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Scientific Computing

Scientific Computing. Dr. Guy Tel- Zur. Version 28-05-2011.12:40. Agenda. Administration Visualization Visualization in Sage VisIt : Tutorial The Silo file format A demo program Animation Demo : AWS – HTC Instance for Parallel Computing and Cellular Automata / NKS demo on the cloud

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Scientific Computing

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  1. Scientific Computing Dr. Guy Tel-Zur Version 28-05-2011.12:40

  2. Agenda • Administration • Visualization • Visualization in Sage • VisIt: • Tutorial • The Silo file format • A demo program • Animation • Demo: AWS – HTC Instance for Parallel Computing and Cellular Automata / NKS demo on the cloud • Parallel Profiling • Home assignment #3 (next week)

  3. Final Projects • Please hurry to choose a topic! • Send an email to gtelzur@gmail.com with: • Your name • Project title • An abstract • Computational tools, e.g. MPI, Condor…

  4. Sage Vmware Player Shared folder under: /mnt/hgfs/shared/

  5. # reference: http://www.packtpub.com/article/plotting-data-sage p1 = plot(sin, (-2*pi, 2*pi), thickness=2.0, rgbcolor=(0.5, 1, 0), legend_label='sin(x)') p2 = plot(cos, (-2*pi, 2*pi), thickness=3.0, color='purple', alpha=0.5, legend_label='cos(x)') plt = p1 + p2 plt.axes_labels(['x', 'f(x)']) show(plt)

  6. # plotting a function with a pole pole_plot = plot(1 / (x - 1), (0.8, 1.2), detect_poles='show', marker='.') print("min y = {0} max y = {1}".format(pole_plot.ymax(), pole_plot.ymin())) pole_plot.ymax(100.0) pole_plot.ymin(-100.0) # Use TeX to make nicer labels pole_plot.axes_labels([r'$x$', r'$1/(x-1)$']) pole_plot.show()

  7. # plotting a parametric function var('t') pp = parametric_plot((cos(t), sin(t)), (t, 0, 2*pi), fill=True, fillcolor='blue') pp.show(aspect_ratio=1, figsize=(3, 3), frame=True)

  8. # making a polar plot # A linear broadside array of short vertical dipoles # located along the z axis with 1/2 wavelength spacing var('r, theta') N = 7 normalized_element_pattern = sin(theta) array_factor = 1 / N * sin(N * pi / 2 * cos(theta)) \ / sin(pi / 2 * cos(theta)) array_plot = polar_plot(abs(array_factor), (theta, 0, pi), color='red', legend_label='Array') radiation_plot = polar_plot(abs(normalized_element_pattern * array_factor), (theta, 0, pi), color='blue', legend_label='Radiation') combined_plot = array_plot + radiation_plot combined_plot.xmin(-0.25) combined_plot.xmax(0.25) combined_plot.set_legend_options(loc=(0.5, 0.3)) show(combined_plot, figsize=(2, 5), aspect_ratio=1)

  9. # plotting a vector field var('x, y') a = plot_vector_field((x*x, y), (x, -3, 3), (y, -3, 3), color='blue') b = plot_vector_field((y, -x), (x, -3, 3), (y, -3, 3), color='red') show(a + b, aspect_ratio=1, figsize=(4, 4))

  10. # making a scatter plot defnoisy_line(m, b, x): return m * x + b + 0.5 * (random() - 0.5) slope = 1.0 intercept = -0.5 x_coords = [random() for t in range(50)] y_coords = [noisy_line(slope, intercept, x) for x in x_coords] sp = scatter_plot(zip(x_coords, y_coords)) sp += line([(0.0, intercept), (1.0, slope+intercept)], color='red') sp.show()

  11. # reference: http://diffusion.cgu.edu.tw/ftp/sage/ # 2D plot plot(sin(x^2-x+1/(x-1)),(x,-pi,pi))

  12. # animation (not working in power point , do the real demo a=animate([sin(x^k)/x^k for k in srange(1,10)], xmin=-pi, xmax=pi, ymin=-0.3, ymax=1) a.show()

  13. # 3D plot for x^2-x*y+y^2+1 and surface x^2+y^2-1=0 var('x, y, z') s1=plot3d(x^2-x*y+y^2+1,(x,-2,2),(y,-2,2),opacity=0.5) s2=implicit_plot3d(x^2+y^2-1,(x,-2,2),(y,-2,2),(z,0,10),color='red',opacity=0.7) show(s1+s2)

