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Parallel Processing Lab 1

Parallel Processing Lab 1. Dr. Guy Tel- Zur. August 2013 edition. מטרות השיעור. התחברות לקלאסטר המקבילי תרגול ביצוע משימות בסיסיות תחת מערכת ההפעלה Linux הרצת תכניות מקביליות בסיסיות המשתמשות ב MPI - שימוש ב - Profiler. יעדים. יישור קו בנושא לינוקס הכרות ראשונית עם MPI פיתוח קוד

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Parallel Processing Lab 1

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  1. Parallel ProcessingLab 1 Dr. Guy Tel-Zur August 2013 edition

  2. מטרות השיעור • התחברות לקלאסטר המקבילי • תרגול ביצוע משימות בסיסיות תחת מערכת ההפעלה Linux • הרצת תכניות מקביליות בסיסיות המשתמשות בMPI- • שימוש ב- Profiler

  3. יעדים • יישור קובנושא לינוקס • הכרות ראשונית עם MPI • פיתוח קוד • קימפול • ניפוי שגיאות • הרצה • ניתוח התוצאה

  4. The Hobbits • Old hobbits: • Hobbit1 132.72.53.1 • Hobbit2 132.72.53.2 • Hobbit3 132.72.53.3 • Hobbit4 132.72.53.4 • Hobbit5 132.72.53.5 • New hobbits: • Hobbit6 132.72.50.36 • Hobbit7 132.72.50.35 • Hobbit8 132.72.55.240 • Hobbit9 132.72.55.241 • Hobbit10 132.72.52.160 • Virtual hobbits: • Hobbit11 132.72.50.68 • Hobbit12 132.72.50.71 • Hobbit13 132.72.50.91 • Hobbit14 132.72.50.93 • Hobbit15 132.72.50.94

  5. Ganglia Monitorhttp://hobbit5.ee.bgu.ac.il/

  6. Enter the system login: username password: passwd Exit the system exit Text editors pico, vi, (x)Emacs, gedit… or Edit on Windows then transfer file using ftp C Compiler gcc –o file file.c Basic Linux Commands – 1/5

  7. DOS Linux See files dir ls ls -l Copy files copy cp Erase files del rm Basic Linux Commands – 2/5

  8. DOS Linux Make directory mkdir mkdir Remove directory rmdir rmdir More/Rename rename mv OS version ver uname -a Basic Linux Commands – 3/5

  9. Basic Linux Commands – 4/5 • Getting help: man topic • Look at the contents of a file: cat, more,head and tail • Quit from man or more: q • Where am I? pwd • Clear the screen: clear

  10. Basic Linux Commands – 5/5 • Redirection: >, >> • Pipe: | • telnet • ftp • ping • chmod • chown

  11. http://www.ctssn.com/linux/linuxfaq.html Linux FAQ

  12. ESC Puts you in command mode h, j, k, l Left, down, up, right or use the arrows keys w, W, b, B Forward, backward by word 0, $ First, last position of current line /pattern Search forward for pattern ?pattern Search backward for pattern n,N Repeat last search in same, opposite direction x Delete character dd Delete current line D Delete to end of line dw Delete word p, P Put deleted text before, after cursor u Undo last command . Repeat the last command i, a Insert text before, after cursor [Puts you into INPUT MODE] o, O Open new line for text below, above cursor [Puts you into INPUT MODE] ZZ Save file and quit :w Save file :q! Quit, without saving changes The vi Editor

  13. vi reference card • Download and print: • http://my.pages.de/vi-refcard.html • http://vh224401.truman.edu/~dbindner/mirror/vi-ref.pdf

  14. Vi for Windows

  15. Vi for windows

  16. nano

  17. Other text editors • Vi, Vim • Pico • Emacs/Xemacs • Nedit (very friendly) • Eclipse IDE‏

  18. Linux: Gathering Information Kernel version: uname –a CPU information:more /proc/cpuinfo Memory Information:more /proc/meminfo

  19. הגנה על הפרטיות – הרשאות גישה לקבצים

  20. Connecting from Windows to a remote node • Secured: SSH SSH client from: http://www.ssh.com/support/downloads/ PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/ Please download Putty!!!!!

