctoral Dissertation]. McMaster University; 2016. Available from: http://hdl.handle.net/11375/19092
Virginia Tech
22.
Kang, Pilsung.
Modular Implementation of Program Adaptation with Existing Scientific Codes.
Degree: PhD, Computer Science, 2010, Virginia Tech
URL: http://hdl.handle.net/10919/28783
► Often times, scientific software needs to be adapted for different execution environments, problem sets, and available resources to ensure its efficiency and reliability. Directly modifying…
(more)
▼ Often times, scientific software needs to be adapted for different execution environments, problem sets, and available resources to ensure its efficiency and reliability. Directly modifying source code to implement adaptation is time-consuming, error-prone, and difficult to manage for today's complex software. This thesis studies modular approaches to implementing program adaptation with existing scientific codes, whereby application-specific adaptation strategies can be implemented in separate code which is then transparently combined with a given program. By using the approaches developed in this thesis, scientific programmers can focus on the design and implementation of adaptation schemes, manage an adaptation code separately from the main program components, and compose an adaptive application whose original capabilities are enhanced in diverse aspects such as application performance and stability. The primary objective of the modular approaches in this study is to provide a language-independent development method of adapting existing scientific software, so that applications written in different languages can be supported when implementing adaptation schemes. In particular, the emphasis is on Fortran, which has been a mainstream language for programming scientific applications.
Three research questions are formulated in this thesis, each of which aims to: design and implement high-level abstractions for expressing adaptation strategies, develop a dynamic tuning approach for
parallel programs, and support flexible runtime adaptation schemes, respectively. The applicability of the proposed approaches is demonstrated through example applications to real-world scientific software.
Advisors/Committee Members: Varadarajan, Srinidhi (committeechair), Ribbens, Calvin J. (committee member), Tilevich, Eli (committee member), Tafti, Danesh K. (committee member), Ramakrishnan, Naren (committeecochair).
Subjects/Keywords: scientic computing; parallel programming; program adaptation
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APA (6th Edition):
Kang, P. (2010). Modular Implementation of Program Adaptation with Existing Scientific Codes. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/28783
Chicago Manual of Style (16th Edition):
Kang, Pilsung. “Modular Implementation of Program Adaptation with Existing Scientific Codes.” 2010. Doctoral Dissertation, Virginia Tech. Accessed February 17, 2020.
http://hdl.handle.net/10919/28783.
MLA Handbook (7th Edition):
Kang, Pilsung. “Modular Implementation of Program Adaptation with Existing Scientific Codes.” 2010. Web. 17 Feb 2020.
Vancouver:
Kang P. Modular Implementation of Program Adaptation with Existing Scientific Codes. [Internet] [Doctoral dissertation]. Virginia Tech; 2010. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10919/28783.
Council of Science Editors:
Kang P. Modular Implementation of Program Adaptation with Existing Scientific Codes. [Doctoral Dissertation]. Virginia Tech; 2010. Available from: http://hdl.handle.net/10919/28783
Virginia Tech
23.
Kannan, Vijayasarathy.
A Distributed Approach to EpiFast using Apache Spark.
Degree: MS, Computer Science, 2015, Virginia Tech
URL: http://hdl.handle.net/10919/55272
► EpiFast is a parallel algorithm for large-scale epidemic simulations, based on an interpretation of the stochastic disease propagation in a contact network. The original EpiFast…
(more)
▼ EpiFast is a
parallel algorithm for large-scale epidemic simulations, based on an interpretation of the stochastic disease propagation in a contact network. The original EpiFast
implementation is based on a master-slave computation model with a focus on distributed
memory using message-passing-interface (MPI). However, it suffers from few shortcomings
with respect to scale of networks being studied. This thesis addresses these shortcomings
and provides two different implementations: Spark-EpiFast based on the Apache Spark big
data processing engine and Charm-EpiFast based on the Charm++
parallel programming
framework. The study focuses on exploiting features of both systems that we believe could
potentially benefit in terms of performance and scalability. We present models of EpiFast
specific to each system and relate algorithm specifics to several optimization techniques. We
also provide a detailed analysis of these optimizations through a range of experiments that
consider scale of networks and environment settings we used. Our analysis shows that the
Spark-based version is more efficient than the Charm++ and MPI-based counterparts. To
the best of our knowledge, ours is one of the preliminary efforts of using Apache Spark for
epidemic simulations. We believe that our proposed model could act as a reference for similar
large-scale epidemiological simulations exploring non-MPI or MapReduce-like approaches.
