Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks on Blocks! Dynamically Rearranging Synteny Blocks in Comparative Genomes Nick Egan’s Final Project Presentation for BIO 131 Intro to Computational Biology Taught by Anna Ritz
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ADDRESS MAPPING (MULTIPLE CHANNELS) C Row (14 bits) Bank (3 bits) Column (11 bits) Byte in bus (3 bits) Row (14 bits) C Bank (3 bits) Column (11 bits) Byte in bus (3 bits) Row (14 bits) Bank (3 bits) Column (11 bits) Byte in bus (3 bits) Row (14 bits) Bank (3 bits) C Column (11 bits) C Byte in bus (3 bits) • Where are consecutive cache blocks? C Row (14 bits) High Column Bank (3 bits) C High Column Bank (3 bits) High Column C Bank (3 bits) High Column Bank (3 bits) High Column 8 bits Low Col. Byte in bus (3 bits) C Low Col. Byte in bus (3 bits) 3 bits 8 bits Row (14 bits) Byte in bus (3 bits) 3 bits 8 bits Row (14 bits) Low Col. 3 bits 8 bits Row (14 bits) Byte in bus (3 bits) 3 bits 8 bits Row (14 bits) Low Col. Bank (3 bits) Low Col. C Byte in bus (3 bits) 3 bits 47
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Advantages and Limitations of CFB  appropriate when data arrives in bits/bytes  most common stream mode  note that the block cipher is used in encryption mode at both ends  errors during transmission propagate for several blocks only (till the “dirty” part is eliminated from the shift register).
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Ron’s Code or Rivest Codes Scorecard Description RC2 RC4 RC5 RC6 Timeline 1987 1987 1994 1998 Type of Algorithm Block cipher Stream cipher Block cipher Block cipher Key size (in bits) 40 and 64 1 - 256 0 to 2040 bits (128 suggested) 128, 192, or 256 Variable key-size block cipher that was designed as a "drop-in" replacement for DES. Use Most widely used stream cipher based on a variable key-size Vernam stream cipher. It is often used in file encryption products and secure communications, such as within SSL. The cipher can be expected to run very quickly in software and is considered secure. © 2012 Cisco and/or its affiliates. All rights reserved. A fast block cipher that has a variable block size and key size. It can be used as a dropin replacement for DES if the block size is set to 64-bit. An AES finalist (Rijndael won). A 128-bit to 256- bit block cipher that was designed by Rivest, Sidney, and Yin and is based on RC5. Its main design goal was to meet the requirement of AES. 104
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Preamble “Post-amble” Block Execution: 3 Detail Observing Block Observing Block “Post-amble” “Post-amble” 3 Observing Block Observing Block ok Measurement Set ready “Post-amble” EVLA Data Processing PDR Observing Observing Block Block Observing Observing Block Block Failed! Preamble “Post-amble” Preamble ok ?4 5 Preamble ready Preamble Observing Observing Block Block Observing Observing Block Block Observing Block Observing Block Measurement Set “Post-amble” “Post-amble” Preamble Preamble “Post-amble” Measurement Set “Post-amble” “Post-amble” “Post-amble” July 18 - 19, 2002 2 2 Observing Observing Block Block Block Observing Observing Observing Block Block ok Archive: Preamble Observing Block Observing Block 34 ready Preamble “Post-amble” 1 3 Observing Block Observing Observing Block Block Observing Block Observing Observing Block Block ready Preamble Execution: Preamble ready Observing Observing Block Block Observing Observing Block Block Preamble Observing Block Observing Block 22 “Post-amble” “Post-amble” Preamble Preamble 1 “Post-amble” Preamble Input Queue: ok Measurement Set Boyd Waters 13
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Cipher FeedBack (CFB)    message is treated as a stream of bits or bytes result is feed back for next stage (hence name) standard allows any number of bit (1,8, 64 or 128 etc) to be feed back   denoted CFB-1, CFB-8, CFB-64, CFB-128 etc most efficient to use all bits in block (64 or 128) Ci = Pi XOR EK(Ci-1) C-1 = IV  Used for stream data encryption
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The 16550 UART registers Base+0 Divisor Latch Register Base+0 Transmit Data Register 8-bits (Write-only) Base+0 Received Data Register 8-bits (Read-only) Base+1 Interrupt Enable Register 8-bits (Read/Write) Base+2 Interrupt Identification Register 8-bits (Read-only) Base+2 FIFO Control Register 8-bits (Write-only) Base+3 Line Control Register 8-bits (Read/Write) Base+4 Modem Control Register 8-bits (Read/Write) Base+5 Line Status Register 8-bits (Read-only) Base+6 Modem Status Register 8-bits (Read-only) Base+7 Scratch Pad Register 8-bits (Read/Write) 16-bits (R/W)
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Transparent Scalability  Hardware is free to assign blocks to any SM (processor)  A kernel scales across any number of parallel processors Device Kernel grid Device Block 0 Block 1 Block 2 Block 3 Block 0 Block 1 Block 4 Block 5 Block 6 Block 7 Block 2 Block 3 Block 4 Block 5 Block 6 Block 7 26 time Block 0 Block 1 Block 2 Block 3 Block 4 Block 5 Block 6 Block 7 Each block can execute in any order relative to other blocks.
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Transparent Scalability Hardware is free to assign blocks to any processor at any time  A kernel scales across any number of parallel processors Device Device Kernel grid Block 0 Block 1 Block 2 Block 3 Block 0 Block 2 Block 1 Block 3 Block 4 Block 5 Block 6 Block 7  Block 4 Block 5 Block 6 Block 7 time Block 0 Block 1 Block 2 Block 3 Block 4 Block 5 Block 6 Block 7 Each block can execute in any CUDA Tools and Threads – Slide order relative 69
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Cipher Block Chaining • cipher block: if input block repeated, will produce same cipher text: t=1 … m(17) = “HTTP/1.1” t=17 • cipher block chaining: XOR ith input block, m(i), with previous block of cipher text, c(i-1) – c(0) transmitted to receiver in clear m(1) = “HTTP/1.1” block cipher c(1) block cipher c(17) m(i) c(i-1) + block cipher c(i) = “k329aM02” = “k329aM02”
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