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Scientific Computing Topics for Final Projects

Scientific Computing Topics for Final Projects. Dr . Guy Tel- Zur. Version 2, 15-05-2011. Best option. Find a computational challenge in your field of research (Math, CS, Biology, Chemistry, Physics…) Think Parallel or Distributed Use advanced Visualization.

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Scientific Computing Topics for Final Projects

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  1. Scientific ComputingTopics for Final Projects Dr. Guy Tel-Zur Version 2, 15-05-2011

  2. Best option • Find a computational challenge in your field of research (Math, CS, Biology, Chemistry, Physics…) • Think Parallel or Distributed • Use advanced Visualization

  3. In the next slides are topics which can candidates for the Final Projects

  4. Class 1: Science topic + a computational tools • Examples: • Map-Reduce Paradigm, http://hadoop.apache.org/core/

  5. Class 2: Study new computational tools + case studies / benchmarks • In class 2 there is less emphasize on the scientific story • Examples: • CFD, learn OpenFoam, http://www.opencfd.co.uk/openfoam/ such projects also include learning how to install the tool

  6. Class 3: Porting a scientific problem to another new software • Examples: • Program the “Game of Life” in Erlang, UPC, Chapel, Fortress • Port the “Game of Life” to GPGPU • “Game of Life” in Microsoft’s Axum, http://msdn.microsoft.com/en-us/devlabs/dd795202.aspx

  7. More topics • Develop distributed code for Grid Mathematica or Maple • Run your project on Amazon’s EC2 Cloud • Find a CPU intensive problem like parameter sweep or Monte Carlo and solve it using Condor • Do your project in “R” • Do your project using MatlabMPI / pMatlab

  8. Cont’ • Performance tools: TAU (Tuning and Analysis Utilities), http://www.cs.uoregon.edu/research/tau/home.php

  9. 2D Ising Model Simulation • DLA – Difussion Limited Aggregation • Parallel Sorting algorithms • Game: the sesmic duck in OpenMP: http://home.comcast.net/~arch.robison/seismic_duck.html • Open|SpeedShop, http://www.openspeedshop.org/wp/ • A strong CS background is needed

  10. The NAS Parallel Benchmark http://www.nas.nasa.gov/Software/NPB/

  11. Parallel Numerical Libraries: Scalapack • Download packages. • Write an example program. • Make benchmarks (speedup & efficiency) • Ref: ScaLAPACK: a portable linear algebra for distributed memory computers – design issues and performance. J.Choi et al. Computer Physics Communications 97 (1196) 1-15 • http://oscinfo.osc.edu/training/parlib/parlib.ls.pdf

  12. Parallel Genetic Algorithms A genetic algorithm (GA) is a search procedure that optimizes some objective function f by maintaining a population P of candidate solutions and employing operations inspired by genetics (called crossover and mutation) to generate a new population from the previous one. Generally, the candidate solutions are encoded as bit strings.

  13. Simulated Annealing (SA) Metropolis Algorithm Example: TSP - Traveling Salesman Problem

  14. פרוייקט גמר – 12 Fractal Dimension Calculation Using the “Box Counting” Method

  15. Neural Networks • Parallel (MPI/OpenMP) or Distributed (Condor) • Search for a Pattern/Optimization

  16. Clustering • Parallel (MPI/OpenMP) or Distributed (Condor) • Classification of Data using Fuzzy Logic

  17. DLA The Diffusion-Limited Aggregation (DLA) is a growth model based on diffusing particles. The growth is started with a single seed A random walker travels about a square lattice; when the walker reaches a site adjacent to the growing cluster it sticks

  18. N-Body Problem Using the Barnes-Hut Algorithm An O(n log n) algorithm based on a hierarchical octree representation of space in three dimensions. It computes interactions between distant particles by means of the first order approximation.

  19. Multi-Grids Solving the Discrete Poisson Equation using Multigrid Divide-and-Conquer Method

  20. IsingModel Spins interactions The Monte Carlo code should be parallel in the sense that each processor will perform work on a separate region of the lattice.

  21. Root - Proof • http://people.web.psi.ch/feichtinger/doc/proof_examples.html

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