Advisors/Committee Members: Marathe, Madhav Vishnu (committeechair), Marathe, Achla (committee member), Vullikanti, Anil Kumar S. (committee member), Chen, Jiangzhuo (committee member).
Subjects/Keywords: computational epidemiology; parallel programming; distributed computing
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APA (6th Edition):
Kannan, V. (2015). A Distributed Approach to EpiFast using Apache Spark. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/55272
Chicago Manual of Style (16th Edition):
Kannan, Vijayasarathy. “A Distributed Approach to EpiFast using Apache Spark.” 2015. Masters Thesis, Virginia Tech. Accessed February 17, 2020.
http://hdl.handle.net/10919/55272.
MLA Handbook (7th Edition):
Kannan, Vijayasarathy. “A Distributed Approach to EpiFast using Apache Spark.” 2015. Web. 17 Feb 2020.
Vancouver:
Kannan V. A Distributed Approach to EpiFast using Apache Spark. [Internet] [Masters thesis]. Virginia Tech; 2015. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10919/55272.
Council of Science Editors:
Kannan V. A Distributed Approach to EpiFast using Apache Spark. [Masters Thesis]. Virginia Tech; 2015. Available from: http://hdl.handle.net/10919/55272
Universitat Autònoma de Barcelona
24.
Vera Rodríguez, Gonzalo.
R/parallel Parallel Computing for R in non‐dedicated environments.
Degree: Departament d'Arquitectura de Computadors i Sistemes Operatius, 2010, Universitat Autònoma de Barcelona
URL: http://hdl.handle.net/10803/121248
► Traditionally, parallel computing has been associated with special purpose applications designed to run in complex computing clusters, specifically set up with a software stack of…
(more)
▼ Traditionally,
parallel computing has been associated with special purpose
applications designed to run in complex
computing clusters, specifically set up with
a software stack of dedicated libraries together with advanced administration tools to
manage co Traditionally,
parallel computing has been associated with special purpose applications designed to run in complex
computing clusters, specifically set up with a software stack of dedicated libraries together with advanced administration tools to manage complex IT infrastructures. These High Performance
Computing (HPC) solutions, although being the most efficient solutions in terms of performance and scalability, impose technical and practical barriers for most common scientists whom, with reduced IT knowledge, time and resources, are unable to embrace classical HPC solutions without considerable efforts. Moreover, two important technology advances are increasing the need for
parallel computing. For example in the bioinformatics field, and similarly in other experimental science disciplines, new high throughput screening devices are generating huge amounts of data within very short time which requires their analysis in equally short time periods to avoid delaying experimental analysis. Another important technological change involves the design of new processor chips. To increase raw performance the current strategy is to increase the number of processing units per chip, so to make use of the new processing capacities
parallel applications are required. In both cases we find users that may need to update their current sequential applications and
computing resources to achieve the increased processing capacities required for their particular needs. Since
parallel computing is becoming a natural option for obtaining increased performance and it is required by new computer systems, solutions adapted for the mainstream should be developed for a seamless adoption. In order to enable the adoption of
parallel computing, new methods and technologies are required to remove or mitigate the current barriers and obstacles that prevent many users from evolving their sequential running environments. A particular scenario that specially suffers from these problems and that is considered as a practical case in this work consists of bioinformaticians analyzing molecular data with methods written with the R language. In many cases, with long datasets, they have to wait for days and weeks for their data to be processed or perform the cumbersome task of manually splitting their data, look for available computers to run these subsets and collect back the previously scattered results. Most of these applications written in R are based on
parallel loops. A loop is called a
parallel loop if there is no data dependency among all its iterations, and therefore any iteration can be processed in any order or even simultaneously, so they are susceptible of being parallelized.
