Unix/Linux Operating System. Introduction to Computational Statistics STAT 598G, Fall 2011

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1 Unix/Linux Operating System Introduction to Computational Statistics STAT 598G, Fall 2011 Sergey Kirshner Department of Statistics, Purdue University September 7, 2011 Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 1 / 13

2 What is Unix/Linux? Unix is an operating system (OS). Multi-user, multitasking. Provides a command line interface and lots of tools for file manipulation. What is Linux? Think of it as an open source version of Unix. expert.ics.purdue.edu is running Solaris 5.10 OS (Unix) Why use Unix? Not everything requires GUI (e.g., batch jobs). Needs fewer resources, uses less bandwidth. Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 2 / 13

3 Navigating UNIX Basic command categories information: uname, man, info, apropos, --version directory management: ls, cd, pwd, mkdir, rmdir file management: cp, mv, rm, touch, chmod searching and displaying: grep, cat/more/less, diff, wc, head/tail, cut, paste redirects: >, <, >>, searching for files: find, which, locate archiving: gzip/bzip, tar process management: top, ps, kill, jobs, &, fg/bg, Ctrl + c, Ctrl + z, nice/renice, time remote file/access management: wget, ssh, scp, sftp Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 3 / 13

4 Help and information commands uname: print system information uname -a man: find and display reference manual pages man uname info: read Info documents (nicer version of man) apropos: locate commands by keyword lookup (same as man -k) apropos who command version: tells the version of the given program R --version, gcc --version Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 4 / 13

5 Directory management Under Unix, there are two ways to represent a path to files. Assume current location is in /usr. absolute path: usr/include relative path: include Commands: ls: list directory contents ls -la cd: change working directory pwd: print name of current/working directory mkdir: make directories rmdir: remove directories Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 5 / 13

6 File management cp: copy files and directories mv: move (rename) files rm: remove files or directories no undo touch: change file timestamp if no file exists, create an empty file chmod: change file mod bits Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 6 / 13

7 Searching in files and displaying grep: print lines matching a pattern cat/more/less: display contents of a file diff: compare files line by line head/tail: output the first/last part of files wc: print newline, word, and byte counts for each file cut: remove sections from each line of files paste: merge lines of files Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 7 / 13

8 Input/output redirects >: redirect the standard output <: redirect the standard input >>: redirect the standard output and append : create an interprocess channel ls -la more Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 8 / 13

9 Search for files, archiving files find: search for files in a directory hierarchy which: locate a command; display its pathname of alias which R locate: list files in databases that match a pattern gzip (also bzip if installed): compress or expand files tar: create tape archives and add or extract files Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 9 / 13

10 Process management top: display and update information about the top cpu processes ps: report process status kill: send signals to processes, or list signals kill -9 <number> jobs: list current jobs command &: run command on the background (return prompt) fg/bg: bring the job to the foreground/execute the job in the background Ctrl + z: suspend the currently running process Ctrl + c: kill currently running process nice/renice: run a program with modified scheduling priority time: time the execution of a script Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 10 / 13

11 Remote file/access management wget: the non-interactive network downloader ssh: secure shell (remote login) scp: secure copy (remote file copy program) sftp: secure file transfer program Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 11 / 13

12 Mini lab Create a directory for the course in your account on expert.ics.purdue.edu: e.g., mkdir stat598g. Go to that directory: cd stat598g. Download courses/fall2011/598g/cvsi.tar.gz file: wget fall2011/598g/cvsi.tar.gz. Extract the files from the archive: tar -xvzf cvsi.tar.gz. Go to the directory cvsi: cd cvsi. Look at the R program what does it do? Compile C program: gcc sum example.c -o sum example Time the execution of both C and R programs time Rscript sum example.r time./sum example Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 12 / 13

13 Interpreter vs Compiler Why is R so much slower than C? R is an interpreted language. Program is interpreted (converted into binary on the fly) as it runs. Conversion is performed on every execution. Slow!, but... good for interactive development. C is a compiled language. Program is converted into binary (compiled). Every execution runs binary code. Fast!, but... cumbersome to modify complex code. Sergey Kirshner (Purdue University) STAT 598G (Fall 2011): Unix/Linux 13 / 13

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