PY410 / 505

Computational Physics 1

Salvatore Rappoccio

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 Technical Lectures
• We will have several technical lectures to get you up to
speed with programming and technical skills
– Using UNIX/LINUX command line
– Compiling, version control
– Data representations, flow of control, object oriented
programming, simple algorithms

 Executing code
• The official environment for the class is a container:
– Docker image for class software (Ubuntu based):
• https://hub.docker.com/r/ubsuny/compphys

• Software for this class:

– https://github.com/ubsuny/CompPhys

• If you want to use your laptop environment directly, you

can but CAVEAT EMPTOR.

I assist students with

personal laptop issues on
best-effort basis
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 Executing code
• Some people that have tablet two-in-one “laptops” will
have trouble with containers
– This is because the tablet is basically a large phone with
a keyboard, and we need a “real” computer capable of
running virtual machines
– For those at UB: If you do not have a powerful enough
laptop, you can use the SENS cluster.
– For those elsewhere: singularity is installed at the LPC
so if you have an account there, instructions can be
provided by the LPC staff to run the container.

 Containers

• Can also make use of containers

– Virtual “machine” but for applications

 Containers
• Why bother?
– So you don’t have to spend time configuring software. It
just works.

• Instructions:
– Get docker : https://docs.docker.com/install/
• (shortcuts: https://download.docker.com)
– Follow installation instructions (OS dependent)
– Once it is running, open your “Terminal” app in your
laptop / host machine, and execute these:
git clone https://github.com/ubsuny/CompPhys.git
chmod a+w CompPhys
cd CompPhys
./runDocker.sh ubsuny/compphys:latest

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 Containers
• You will get a command line just like a linux computer
(running Ubuntu)

% ./runDocker.sh srappoccio/compphys:latest
192.168.1.231 being added to access control list
compphys@55d39ad05e02:/Users/rappoccio/dockers/CompPhys$

• (Your IP, hash details, and user directory will be different)

 UNIX/LINUX
• Operating systems (like Windows or Mac OS)

• We will be using LINUX (an offshoot of UNIX)

– Invented by Linus Torvalds in 1991
– Mac OS X is built upon LINUX
• EdX course from the creator here :
– https://www.edx.org/course/introduction-linux-
linuxfoundationx-lfs101x-0#!
• Linux is completely open source : you can modify it at your
will and debuggers are also free

• Predominantly command line tools

• Cheat sheet on UBLearns (or indico for FNAL people) 8

 Linux Shells
• We will be using an interface to Linux called a “shell”
• It is a command-line interpreter : you type, it executes

• Two major options are “bash” (as in, smash) and “csh” (like
“sea shell”, modern version is “tcsh”, “tea sea shell”)
• For the most part, few differences with respect to this
class, you can use either one.

• Major difference : environment variables syntax

– bash: export X=value
– tcsh: setenv X value
• That’s about it for the purposes of this class

 Jupyter
• We will (judiciously) use Jupyter notebooks
• Also can be installed on your own machines if you want
• Nice little package for code and documentation at once
– Note: This is usually not for “industrial strength” software,
but for prototyping and communication!

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 Jupyter
• We will (judiciously) use Jupyter notebooks
• Also can be installed on your own machines if you want
• Nice little package for code and documentation at once
– Note: This is usually not for “industrial strength” software,
but for prototyping and communication!
• To run: jupyter notebook --ip 0.0.0.0 --no-browser

compphys@e0e70fd1831c:/Users/rappoccio/dockers/CompPhys$ jupyter notebook --ip 0.0.0.0 --no-browser

[I 19:59:18.332 NotebookApp] Writing notebook server cookie secret to /results/.local/share/jupyter/runtime/notebook_cookie_secret
[I 19:59:18.499 NotebookApp] Serving notebooks from local directory: /Users/rappoccio/dockers/CompPhys
[I 19:59:18.499 NotebookApp] Jupyter Notebook 6.4.12 is running at:
[I 19:59:18.499 NotebookApp] http://e0e70fd1831c:8888/?token=a31edcbb72eb3b6f3678471fd6ed9fbe98a7b7e419193cb1
[I 19:59:18.499 NotebookApp] or http://127.0.0.1:8888/?token=a31edcbb72eb3b6f3678471fd6ed9fbe98a7b7e419193cb1
[I 19:59:18.499 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 19:59:18.502 NotebookApp]

To access the notebook, open this file in a browser:

file:///results/.local/share/jupyter/runtime/nbserver-10-open.html
Or copy and paste one of these URLs:
http://e0e70fd1831c:8888/?token=a31edcbb72eb3b6f3678471fd6ed9fbe98a7b7e419193cb1
or http://127.0.0.1:8888/?token=a31edcbb72eb3b6f3678471fd6ed9fbe98a7b7e419193cb1
[I 19:59:26.391 NotebookApp] 302 GET /?token=a31edcbb72eb3b6f3678471fd6ed9fbe98a7b7e419193cb1 (172.17.0.1) 0.500000ms

Copy and paste into web browser

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 Jupyter
• Now you’re running jupyter locally:

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 Jupyter

New —> Python3

Gives you a notebook:

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 Jupyter

Type python

Shift+Enter: It executes

Copy-and-paste-able:
import matplotlib.pyplot as plt
import array
x = array.array('f', [1,2,3])
y = array.array('f', [1,4,9])
plt.plot(x,y)
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plt.show

 Jupyter

2. Change cell to “Markdown”

1. Select the cell.

3. LaTeX goes in “$(stuff here)$”

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Jupyter

4. Shift+Click, and you get the markdown

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 Jupyter
• But wait, it gets better! If you want, you can use the Jupyter
terminal directly instead of the linux shell.

