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Linux OverView
NCBI
Chuong Huynh
NIH/NLM/NCBI
New Delhi, India
Sept 28, 2004
[email protected]
What is UNIX?
•A family of operating systems
•Multitasking
IRIX
•Multiuser
Runs more than one program at
SOLARIS
the same time.
•Networked
Many different people can use
BSD
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thebusy
A
system
system
at the
cansame
be running
time.
LINUX
It
is designed
to be
several
hundred
or linked
even to
other
computers
and to at
allow
thousands
of programs
the
Digital
UNIX
people
to work over a network.
same time.
HP-UX
The network IS the computer.
...
Linux History
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• Linux was written by Linus Torvalds while he
was a grad student at the University of
Helsinki.
• He received a new 386, and he found the
existing DOS and UNIX too expensive and
inadequate.
• In those days, a UNIX-like
tiny, free OS called Minix was
extensively used for academic
purposes. Since its source code
was available, Linus decided to
take Minix as a model.
Unix/Linux Basic Architecture
SHELL
Utility
Kernel
Hardware
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• Unix is a
layered
operating
system
• Unix is a
multi-user,
multi-tasking
operating
system
Linux kernel
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• Linux is the kernel or core of a free
computer operating system that runs on
many different Central Processing Units
(CPUs).
• It is constantly being updated and
improved; and new versions can appear
daily, several times a day, or every other
day. .
Linux Distribution
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• Linux, combined with thousands of other free
software packages—especially those from the
Free Software Foundation and The XFree86
Project, Inc.—becomes a Linux distribution.
• There are hundreds of different Linux
distributions (distrowatch.com), but the most
popular are Red Hat (Fedora); SuSE from
SuSE, Inc.; Debian (named after Ian Murdock
and his girlfriend, Deb) from The Debian
Project; Slackware from the Slackware Linux
Project; and Mandrake from MandrakeSoft.
Linux and Open Source
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• Linux and most of its accompanying software is
free and distributed with source code.
• The source code is distributed under a unique
"copyleft" license named the GNU General
Public License (GPL), which ensures that the
software will forever be free and available in
source form.
• There are many different software licenses
used for software included with a Linux
distribution
• And some Linux distributions include
proprietary software as value-added purchase
incentives.
Linux Support
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• If you want support for Linux, you can pay for such
support, hire a consultant, or learn more about Linux on
your own.
• There is plenty of information about Linux available on
the Internet.
• You can purchase various support options from vendors
such as Red Hat, Inc.
• One of the best and cheapest ways to get help is to
join a Linux Users Group, or LUG.
• Or search the search engines, especially in the
newsgroup, someone is bound to have already asked the
same question.
• Every experienced Linux user starts out as a beginner,
but with the help of newly found friends and practice,
a new Linux user (known as a newbie) can learn a lot
faster.
Installing Linux?
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• Linux may be installed from optical media; by floppy
disk; via a local network or over the Internet using
FTP, HTTP, or NFS; from a hard drive partition; via a
parallel-port cable or null-modem cable and serial
interface; from a USB Zip drive; or by other methods.
• You don't even have to install Linux in order to run
Linux because it does not require a hard drive in order
to run, and you can run Linux on your PC without
installing by using a "live filesystem" CD-ROM, such as
one in distribution from KNOPPIX or SuSE's
evaluation CD.
• You can download, burn, and boot from such a CD
directly to a Linux session with a graphical desktop.
Linux and Internet Connection
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• Linux can be used to connect with many different
Internet Service Providers (ISPs).
• Most Linux dial-up (modem) users connect to an ISP
by using the Point-to-Point Protocol (PPP), which is
readily supported. Linux cable modem users can usually
connect by using the Dynamic Host Control Protocol
(DHCP). Digital Subscriber Line (DSL) users connect
by using PPP-over-Ethernet (PPPoE) because Linux
supports PPP, DHCP, and PPPoE.
• Millions of Linux user to connect to the Internet
every day, and browse the Web, download and upload
files, and send and receive electronic mail—along with
many other types of common Internet-related
activities.
Linux at the Enterprise Level
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• Linux is used by enterprise-level
companies, such as those in the Fortune
500, many governments on various levels,
academia, small businesses, Small Office
Home Office (SOHO) users, and millions
of users around the world.
• Linux is destined to host more than half
of the server computers connected to
the Internet, but gauging exactly how
many Linux users exist can be hard
because Linux is free.
Where do I find more
information about Linux?
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http://www.linux.org
A definitive Linux portal for all kinds of information
http://www.tldp.org
The Linux documentation project
http://www.unix-vs-nt.org/kirch/ An impartial comparison of UNIX / NT
http://www.tir.com/~sorceror/mdlug/mdlug.zip A HTML slideshow onLinux
http://www.oreilly.com/catalog/opensources/book/toc.html
Open-source essays
http://www.cuug.ab.ca/~leblancj/nt_to_unix.html
It’s good to migrate to Linux
http://www.linuxmall.com/resources/nlm Newbies Linux manual
http://www.cs.helsinki.fi/~torvalds/
Linus Torvalds’ home page
http://www.ssc.com/lj/index.html Linux Journal is a nice Linux periodical
http://www.gnu.org/
Official GNU web-site
news://comp.os.linux
The Linux USENET newsgroup
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Networked with other computers
Multiple asynchronous task
Unique profile for each user’s environment
Protecting info stored from another user on the same
system
WWW uses Unix prevalently; most web servers run
under Unix.