  14. Visualization: The Silo file format • References: • Download: https://wci.llnl.gov/codes/silo/release_notes.html (BSD License) • http://www.e-science.le.ac.uk/format/silo.shtml • http://www.e-science.le.ac.uk/format/silocode.shtml

  15. Visualization: A demo program • Use VirtualBox Ubuntu  Install Silo and VisIt • Installation was not smooth on Ubuntu 10.4, I had to install libstdc++5 manually (an older version) • Let’s look at “wave.c” • Open DevC++ with: C:\Users\telzur\Documents\My Talks\MIL_OSS\silo\silo-4.8-bsd\tests\wave.c

  16. Silo • Discuss in class the wave.c program • Run the program on the Virtual Machine • Make plot using VisIt • Make a mpeg movie! Bulding silo: ./configure make sudo make install cd ./tests make wave ./wave

  17. wave.c silo file

  18. Mini Course: Performance Tuning • Open VirtualBox SC10 demos: • Vampir (commercial, only a free viewer) • TAU – Paraprof (free) • Scalasca (free) • Marmot (free)

  19. pprof profiler /home/livetau/workshop-point/ring$ mpirun -np 4 ./ring 0 started. 2 started. 3 started. 1 started. 0 done. 2 done. 3 done. 1 done. /home/livetau/workshop-point/ring$ pprof …

  20. NODE 3;CONTEXT 0;THREAD 0: --------------------------------------------------------------------------------------- %Time Exclusive Inclusive #Call #Subrs Inclusive Name msec total msecusec/call --------------------------------------------------------------------------------------- 100.0 0.363 1,070 1 5 1070955 MAIN 97.3 1,041 1,041 1 0 1041995 MPI_Init() 1.8 0.26 19 1 4 19144 FUNC 1.6 17 17 1 0 17531 MPI_Barrier() 0.9 9 9 1 0 9439 MPI_Finalize() 0.1 1 1 1 0 1009 MPI_Bcast() 0.0 0.323 0.323 1 0 323 MPI_Recv() 0.0 0.021 0.021 1 0 21 MPI_Send() 0.0 0.007 0.007 1 0 7 MPI_Comm_rank() 0.0 0.007 0.007 1 0 7 MPI_Comm_size() ---------------------------------------------------------------------------------------

  21. FUNCTION SUMMARY (mean): --------------------------------------------------------------------------------------- %Time Exclusive Inclusive #Call #Subrs Inclusive Name msec total msecusec/call --------------------------------------------------------------------------------------- 100.0 0.242 1,087 1 5 1087028 MAIN 97.7 1,062 1,062 1 0 1062336 MPI_Init() 1.5 1 16 1 4 16716 FUNC 1.3 14 14 1 0 14208 MPI_Barrier() 0.7 7 7 1 0 7708 MPI_Finalize() 0.0 0.427 0.427 1 0 427 MPI_Bcast() 0.0 0.228 0.228 1 0 228 MPI_Recv() 0.0 0.0307 0.0307 1 0 31 MPI_Send() 0.0 0.0155 0.0155 1 0 16 MPI_Comm_size() 0.0 0.0105 0.0105 1 0 10 MPI_Comm_rank()

  22. TAU –pprof, paraprof cd to: workshop-point/ring

  23. HPC – Performance Optimization Cycle Source: Scalasca user guide

  24. Scalasca Step1: scalasca –instrument mpicc –o jacobi ./main.c ./jacobi.c Step 2: scalasca –analyze mpirun –np 4 ./jacobi Step 3: scalasca –examine epick_<title> Users guide: http://www.fz-juelich.de/jsc/datapool/scalasca/UserGuide.pdf BTW: Virtual Box file sharing: as root: mount –t vboxsfguytmp ./guytmp

  25. HTC Cloud Computing Demo Goal: Install Condor on the HPC cloud machine Run many Cellular Automata jobs Check graphical output How to install Condor on Debian: http://www.cs.wisc.edu/condor/debian/

  26. AWS - CloudWatch

  27. 8 cores !

  28. NKS Reference: http://telzur.blogspot.com/2008/01/mysteries-of-cellular-automata.html

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