An Introduction to Linux for Windows Users

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An Introduction to Linux for Windows Users

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1. An Introduction to Linux for Windows Users http://www.engr.uconn.edu/becat/hpc

3. Equipment SGI Altix 3700 BX2 System (sgi1) 64 Intel Itanium 2 Processors (1.5GHz/4MB) 64 GB RAM SGI Altxi 350 Server (sgi2) 8 Intel Itanium 2 Processors (1.5GHz/6MB) 8 GB RAM SuSE SLES 9/SGI ProPack 4

4. Software GNU Compilers, Intel C++/Fortran Compilers Libraries : BLAS, LAPACK, SCSL, MKL, MPT, OpenMP etc. Applications: Scilab, Octave, VTK, Paraview, R, etc.

5. Accessing the System OpenSSH SSH Client – Putty http://www.chiark.greenend.org.uk/~sgtatham/putty/ SFTP Client – WinSCP http://winscp.net/eng/index.php Other SSH Clients http://www.ssh.com

6. Accessing the System - Putty

7. Accessing the System - Putty

8. Accessing the System - Putty

9. Accessing the System - Putty

10. FAQs Where is my home directory? /u/home/{username} What is the disk quota limit? 500 MB for the home directory Up to 500 GB for /data/scratch How do I navigate the file system? cd dir

11. FAQs How do I create directories/files? nedit, pico, vi, emacs mkdir dir How do I delete directories/files? rm –rf dir/files How do I protect my directories/files from being viewd by other users? chmod 700 dir/file

12. FAQs Are my files backed up automatically? For the time being, no. How do I back up my files? Use tar, gzip and transfer backup files to a safe place How do I transfer files between sgi1 and my PC? Sftp, WinSCP How do I access the system from home? Through fester or VPN

13. Transferring Files - WinSCP

14. Transferring Files - WinSCP

15. Passwords Every account must have a password. Passwords can be composed of letters, numbers, the space character and other special symbols. It is essential for users to choose a strong password. Passwords are case-sensitive.

16. Changing Your Password Standalone systems: passwd NIS: yppasswd The SoE systems: Method 1: USING SOE WEB MAIL Go to www.engr.uconn.edu/mail Enter your SOE email ID, hit Enter Click on Read Mail Enter ID and Pass Word Click on the Options Icon located in the bottom left Scroll down to Change Password Enter Account, Old Password, New Password and Confirm new password Method 2: USING ECS LC Come to any ECS LC and login into any PC, then press CTRL, ALT & DEL again while logged in. You will be able to select Change Password from the Task Menu.

17. The Shell Shell – command processor Korn shell (/bin/ksh) C shell (/bin/csh) Bourne Shell (/bin/sh) Bourne Again Shell (/bin/bash) Switch between shells

18. BASH Bash is a command language interpreter Bash is the most popular shell under Linux The prompt: %, #, $, ~> Everything you type before return is consider to be the command line The first word is taken to be the command Everything else on the command line is information for either the command itself or for the shell. Options usually begin with a minus sign

19. BASH: Startup Environment When a login shell starts, BASH reads and executes commands from: /etc/profile ~/.bash_profile When an interactive shell (not login shell) starts, BASH reads and executes commands from: ~/.bashrc

20. BASH: Startup Script Example

21. BASH Some useful shell commands: ls – lists the files you have in the current directory date – gives the date and time who – gives information about who is currently logged on man – access to the on-line manual when you need to check the syntax of a command

22. BASH cat - concatenates files together and sends the result to stdout more - gives you one screenful of the files at a time. Type the SPACE bar to get another screenful. find - search for files in a directory hierarchy

23. BASH Controlling the flow of input and output Redirection: To redirect input to come from a specified file (instead of stdin), type: command < filename To redirect output to a specified file (instead of stdout), type: command > filename Example : $ ls –lct > list.txt

24. BASH Piping – connecting stdout of one command to stdin of another One can pipe the output of one command into the input of another command by using the vertical bar character (|). Example: $ cat file1 file2 | more Concatenate the files file1 and file2 and use the results as input to the more program

25. Processes A process is a shell command or a program in execution. When you log in, a process is created. This process is executing the shell When you execute a shell command, a new process is created. When the command terminates, the new process dies. A single user can have many processes executing at the same time

26. Processes The command ps is used to determine the status of active processes. The command returns the process id (PID) number and other information such as the amount of CPU time the process has used (TIME) and the command which invoked the process (CMD). Options may be combined. UNIX options; BSD options; GNU options

27. Examples of the ps Command

28. Top The command top is used to show a real-time view of Linux tasks top can be used to display the CPU/memory usage of each task and the CPU the task is running on in a SMP system $ top $ top -u

29. Top

30. Top: Options

31. Top

32. Terminate Processes kill is used to terminate processes or to send signal to processes. Examples: $ kill PID Terminate the process with the process id (PID). $ kill –HUP PID Restart the process with the process id (PID). $ kill -9 -1 Terminate all processes. Useful when you want to clean all the tasks you initiated.

33. The File System Ext2, ext3, reiserfs, xfs and more Journaling file system is a file system which records changes to a journal before writing to the main system, e. g. ext3, reiserfs etc.

34. The File System UNIX file name can be very long. Use alphabetic, numeric and some special characters. Files started with a .(dot) are hidden. Use $ ls –a to display hidden files. Hierarchical file structure (tree structure).

35. The File System You are automatically placed in your home directory after logging in. e.g. /u/home/hpc, /home/hpc You can move up and down in the tree to other directories if you have permission to do so.

