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Introduction to Bioinformatics

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Introduction to Bioinformatics Computer Architecture Course Details • Course Code: COMP303 Prof. Dr. Nizamettin AYDIN • Course Name: Computer Architecture • Credit: 3 • Nature of the course: Lecture [email protected] • Course web page: http://www.yildiz.edu.tr/~naydin/na_CAr.htm http://www.yildiz.edu.tr/~naydin • Instructors: Nizamettin AYDIN Room: …. Email: [email protected], [email protected] 1 2 Assesment Rules of the Conduct • No eating /drinking in class • Midterm : 30% – except water • Cell phones must be kept outside of class or • Final : 40% switched-off during class • Project : 10% • No talking with your peers • Homework : 15% • No late arrival or early leave to/from the • Attendance & participation : 05% lecture • No web surfing and/or unrelated use of computers – when computers are used in class or lab 3 4 Rules of the Conduct Recommended Texts • You are responsible for checking the class web • Computer Organization and Design, David A. page often for announcements. Patterson and John L. Hennessy – http://www.yildiz.edu.tr/~naydin/na_CAr.htm • Computer Architecture: A Quantitative Approach, John L. Hennessy, David A. Patterson • Academic dishonesty and cheating • Computer Organization and Architecture: – will not be tolerated Designing for Performance, William Stallings – will be dealt with according to university rules and • Computer System Architecture, M. Morris Mano regulations • Logic and Computer Design Fundamentals, M. • http://www.yok.gov.tr/content/view/475/ Morris Mano, Charles Kime • Presenting any work that does not belong to you is also • … considered academic dishonesty. 5 6 Copyright 2000 N. AYDIN. All rights reserved. 1 Week’s Agenda Objectives • What is computer architecture? • Know the difference between computer organization and computer architecture. • Why study computer architecture? • Understand units of measure common to • HW/SW abstractions computer systems. • Manufacturing of a chip • Appreciate the evolution of computers. • Course Info • Understand the computer as a layered system. • … • Be able to explain the von Neumann architecture and the function of basic computer components. 7 8 Why study Computer Architecture? What is Computer Architecture? • Design better programs, including system software such as • Fred Brooks (IBM) – compilers, operating systems, and device drivers. – “Computer architecture, like other architecture, is the • Optimize program behaviour. art of determining the needs of the user of a structure • Parallelism and then designing to meet those needs as effectively – Primary source of performance is now parallelism as opposed to the speed of transistors, clock frequency, instruction level as possible within economic and technological parallelism or pipelining constraints.” • Programmer has to be aware of the parallel architecture • Source: Wikipedia • Evaluate (benchmark) computer system performance. – Employers are looking for people who know ‘how’ things work • Understand time, space, and price trade-offs. • Required Class 9 10 Computer Organization vs Computer Architecture Computer Organization vs Computer Architecture • There is no clear distinction between matters • Computer organization related to computer organization and matters – Encompasses all physical aspects of computer systems. relevant to computer architecture. • Control signals, interfaces, memory technology. – e.g. Is there a hardware multiply unit or is it done by repeated addition? • Principle of Equivalence of Hardware and – How does a computer work? Software: • Computer architecture – Anything that can be done with software can also be – Logical aspects of system implementation as seen by the done with hardware, and anything that can be done programmer. with hardware can also be done with software, • Instruction set, number of bits used for data representation, I/O • assuming speed is not a concern. mechanisms, addressing techniques. – e.g. Is there a multiply instruction? – How do I design a computer? 11 12 Copyright 2000 N. AYDIN. All rights reserved. 2 Computer Organization vs Computer Architecture Computer Components - Structure & Function • All Intel x86 family share the same basic • Structure is the way in which components relate to architecture each other – Processor • The IBM System/370 family share the same basic – Memory architecture – IO – System Interconnection • This gives code compatibility • Function is the operation of individual components as part of the structure – at least backwards – Data processing – Data movement • Organization differs between different versions – Data storage – Control 13 14 An example system An example system • Consider this advertisement: • Measures of capacity and speed: Decimal Binary Kilo (K) = 1 thousand = 103 210 Mega (M) = 1 million = 106 220 Giga (G) = 1 billion = 109 230 Tera (T) = 1 trillion = 1012 240 Peta (P) = 1 quadrillion = 1015 250 • Whether a metric refers to a power of ten or a power of two typically depends upon what is • What does it all mean?? being measured. 