Hello.

I am a geek.

I use SAS & Linux all day.

I build software for it.

I rarely teach.

 

We are here

 

 

ssid

[removed]

password

[removed]

 

The Plan

Day 1

Course (mostly)

standard linux 101

 

Day 2

Workshop (mostly)

objective driven

Checklist:

 

Most places teach this as a 3 to 5 day course, without the SAS bit. 

 

So it's cut down quite a lot to the relevant bits.

 

For now anyway.

 

Focused on trying & doing. Interrupt me if I gloss over something that I obviously shouldn't. 

Disclaimer:

 

Come Up With Your Own
Success Criteria

Getting Started

 

Connectivity

The Terminal

The Shell

The Unix 'Philosophy'

Looking for Help

Connecting to Linux

The Terminal

The Shell

The Nice Things I mentioned

 

The UNIX 'Philosophy'

Seeking and Getting Help

 

Basic Commands & Streams

 

Commands

Syntax

Parameters / Arguments

Input and Output

Pipes and Redirects

 

Run some commands

go on

date

(return the date)

echo

(return the input)

hostname

(returns hostname)

passwd

(changes password)

clear

(clears terminal)

history

(return the shell history)

Commands & Syntax

Add some parameters

date -I

(return the ISO date)

man date

(not like that)

hostname -s

(returns short hostname)

uptime -p

(uptime in 'pretty format')

echo {con,pre}{sent,fer}{s,ed}

(just because bash brace expansion is cool)

Command Input and Output

 

https://en.wikipedia.org/wiki/Standard_streams

Pipes

Again fundamental to Unix Philosophy, all programs do this. 

(even sas -stdio)

 

stdout of one program feeds stdin of the next (chaining).

 

Command Syntax uses the vertical bar:

|

 

Chaining commands using Pipes

who | sort -r

(show who is logged on and then sorts lines)

echo Alright World? | rev

(passes Alright World? as stdin to rev which reverses it)

ps aux | grep sas

(lists all running processes and then filters on sas)

Stream Redirection

https://en.wikipedia.org/wiki/Redirection_(computing)

stdout and stderr streams can also be redirected to a file.

 

This is done with the > operator (greater than).

 

echo Hello! > myfile.txt

The contents of a file can be redirected to the stdin stream of a program.

 

This is done with the < operator (less than).

 

rev < myfile.txt

 

They can be used at the same time:

rev < myfile.txt > reversedFile.txt

Appending to files

 

Redirecting to a file using the > command always creates a new file.

 

To append the output of a command to the end of a file while keeping previous contents, use >>.

 

rev < myfile.txt >> reversedFiles.txt

 

This will also create the output file if it doesn't already exist.

Exercise?

Create a file by redirecting to it.

 

Append some echoed text to it.

 

Use pipes or redirects to read the contents of that file and write it to a second file

 

 

Ready for SAS Studio at this point.

Files and Directories

 

Directory Structure

Relative and Absolute Paths

Navigating the Filesystem

Creating Directories

Permissions

Changing Ownership

Users

Home Directories

 

Directory Structure

 

Same concept as Windows - a hierarchical collection of files and/or other directories, with some differences:

 

• Linux uses forward slash (/) instead of backslash (\) 
• No drive letters, just one root directory, /
• Paths are case sensitive
• Files can be more than just files
  (symbolic links, devices, special kernel 'files')

 

Absolute and Relative Paths

 

 

Again similar to Windows, an absolute path is the full path to a file or directory. For example, /usr/share/doc always points to the shared documentation directory.

 

A relative path refers to a file from the perspective of the current directory. Simple example:

 

cd /usr navigates to /usr using its absolute path

cd share/doc then navigates to /usr/share/doc using relative path   

Special Paths

Your shell has a Current Directory, where you are currently working. pwd returns your current directory to stdout.

Commands like ls also use the current directory as default input. 

The special relative paths . and .. refer to current directory and its parent directory respectively (same as in Windows).

The special path ~ always refers to your home directory. 

Try this:

The cd command, by default, will take you to your home directory. cd and cd ~ will both navigate to your home directory.

Type cd . or cd ./ and you will stay where you are. Type cd .. and you will navigate to /home. Check where you are with pwd.   

Directories & Navigation

Useful arguments / one-liners:

cd - returns to your previous directory

ls -la lists (a)ll files in (l)ong format

mkdir -p creates a full directory path, including all (p)arents

rm -r deletes non-empty directories (r)ecursively

cd

(changes directory)

ls

(lists directory contents)

mkdir

(creates directory)

rmdir

(removes directory)

Overview of 'Standard' Linux Directory Structure

https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard

a nice wallpaper

'Filesystem Hierarchy Standard' is a real standard that's been around for ages. maintained by the Linux Foundation.

Mini Exercise

Look around, navigate to and list some of the directories we talked about.

 

Make some directories in your home directory. Make some recursively.

 

Use tree to visualise them.

 

Then clean them up. You don't need them.

