Introduction to the Linux Command Line for High-Performance Computing

Introduction to theLinux Command Line for

High-Performance Computing

Dr. Charles J AntonelliLSAIT ARSJune, 2014

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RoadmapLinux overviewThe command shellNavigating the filesystemBasic commands & wildcardingShell redirection & pipeliningEditing text filesPermissionsProcesses

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PollHow many here to learn the command line

For HPC, specifically Flux, work?For other computing cluster work?For desktops/other Linux/Unix/Mac OS X?Other?

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Course TextWilliam E Shotts, Jr.,“The Linux Command Line: A Complete Introduction,”No Starch Press, January 2012.

Download Creative Commons Licensed version athttp://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf.

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Linux Overview

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A compute node

12 Intel cores

48 GB RAM

Local disk

Network06/14

cja 2014 7 06/14http://linuxforums.org.uk/index.php?action=media;sa=item;in=262

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The command shell

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The command lineA basic way of interacting with a Linux system

Execute commandsCreate files and directoriesEdit file contentAccess the webCopy files to and from other hostsRun HPC jobs

… do things you can’t do from the conventional point-and-click Graphical User Interface (GUI)

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Why command line?1. Linux was designed for the command line2. You can create new Linux commands using the

command line, without programming3. Many systems provide only the command line, or

poorly support a GUI interface• Such as most HPC systems

4. Many things can be accomplished only through the command line• Much systems administration & troubleshooting

5. You want to be cool

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The command shellThe command shell is an application that reads command lines from the keyboard and passes them to the Linux operating system to be executedWhen you login to a remote Linux system using a tool like ssh, you will automatically be connected to a shellOn your desktop, laptop, or tablet, you may have to find and execute a terminal emulator application to bring up a shell in a window

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The command shell

06/14http://www.livefirelabs.com/208_global/images/unix-operating-system.gif

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Types of shellsStandard Linux shell (used in this course)

bash “Bourne-again” shellOther shells

tcsh “Enhanced C shell”, better version of cshcsh “C shell”, common on older Unix systemssh Bourne shell, original AT&T Unix shell

What shell am I using?echo $SHELL

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Connecting via sshTerminal emulators

Linux and Mac OS XStart TerminalUse ssh command

WindowsSSH Secure Shell (deprecated)U-M PuTTY/WinSCP (U-M Blue Disc)https://www.itcs.umich.edu/bluedisc/PuTTYhttp://www.chiark.greenend.org.uk/~sgtatham/putty/

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Lab 0Task: Start a local shell on Mac OS X1. Login to Mac OS X with your uniqname and Kerberos password2. If there is a Terminal icon in the Dock , double-click it

Otherwise:a. Bring up a Finder window:

Click on the desktop, type Command-Nb. Start the Terminal Application:

In the Finder window, click on Applications on the left, scroll down on the right until you find the Utilities folder, double-click on the Utilities folder, scroll down on the right until you find the Terminal application, double-click it

3. This creates a Terminal window with a shell running inside it4. From a Terminal window, Command-N will start a new Terminal

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Lab 0

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The shell promptThe “~$ “ is the shell prompt

This means the shell is waiting for you to type somethingFormat can vary, usually ends with “$” , “%” or “#”

If $ or %, you have a normal shellThis shell has your privileges

If #, you have a so-called “root shell”This shell has administrator privileges You can do a great deal of irreversible damage

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Typing into the shellBasic input line editing commands

Backspace erases previous characterLeft and right arrow move insertion point on the lineControl-U erases the line so you can start overEnter executes the line you typedControl-C interrupts whatever command you started and returns you to the shell prompt (usually)Up and down arrow will access your command historyType “exit” without the quotes to exit the shellClick the red circle at upper left of the Terminal window to close it

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Lab 1Task: Enter some basic commands~$ date~$ id~$ ps~$ df -kh~$ who~$ top

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Interlude: Flux

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FluxFlux is a university-wide shared computational discovery / high-performance computing service. Interdisciplinary

Provided by Advanced Research Computing at U-M (ARC)Operated by CAEN HPCHardware procurement, software licensing, billing support by U-M ITSUsed across campus