  21. Putty

  22. Putty + Xming (option 1) Install xmingand xming fonts

  23. Connecting with cygwin X (option 2) • Connect with PuTTY • Programs  cygwin  xwin server • xhost + • From PuTTY’swindow: open X application

  24. For a secured connection from home http://vpn.bgu.ac.il

  25. For a secured connection from home

  26. For a secured connection from home IPconfig

  27. Configuring PuTTY

  28. Download links • Putty: • http://www.putty.org/ • Xming: • http://sourceforge.net/projects/xming

  29. Password-less SSH: http://telzur.blogspot.co.il/2006/03/password-less-ssh-connection.html

  30. תרגיל מס' 1 • התחבר לאחת מהתחנות תוך שימוש ב- ssh • כתוב תכנית מחשב קצרה שמדפיסה: Hello World • בצע קומפילציה: gcc –o hello_worldhello_world.c • הרץ את התכנית ושמור הפלט: % ./hello_world > hello.txt • בדוק את הפלט על-ידי: • more hello.txt

  31. The GNU compilerhttp://gcc.gnu.org/ • gcc filename.c • Will produce an executable “a.out” • gcc –o runme filename.c • Will produce an executable “runme” • Optimization: gcc –O3 –o runme filename.c • gcc –c filename.c will produce an object file “filename.o”

  32. פתרון תרגיל מס' 1 – 1/3

  33. פתרון תרגיל מס' 1 – 2/3

  34. פתרון תרגיל מס' 1 – 3/3

  35. MPI

  36. MPI-Quick reference card 1/2

  37. MPI-Quick reference card 2/2

  38. MPI Quick Reference Card: http://web.eecs.utk.edu/~dongarra/WEB-PAGES/SPRING-2006/mpi-quick-ref.pdf

  39. Data Process 0 Data May I Send? Data Data Data Data Data Data Data Process 1 Yes Time What is message passing? • Data transfer through messaging • Requires a sender and a receiver cooperation

  40. תהליך מס' 1 תהליך מס' 2 x y הזזת נתונים Send(&x,2); Recv(&y,1); Point to Point: Basic Send/Receive

  41. Space-Time Diagram of a Message-Passing Program

  42. MPI - Message Passing Interface API • MPI is a standard not an implementation • Popular implementations are LAM and MPICH • MPICH is installed under /usr/local/mpich • Always put in the code: #include “mpi.h” • Compilation: mpicc –o filename file.c • Execution: mpirun –np N filename • Help: man mpirun

  43. MPI Naming Conventions MPI_Xxxxx(parameter,...)‏ Example: MPI_Init(&argc,&argv)‏

  44. The First 4 Functions of MPI • MPI_Init • MPI_Finalize • MPI_Comm_size • MPI_Comm_rank • …and don’t forget the #include “mpi.h”

  45. The First 4 Functions Syntax • int MPI_Init(int argc, char *argv[] )‏ • int MPI_Finilize()‏ • int MPI_Comm_size(MPI_Comm comm, int *size)‏ • int MPI_Comm_rank(MPI_Comm comm, int *rank)‏

  46. MPI Communicator A communicator is a handle representing a group of processors that can communicate with one another. The communicator nameis required as an argument to all point-to-point and collective operations. The communicator specified in the send and receive calls must agree for communication to take place. Processors can communicate only if they share a communicator.

  47. Basic Point to Point Functions • MPI_Send • MPI_Recv • MPI_Send(void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm); • MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Status status);

  48. MPI_Send int MPI_Send(void *buf, int count, MPI_Datatype dtype, int dest, int tag, MPI_Comm comm);

  49. MPI Data types MPI data typeC Type MPI_CHAR signed char MPI_SHORT signed short int MPI_INT signed int MPI_LONG signed long int MPI_UNSIGNED_CHAR unsigned char MPI_UNSIGNED_SHORT unsigned short int MPI_UNSIGNED unsigned int MPI_UNSIGNED_LONG unsigned long int MPI_FLOAT float MPI_DOUBLE double MPI_LONG_DOUBLE long double MPI_BYTE (none)‏ MPI_PACKED (none)‏

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