New —> Terminal

Gives you:

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 Jupyter

Click to “JupyterExamples”,

Then open example_jupyter.ipynb

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 Jupyter

To run:

Kernel:
Restart and Run All

Boom! Jupyter-ed.

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 Linux Command Line
• Basics : Listing directory contents : “ls”, like “list”
$ ls
$

• Empty right now

• Basics : Echoing content : “echo” :
$ echo "Why am I here?"
Why am I here?

• Basics : Saving what you type: the “pipe” command : “>”

$ echo "Who am I?" > stuff.txt
$ echo “Why am I here?” > stuffagain.txt

• No output… what happened? “ls” again:

$ ls
stuff.txt stuffagain.txt
• Aha, there it is. What’s in it?
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 Linux Command Line

• Reading files : “more”, “less”, and “cat”:
– “cat” : concatenates files together (if just one, reads it)
$ cat stuff.txt
Who am I?
– “less”: reads a file and paginates it
$ less stuff.txt
Who am I?
~

– “more” : reads multiple files separately

$ more stuff.txt
Who am I?

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 Linux Command Line

– “cat” will concatenate:
$ cat stuff.txt stuffagain.txt
Who am I?
Why am I here?

– But “more” does more:

$ more stuff.txt stuffagain.txt
::::::::::::::
stuff.txt
::::::::::::::
Who am I?
::::::::::::::
stuffagain.txt
::::::::::::::
Why am I here?
$

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 Linux Command Line

• What if you want to copy or move files?
• Copy : “cp” :
$ cp stuff.txt stuff1.txt
$ ls
stuff1.txt stuffagain.txt stuff.txt
$ cat stuff1.txt
Who am I?
– File “stuff1.txt” is a copy of “stuff.txt”
– They are duplicates. “stuff.txt” is retained.

• Move : “mv” :
$ ls
stuff2.txt stuffagain.txt stuff.txt
$ mv stuff1.txt stuff2.txt
$ cat stuff2.txt
Who am I?
– File “stuff2.txt” is there, but “stuff1.txt” is gone
– Also known as “renaming”! 23

 Linux Command Line

• Removing files : “rm”
$ rm stuff2.txt
rm: remove regular file `stuff2.txt'? y
$ ls
stuffagain.txt stuff.txt
– Gone forever. Really, really, really gone. No “trash bin”.
No “restore”. No “but professor, can’t I undo that?” No.
You cannot. Bits are gone.
• Backups in LINUX are VERY IMPORTANT TO HAVE

– Example:
$ cp stuff.txt stuff_backup_27jan2017.txt
– OR! Use version control (more on that later)

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 Linux Command Line

• What if I hate typing files one at a time?
– Then Linux is the best operating system for you

• Huge number of shortcuts in LINUX :

– tab completion : If you start typing and press “TAB”, it will
list the possible completions, or if there is only one,
complete it for you
– “up” key : reproduces previous line in Terminal
– aliases : can define your own shortcuts

– wildcards!

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 Hands on!
• Open terminal, go to “CompPhys/LinuxOverview”
• Look at “commandline1.sh” file:
% more commandline1.sh
echo "Always look on the bright side of life" > bright.txt
echo "If life is jolly rotten, there's something you've
forgotten" > forgotten.txt
cat bright.txt forgotten.txt > song.txt
cat song.txt=
• Execute:
% bash commandline1.sh
• Output:
Always look on the bright side of life
If life is jolly rotten, there's something you've forgotten
• Type “ls”:
bright.txt commandline1.sh forgotten.txt song.txt

• Demonstrates: more, ls, and cat commands, files, and piping

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 Linux Command Line

• Wildcards : http://www.tldp.org/LDP/GNU-Linux-Tools-Summary/html/x11655.htm
– ? : single character
$ ls ?right.txt
bright.txt
– * : any number of characters
$ ls *.txt
bright.txt forgotten.txt song.txt stuffagain.txt
stuff_backup_27jan2017.txt stuff.txt

$ ls s*.txt
song.txt stuffagain.txt stuff_backup_27jan2017.txt stuff.txt

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 Linux Command Line

• Wildcards:
– [] : specifies a range
$ echo "song1" > song1.txt
$ echo "song2" > song2.txt
$ echo "song3" > song3.txt
$ cat song[1-2].txt
song1
song2
– {} : name or wildcard
$ echo "song4" > whoops.ugh
$ cat {song*.txt,whoops.ugh}
song1
song2
song3
Always look on the bright side of life
If life is jolly rotten, there's something you've forgotten
song4

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 Linux Command Line

• Command line options :
– What if you like “rm”, but hate to confirm each removal?

