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74 CHAPTER 3. A C++ FRAMEWORK FOR HIGH-THROUGHPUT DNA SEQUENCING (a) serial parallelizer parallel sync serial desync parallel Source multiplexer track Pipe multiplexer thread Pipe lock_link . . . . . . . . . . . . track Sink . . . . . . (b) serial parallelizer parallel sync serial desync parallel multiplexer track multiplexer thread Pipe lock_link . . . . . . . . . . . . track Sink . . . . . . Signal data ush Slot postlock preunlock postunlock join Figure 3.3: Connections between Parallel Processing Objects the respective thread. An auxiliary flush signal in addition conveys the thread-specic ush state across synchronized sections of the processing pipeline. Finally, a connection join is supported by all parallel processing modules to ensure correct termination of processing across all threads. For distributed memory architectures, data are distributed from a single root process to several worker processes. Worker processes must receive the data to be processed concurrently from the root process, and must subsequently return their output data for processing by serial modules (gure 3.3(b) ). Objects of parallelizer, sync and desync initialized in worker processes automatically establish connections for exchange of data with their respective counterpart in the root process, where each connection is associated with an additional thread in the root process. To prevent initialization conicts and overhead, serial objects are associated with the additional function of preventing creation of their respective incorporated processing module when
3.3. A SIMPLIFIED PARALLELIZATION INTERFACE 75 not in the root process. Threads of worker processes' parallelizer objects operate by requesting data from the respective counterpart in the root process. Failure to retrieve data indicates that processing is complete, and triggers invocation of the thread's ush signal and subsequently thread termination. Otherwise, data received are transmitted to the subsequent parallel object, identical with threaded operation. Subsequent sync objects submit received data and ush signals to the corresponding object of the root process. Sections formed by serial objects however cause an interruption in the pipelines of worker processes. Therefore, sync objects must exploit the postlock signal transmitted through serial modules to trigger a downstream desync object to request data generated by serial processing from its counterpart in the root process.
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An Integrated Data Analysis Suite a
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Erklärung Hiermit erkläre ich, da
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Acknowledgment First of all I would
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Abstract The various parallel DNA s
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xii CONTENTS 2.6 A Parallelization
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2 CHAPTER 1. INTRODUCTION 1.2 Appro
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4 CHAPTER 1. INTRODUCTION genetic a
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6 CHAPTER 1. INTRODUCTION Instrumen
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8 CHAPTER 1. INTRODUCTION biases. S
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10 CHAPTER 1. INTRODUCTION To achie
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12 CHAPTER 1. INTRODUCTION quantiti
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14 CHAPTER 1. INTRODUCTION of featu
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16 CHAPTER 1. INTRODUCTION Our appl
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20 CHAPTER 2. A HIGH-THROUGHPUT DNA
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22 CHAPTER 2. A HIGH-THROUGHPUT DNA
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Page 91 and 92: 4 Closing Remarks Routine analysis
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Page 96 and 97: 82 BIBLIOGRAPHY [9] S. Brenner, M.
Page 98 and 99: 84 BIBLIOGRAPHY [29] N. Cloonan, A.
Page 100 and 101: 86 BIBLIOGRAPHY [48] B. A. Methe, K
Page 102 and 103: 88 BIBLIOGRAPHY [72] S. Andrews. Fa
Page 104 and 105: 90 BIBLIOGRAPHY [98] M. A. DePristo
Page 106 and 107: 92 BIBLIOGRAPHY [124] W. J. Kent, C
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