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Intro to Linux - getting around HPC systems

QuickTime™ and aTIFF (Uncompressed) decompressor

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Himanshu Chhetri

March 12, 2007

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Introduction to Linux

In 1990, Linus Trovalds, a Finnish Computer Science student developed Linux.

He created the kernel but most of the supporting utilities was made by the GNU project of the Free Software Foundation.

He was inspired by Minix, a classroom teaching tool which closely resembled the Unix OS.

Linux is the result of the combined effort of many developers worldwide.

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HPCI Clusters

• HPCI maintains two clusters based on Linux distributions:

1.AZULazul.hpci.latech.edu (head node)138.47.102.117

2.ITANIUMitanium.hpci.latech.edu (head node)138.47.102.161

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Connecting to HPCI Cluster

From Windows 9x / 2003 Server / 2000 / XP / Vista:• PuTTY is a free software SSH, Telnet, rlogin, and

raw TCP client :

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Connecting to HPCI Cluster

From Linux/ Mac Os:• Open the terminal and use the command line

based ssh client:

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Accessing user files remotely:

From Windows 9x / 2003 Server / 2000 / XP / Vista:• WinSCP is an open source free SFTP client for

Windows using SSH.

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Accessing user files remotely:

From Linux/ Mac Os:• Open the terminal and use the command line

based scp client:

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Filesystem

• You are automatically placed in your home directory after logging in.

i.e. /home/user_name

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Directories

• Listing files/directories:

$ls

• Creating new directory and changing to it:

$mkdir dir_name

$cd dir_name

• Removing directory and all the files/subdirectories:

$rm -rf dir_name

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Working with permissions

• Display the permissions of current directory content:

$ls -la

• Safely changing permissions to allow read,write and execution of file:

$chmod 700 name_of_file

• Change permissions recursively:

$chmod -R dir_name

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File archiving : tar

• tar can save multiple files in a single file or do the vice versa

• Archiving a directory recursively:

$ tar cvf name_of_archive.tar directory_name/

• Extracting a tar archive contents:

$tar xvf name_of_archive.tar

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File Compression : gzip

• gzip is frequently used together with tar to archive and compress files:

$gzip name_of_archive.tar

name_of_archive.tar.gz is the resultant file

• Uncompressing “.tar.gz” files:

$tar xzvf name_of_archive.tar.gz

• gunzip command uncompresses “.gz” files.

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Text Editors:

The systems have different kinds of text editors for editing source code,configuration files or plain text:

• vim : improved version of vi. Widely used.• nano : enhanced version of pico editor.• emacs : advanced text editor that offers additional

features like sending/receiving emails and lisp interpreter

• ed : It is a simple line-oriented text editor

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Managing processes : ps

• report a snapshot of all the current processes:

$ps -ef| more

• show processes only run by certain user. Eg: show all processes being run by user hch018

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Managing processes : top

• top command displays real time view of running processes and other related information:

• $top -u user_name

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Managing processes : kill

• kill command terminates a process• Process need to terminated in situations like if it

cannot terminate normally. Eg : $kill -9 PID

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User security : password

• passwd command can be used to change the user's password:

• Compromise of a user account can be prevented to a great extent with a strong password.

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User Security : permissions

• chmod can be used to prevent other users from accessing files/directories owned by a rightful user.

• In above example chmod recursively gives appropriate permission only to user : hch018

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User security : file integrity

• md5sum command generates a unique 128 bit checksum for a file. This is useful in verifying file integrity.

• Many open source projects provide md5 checksum for their packages.

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Help/Documentation : man

• man command displays the manual page for a particular command/utility. Eg:

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Network utilities : ping

• ping is a useful utility to check network connectivity.

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Available compilers:

• gcc (GNU C Compiler):

This is used to compile C programs

• g++(GNU C++ Compiler):

This is used to compile C++ programs

• as / ld

These are used to assemble and link assembly programs.

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Available Interpreters / Scripting:

• python

Compiler for the high level programming language.

• perl

Compiler for the dynamic,interpreted high level language.

• gawk

Compiler for awk : designed to process text data.

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Resources :

• Official HPCI website:

http://hpci.latech.edu

• Official HPCI mailing list:

http://hpci.latech.edu/mailman/listinfo/hpc_users

• Alphabetical Directory of Linux Commands

http://www.linuxdevcenter.com/linux/cmd/

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Downloads:

• Putty

http://www.chiark.greenend.org.uk/~sgtatham/putty/

• Winscp

http://winscp.net/eng/download.php

• Linux FAQs, Guides and HOWTOs

http://tldp.org/

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END

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