Physics 2660: Fundamentals of Scientific Computing Lecture 1
Announcements
•  Weekly readings will be assigned and available through the class wiki home page
•  HW01 will be assigned there as well
–  Will be assigned on Thursday this week after labs
–  Due Thursday 4 February
•  Electronic submission: by 12:00 noon EST
•  Last week: Lab00
–  Work through these exercises if you registered late to the class and have not yet completed them
•  This week: Lab01
–  Will be posted on Thursday
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Connecting to galileo
•  The galileo computer cluster is where we will do all of our work this semester
–  Everyone has an account there now
–  Do not lose this information or forget how to connect
•  The best methods for connecting to galileo:
–  Use ‘ssh’ from the terminal application from one of the desktop PCs in the computer lab
–  Use ‘ssh’ and ‘NXClient’ from a computer in an ITC hosted computer lab
–  Use ‘ssh’ and an Xserver app from a personal computer
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GeBing Help
•  My office hours:
–  3:30-­‐‑5pm Tuesdays in Room 022-­‐‑C (our computer lab)
•  TA office hours
–  In Room 022-­‐‑C
•  Mondays 5:00-­‐‑8:00 pm
•  Tuesdays 5:00-­‐‑8:00 pm
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Last Time and This Time
•  Last time:
–  Intro to course objectives and expectations
•  Today:
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–
–
–
–
–
–
–
–
Computer hardware
What is an operating system?
Example: Linux
Command line interface
Shells
Basic linux commands
Intro to the galileo cluster – where we will do all our work!
Computer programs and compilers
The basics of C:
•
•
•
•
example program
variables and definitions, arithmetic
comments inside code
functions
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Computers
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Computer Hardware
CPU
and cache
Memory
fast
(aka RAM)
fast
PCIe Bus
(for graphics card)
Northbridge
fast
(aka front side bus, MCH)
“MCH” = memory controller hub slow
slow
Peripherals
(keyboard, mouse) Hard drive / disk
Southbridge slow
(aka back side bus, ICH)
“ICH” = I/O controller hub
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Computer Hardware
•  Since the advent of the personal computer (PC) in the early 80s, the architecture has not changed much:
–  Central Processing Unit (CPU): does the computer’s actual work
–  Northbridge / Southbridge: middlemen, handling fast and slow input/output and inter-­‐‑component communications
–  Memory: temporary storage of data needed rapidly when running programs
–  Hard drive / disk: permanent, long-­‐‑term storage of data
–  Input devices: enables interaction with users
–  Graphics card: middleman to allow for visual output to be displayed
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Disk, Memory and Cache
•  These are confusing to many computing newcomers
•  Disk: large capacity, slow access
•  Memory: reasonable capacity, fast access
•  Cache: meager capacity, really fast access (internal to CPU)
–  Computers are designed to predict what data from the disk one needs when running a program. This is stored in memory.
–  Similar prediction game is played when puding select important data into the cache.
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How a Program Runs
•  Users write programs in some human-­‐‑readable language
–  Ex: C, C++, java, FORTAN, etc.
•  Problem: CPUs don’t speak any human readable language!
•  Compiler translates into low-­‐‑level instructions for the CPU
•  CPU gets ordered instructions from memory
•  Location in memory stored in a register on CPU
•  CPU executes instructions in number order and moves on
CPUs are all different, depending on manufacturer and specifications èinstructions need to be matched to CPU.
Different compilers are necessary for different computers. Not an issue on galileo.
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CPUs
•  The story behind the CPU is rich and interesting in its own right
•  We will not get deep into it here and now
•  There have been many different CPU architectures over the years
•  Two most prominent modern examples:
–  x86-­‐‑32 (aka i386 or x86): 32-­‐‑bit CPUs made by Intel and AMD (declining utility)
–  x86-­‐‑64: 64-­‐‑bit CPUs made by AMD and Intel
•  Multicore processors
–  Multiple CPUs (cores) in one motherboard
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Operating Systems and Linux
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What is an Operating System?
•  Beyond the hardware, we need some management structure to tie all the pieces together
–  This is the role of the operating system
•  Functions: many handled by the kernel
–
–
–
–
–
middleman for handling I/O
middleman for handling memory allocation
order of execution of processes
parallelization of processes
handling of network information
•  Every standard computer has some sort of operating system
•  Examples: Windows, Mac OS X, Android, iOS, Linux…
hdp://upload.wikimedia.org/wikipedia/commons/e/e1/Operating_system_placement.svg
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What is Linux?
•  Linux is an operating system borne out of the desire to have a freely available computer programming environment
–  In the early days of computing, many saw the need to ensure freely open software – proprietary nature of some software was very off-­‐‑
puding to many developers
–  Many tools existed (see the GNU project) that were “open-­‐‑source” –  Linus Torvalds in 1991 wrote an operating system+kernel and brought together these disparate pieces…and Linux was born
•  Features:
–  can run programs for any purpose (no usage restrictions) –  can edit programs (open source)
–  can redistribute without oversight
•  Rich interesting history starting from Unix, on to GNU and late 60s
70s-­‐‑80s eventually Linux
90s 14
What is Linux?
