Linux

Misc Links

These topics have their own pages.

Getting Started

Gnuplot

Common C, C++, FORTRAN Libraries

The Command Line

Useful Commands

The following is a (short) list of useful command when manipulating data in text files. Some common options are listed, but may not be explained. For full descriptions of each command, see the man page. stdin, stdout, and stderr refer to standard input, output and error, respectively. ====File Management: Creating, Viewing, Moving, Deleting, Etc.

ls [dir]

list the contents of a directory to stdout

if no directory is given, the contents of the current directory are listed

common options: -l, -a

cd [dir]

change current working directory to a directory. i.e. go into a directory

used to navigate the filesystem

mkdir dir

make directory named 'dir'

rm file1 [file2 [...] ]

remove one or more files

if trying to remove a directory, the -r option must be given

mv source [source2 [...] ] dest

move a file or files. if multiple files are given, then the last argument must be a directory.

examples

cat [file1 [ file2 [...] ] ]

print text file(s) to stdout. if multiple files are given, their text is concatenated

useful for starting a pipeline of commands from the contents of a text file

Processing Text Files

grep "pattern" [ file1 [ file2 [...] ] ]

find text matching 'pattern' in files, or from stdin, and print matching lines to stdout

useful for finding a file containing a specific configuration options

useful for filtering output of a program to only those lines that are interesting

echo [args...]

print arguments to stdout

useful for starting a pipeline of commands from a variable's value

useful for printing output to the terminal from inside a script

sort

read from stdin, sort lines, and write to stdout

common options: -k, -t, -n, -g

cut

read from stdin and write selected columns to stdout.

common options: -d, -f

column

read from stdin and write to stdout such that columns are aligned

common options: -t

head [file]

read from stdin, or from a file, and print the first 10 lines

useful for taking a peak at the contents of a large file

useful for limitng the output of a pipeline

common options: -n

tail [file]

read from stdin, or from a file, and print the last 10 lines

similar uses to head

can be used with head to print a single line, or range of lines, in a file

common options: -n

sed 's/old/new/g' [file]

read from stdin, or from a file, and replace all instances of 'old' with 'new', then print to stdout

Pipes

Pipes allow you to use multiple commands together. Any command that reads input from stdin and writes to stdout can be used in a pipe.

Shell Scripts

Shell scripts are just text files that contain a list of commands for the shell to run. Anything you can run at the command line can be ran in a shell script. To create a shell script, you must do two things.

1. create a text file with the comment #! /bin/bash on the first line.
2. make the text file "executable" with the chmod command.

Here is an example of a simple "hello world" script.

#! /bin/bash

echo "hello world"

If you save this in a file named 'hello.sh', then to run it you must first make it executable.

user@host:~$ chmod +x hello.sh
user@host:~$ ./hello.sh

You may find some more information on the scripting page.