Filesystem Permissions

ls -l returns a listing of files in this format:
 

drwxrwxr-x.  2 nik  nik       4096 Mar  5 13:28 adirectory
-rw-rw-r--.  1 nik  nik        187 Aug 29  2015 someotherfile.txt
-rwxrw-r--.  1 nik  sas     213835 Jul 13  2015 athirdfile.txt

https://en.wikipedia.org/wiki/File_system_permissions#Notation_of_traditional_Unix_permissions

https://en.wikipedia.org/wiki/Umask​

good stackoverflow explanation of ls

File and Directory Permissions

Read
Permission to read the data stored in the file

Write
Permission to write new data to the file, to truncate the file, or to overwrite existing data

 

Execute

Permission to attempt to execute the contents of the file as a program

Read
Permission to get a listing of the directory

Write
Permission to create, delete, or rename files (or subdirectories) within the directory

 

Execute

Permission to change to the directory, or use the directory as an intermediate part of a path to a file

Changing Ownership and Permissions

chmod

(changes permissions of a file or dir)

chown

(changes the owner of a file or dir)

chgrp

(changes the group owner of a file or dir)

Permissions Notation

rwx is 4+2+1=7
rw- is 4+2+0=6
r-- is 4+0+0=4
r-x is 4+0+1=5
(etc)

Notation can also be Numeric.

https://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation

chmod

chmod

chown

chgrp

Users

(briefly, just because we haven't really covered it)

Home Directories

exercise - make some public files

that everyone can read but only you can edit

make a directory where people can add their own files but can't delete those of others

try to delete someone else's files in your directory

Do some stuff

Working with Files

 

What are files

Common file operations

Opening / Inspecting

Searching within files

Executables and Executing

 

Filesystem Objects

(bit of a recap)

a file is place to store data - a (possibly empty) sequence of bytes

a directory is a collection of files or other directories

together they're organised into the filesystem

each file or directory can be referenced with an absolute path (starting with /) or with a relative path (from some current directory)

Extensions

Similar to Windows - it is common to put a filename extension, beginning with a dot (.) on the end of the filename. 

However here they are informational and a user convention, treated no differently by the OS. A few programs use them. 

Filename completion

Remember - tap Tab twice to get filename completion.

Using Wildcards

Use wildcards to refer to multiple files when specifying them

use * to match any part of a filename

ls *.txt

returns
myfile1.txt  myfile12.txt myfile3.txt

use ? to match a single character in a filename

ls myfile?.txt

returns
myfile1.txt  myfile3.txt

Wildcards are handled by the shell and the actual filenames are passed to the program without it knowing.

File Operations

cp

(copies files)

mv

(moves, or 'renames' files)

rm

(deletes files)

grep

(searches the contents of a file
or list of files)

file

(identifies files types)

rmdir

(deletes directories)

cp

cp [options] sourcefile destinationfile

(copies source file to destination file)

cp [options] file1 file2 file3 destinationdir/

(copies source files 1 to 3 to to destination directory)

Common Options:

-f forces overwriting of destination files without prompting

-i interactively prompts before overwriting each file

-r or -R copies directories and contents recursively

 

mv

renames files or directories, or moves them to a different location  

mv mycode.sas myoldcode.sas

(example of a 'rename' like operation)

Common Options:

-f forces overwriting of destination files without prompting

-i interactively prompts before overwriting target

mv *.sas ~/myPrograms/

(example of how to move multiple files using a wildcard to a directory in your home dir using relative home path)

rm

Deletes, or removes the specified files. There is no undo or recycle bin here. You must have write permission on the directory to remove file

rm -rf ~/hateThisDirectorySoMuch

Permanently removes that directory you really don't like any more. And everything in it. Without asking.

Common Options:

-f forces deletion of write-protected files without prompting

-i interactively prompts before deleting each file

-r recursively deletes files and directories

rm -i myProgram_v*.sas

prompts you for each file where not all matching files are to be deleted

grep

searching contents of a file for a string

https://en.wikipedia.org/wiki/Grep

https://en.wikipedia.org/wiki/Regular_expression​

-i case insensitive

-r recursive

-l prints just names 

-n numbers the output

-v reverses test (not matching)

grep drjim /etc/passwd

grep 'ˆdrjim' /etc/passwd

pattern matching beginning

'drjim$' pattern match end

 

Regular expressions

file

simple utility, tries to guess the file type

try it with SAS Foundation executable

file /pub/sas/SASFoundation/9.4/sas

[drjim@apps ~]$ file dirs
dirs: empty
[drjim@apps ~]$ file things
things: ASCII text
[drjim@apps ~]$

more or less it

 

Exercises

 

Do some actual relevant stuff with SAS now. 

 

Access to playpen?

Editing, Executing and Variables

 

How to run an executable

Editing files and scripts (executables)

Command Substitution

Environment Variables

Recursion and Shell Programming

Editing files

Running an executable

Environment Variables

similar to windows

 

Command Substitution

Recursion & Conditionals

The idea of bash programming

if [ -f /etc/bashrc ];
  then . /etc/bashrc
fi

Testing for file existence

for file in *.txt; do
  mv -v $file $file.old; 
done

Looping

nixCraft link to looping

https://en.wikipedia.org/wiki/Shebang_(Unix)

Processes

 

What is a process

Listing processes

Forking, Foreground, Background, Pausing

Signalling (killing)(!)

What is a Process

What is a Process

Process Operations

ps

(all processes currently running)

htop

(top but way better)

top

(full screen, updates constantly)

pstree

(return the process tree)

esm

(the one and only)

pidof

(gets pid(s) of a given executable)

Process Management

(signalling)

Common Signals

 

Signalling a process

 

Background, Foreground, Pause

Scheduling a process to run later

 

 

at command

 

no access to cron probably

 

You'll probably use LSF.