Getting Familiar with Unix Environments

This page is designed to provide an introduction to Unix-type shell commands. On MacOS, the standard Terminal is zsh (as of 2019) which is a Unix-type shell. On Windows, the cygwin project provides a Unix-like environment that uses the same commands.

Summary of Commands

The commands introduced in this page are summarized in the following table for convenience:

Command	Description	Commonly-Used Options
pwd	Obtains the present working directory
ls	Lists the contents of the present working directory	-l (verbose); -a (show hidden)
cd	Changes directory to a different location
cp	Copies files from one location to another	-r (recursively copy from directories)
ln	Links one file to another	-s (symbolic)
cat	Print contents of a file to the terminal
head	Print contents of the start of a file	-n (number of lines)
tail	Print contents of the end of a file	-n (number of lines)
mkdir	Make a directory
rm	Removes file(s) from the system	-r (recursively remove from directories)
rmdir	Remove directory	-R (remove a directory and all of the files inside of it)

Tutorial

Getting Started

To get started with this introductory tutorial, use the following steps:

1. Download the model_config_example.zip example file set from the Github repository for this book and unzip it.

2. Open the Unix shell you use on your machine.

The model_config_example directory contains several subdirectories containing various files in the following format:

This directory structure mimics the typical structure used for MITgcm models.

Navigating the File System

Determining your path

When you open your terminal, one of the first thing you want to determine is where in your file system you are. The command pwd, which stands for present working directory, will show you where you are located.

pwd

From the above command you may see something like the following:

/Users/mike

Typically, the terminal is configured to open in your home directory. You can check your home directory with the following command:

echo $HOME

This location is typically the location where your shell will open when you launch your terminal

Listing contents of your directory

Wherever you are, you can determine what files, folders and other items are in your current folder using the ls command.

ls

The output of your ls command will look something like the following:

Applications         Library              Pictures             bin
Documents            Movies               Public               opt
Desktop              Downloads            Music               

Note

All Unix commands have the structure command -(options) (arguments) where options and arguments may or may not be present.

🤔 Try it for yourself:

Try the ls command with the following and consider how they affect the output:

• option -l

• option -a

• argument Documents

• argument D*

💡 Solution:

• The -l option gives verbose output

• The -a option shows hidden files

• Providing Documents as an argument will list all files in the Documents folder rather than the current directory

• Providing D* as an argument will list all files in directories starting with the letter D. Here, we see that * is a wildcard character and can be used to find directories that match a given pattern.

Changing Directories

To move from one directory to another, use the cd command (short for change directory):

cd Documents

You can move up one folder in your directory using two dots in your path as

cd ..

You can repeat the cd command in succession to move around your computer, or you can string together a full path to move to a different location, e.g.:

cd model_Files/model_config_example

🤔 Try it for yourself:

Move into the run subdirectory of the model_config_example directory.

💡 Solution:

Your exact solution will depend on the location of your home directory and where you saved and unzipped your model_config_example files.

You may choose to enter individual commands such as cd model_config_example and then cd run. Or you can string your commands together to make a long path to your destination, e.g. cd model_config_example/run

Note

You can use the Tab key to complete the name of a directory after typing a few characters of its name.

Copying and Linking Files

Copying Files

Files can be copied with the cp command (short for copy). The syntax for the copy command is to first list the path of the file to copy and then the destination for that file. For example, suppose you are in the run directory and would like to copy the file eedata from folder namelist. In this case, the copy can be completed with:

cp ../namelist/eedata eedata

The first argument is the source file and the second is the destination file. If you want the file name to stay the same, then you can optionally provide a directory. For example, you can use the . symbol to indicate the current directory as the destination as:

cp ../namelist/eedata .

Just like with file paths, wildcards can be used to copy multiple files at once that follow the same pattern.

🤔 Try it for yourself:

Copy all files from namelist that start with data to the run directory:

💡 Solution:

Top copy all of the files starting with the characters data from the namelist directory to the current directory, use cp ../namelist/data* .

Linking Files

Often we would like files to be in multiple locations at the same time. For example, two different models may rely on the same underlying data. In this case, we don’t need two complete copies of the data - each model just needs to know where the data located. In these circumstances, a symbolic link is desirable.

We can symbolicly link files with the ln -s command. For example, suppose we wanted to link the bathymetry.bin file from the input directory into the run directory. In this case, we could use

ln -s ../input/bathymetry.bin .

🤔 Try it for yourself:

Link the rest of the folders and files from the input directory into your run directory.

💡 Solution:

To see what other files are in the input directory, we can use the ls ../input command.

After discovering the names of the three other items, we can use

• ln -s ../input/exf .,

• ln -s ../input/obcs ., and

• ln -s ../input/tile001.mitgrid ..

Making and Editing Files and Directories

Editing Files

We can make and edit files with a variety of different editors that often come pre-installed on command line interfaces.

One popular editor is the nano editor which can be opened with the nano command. For example, we can create and edit a README.txt file with the following call:

nano README.txt

The nano text editor will open in the terminal directly and will have the following appearance.

You can edit the text in the file directly. Then, when your edits are complete, use CTRL-X to save and exit.

Alternatively, we can use our native text editors to edit files directly. To create a file, we can use the touch command.

touch notes.txt

Then, in MacOS, we can use TextEdit open and edit this file with

open -a TextEdit notes.txt

Similarly, on Windows, we can use the Notepad program with:

notepad.exe notes.txt

🤔 Try it for yourself:

Create a file called notes.txt and add some notes to the file.

To see the text that the file contains, you can use cat:

cat README.txt

The code above returns the following contents, assuming that the file was created with nano as shown above:

This file contains information about the model configuration

To see just the start of the file, you can use head:

head README.txt

To see just the end of the file, you can use tail:

tail README.txt

Creating Directories

Directories can also be creates and removed using tools on the command line.

To make a directory, we use use the mkdir command (short for make directory). For example, suppose you wanted to make a directory called diags. This can be achieved with

mkdir diags

Shell Profiles

Each shell has a given profile - a script that is automatically run when you open a terminal. For example, the default terminal on MacOS is zshell which has the default shell profile in the .zshrc file. Similarly, bash shells have profiles in .bashrc and/or .bash_profile. Note that the . in front of each file ensures that the file is hidden.

All shell profiles should be placed in your home directory.

You can see your hidden profile in your home directory using the -a flag on the ls command with:

ls -a $HOME

To edit your profile, you can use the nano editor as described above.

🤔 Try it for yourself:

Add a welcome message for yourself in your profile. Then, open a new terminal window to double check that your profile is working.

💡 Solution:

Use your favorite text editor to open your profile file. Then, use the echo command to print a message, e.g. echo "Welcome Mike".

Deleting Files and Directories

We can delete files with the rm command - short for remove. For example, if we no longer wanted the temporary note that we made before, we could remove it with

rm tmp_note.txt

Warning

Deleting files in a Unix Environment is PERMANENT. There is no Trash or Recycle bin and there will not be a note asking you if you’re sure you would like to delete that file. Before using the rm command, be sure to think for an extra second or two about what you intend to do.

To remove a directory, such as diags, we can use the similar rmdir command as

rmdir diags

One caveat (or perhaps safety net) of this command is that the directory must be empty before it is deleted. If you would like to remove the directory and all of the files inside of it, you can use the recursive option for the command as

rmdir -r diags

Again, caution should be used with deleting directories because the contents cannot be recovered after they are gone.

🤔 Try it for yourself:

Suppose you made some changes to the exf package and need to recompile the model to reflect these changes. Remove all exf files from the build directory.

💡 Solution:

rm ../build/exf*