Homework #2

Homework #2#

Completing this assignment

For the problems below, create a single text file in nano called homework2.txt and record the commands that you need to do to accomplish the goal of each problem. If the problem asks for your to capture the output of a command, copy-paste it into this same text file.

Upload your homework2.txt to Brightspace as well as the script that you write in the last problem.

Important

All work must be your own.

You may not use generative AI / large-language models for any part of this assignment.

  1. scp practice

    • On your laptop or one of the MathLab machines, create a file of the form username.txt, where you replace username with your portal username / NetID.

    • Using scp (or pscp if you are using Windows / PuTTY), transfer the file to portal.mathlab.stonybrook.edu into the directory /home/phy277_spr26.

      This is a directory that is world readable / writable.

    • Copy the exact scp command you used and the output from the transfer when you did it on the command line (this will show, for instance, the transfer speed, percentage complex, etc.) and put it in your homework2.txt file that you will submit for this assignment.

    • Finally, ssh into portal and do an ls -l on the directory you copied the file to. What are the permissions on your file, and who (user, group members, and others) has access to read and write it?

    Important

    This directory only exists on portal and not portal2.

    solution

    The scp command I would use is:

    touch mzingale.txt
scp mzingale.txt mzingale@portal.mathlab.stonybrook.edu:/home/phy277_spr26

    The output will look like:

    Authorized uses only. All activity may be monitored and reported.
mzingale@portal.mathlab.stonybrook.edu's password:
mzingale.txt                                  100%    0     0.0KB/s

    When I ssh into portal, I should see:

    -rw-r-----. 1 mzingale     mzingale       0 Feb 17 11:44 mzingale.txt

    This indicates that I (as the user) can read and write to the file, and group members can read the file. Anyone else on the computer cannot access the file.

  2. pipes

    In class, we learned the sort and wc commands, and how they work with pipes (|). Now for two new commands:

    • uniq : remove repeated lines from the input

    • cut : this will extract just a portion of a line from input

    Here’s an example. Go to ~/shell-lesson-data/exercise-data/animal-counts

    The file animals.csv is a command-separate values file. If we look at the file (just use cat) we see that the first column is the date, the second column is an animal, and the third column is a count (number of times the animal was seen). These columns are separated by a comma, ,.

    If we do:

    cut -d , -f 2 animals.csv

    Then we get just the middle column. Here the -d flag specifies the delimiter separating the columns, and the -f flag specifies which field we want (the second).

    Tip

    Remember, you can do man cut to learn these options.

    The output of this is:

    deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear

    We want to get just the types of animals that were seen, so any duplicates should be removed.

    If you just pipe the output to uniq it doesn’t work, since uniq only looks at the previous line. So you need to sort the output first.

    Your task: Give the bash one-line sequence (several commands connected with pipes) that will give you just the list of animals observed, with no duplicates.

    solution

    cut -d , -f 2 animals.csv | sort | uniq

  3. a script

    In ~/shell-lesson-data/exercise-data/alkanes, you’ll find a collection of files that describe different alkane molecules. Your task here is to write a simple shell script that takes the name of a file and outputs how many atoms is has.

    You can find the lines containing an atom in the file by using grep to look for ATOM.

    For our script, we want to run it like:

    ./myscript cubane.pdb

    In the script, we can reference the filename that follows our script using the variable $1. For instance, a script that had this:

    #!/bin/bash

echo $1

    would just echo whatever the first argument to your script was.

    Your task:

    • Create a file called myscript.sh in nano. It should start with

      #!/bin/bash

      as we discussed in Executable scripts.

    • Add the sequence of commands that grep the input file ($1) and count the number of lines that have an atom.

    • Finally, modify the file permissions, giving you (and only you—not group or other users) the ability to execute your script simply as ./myscript.sh

    solution

    Your script will look like:

    #!/bin/bash

grep ATOM $1 | wc -l

    and you would change the permissions as:

    chomd u+x myscript.sh

    For this problem, in your homework2.txt file, share the command you used in the last step for the permissions. Also upload your script separately to Brightspace.