Unix lecture1
- 1. UNIX Operating System Unit 1 410.634, Johns Hopkins University ©John M. Greene, Ph.D., 1999-2011 All Rights Reserved
- 2. What is an operating system? • Hardware • OS • Applications • OS is the interface between the applications and the hardware - takes care of hardware initialization and shutdown, manages processes, and allocates resources
- 3. What is UNIX, and Why Is It Used in Bioinformatics? • UNIX is an interactive, reliable, multi-user operating system which optimizes available hardware power. • UNIX experienced renewed interest due, in part, to the availability of computer systems designed to run it which offer better performance at a lower price than their proprietary counterparts. • Most real bioinformatics software (BLAST, FASTA; relational databases) is written for UNIX.
- 4. The Mouse Is For Wimps The quickest way to do something on a computer is with the keyboard, not the mouse. Many times for UNIX, there is no mouse!
- 5. UNIX • OS, plus a set of standard libraries and standard applications • Kernel - hardware and process management – UNIX sees each device as a file – implements security – allocates resources, including use of the CPU • Shell - program that talks to the kernel and passes on requests
- 6. UNIX Philosophy • Open source (not proprietary) - more or less • Simple, orthogonal commands - each tool does one thing really well • Commands connected through pipes • Common interface style - mainly command- line, but there is the X Window System - a large program from MIT allowing computers to create graphical windows, used on many different Unix platforms • No file types required
- 7. UNIX drawbacks • Inconsistencies and overlapping functions - too many cooks over 25 years • Much higher learning curve than Mac/Windows • Few popular programs currently available - Netscape,WordPerfect, and Star Office (from Sun Microsystems; can read Microsoft formats) • Until Linux and open source, relatively expensive
- 8. UNIX History • Unix history goes back to 1969. Ken Thompson and Dennis Ritchie sketched out a new operating system that would meet Bell Labs' needs. • For the first 10 years, Unix development was essentially confined to Bell Labs. The C language was originally designed for the Unix operating system, and hence there is a strong synergy between C and Unix. In fact, the UNIX OS was re-written into C. • The name "Unix" was intended as a pun on Multics, an effort to develop a multiplex user system that could do time-sharing (UNIX was written "Unics" at first -- UNiplexed Information and Computing System).
- 9. UNIX Families • System 5 Release 4 ; SVR4 (AT&T Bell Labs origins) • BSD (UC Berkeley origins) • Linux (LIH-nucks) • UNIX is available for mainframes, workstations, Windows PCs, and even Macs! (Mac OS X has a Berkeley-derived UNIX kernel - Darwin)
- 10. UNIX Family Tree Linux Berkeley (BSD) SVR4 Bell Labs 1969 ~1979 ~1990?
- 11. UNIX Vendor Versions • IRIX - SGI (SVR4) • SunOS, Solaris – Sun (SVR4) • HP-UX - Hewlett-Packard • AIX - IBM • Red Hat, Caldera, SuSE (Linux) • FreeBSD – bio.pgp.jhu.edu (Berkeley) • MacOS X – Darwin (Berkeley)
- 12. Login • Username • Password • Receive shell prompt • UNIX IS CASE SENSITIVE!!!! • Root (superuser) - can do anything; usually the system administrator
- 13. UNIX Shells • Shell interprets commands and talks to kernel • Bourne (sh) - lacks job control • C shell (csh) - job control but difficult for shell scripts • Korn (ksh) - C/Bourne hybrid • Bourne-Again (bash) • tcsh - extended C shell • zsh
- 14. Control characters • Hold down Ctrl key and press letter simultaneously • Ctrl-C Interrupt (terminates current job) • Ctrl-H Backspace • Ctrl-Z Quit; suspend job • Ctrl-S Pause output (but not on JHUNIX) • Ctrl-Q Resume output (“) • Ctrl-D logout/exit; end of input • Ctrl-U kill; erases entire line • Can use stty erase Ctrl-H to set backspace key, if different on a given terminal
- 15. Getting out • exit • Logout (on some systems) • CTRL-D
- 16. UNIX command syntax command option(s) filename(s) – commands are entered in lowercase – options modify how the command works; often they are preceded by a - (dash) and separated by spaces. They are also called flags – options come before filenames – options and filenames are called arguments
- 17. Simple commands • date • who - lists users logged on • whoami – lists logged-in user • uname -a - name of computer, OS • passwd - changing your password • ls – list all files in the current directory • ls –a – list all files, including hidden files • ls –l - list all files in long format
- 18. Weird vocabulary • ! Bang • * Splat, star • " Double quote • ' Single quote, tick • ` Backtick • . Dot, point • # Sharp
- 19. UNIX error messages Segmentation fault(core dumped) - memory error; creates a large file named core - please delete it! Broken pipe - one part terminates before the rest