Parallel loops are found in a large number of scientific applications. Previous contributions deal with partial aspects…
Advisors/Committee Members: [email protected] (authoremail), true (authoremailshow), Suppi Boldrito, Remo (director), true (authorsendemail).
Subjects/Keywords: Parallel loops; Oportunistic computing; Bioinformatics; Tecnologies; 004
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to Zotero / EndNote / Reference
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APA (6th Edition):
Vera Rodríguez, G. (2010). R/parallel Parallel Computing for R in non‐dedicated environments. (Thesis). Universitat Autònoma de Barcelona. Retrieved from http://hdl.handle.net/10803/121248
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Vera Rodríguez, Gonzalo. “R/parallel Parallel Computing for R in non‐dedicated environments.” 2010. Thesis, Universitat Autònoma de Barcelona. Accessed February 17, 2020.
http://hdl.handle.net/10803/121248.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Vera Rodríguez, Gonzalo. “R/parallel Parallel Computing for R in non‐dedicated environments.” 2010. Web. 17 Feb 2020.
Vancouver:
Vera Rodríguez G. R/parallel Parallel Computing for R in non‐dedicated environments. [Internet] [Thesis]. Universitat Autònoma de Barcelona; 2010. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10803/121248.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Vera Rodríguez G. R/parallel Parallel Computing for R in non‐dedicated environments. [Thesis]. Universitat Autònoma de Barcelona; 2010. Available from: http://hdl.handle.net/10803/121248
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Cornell University
25.
Ni, Cao.
Efficient Ranking And Selection In Parallel Computing Environments
.
Degree: 2016, Cornell University
URL: http://hdl.handle.net/1813/43581
► The goal of ranking and selection (R&S) procedures is to identify the best stochastic system from among a finite set of competing alternatives. Such procedures…
(more)
▼ The goal of ranking and selection (R&S) procedures is to identify the best stochastic system from among a finite set of competing alternatives. Such procedures require constructing estimates of each system's performance, which can be obtained simultaneously by running multiple independent replications on a
parallel computing platform. However, nontrivial statistical and implementation issues arise when designing R&S procedures for a
parallel computing environment. This dissertation develops efficient
parallel R&S procedures. In this dissertation, several design principles are proposed for
parallel R&S procedures that preserve statistical validity and maximize core utilization, especially when large numbers of alternatives or cores are involved. These principles are followed closely by the three
parallel R&S procedures analyzed, each of which features a unique sampling and screening approach, and a specific statistical guarantee on the quality of the final solution. Finally, in our computational study we discuss three methods for implementing R&S procedures on
parallel computers, namely the Message-Passing Interface (MPI), Hadoop MapReduce, and Apache Spark, and show that MPI performs the best while Spark provides good protection against core failures at the expense of a moderate drop in core utilization.
Advisors/Committee Members: Martinez,Jose F. (committeeMember), Frazier,Peter (committeeMember).
Subjects/Keywords: ranking and selection;
simulation optimization;
parallel computing
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Manager
APA (6th Edition):
Ni, C. (2016). Efficient Ranking And Selection In Parallel Computing Environments
. (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/43581
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ni, Cao. “Efficient Ranking And Selection In Parallel Computing Environments
.” 2016. Thesis, Cornell University. Accessed February 17, 2020.
http://hdl.handle.net/1813/43581.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ni, Cao. “Efficient Ranking And Selection In Parallel Computing Environments
.” 2016. Web. 17 Feb 2020.
Vancouver:
Ni C. Efficient Ranking And Selection In Parallel Computing Environments
. [Internet] [Thesis]. Cornell University; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/1813/43581.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ni C. Efficient Ranking And Selection In Parallel Computing Environments
. [Thesis]. Cornell University; 2016. Available from: http://hdl.handle.net/1813/43581
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Melbourne
26.
