Basic Linux Commands
In this section, we will review more commands to get you comfortable do basic things on HYAK. This section has sampled some of the data and exercises for this tutorial were sampled from The Unix Shell by Software Carpentry, but have been tailored to fit most HYAK users. Sampled materials are under the Copyright of Software Carpentry and are made available under the Creative Commons Attribution license (CC BY 4.0).
Your Working Directory#
We have discussed storage on HYAK a bit in this tutorial, but it is important to emphasize here, that you should avoid storing data, scripts, and software in your Home directory where you will quickly run out of storage due to its 10GB quota. For this reason, it is important to understand your other storage options on HYAK, which are as follows:
- If you are part of a lab group who contributed resources to HYAK (slices) then you have storage under their directory in
/mmfs1/gscratch/labname. Where the wordlabnameis replaced by the name of your lab group on HYAK. Check with your PI or labmates to find out what that directory is called., or use thehyakalloccommand which will show thelabnameand the directory name for your lab. - If you are a student and you have applied to be part of the Research Computing Club (RCC), you have have storage under
/mmfs1/gscratch/stf/. The RCC has set storage quotas for users there. Please inquire with the RCC aboutstfstorage quotas. Apply for anstfaccount [HERE] - If you don't fall into any of these categories, we have temporary community storage under
/gscratch/scrubbed/; however, directories and files here will be automatically deleted if not used after 21 days. Please review our documentation about/gscratch/scrubbed/HERE.
For this tutorial, we will make a working directory under /gscratch/scrubbed/ and perform the exercises there. You can do the same, or perform the following command in another storage area you have access to (i.e., a lab group directory or under stf).
mkdir#
"make directory" or mkdir to make am empty directory you can work in.#
First navigate to /gscratch/scrubbed/ or the location you have selected for your working directory.
If you are following along and are in the right place the output of the pwd command should be:
Then make your working directory with the following, but replacing the word UWNetID with your UW Net ID.
Change directory to enter your new directory.
Double check your location on klone and the absolute path to your working directory for this part of the tutorial.
If you are following along and are in the right place the output of the pwd command should be:
wget#
"web get" or wget to download data from a webpage.#
Now we are going to download some data from the Software Carpentry github repository for the next exercises.
List your working directory to show the zipped version of the lesson directory.
ls should show a zipped version of the shell-lesson-data directory.
Unzip the lesson directory with the unzip command.
List your working directory again to show the unzipped version of the lesson directory and the zipped version.
ls should show a unzipped version of the shell-lesson-data directory as well as the zipped version.
Change directory to go into shell-lesson-data/exercise-data/writing/
Print your working directory to understand where you are.
If you are in the right place to continue your output of pwd should show the absolute path to the data we will use in the next activity and read:
List the writing directory
The expected result is:
../
Another way to move around the directories on the filesystem is to move backwards (toward the root) one directory at a time with ../.#
Print your working directory to understand where you are.
The expected result is:
Print working directory again to see the result of cd ../
The expected result is:
Use cd and ../ to go backward 2 directories
Print working directory again to see the result of cd ../
The expected result is:
Let's go back to shell-lesson-data/exercise-data/writing and practice making a directory again.
Make a directory called thesis
Note that mkdir is not limited to creating single directories one at a time. The -p option allows mkdir to create a directory with nested subdirectories in a single operation:
You can list the contents of the directory "above" where we are now without changing directory.
The expected result is:
-F option with ls puts a / after directories to differentiate them from other objects.
The expected result is:
The -R option to the ls command will list all nested subdirectories within a directory. Letās use ls -FR to recursively list the new directory hierarchy we just created in the project directory:
You should see:
caution
Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files and directories.
Donāt use spaces.
Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test this out, try typing mkdir north pacific gyre and see what directory (or directories!) are made when you check with ls -F.
Donāt begin the name with - (dash). Commands treat names starting with - as options.
Stick with letters, numbers, . (period or āfull stopā), - (dash) and _ (underscore).
Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.
If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in single quotes ('').
Editing files on klone#
use nano text editor on klone#
To edit files on klone we need to go back to basic text editors. You will not have access to a word processer and formatting and syntax doesn't always translate from Microsoft Word or similar software to executable commands on klone. With the next command, we will create a file called draft.txt and open it in the text editor nano.
First change directory to thesis:
The create and open a file called draft.txt with the command:
note
There are other text editors you could choose from. vim is a popular choice. In the opinion of the author, nano is more beginner friendly, so that is what we will use here.
Let's type a few lines of text.
Once weāre happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk. We will be asked to provide a name for the file that will contain our text. Press Return to accept the suggested default of draft.txt.
Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.
cat#
"concatenate" or cat a file to print its contents to the screen for review.#
Let's view our work. List the directory to see our new file, draft.txt there.
Now let's view the contents of draft with cat
important concept: Paths and Access
In the last section we talked about your "location" or "places" in the klone filesystem. On the command line, your location determines what you have access to. To demonstrate this important concenpt, consider the following example:
There is a dataset of sequences from a mythical creatue called a Basilisk (from the Harry Potter Universe). The dataset is called basilisk.dat. If you wanted to execute anything on basilisk.dat you would not be able to unless you are inside of the directory where it is stored. Let's go find it and print its contents to the shell with cat.
If you have been following along and you are in the thesis directory, change directory to two directories "above" thesis (i.e., two directories closer to the root directory (/)) and enter a directory called creatures/
List the directory.
cat the Basilisk data
The expected output:
To illustrate the concept of paths and access. Let's go back to thesis and try to do the same thing. Change directory to one directory "above" the cretures, then go into writing and finally thesis.
The expected output:
We get an error because we can't access basilisk.dat from our location without more information. However, we can provide more complete information and view basilisk.dat
Will return:
In this example, we have provided more information about the location of basilisk.dat relative to our location (i.e. using ../ to indicate the position relative to our current directory location) and are able to access it and execute the cat command upon it. This illustrates, using a relative path, or an address to that file relative to our own location.
We can also use absolute paths to access a file from ANY location on the klone filesystem. This is a error-proof method of making sure you can execute commands on files no matter where on the filesystem the command is issued. Let's use an absolute path to see a file from elsewhere on the filesystem. There is a dataset called animals.csv under /mmfs1/sw/hyak101/basics/data/. Let's view it with cat from our current directory.
Now use the absolute path to animals.csv to cat it
To summarize, you either have to be inside of the directory where a file is to execute commands on it, provide a relative path to the item from your current directory, or provide an absolute path to the file.
In the next section, we'll review additional Linux commands that you might find helpful.