Collaborative since 2010Advanced Research Computing at U-M (ARC) College of Engineering’s IT Group (CAEN)Information and Technology ServicesMedical SchoolCollege of Literature, Science, and the ArtsSchool of Information

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http://arc.research.umich.edu/resources-services/flux/

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The Flux clusterLogin nodes Compute nodes

Storage…

Data transfernode

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A Flux node

12 Intel cores

48 GB RAM

Local disk

Network06/14

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Logging in to Fluxssh flux-login.engin.umich.edu

MToken (or Software Token) requiredYou will be randomly connected a Flux login node

Currently flux-login1 or flux-login2Firewalls restrict access to flux-login.To connect successfully, either

Physically connect your ssh client platform to the U-M campus wired or MWireless network, orUse VPN software on your client platform, orUse ssh to login to an ITS login node (login.itd.umich.edu), and ssh to flux-login from there

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A shell on a login nodeNow you have a shell on the login nodeYour shell prompt has changed to something like[flux-login1 ~]$ Try those simple commands here!Flux is for HPC work

The login nodes are reserved for copying data, editing and compiling programs and scripts, and short test runsFor HPC computation, you should run on the compute nodes

A batch job will always run on the compute nodesAn interactive batch job will get you a shell on a compute node

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A shell on a compute node

Getting a shell on a compute nodeEnter this command on the login node:[flux-login1 ~]$ ~cja/hpc100/getshellAfter a short delay, you’ll get an interactive shell:qsub: waiting for job 11147004.nyx.engin.umich.edu to startqsub: job 11147004.nyx.engin.umich.edu ready[nyx5509 ~]$ You can type commands into this shell for all of our in-class experimentsType “exit” to exit this shellAfter two hours, your interactive shell will be killed

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Navigating the filesystem

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Linux Filesystem Concepts

Files are stored in a directoryDirectories may contain other directories as well as files

A hierarchy of these directories is called a directory treeA directory tree (a connected graph with no cycles) has a single topmost root directory

A directory tree rooted at the system root directory “/” is called a filesystem

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cja 2014 29 06/14http://redhatlinux4u.blogspot.com/2011/11/file-hierarchy-system.html

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Linux Filesystem ConceptsA file is accessed using its path name

Absolute path name/dir1/dir2/…/dirn/filename/usr/X11R6/bin

Relative path namecurrent-working-directory/filenamebin

Every shell maintains a notion of a current working directoryInitialized at login to your home directoryChanged via cd command

Two special directories. refers to the current directory.. refers to the current directory’s parent directory

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Basic commands

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PrerequisitesSome fundamental commands:~$ file file # what kind of file is file?

~$ cat file # display contents of text file

~$ less file # paginate text file

~$ man command # get info about command

Exercise: figure out how to make the date command display the date in Coordinated Universal Time (UTC)

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Lab 2Task: navigate the file systemCommands:~$ cd # make your home directory the current working directory

~$ pwd # print working directory

~$ mkdir foo # create directory foo

~$ cd foo # cd to the foo directory

~$ mkdir bar # create directory bar

~$ cd .. # cd back to the foo directory

~$ tree # display foo’s directory tree

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Navigating the filesystem

Some fundamental commands:~$ pwd # print working directory

~$ cd dir # make dir the current working directory

~$ cd # cd to your home dir

~$ cd ~cja # cd to cja’s home dir

~$ mkdir dir # create directory dir

~$ rmdir dir # remove (empty) directory dir

~$ tree # display dir tree

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Listing info on filesls – list information about files~$ ls # list contents of cur dir

~$ ls dir # list contents of dir

~$ ls –l # list details of files in cur dir

~$ ls –t # list newest files first

~$ ls –R dir # list all files in tree dir

~$ ls –lt dir # options can be combined

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Working with filesThese commands manipulate files~$ mv foo bar # rename file foo to bar

~$ cp foo bar # copy file foo to bar

~$ cp –r dir1 dir2 # copy dir tree dir1 to dir2

~$ cp f1 f2 dir # copy f1 and f2 to directory dir

~$ mkdir dir # create empty directory dir

~$ rmdir dir # remove empty directory dir

~$ rm file # remove file file

~$ rm –r dir # remove directory tree dir

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Lab 3Exercise:Create a directory named tutorial in your home directory. In that directory, create a directory named sample and a directory named test . Create a file named msg in directory test that contains a copy of the file /etc/motd .