Stivala, Alexander David.
Algorithms for the study of RNA and protein structure.
Degree: 2010, University of Melbourne
URL: http://hdl.handle.net/11343/35772
► The growth in the number of known sequences and structures of RNA and protein molecules has led to the need to solve many computationally demanding…
(more)
▼ The growth in the number of known sequences and structures of RNA and protein molecules has led to the need to solve many computationally demanding problems in the analysis of RNA and protein structure. This thesis describes algorithms for structural comparison of RNA and protein molecules. In the case of proteins, it also describes a technique for automatically generating two-dimensional diagrammatic representations for visual comparison.
A general technique for parallelizing dynamic programs in a straightforward way, by means of a shared lock-free hash table implementation and randomization of subproblem ordering is described. This generic approach is applied to several well-known dynamic programs, as well as a dynamic program for structural alignment of RNA molecules by aligning their base pairing probability matrices.
Two algorithms for protein structure and substructure searching are described. These algorithms are also capable of finding non-sequential matches, that is, matches between structures where the sequential order of secondary structure elements is not preserved. The first algorithm is based on the relaxation of an earlier quadratic integer problem (QIP) formulation to a quadratic program (QP).
The second algorithm uses the same formulation but approximates it using simulated annealing. It is shown that this results in significant increases in speed. This algorithm is also capable of greater accuracy when assessed as a fold recognition method. A parallel implementation of this algorithm on modern graphics processing unit (GPU) hardware is also described. This parallel implementation results in a further significant speedup, and, to the best of our knowledge, is the first use of a GPU for the protein structural search problem.
Finally, a system to automatically generate two-dimensional representations of protein structure is described. Such diagrams are particularly useful in analysing complex protein folds. A method for using these diagrams as an interface to the protein substructure search methods is also described.
Subjects/Keywords: RNA; protein; bioinformatics; dynamic programming; parallel computing
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APA (6th Edition):
Stivala, A. D. (2010). Algorithms for the study of RNA and protein structure. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/35772
Chicago Manual of Style (16th Edition):
Stivala, Alexander David. “Algorithms for the study of RNA and protein structure.” 2010. Doctoral Dissertation, University of Melbourne. Accessed February 17, 2020.
http://hdl.handle.net/11343/35772.
MLA Handbook (7th Edition):
Stivala, Alexander David. “Algorithms for the study of RNA and protein structure.” 2010. Web. 17 Feb 2020.
Vancouver:
Stivala AD. Algorithms for the study of RNA and protein structure. [Internet] [Doctoral dissertation]. University of Melbourne; 2010. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/11343/35772.
Council of Science Editors:
Stivala AD. Algorithms for the study of RNA and protein structure. [Doctoral Dissertation]. University of Melbourne; 2010. Available from: http://hdl.handle.net/11343/35772
California State University – Sacramento
27.
Saxena, Ankita.
Acceleration of Bellman-Ford single source shortest path using parallel computing.
Degree: MS, Electrical and Electronic Engineering, 2019, California State University – Sacramento
URL: http://hdl.handle.net/10211.3/207661
► With the advancement in technology these days, we need our work to be done in a faster and efficient way, especially in the areas of…
(more)
▼ With the advancement in technology these days, we need our work to be done in a faster and efficient way, especially in the areas of telecommunication and VLSI technologies. We need our problems to be rapidly resolved. Hence, in the world of
computing, a new concept of parallelism in CPU was introduced. The computer hardware is made to perform a task more resourcefully either using a CPU or a GPU. We can achieve better performance on CPU???s by parallelizing the workload using multiple thread, utilizing several processors to execute different stages. It can be done by data parallelism, by creating and distributing threads to cores. Each processor executes various threads or processes on same or different data. For instance, if in 2 core processor, we can ask CPU1 to perform Task1, simultaneously with the CPU2 performing task2. Multiple tasks are done at the same time by quickly switching between various CPU cores. The same code runs independently on different machines by data sharing embedded in the code. One of the challenges faced here is to make sure that no data in lost in the process of sharing data amongst different CPU cores. This parallelization helps reducing run time execution, thus scaling up the performance of hardware.