15 16 An example system An example system • Measures of time and space: • Hertz = clock cycles per second (frequency) Milli (m) = 1 thousandth = 10 -3 – 1MHz = 1,000,000 Hz Micro () = 1 millionth = 10 -6 – Processor speeds are measured in MHz or GHz. Nano (n) = 1 billionth = 10 -9 • Byte = a unit of storage Pico (p) = 1 trillionth = 10 -12 – 1KB = 210 = 1024 Bytes Femto(f) = 1 quadrillionth = 10 -15 – 1MB = 220 = 1,048,576 Bytes • Millisecond = 1 thousandth of a second – Main memory (RAM) is measured in MB – Hard disk drive access times are often 10 to 20 milliseconds. • Nanosecond = 1 billionth of a second – Disk storage is measured in GB for small systems, – Main memory access times are often 50 to 70 nanoseconds. TB for large systems. • Micron (micrometer) = 1 millionth of a meter – Circuits on computer chips are measured in microns. 17 18 Copyright 2000 N. AYDIN. All rights reserved. 3 An example system An example system • We note that cycle time is the reciprocal of clock frequency: The microprocessor is the “brain” of the system. It executes program T = 1/f instructions. This one is a Pentium III • A bus operating at 133 MHz has a cycle time (Intel) running at 667MHz. of 7.52 nanoseconds: T = 1/f = 1/(133×106) = 0.00751879×10-6 T = 7.51879×10-9 second/cycle A system bus moves data within the T = 7.52 nanosecond/cycle computer. The faster the bus the better. This one runs at 133MHz. Now back to the advertisement ... 19 20 An example system An example system • Computers with large main memory capacity can run larger programs with greater speed This system has 64MB of (fast) synchronous dynamic RAM than computers having small memories. (SDRAM) . • RAM is an acronym for random access memory. – Random access means that memory contents can be accessed directly if you know its location. … and two levels of cache memory, the level 1 (L1) cache is smaller and (probably) faster than the L2 cache. • Cache is a type of temporary memory that can Note that these cache sizes are measured in KB. be accessed faster than RAM. 21 22 An example system An example system Hard disk capacity determines the amount of data and size of EIDE stands for enhanced integrated drive electronics, which describes how the hard disk interfaces with (or programs you can store. connects to) other system components. This one can store 30GB. 7200 RPM is the rotational speed of the disk. Generally, the faster a disk rotates, A CD-ROM can store about 650MB of data, making the faster it can deliver data to RAM. (There are many it an ideal medium for distribution of commercial other factors involved.) software packages. 48x describes its speed. 23 24 Copyright 2000 N. AYDIN. All rights reserved. 4 An example system An example system Ports allow movement of System buses can be augmented by • Serial ports send data as a series of pulses data between a system and its dedicated I/O buses. PCI, peripheral along one or two data lines. external devices. component interface, is one such bus. • Parallel ports send data as a single pulse along This system has at least eight data lines. four ports. • USB (universal serial bus) is an intelligent serial interface that is self-configuring. This system has two PCI – It supports “plug and play.” devices: a sound card, and a modem for connecting to the Internet. 25 26 An example system An example system The number of times per second that the image on • Throughout the remainder of this course you the monitor is repainted is its refresh rate. The dot will see how these components work and how pitch of a monitor tells us how clear the image is. they interact with software to make complete This monitor has a dot pitch of computer systems. 0.28mm and a refresh rate of 85Hz. • The above statement raises two important questions: – What assurance do we have that computer components will operate as we expect? The graphics card contains memory and – And what assurance do we have that computer programs that support the monitor. components will operate together? 27 28 Standards Organizations Standards Organizations • There are many organizations that set computer • The Institute of Electrical and Electronic hardware standards Engineers (IEEE) – to include the interoperability of computer – Promotes the interests of the worldwide electrical components. engineering community. • Throughout this course, and in your career, you – Establishes standards for will encounter many of them. • computer components, • data representation, • Some of the most important standards-setting • signaling protocols, groups are . •
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