Computational Science I

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Computational Science I

• Lecture 2
• CAAM 420, Fall 2004
• Instructor Tim Warburton

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Syllabus Part 1
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Homework due 08/25/04

• Make sure you can log on to a unix or linux
  system of your choice, which I will refer to as
  nix from now on.
• (Apply for a ruf account at apply.rice.edu for an
  account if necessary.)
• Read one of the listed unix quick guides and one
  of the emacs quick guides listed on the next
  page.
• Download the following file to your home
  directory http//www.math.unm.edu/timwar/CAAM420
  /ExerciseA.tar.gz
• Uncompress this file using gzip or gunzip
• Expand the archive with tar
• Navigate in the directory structure to find the
  following file target.text you may wish to use
  the nix command find as this file is well
  hidden.
• Open, edit and save this file with emacs to
  change the name in the file to be your name.
• Use one of the nix mail programs to send only
  the modified file to me.

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Homework Quick References

• Unix
• http//www.rice.edu/it/help/documents/training_doc
  s/index_platform.html
• http//www.ee.surrey.ac.uk/Teaching/Unix/
• http//www.unixtools.com/tutorials.html
• http//www.cs.washington.edu/orgs/acm/tutorials/in
  tro-unix/cheat-sheet.html
• http//wwwtheor.itep.ru/computing/unix.html
• http//www.uni.edu/its/us/document/sun/unixref.htm
  l
• http//www.cs.utk.edu/help/unix/quickref.php
• http//www.decf.berkeley.edu/help/handouts/unix-in
  tro.pdf
• Emacs
• http//www.cs.utah.edu/alee/emacs/emacs_quick.pdf
  
• http//seamons.com/emacs/
• http//rgrjr.dyndns.org/emacs/emacs_cheat.html
• http//www.cat.pdx.edu/tutors/tutorials/tutorials.
  php?gotoemacs

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Step 1 starting ssh

• First bring up a ssh client under windows (this
  allows us to log in to a nix server in a secure
  way)

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Step 2 choosing the nix server

• Left mouse click on Quick Connect
• Next select the server you want to log in to by
  typing in the host name in the pop up
• Also type in your user name in the 2nd box
  (replace timwar with your own user name)

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Step 3 successful log in

• You should see two things
• 1)
• 2)

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Step 4 setting up a profile

• Click in the box
  and enter in a nickname for this server/user name
  pair (I might use timwarruf). The next time you
  log in from this computer you can click on
  Profiles and just choose the nickname
  (hopefully).

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Step 5 the text prompt

• You are now in control of the nix session
• Anything you type will be taken as a command

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Rice Unix Cheat Sheet

• We will discuss the Rice Unix cheat sheet
• The only way to learn nix commands is to
  practice

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Step 6 who else is logged in?

• Q) Are you the only person logged into this
  machine?
• A) Check by typing who

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Step 7 shared resource

• You will see a large number of user names and
  info scrolling past.
• This tells you that the ruf machine is very much
  a shared resource.
• In later classes we will start to need a certain
  amount of computational resource demands one
  may wish to find an account elsewhere in a few
  weeks.
• In the meantime use ruf so we are all on the same
  page.

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Step 8 viewing all the names

• The output from the who command whizzed past and
  we could not read it all.
• A nix feature is we can pipe output from one
  command into a second command.
• This means instead of being displayed as output
  on the screen, the text is sent as input to a
  different command

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Step 9 -- piping

• Following who with (probably shift-\) tells
  nix to pipe the output from who to the nix
  command less

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Step 10 less is more

• less is a nix command which takes input from a
  file or a pipe and displays it in an interactive
  way
• We can navigate through the output using the b
  and spc keys to move up and down.
• Try it

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Step 11 Try homework

• A solution to the first part of the homework

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Disection of the Homework

• 1) ls tells us what is the current directory (in
  this case my home directory)

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2) Using gzip

• We next invoked gzip with the d argument and the
  ExerciseA.tar.gz file name which decompresses the
  ExerciseA.tar.gz to a new file ExerciseA.tar

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3) Using tar

• We next invoked tar to unarchive the tar file.
• The arguments xf says expand a file.

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4) Using find

• We next use find to locate the target.text file.
• find does a recursive search starting in the
  specified ExerciseA directory.
• find is looking for target.text
• When find locates any instance of target.text it
  executes the cp / command.

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5) Using cp

• We asked find to invoke a cp command if it found
  target.text
• Suppose we have a file foo which we want to copy
  to foo1

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5a) Using cp from find

• Recall we asked find to execute
• cp / \
• This is nix short hand

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-exec arguments disected

• cp / \
• cp is the copy command
• is a wild card denoting any file find finds
  which matches your description (in this case
  nametarget.text)
• / is a short hand notation for the users home
  directory.
• \ says two things
• \ instructs nix to pass this argument to find
  without doing anything to
• is the end of command instruction for the exec
  argument

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Emacs

• Invoke emacs by typing it at the text prompt

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Emacs cont

• So now you can start typing or issuing emacs
  commands

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Emacs cont

• We will discuss the Rice emacs cheat sheet here

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Class Exercise B

• 1) Make a new directory CAAM420
• 2) Make a sub-directory CAAM420/ExerciseB
• 3) Change directory to this new sub-directory
• 4) Create a file using emacs called foo.txt
• 5) Write a paragraph on what your research dreams
  are (or some such random text)
• 6) Save the file
• 7) Make a copy of the foo.txt file called
  other.txt
• 8) Use ls to find out how large foo.txt is
• 9) Use chmod to make it so that all users and
  groups can read this file
• 10) Ask the person next to your for their user
  name and use cp to copy their other.txt file into
  your ExerciseB directory
• 11) Use less to read the new other.txt
• 11) You have just discovered that if permissions
  are set right you can share files on the same
  system but also that your files are visible.

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Homework

• Browse through the unix and emacs cheat sheets.
• We will go through new examples next time.