In this project, a single source shortest path Bellman ??? Ford Algorithm is implemented using an execution model, POSIX threads in C. In a given shortest path problem, we need to determine the path between 2 nodes or vertices in a graph, such that the sum of weights on each edge is minimum. For example, if a salesman has to travel from place A to B which has various intermediate points and different cost, we deal with shortest path problem. Here, weight will not only be the physical distance, but time and monetary cost as well. For the project, this algorithm has been executed both in series (1 processor) and in
parallel (multiple processors), performances were compared to calculate the speed-up.
Performance was tested on bigger graphs to see how well larger workloads would benefit from parallelism. A speed up of 18 was achieved using 16 processors. To ensure the correctness, the execution on 1 processor versus 16 processor was tracked and verified the correctness of the results. As noted, there???s scope for improvement by employing node-based workload distribution as groups of outgoing edges and also dynamic load balancing. As seen in results, the solution is scalable with both the size of input graph and the number of processors.
Advisors/Committee Members: Vadhva, Suresh.
Subjects/Keywords: Parallel computing; Operating system; Bellman-Ford algorithm
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APA (6th Edition):
Saxena, A. (2019). Acceleration of Bellman-Ford single source shortest path using parallel computing. (Masters Thesis). California State University – Sacramento. Retrieved from http://hdl.handle.net/10211.3/207661
Chicago Manual of Style (16th Edition):
Saxena, Ankita. “Acceleration of Bellman-Ford single source shortest path using parallel computing.” 2019. Masters Thesis, California State University – Sacramento. Accessed February 17, 2020.
http://hdl.handle.net/10211.3/207661.
MLA Handbook (7th Edition):
Saxena, Ankita. “Acceleration of Bellman-Ford single source shortest path using parallel computing.” 2019. Web. 17 Feb 2020.
Vancouver:
Saxena A. Acceleration of Bellman-Ford single source shortest path using parallel computing. [Internet] [Masters thesis]. California State University – Sacramento; 2019. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10211.3/207661.
Council of Science Editors:
Saxena A. Acceleration of Bellman-Ford single source shortest path using parallel computing. [Masters Thesis]. California State University – Sacramento; 2019. Available from: http://hdl.handle.net/10211.3/207661
28.
-1801-637X.
High-Performance Sparse Fourier Transform on Parallel Architectures.
Degree: Computer Science, Department of, 2016, University of Houston
URL: http://hdl.handle.net/10657/3269
► Fast Fourier Transform (FFT) is one of the most important numerical algorithms widely used in numerous scientific and engineering computations. With the emergence of big…
(more)
▼ Fast Fourier Transform (FFT) is one of the most important numerical algorithms widely used in numerous scientific and engineering computations. With the emergence of big data problems, however, in which the size of the processed data can easily exceed terabytes, it is challenging to acquire, process and store a sufficient amount of data to compute the FFT in the first place. The recently developed it{sparse} FFT (sFFT) algorithm provides a solution to this problem. The sFFT can compute a compressed Fourier transform by using only a small subset of the input data, thus achieves significant performance improvement.
Modern homogeneous and heterogeneous multicore and manycore architectures are now part of the mainstream
computing scene and can offer impressive performance for many applications. The computations that arise in sFFT lend it naturally to efficient
parallel implementations. In this dissertation, we present efficient
parallel implementations of the sFFT algorithm on three state-of-the-art
parallel architectures, namely multicore CPUs, GPUs and a heterogeneous multicore embedded system. While the increase in the number of cores and memory bandwidth on modern architectures provide an opportunity to improve the performance through sophisticated
parallel algorithm design, the sFFT is inherently complex, and numerous challenges need to address to deliver the optimal performance. In this dissertation, various parallelization and performance optimization techniques are proposed and implemented. Our
parallel sFFT is more than 5x and 20x faster than the sequential sFFT on multicore CPUs and GPUs, respectively. Compared to full-size FFT libraries, the
parallel sFFT achieves more than 9x speedup on multicore CPUs and 12x speedup on GPUs for a broad range of signal spectra.