– “rm” has OPTIONS you can add

• Options usually come in two forms :

– Single dash, single letter : “ls -r”

– Two dashes, many letters: “ls —help”

– Most commands come with “—help”, so you can read

the options you have

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 Linux Command Line

• Example : “ls”:
$ ls --help
Usage: ls [OPTION]... [FILE]...
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 ..
--author with -l, print the author of each file
-b, --escape print octal escapes for nongraphic characters
--block-size=SIZE use SIZE-byte blocks. See SIZE format below

• Common options
– “-l” : long listing
– “-a” : list all
– “-t” : list by time
– “-r” reverse

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 Linux Security

• What the heck is all this stuff?

-rw------- 1 srrappoc phyfac 6 Jan 27 11:14 whoops.ugh

Filename

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 Linux Security

• What the heck is all this stuff?

-rw------- 1 srrappoc phyfac 6 Jan 27 11:14 whoops.ugh

Time/date Filename
of last mod.

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 Linux Security

• What the heck is all this stuff?

-rw------- 1 srrappoc phyfac 6 Jan 27 11:14 whoops.ugh

“group” Time/date Filename

of last mod.

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 Linux Security

• What the heck is all this stuff?

-rw------- 1 srrappoc phyfac 6 Jan 27 11:14 whoops.ugh

“permissions” “owner” “group” Time/date Filename

of last mod.

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 Linux Security
• Levels of security :
– All : everyone
– Group : a group of users
– Owner : the owner of the file

• Access levels :
– Read : Can read from file
– Write : Can write to file
– Execute : Can execute if it is a program

• Can set different access levels for different levels

– Most common example: “Owner” can read+write,
“Group” can read, “All” can do nothing
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 Linux Security
• You can change the permissions, the owners, or the
groups of files:

– chown (change owner or group) :

• usage : chown user:group file
• change owner of file to “user” and group to “group”
– chmod (change permission)
• usage examples :
– chmod a+x file (give execute permission to “all”)
– chmod g+w file (give write permission to “group”)
– chmod a+wrx file (give read/write/execute permission to anyone)

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 Linux Directories
• To make directories, use “mkdir”:
$ mkdir testdir
$ ls
bright.txt commandline1.sh forgotten.txt song.txt testdir

– To remove them, “rmdir” (must be empty)

• You can move files from one directory to another with “mv”
just like before:
$ mv song.txt testdir/

• And you can use “ls” to look at the directory:

$ ls testdir/
song.txt
•

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 Linux Directories
• The directory you are “in” is called the “current directory”
• To change your current directory, use “cd”:
$ cd testdir
/nsm/home/srrappoc/testdir
$ ls
song.txt

• To go to the directory “up” the chain, do “cd ..”:

$ cd ..

• There are shortcuts for “cd” :

– “cd -“ go to previous directory
– “cd” (no arguments) go to home directory

• You can also print the working directory (pwd)

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 Editors
• AKA : why is it so f*ing hard to type stuff in Linux?
– It isn’t, you’re just not thinking about it right :)
– If you’re sitting at the same terminal you’re executing
commands on, your server is the same as your client
– If you’re using ssh, you are trying to send a ton of
graphical information over the net to type

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 Editors
• Linux comes with the “X11” graphics package : that’s how
everything works
– This is also the basis for Mac OS’s GUI

• Many editors are available, and many have “inline text”

and “X11” modes

• Now we come to one of the greatest scientific

controversies of all time:

THE EDITOR WARS

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 Editors

http://cube-drone.com/comics/c/holy-war

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Editors

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 Editors
• I am personally firmly in the “Emacs” zone of the world
• If you are a vi or ed user, you can leave now
– Kidding!!! *coughsortofcough*

• I can teach you the basics of emacs, and you should learn
the rest on your own. You’re scientists, that’s how it goes.
It’s like learning to walk, or ride a bike, or hazing or
something.

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 Editors
• emacs :
– X mode : emacs filename.txt &
• Edit away as you want.
– Terminal mode : emacs -nw filename.txt
• “-nw” is “no window”
– Tutorial : https://www.gnu.org/software/emacs/tour/
• vi / vim:
– vi filename.txt
– I suck at vi, so just go here:
• https://scotch.io/tutorials/getting-started-with-vim-an-interactive-
guide

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 Editors
• If you’re terrified of learning how to use these, just use
“nano”. The interface is straightforward, but has extremely
few features.

• Some of you young whipper snappers will want to use a

more modern editor like sublime or xcode
– If you know out how to use them, go for it, but I won’t
help you! :)

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 Editing: Docker
• There is no emacs in our docker image
• There is no vi in our docker image
• There is no editor at all

• WTH Sal?!!?

Use the host operating

system’s editing
tools, silly!

This is the docker image

Your computer is here

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 Editing: Docker
• Open the files directly in your host operating system (i.e.
the normal way you edit stuff on your computer)
compphys@d4fa2e3932fb:/Users/rappoccio/dockers/CompPhys$

The file is here on your host operating system, just edit in a different terminal!

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