ETD

Digital archive of theses discussed at the University of Pisa

 

Thesis etd-09042020-140441


Thesis type
Tesi di laurea magistrale
Author
YAGUBLU, AYTAN
URN
etd-09042020-140441
Thesis title
Parallelization of Stochastic Simulation of Biochemical Reaction Systems on Multi-Core Processors
Department
INFORMATICA
Course of study
INFORMATICA
Supervisors
relatore Prof. Danelutto, Marco
Keywords
  • Parallelization on CPUs
  • SSA
  • Stochastic Simulation Algorithms
  • Gillespie's Direct Method
  • Next Reaction Method
  • Rejection-based SSA
  • Domain Decomposition method
  • Partition reactions into subdomains
  • C++ threads
  • FastFlow
Graduation session start date
09/10/2020
Availability
Withheld
Release date
09/10/2090
Summary
The Gillespie’s Stochastic Simulation Algorithm (SSA) is a compact, computer-oriented Monte Carlo simulation procedure that is useful for modeling simulation of well-stirred biochemical systems. This thesis describes different sequential methods of SSA such as Direct Method, Next Reaction Method, Rejection based SSA and different methodologies of parallelization of these methods on CPUs. The thesis investigates different parallelization strategies and discusses experimental results on two states of the art multicore architectures.
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