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Compressing and archiving

These commands compress and archive files~$ gzip foo # compress foo to foo.gz

~$ gunzip foo # uncompress foo.gz to foo

~$ tar cf foo.tar bar# archive subtree bar in file foo.tar

~$ tar xf foo.tar # restore archive from file foo.tar

~$ tar zcf foo.tgz bar # archive and compress

~$ tar jcf foo.tjz bar # archive and compress better

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WildcardsAll Linux commands take wildcarded argumentsWildcards:

? Matches a single character* Matches zero or more characters[chars] Matches any of the chars[c1-c2] Matches chars ‘c1’ through ‘c2’[^chars] Matches any but the chars

~$ ls foo.? # match files named foo.x, where x is any character

~$ echo *.[cs] # echo files that end in .c or .s

~$ mv [o-z]* save # move files starting with o through z to directory save

~$ echo [^A-Z]? # ???

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Shell redirection & pipelining

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Shell redirectionA Linux command can have its inputs and outputs redirected~$ ls >foo # put list of files in current

directory into file foo

~$ ls >>bar # add list of files in current directory to end of file foo

~$ sort <bar # sort lines from file bar

~$ sort <<EOF # sort lines entered at keyboardwhiskeybravotangoEOF

~$ wc -l </etc/motd >~/mycounts# count number of lines from file /etc/motd and put result in file mycounts in my home directory

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More Linux commands

More useful Linux tool commands~$ grep string # show lines of input containing

string

~$ tail # show last few lines of input

~$ head # show first few lines of input

~$ sort # sort the input

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Shell pipeliningA Linux command can have its output connected to the input of another Linux command~$ ls | wc –l # count files in current

directory

~$ last | grep reboot # when did we reboot?

Exercise:How many people are running MATLAB on your compute node?

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Editing text files

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Editing text files

Simple editornano or pico

"What you see is what you get” editorSimple to learn if you want to get started quickly

Supported editorsvi or vimemacs

Powerful but more complexIf you have time and inclination to become proficient, spend time here

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Text filesWatch out for source code or data files written on Windows systems

Use these tools to analyze and convert source files to Linux formatfiledos2unix

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Permissions

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File PermissionsThree permission bits, aka mode bits

Files: Read, Write, ExecuteDirectories: List, Modify, Search

Three user classesUser (File Owner), File Group, Other

man chmod

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File Permissions, examples

-rwxr-xr-x cja lsaitfile read, write, and execute rights for the owner, read and execute for others

-rwxr-x--x cja lsaitsame permissions as above, except only the owner can read the file, while all can executechmod u=rwx,g=rx,o=x file

drwxr-x--x cja lsaitlist, modify, and search for the owner, list and search for group, and execute only for others

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Processes

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Processes

On Linux, every program runs in a process

You can examine these processes

man pspsps axtop

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Processes

You can signal a running processTo stop it, or "kill" it

man kill

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Any Questions?Charles J. AntonelliLSAIT Advocacy and Research [email protected]://www.umich.edu/~cja734 763 0607Please evaluate our course:

http://umichlsa.qualtrics.com/SE/?SID=SV_3pzjrMdjGXtUDAh

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References1. http://en.wikipedia.org/wiki/History_of_Linux2. http://redhatlinux4u.blogspot.com/2011/11/file-hierarchy-system.html3. William E Shotts, Jr., “The Linux Command Line: A Complete Introduction,” No

Starch Press, January 2012. Download Creative Commons Licensed version athttp://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf.

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ExtraTask: compile and execute simple programs on the Flux compute node

Copy sample code to your login directory:cdcp ~brockp/cac-intro-code.tar.gz .tar -xvzf cac-intro-code.tar.gzcd ./cac-intro-code

Examine, compile & execute helloworld.f90:ifort -O3 -ipo -no-prec-div -xHost -o f90hello helloworld.f90./f90hello

Examine, compile & execute helloworld.c:icc -O3 -ipo -no-prec-div -xHost -o chello helloworld.c./chello

Examine, compile & execute MPI parallel code:mpicc -O3 -ipo -no-prec-div -xHost -o c_ex01 c_ex01.cmpirun -np 2 ./c_ex01

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