Advisors/Committee Members: Chapman, Barbara M. (advisor), Gnawali, Omprakash (committee member), Shah, Shishir Kirit (committee member), Shi, Weidong (committee member), May, Elebeoba E. (committee member).
Subjects/Keywords: Sparse FFT; Parallel Computing; Compressive Sensing; GPU
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APA (6th Edition):
-1801-637X. (2016). High-Performance Sparse Fourier Transform on Parallel Architectures. (Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/3269
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
-1801-637X. “High-Performance Sparse Fourier Transform on Parallel Architectures.” 2016. Thesis, University of Houston. Accessed February 17, 2020.
http://hdl.handle.net/10657/3269.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
-1801-637X. “High-Performance Sparse Fourier Transform on Parallel Architectures.” 2016. Web. 17 Feb 2020.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
-1801-637X. High-Performance Sparse Fourier Transform on Parallel Architectures. [Internet] [Thesis]. University of Houston; 2016. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10657/3269.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
-1801-637X. High-Performance Sparse Fourier Transform on Parallel Architectures. [Thesis]. University of Houston; 2016. Available from: http://hdl.handle.net/10657/3269
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation
University of Houston
29.
Chitral, Pooja 1986-.
Accelerator Benchmark Suite Using OpenACC Directives.
Degree: Computer Science, Department of, 2014, University of Houston
URL: http://hdl.handle.net/10657/1686
► In recent years, GPU computing has been very popular for scientific applications, especially after the release of programming languages like CUDA, OpenCL, and OpenACC. The…
(more)
▼ In recent years, GPU
computing has been very popular for scientific applications, especially after the release of programming languages like CUDA, OpenCL, and OpenACC. The growing popularity of GPU computation in commercial and scientific fields is attributed to the high computational power of GPU cores. The accelerator benchmark suite using OpenACC 2.0 is a combination of very popular benchmarks – the Parboil and NAS
Parallel benchmarks. These benchmarks contain a wide range of throughput
computing applications, which are useful for studying the performance of
computing architectures and compilers. The Parboil benchmark includes applications from different scientific and commercial fields including image processing, biomolecular simulation, and astronomy. The NAS
Parallel benchmark has a set of applications that target different areas of computational fluid dynamics.
The accelerator benchmark suite that has been designed exploits the computational power of GPU architecture by using the emerging directives and clauses provided by OpenACC 2.0. This benchmark can act as a reference point for new programmers in GPU
computing, reducing the time taken to understand one of the most powerful
parallel programming paradigms.
Finally, the goal of the accelerator benchmark is to evaluate the applicability of one of the high-level programming models OpenACC for accelerators. This benchmark will help provide the OpenACC community with valuable feedback to improve the model further.
Advisors/Committee Members: Chapman, Barbara M. (advisor), Gnawali, Omprakash (committee member), Gurkan, Deniz (committee member).
Subjects/Keywords: GPU computing; OpenACC; Parboil; NAS Parallel Benchmark
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Manager
APA (6th Edition):
Chitral, P. 1. (2014). Accelerator Benchmark Suite Using OpenACC Directives. (Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/1686
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Chitral, Pooja 1986-. “Accelerator Benchmark Suite Using OpenACC Directives.” 2014. Thesis, University of Houston. Accessed February 17, 2020.
http://hdl.handle.net/10657/1686.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Chitral, Pooja 1986-. “Accelerator Benchmark Suite Using OpenACC Directives.” 2014. Web. 17 Feb 2020.
Vancouver:
Chitral P1. Accelerator Benchmark Suite Using OpenACC Directives. [Internet] [Thesis]. University of Houston; 2014. [cited 2020 Feb 17].