Unix used extensively in universities where software
was originally developed for bioinformatics began
Until the mid 1990’s the only workstation capable for
bioinformatics of visualizing protein structure data in
real time were SGI and Sun Unix Workstation
Command line richness with a graphical user interface
– provides options and possibilities
Many pre-built software prepackaged with various
Linux distribution from word processing to web
servers.
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•
Why use Unix for bioinformatics?
Then why use Linux?
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• Free Unix clone for personal computers
with full multitasking, X Window system,
TCP/IP networking, etc.
• Cost effective
• Runs all of the bioinformatics programs
effectively
• Samba software suite – Linux acts as a
Windows file/print server
• Linux is a free Unix clone
Fedora Core 2 Linux
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Why use Cygwin?
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• Provides a Unix like environment on top
of Microsoft Windows operating
system. Cygwin is not an operating
system, but an Application Programming
Interface on top of an existing
operating system.
• Ease the transition of learning
Unix/Linux for those familiar with
Microsoft Windows
Cygwin CD Installation Exercise
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• Install cygwin CD on your MS Windows
machine
• Ask the instructor or the Teaching
Assistant to login as an administrator to
allow you to have administrative privilege
to install cygwin
• All the documentation required is in the
index.html in the cygwin CD
• There are many packages which one?
• KDE for cygwin?
Why Use Live Linux CD distro?
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• Non-destructive method to demo Linux for any
Intel/AMD based PC
• Linux operating systems residing on the CD
• Boots and autoconfigures itself without user
interaction
• The CD is the primary boot device and needs a
lot of RAM. Anything save in memory is
temporary. Generally more memory = better.
• Save to hard drive
• Autoconfiguration process identifies hardware
and selects the best configuration for the
hardware it finds.
What is Knoppix?
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• Knoppix is an example of a Live Linux CD
distribution
• Knoppix is created by Klaus Knopper
• Excellent hardware detection and
autoconfiguration abilities
• The packages and OS structure are
based on the Debian distribution, but the
hardware-discovery process uses kudzu,
Redhat's hardware probing utility
Knoppix Hardware Requirements?
NCBI
• Knoppix has fairly standard hardware
requirements.
• It needs an Intel-compatible CPU (i486 or
later) and 20MB of RAM for text mode, with at
least 96MB for graphics mode with KDE.
• 128MB of RAM is recommended when using
applications as resource-hungry as
OpenOffice.org.
• It requires a bootable CD-ROM drive, or a boot
floppy and standard drive CD-ROM
(IDE/ATAPI or SCSI).
• Finally, it also requires a standard SVGAcompatible graphics card and a serial, PS/2
standard, or IMPS/2-compatible USB mouse.
How Knoppix Works?
Put Knoppix CD in a bootable CD-ROM
Reboot computer
Wait
Done
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Knoppix Booting
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Knoppix Autoconfiguration
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How Knoppix Works (1)?
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• The boot process resembles a standard CD
distribution, but uses virtual drives in RAM.
• It can boot into either text or graphics mode
(KDE Graphical User Interface desktop
environment), requiring more memory in
graphics mode.
• The OS file system is a single, compressed,
read-only file that uncompresses applications
and utilities as required. This allows 2GB of
binaries to be stored on a 700 MB CD.
• The rest of the CD contains documentation and
the boot kernel.
• Boot time can be anywhere from 30 seconds to
two minutes, depending on your hardware.
How Knoppix Works (2)?
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• The CD's bootloader offers you the opportunity to add
kernel commands. These "cheat codes" control
everything from device discovery to desktops and local
language selection.
• You can view the options yourself by pressing F2 at
boot-up time.
• The default booting process chooses a KDE GUI
desktop environment.
• As the boot process continues, it creates the RAM disk,
which is followed by the "hotplug" autoconfiguration
process.
• Shell scripts automatically put in the correct settings
for the services once the hardware has been identified.
• DHCP support is enabled.
So why use Knoppix
Live Linux CD for the course?
NCBI
• The focus of the course is on data
interpretation. Ideally, you would want
your own bioinformatics workstation with
the operating system installed to the hard
drive (much faster and larger).
• And when you return home, you can easily
demo the same programs you learned here
for review
Vigyaan biochemical software workbench
• One example of a Knoppix based
“bioinformatics” distribution –
Vigyaan CD or BioKnoppix
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Pymol on vigyaancd
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PyMOL is a biomolecular structure visualizer with high-quality image output.
GROMACS
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GROMACS is a collection of programs for molecular modeling of proteins.