36. The File System Commands for moving around in the directory structure pwd – no argument needed. Tells you the current directory/path cd dir_name – this changes your position to the specific directory You can specify directory names in two ways: The full pathname from the root of the tree $ cd /u/home/hpc/test/bin A pathname relative to you current directory $ cd . $ cd .. $cd test/bin

37. The File System Creating new directories and removing old ones $ mkdir dir_name This command creates a new directory. $ rmdir dir_name This command is used to delete the directory, which must be empty. $ rm –rf dir_name This command is used to delete the directory and all the files in it.

38. The File System: Pathnames The root of the tree is specified by the character / All levels of a subtree are separated by the character / Examples of complete pathnames are: /u/home/hpc/ee401/homework /usr/home/hpc/.bashrc Examples of relative pathnames are: ../homework/hw1 ee401/homework

39. The File System – ls -l

40. File Access Rights The command ls -l displays the access right to a file. Example: drwxr-xr-x The first single character specifies whether the entry is a directory (d), a simple file (-) or a link (l). r : read permission w : write/modify permission x : execute permission for a file or search permission for a directory - : no permission

41. File Access Rights Example: drwxr_xr_x The first group (rwx) specifies the access privileges of the owner of the file or directory The next group (r_x) specifies the access privileges of a group in which the owner is a member The last group (r_x) specifies the access privileges of the rest of the world (i.e. everyone on the system)

42. Changing the Access Rights: chmod The command changes the access rights to a file or directory. There are two ways to do this: 1. symbolically 2. using octal notation

43. Changing the Access Rights: Symbolically $ chmod [who]permission filename who is specified by u (user/owner), g (group), o (others), a (all three) Examples: Add execute permission to the owner of the file file1: $ chmod u+x file1 Remove execute permission from everyone including the owner on the file file2: $ chmod a-x file2

44. Changing the Access Rights: Using OCTAL notation $ chmod mode filename The mode is specified by treating each of the groups of three rwx fields as an octal digit. Read permission has a value of 4 Write permission has a value of 2 Execute permission has a value of 1 Examples: $ chmod 700 file1 changes access rights of file1 to -rwx------ $ chmod 644 dir2 changes access rights of dir2 to drw-r--r--

45. File Archiving: tar Saves and restores multiple files to/from a single file. Directories followed recursively. Format: tar [opitions] [options_values] [files] Examples: $ tar cvf /tmp/backup.tar ~/data ~/test $ tar xvf backup.tar

46. File Compression: gzip Compressing files: gzip filename $ gzip backup.tar The resulted file is backup.tar.gz Uncompressing files: gzip –d filename.gz $ gzip –d backup.tar.gz The uncompressed file is backup.tar GUN Tar combines uncompress and untar $ tar zxvf filename.tar.gz

47. Example: Back Up Files can be drag and drop to your PC using WinSCP. To back up all the files in a directory: Create a directory to hold the backup file Use tar to save files into a single tar file Compress the tarball using gzip Transfer the compressed backup file (filename.tar,gz) to your PC Delete the backup file or folder on the server The backup file can be expanded on PC using WinZip and other utilities Relative path and full path

48. Example: Back Up

49. Editors vi - a universal text editor in UNIX/Linux $ vi filename nano – a free pico clone in the style of the Pine composer $ nano filename emacs – an extensible, customizable, self-documenting real-time display editor nedit - a multi-purpose text editor for the X Window System

50. Editors - nano

51. Editors - nedit

52. Summary of Useful Commands/Utilities man [command] – display the manual page for the command ls –al | more – list all the files in the current directory cd [dir] – change the current directory cd .. – go to the parent directory pwd - print the current directory rm [file] – delete a file rm –rf [file,dir] – force delete files or directories

53. Summary of Useful Commands/Utilities cp [file1] [file2] – copy file1 to file2, the paths need to be added if the files are not in the current directory mv [oldname] [newname] – rename the file or directory mkdir [dir] – create a directory du –ks – print the space used by the current directory quota –v – display the disk usage by the current users

54. Summary of Useful Commands/Utilities find [dir] –name [filename] – search files with the filename under the directory chmod 700 [file] – change the permission of the file so only the owner can read, write and execute the file chmod –R mode [dir] – change the permissions recusively tar – archive files gzip – compress and expand file(s) export – display the current environment

55. Summary of Useful Commands/Utilities ps –ef | more – display all the processes top – show real-time view of tasks top –u [username] – show tasks owned by the user kill [pid] – terminate the process kill -9 -1 – terminate all the processes owned by you

56. Summary of Useful Commands/Utilities who – displays who is logged on which [command] – shows the full path of the command

57. Examples: Compiling and Running Simple Programs $ g77 hello.f $ ./a.out $ icc –o foobar foobar.c -lmkl_lapack -lmkl_ipf -lguide -lpthread $ ./foobar $ icc –o hello hello.c –lmpi $ mpirun –np 4 hello

58. X and Cygwin/X X Window System (X11 or X) presents the toolkit and protocol to build GUI on Unix, Unix-like systems. To display the remote X GUI applications on your local PC, an X server program (Hummingbird Exceed, XWin32, Cygwin/X etc.) needs to be running on the PC. Cygwin/X provides X Window System for Microsoft Windows. X11 Forwarding/Tunneling through SSH Another seminar will be offered regarding Cygwin/X

59. More Information For supercomputer issues (sgi1, sgi2) [email protected] http://www.becat.uconn.edu/hpc http://www.engr.uconn.edu/becat/hpc For SoE Email/UNIX accounts, VPN ECS Help Desk [email protected]

60. Acknowledgement Some materials in this presentation are based on seminar notes prepared by Sue Lipsky and other Booth Research Center technical staff Jerry Peek et al, UNIX Power Tools, 2nd, O’Reilly, 1997

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