Intro to Linux - getting around HPC systems

Himanshu Chhetri QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.

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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.AZUL

azul.hpci.latech.edu (head node) 138.47.102.117

2.ITANIUM

itanium.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 : March 12, 2007 4

Connecting to HPCI Cluster

From Linux/ Mac Os: • Open the terminal and use the command line based ssh client: March 12, 2007 5

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: March 12, 2007 7

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 March 12, 2007 13

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 March 12, 2007 16

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 March 12, 2007 18

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: March 12, 2007 20

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/ March 12, 2007 24

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/ March 12, 2007 25

END

Demo Of HPCI website and account request

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