•  Linux is an operating system borne out of the desire to have a freely available computer programming environment
–  In the early days of computing, many saw the need to ensure freely open software – proprietary nature of some software was very off-­‐‑
puding to many developers
–  Many tools existed (see the GNU project) that were “open-­‐‑source” –  Linus Torvalds in 1991 wrote an operating system+kernel and brought together these disparate pieces…and Linux was born
•  Features:
–  can run programs for any purpose (no usage restrictions) –  can edit programs (open source)
–  can redistribute without oversight
•  Rich interesting history starting from Unix, on to GNU and late 60s
70s-­‐‑80s eventually Linux
90s 15
What is Linux?
•  Linux is an operating system borne out of the desire to have a freely available computer programming environment
–  In the early days of computing, many saw the need to ensure freely open software – proprietary nature of some software was very off-­‐‑
puding to many developers
–  Many tools existed (see the GNU project) that were “open-­‐‑source” –  Linus Torvalds in 1991 wrote an operating system+kernel and brought together these disparate pieces…and Linux was born
•  Features:
–  can run programs for any purpose (no usage restrictions) –  can edit programs (open source)
–  can redistribute without oversight
Why a penguin?
•  Rich interesting history starting from Unix, on to GNU and late 60s
70s-­‐‑80s eventually Linux
90s hdp://www.sjbaker.org/wiki/index.php?title=The_History_of_Tux_the_Linux_Penguin
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The Command Line
•  More emphasis in Linux than in other OS’s in user-­‐‑interactions executed through the command line rather than through graphical user interface (GUI) than eg Windows
prompt
[phys2660@node5 ~]$
[phys2660@node5 ~]$ ls
total 9748
drwxr-xr-x 4 phys2660
drwxr-xr-x 4 phys2660
drwxr-x--- 2 phys2660
drwxr-xr-x 11 phys2660
write
commands
here
a command:
running a
program
-lrt
phys2660
phys2660
phys2660
phys2660
4096
4096
4096
4096
Feb 22
Apr 4
Aug 10
Mar 20
2007
2007
2007
2008
lib
local
Desktop
usr
output
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Command Line Shells
•  Virtues of the command line:
–  Can narrow results with wildcard expressions using “*”
–  Text interactions are easily reproduced user-­‐‑to-­‐‑user or session-­‐‑to-­‐‑
session (command history) whereas it is more awkward to describe graphical interactions
–  Allow for aliasing commands to more familiar, user-­‐‑defined choices
–  Establishment of environment variables for convenient consistent functions
–  Graphical interactions are nice but typically of limited use
–  Linux has graphical interfaces but they are inconsistent among different Linux variants
–  Not every computer has graphical tools installed, especially if it was built for performance – but there will ~always be command-­‐‑line interactions
–  Many simple things do not need a fancy graphical output (think ‘ls’ instead of Windows Explorer..)
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The Shell
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Commands and Arguments
ccn4g@galileo /home/ccn4g] ls
btag/ Desktop/ mail/ phys2660_spring2012/
public_html/ ROOT_intro/
ccn4g@galileo /home/ccn4g] ls -1
btag/
Desktop/
mail/
phys2660_spring2012/
phys5630_fall2010/
public/
public_html/
ROOT_intro/
ccn4g@galileo /home/ccn4g] ls -lrt
total 32
drwxr-x--- 2 ccn4g ccn4g 4096 Aug 10 2007
drwx------ 2 ccn4g ccn4g 4096 Feb 15 2010
drwxr-xr-x 2 ccn4g ccn4g 4096 Feb 16 2010
drwxr-xr-x 2 ccn4g ccn4g 4096 Feb 16 2010
drwxr-xr-x 2 ccn4g ccn4g 4096 Aug 24 2010
drwxrwxrwx 2 ccn4g ccn4g 4096 Sep 19 2010
drwxr-xr-x 5 ccn4g ccn4g 4096 Sep 19 2010
drwxr-xr-x 3 ccn4g ccn4g 4096 Jan 23 14:46
phys5630_fall2010/ public/
Look at the different output of the program ‘ls’ when passing different arguments
Desktop/
mail/
ROOT_intro/
btag/
public_html/
public/
phys5630_fall2010/
phys2660_spring2012/
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Illustration of the Linux Filesystem
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Navigating Filesystem and Special Directories
•  Think of the filesystem as a nested collection of folders, a user has a home location and a current location
•  How to tell your current location: pwd
[phys2660@node1 phys2660_spring2012]$ pwd
/home/ccn4g/phys2660_spring2012
•  Change to a different directory: cd
[phys2660@node1 phys2660_spring2012]$
ls
prelab_01
[phys2660@node1 phys2660_spring2012]$ cd prelab_01/
[phys2660@node1 prelab_01]$
•  A user’s “home” directory: ccn4g@galileo /home/ccn4g/phys2660_spring2012] echo $HOME
/home/ccn4g
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The PATH Environment Variable
ccn4g@galileo /home/ccn4g/phys2660_spring2012] echo $PATH
/home/phys2660/usr/bin:.:/usr/lib/qt-3.3/bin:/usr/kerberos/bin:
.:/local/bin:/cluster/bin:/common/bin:/bin:/usr/bin:/usr/games:
/usr/X11R6/bin:/usr/openwin/bin:/common/CERN/pro/bin:
/common/lib/scilab/bin:/common/lib/LASSP/bin:/usr/NX/bin:
/opt/real/RealPlayer
•  Typing commands = running a program
•  Compiled version of program can be anywhere on the disk
•  PATH variable tells your shell what locations within the context of the filesystem to look for these executables
•  For instance, most common Linux commands reside under /bin or /usr/bin
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Convenience: Command History
ccn4g@galileo /home/ccn4g/phys2660_spring2012] history 10
559 9:12
su phys2660
560 9:16
echo $HOME
561 9:16
ls
562 9:16
cd phys2660_spring2012/
563 9:16
echo $HOME
564 9:19
echo $PATH
565 9:24
history
566 9:24
man history
567 9:24
history --help
568 9:24
history 10
•  On galileo, one can use up arrow to access commands in your history
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Convenience: Manual Pages Within Linux
ccn4g@galileo /home/ccn4g/phys2660_spring2012] man ls
LS(1)
User Commands
NAME
ls - list directory contents
SYNOPSIS
ls [OPTION]... [FILE]...
DESCRIPTION
List information about the FILEs (the current directory by
default). Sort entries alphabetically if none
of -cftuvSUX nor --sort.
Mandatory arguments to long options are mandatory for short
options too.
-a, --all
do not ignore entries starting with .
-A, --almost-all
do not list implied . and ..
•  good programs have easy-­‐‑to-­‐‑read manual pages, called man pages. Use: man <commandname>
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Some Common Linux Commands
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Editing Files
•  One of the main tasks you will do is edit human-­‐‑readable files
•  Many tools available to you to do this:
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nano (lab00)
pico (similar to nano)
nedit
emacs (lab01)
See this wiki page for some more discussion
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Caution on Caps
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Galileo: Where We Will Do Our Work
hBp://galileo.phys.virginia.edu/
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Remote Shells
•  So far we have tacitly overlooked one key component:
–  What if I am not siding in front of the specific computer / Linux machine I want to work on?
–  How do I establish a connection to that machine?
–  Use the network!
•  Remote shell access:
–  We will use a program called ssh
•  Secure Shell
•  Replaced an old lovable program called telnet, which, in terms of security, had more holes than swiss cheese! Totally Unencrypted
•  Tip: Never ever type the command telnet or even consider typing it
–  FYI There is no ssh version for Windows by default but you can install a Windows version for free. See Software for home on the class home page.
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Galileo: Where We Will Do Our Work
•  The computer / Linux “machine” where we will do all our work is in the physics department and goes by the name galileo
•  galileo is actually the head node of a cluster of computers running Linux
d-172-25-103-246 /Users/neu] ssh -Y -l ccn4g
galileo.phys.virginia.edu
ccn4g@galileo.phys.virginia.edu's password:
Warning: No xauth data; using fake authentication data for X11
forwarding.
Last login: Mon Jan 23 14:08:26 2012 from
d-128-100-66.bootp.virginia.edu
.cshrc sourced
ccn4g@galileo /home/ccn4g]
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A Note on Our Computer Lab
Room 022
Room ??
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The Computers in the Lab
•  The desktop machines in our computer lab run Lubuntu v12.04, kernel v3.2.0-­‐‑24-­‐‑
generic
–  a “lightweight” Linux operating system based on Ubuntu.
–  Ubuntu is a popular (most popular?) type of Linux OS distributions with its own desktop environment.
–  There are several such distributions popular in the community today, Ubuntu is just one
The actual nodes on galileo run a Linux distribution called CentOS, release 5-­‐‑11.
The kernel is v 2.6.18-­‐‑407.el5
Use ‘lsb_release –a’
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Remote Graphics
•  X Server: running on your local computer
•  X Client: program to display graphics from any other program
•  Can be on different computers! 34
Connecting to galileo from other locations/laptops
•  It would be nice to connect to galileo to do your work from say, your laptop while siding in the library for instance
•  Many hints on how to do this are located here: hdp://faculty.virginia.edu/comp-­‐‑phys/phys2660/wiki/
doku.php?id=software:sw_main
•  If you run Windows
–  I recommend installing and using pudy with Xming
–  Another option for Windows: NXClient for speedier graphics connections. See me if interested – might be beder than pudy
+XMing
•  If you run Mac OS X
–  ssh is installed but you still need an X Server to see graphics. See ssh and X11 for Mac
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We’ll pick up from here next time. Don’t forget lab on Thursday! See you then.
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