Introduction to OSes and UNIX

Transcription

1 Introduction to OSes and UNIX 1

2 Quiz Friday 9/5/ minutes 4 questions L1, L2, and L3 2

3 Editor and Perl Has everyone found an editor and perl? 3

4 Bioinformatics is Unix? Why would anyone, even jokingly, propose such an idea? 1) Variants of Unix are open source can view and manipulate code with great control, comes great responsibility example: which services are initiated by default attractive development platform some variants not open source SCO HPUX 2) Free attractive development platform 3) An operating system easy enough to use by everyone may come with features and overhead not required to perform scientific calculations and its not free. example) rendering a graphical user interface 4) Because of 1, 2, and 3, academic developers often choose Unix 4

5 Bioinformatics is Unix? 5) Unix has a long and steep learning curve (and may even be evolving faster now), and a reasonable understanding is required to access or manipulate some of the tools being developed. 6) Web interfaces (and porting) provide limited access Example) BLAST Basic Local Alignment Search Tool 7) However, Unix is not bioinformatics. It is the ability to know and understand the inter-workings of a tool/application, and have the ability and access to manipulate that tool to meet your needs. With this ability to make tools, you can assemble or string together collections of tools to make large and complicated systems. From this tool set (and an understanding of biological problems), we can attempt to solve problems described by large and complex data sets in genetics, biology, and genomics. 5

6 Definitions program, application, script the implementation of an algorithm algorithm set of rules and instructions to accomplish a task (defined more formally later) example) dressing do I have clothes 1 If no, then obtain clothes 2 if yes, are these my clothes 3» if no, go to 2 4» if yes,. 5» (socks before shoes, etc) 6 6

7 Definitions Operating System provides a uniform interface between a computer s hardware and user-level programs. manages the low-level functionality of the hardware automatically. a program (or collection of programs) that controls the hardware of a computer examples manage network traffic memory management Programming Language (perl, java, C, C++, python, PHP, ML, etc) provides a formal structure/syntax for implementing algorithmic procedures that can be mapped onto the hardware abstraction from hardware enables portability i.e., search the homo sapiens genome for any occurrence of the gene (FOXC1) does not work 7

8 What is UNIX (and other OS s)? Operating System : /n./ [techspeak] (Often abbreviated `OS') The foundation software of a machine, of course; that which schedules tasks, allocates storage, and presents a default interface to the user between applications. The facilities an operating system provides and its general design philosophy exert an extremely strong influence on programming style and on the technical cultures that grow up around its host machines. - The Jargon Dictionary* Operating system developed at AT&T Bell Labs early 70 s originally written in assembly code the C programming language was designed to implement a more portable version of UNIX Multi-user multiple users can access and execute instructions (example login) Multi-tasking the ability to distribute computational resources to multiple request complicated issues scheduling allocation of resources (CPU cycles, memory access and utilization, 8 disk access)

9 Unix and Other OS s Microsoft QDOS Quick and Dirty Operating System for $50, written by Tim Paterson of Seattle Computer Products (6 wks) Licensed MS-DOS to IBM 1981 M$ hired Tim Paterson Windows (95,98,2000,XP, ME, NT, ) Apple MaCOS OSX (BSD Unix at University of California, Berkeley) Many others 9

10 UNIX AT&T s Unix distribution made available with source code at no cost could fix bugs, add features or just test alternative methods EXCELLENT for learning or teaching adopted by CS and EE departments for learning Adopted by Berkeley to make BSD (Berkeley Standard Distribution) with the following added features virtual memory paging networking (TCP/IP) 10

11 What is UNIX? (part 3) By programmers, for programmers extensive facilities to allow people to work together and share information in controlled ways time sharing system multiple programs running concurrently robust environment capable of supporting mission critical computations and remaining operational for years Example web servers multi-user, multi-tasking, networked very early in design contrasted to windows-based OS which are generally designed to be easy to use (but they ve come a long way) Every program should do one thing, and do it well example) unix network configuration counter example) windows network configuration 11

12 UNIX hierarchy User i/f Library i/f System call i/f Standard Libr. Users Std. Utility Programs (shell, editor, compiler) (open, close, fork, read, print, etc.) UNIX O/S (process mgmt, memory mgmt, file system, I/O, etc.) Hardware (CPU, memory, disks, keyboard, etc.) Adapted from Tanenbaum, p

13 Windows Hierarchy? cannot know architecture other dilemmas faced by Windows users and developers Microsoft has inherent advantage to developing and distributing application software (DOJ monopoly case) competing application developers have to license access to OS because of this, developers of development software also license their software DELPHI V7 PERSONAL CD-W98/WXP $100 Microsoft Visual C++.NET Standard 2003 $92 13

14 NEWS.COM has an article describing Office 2003's DRM features for documents. This will not only coerce those running older versions of Office to upgrade, which has been a problem for MS in the last few years, but it will also shut out competing software, such as OpenOffice. Now think about this for a second. Even if the developers of a competing office suite could figure out how to get their software to open an Office 2003 document, doing so would be a DMCA violation, since they'd be bypassing an anti-circumvention device. I certainly hope the OpenOffice team will kick development into high gear. If there was a time we need a viable competitor to Office, it's now. 14

15 Memory Management of 386 limited access between levels user programs shared libraries System calls kernel shared library (perl) example: Getopt::Long usage: getaccession.pl f accesion_file o out_file Tanenbaum 15

16 UNIX Basics User Accounts - required to log-on to the computer with username and password (relatively recent for Windows) Groups - entity made up of one or more users. Sharing... Bob Stacie group1 Bill group2 Diane Mike 16

17 UNIX Basics File Sharing - Regulated by three sets of permissions. Permissions: read, write, execute Subjects: owner, group, all User (u) Group (g) All (a) R W X user group world -rwxr-xr-x -r-xr-xr-x -rw rw-r--r-- -rwxrwxrwx foo.pl bar.pl secret public danger 17

18 UNIX Basics Super-user account -complete access to all files -with great power comes great responsibility -example accidentally delete a file Required for system administration tasks add accounts/groups change permissions/owners of any file change password of any account shutdown a machine 18

19 UNIX Basics UNIX Filesystem Hierarchy / analogous to c: bin dev etc lib tmp usr var Two shortcuts. - the current directory.. - the directory one level up /usr /usr/bin /usr/local /usr/local/bin bin doc lib local bin etc lib tmp 19

20 What is UNIX? Processes (computing dictionary) 1. The sequence of states of an executing program. A process consists of the program code (which may be shared with other processes which are executing the same program), private data, and the state of the processor, particularly the values in its registers. It may have other associated resources such as a process identifier, open files, CPU time limits, shared memory, child processes, and signal handlers. Each program executes as a process 20

21 Unix A process provides encapsulation for the program Under UNIX, multiple processes can be running at the same time! foreground (fg) and background (bg) memfill.pl example How to control processes: ^C -- break ^Z -- suspend & -- start in background ps -- show which processes are running kill -- kill a process 21