Available from: http://hdl.handle.net/10657/1686.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Chitral P1. Accelerator Benchmark Suite Using OpenACC Directives. [Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/1686
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of New South Wales
30.
Di, Peng.
Automatic Parallelization of Tiled Stencil Loop Nests on GPUs.
Degree: Computer Science & Engineering, 2013, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/53495
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:12190/SOURCE02?view=true
► This thesis attempts to design and implement a compiler framework based on the polyhedral model. The compiler automatically parallelizes loop nests; especially stencil kernels, into…
(more)
▼ This thesis attempts to design and implement a compiler framework based on the polyhedral model. The compiler automatically parallelizes loop nests; especially stencil kernels, into efficient GPU code by loop tiling transformations which the polyhedral model describes. To enhance
parallel performance, we introduce three practically efficient techniques to process different types of loop nests. The experimental results of our compiler framework have demonstrated that these advanced techniques can outperform previous approaches.Firstly, we aim to find efficient tiling transformations without violating data dependences. How to select a tile's shape and size is an open issue that is performance-critical and influenced by GPU's hardware constraints.We propose an approach to determine the tile shapes out of consideration for improving two-level parallelism of GPUs. The new approach finds appropriate tiling hyperplanes by embedding parallelism-enhancing constraints into the polyhedral model to maximize intra-tile, i.e., intra-SM parallelism. This improves the load balance among the streaming processors (SPs), which execute a wavefront of loop iterations within a tile. We eliminate parallelism-hindering false dependences to optimize inter-tile, i.e., inter-SM parallelism. This improves the load balance among the streaming multiprocessors (SMs), which execute a wavefront of tiles.Furthermore, to avoid combinatorial explosion of tile size's configurations, we present a model-driven approach to automating tile size selection that is performance-critical for loop tiling transformations, especially for DOACROSS loop nests. Our tile size selection model accurately estimates the execution times of tiled loop nests running on GPUs. The selected tile sizes lead to the performance results that are close to the best observed for a range of problem sizes tested.Finally, to address the difficulty and low-performance of parallelizing widely used SOR stencil loop nests, we present a new tiled
parallel SOR method, called MLSOR, which admits more efficient data-
parallel SIMD execution on GPUs. Unlike the previous two approaches that are dependence-preserving, the basic idea is to algorithmically restructure a stencil kernel based on a non-dependence-preserving parallelization scheme to avoid pipelining for higher parallelism. The new approach can be implemented in compilers through a pattern matching pass to optimize SOR-like DOACROSS loop nests on GPUs.
Advisors/Committee Members: Xue, Jingling, Computer Science & Engineering, Faculty of Engineering, UNSW.
Subjects/Keywords: Compiler; GPU; Loop tiling; Parallel computing
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APA ·
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Export
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APA (6th Edition):
Di, P. (2013). Automatic Parallelization of Tiled Stencil Loop Nests on GPUs. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/53495 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:12190/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Di, Peng. “Automatic Parallelization of Tiled Stencil Loop Nests on GPUs.” 2013. Doctoral Dissertation, University of New South Wales. Accessed February 17, 2020.
http://handle.unsw.edu.au/1959.4/53495 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:12190/SOURCE02?view=true.
MLA Handbook (7th Edition):
Di, Peng. “Automatic Parallelization of Tiled Stencil Loop Nests on GPUs.” 2013. Web. 17 Feb 2020.
Vancouver:
Di P. Automatic Parallelization of Tiled Stencil Loop Nests on GPUs. [Internet] [Doctoral dissertation]. University of New South Wales; 2013. [cited 2020 Feb 17].
Available from: http://handle.unsw.edu.au/1959.4/53495 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:12190/SOURCE02?view=true.
Council of Science Editors:
Di P. Automatic Parallelization of Tiled Stencil Loop Nests on GPUs. [Doctoral Dissertation]. University of New South Wales; 2013. Available from: http://handle.unsw.edu.au/1959.4/53495 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:12190/SOURCE02?view=true
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Open Access Theses and Dissertations
