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Becoming Familiar with Unix Commands
====================================

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Familiarity with common `Unix <https://unix.org/>`_ commands makes the practice exercises easier to work through. If you're already comfortable with Unix, skip ahead to the `Initial Exercise <./initial_exercise.html>`_. Otherwise, work through this short exercise first to learn the basics.

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Changing Directories
====================

The command for changing directories is ``cd``.

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#.   In Derecho, move to the *practice_exercises* directory in your *scratch* space:

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        cd /glade/derecho/scratch/$USER/practice_exercises

     Use this command any time you need to move to a different directory.

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#.   A useful shortcut for moving up one directory, regardless of your current location, is typing two periods in a row (..). 

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        cd ..

     You can also move up through multiple directories at once using this command. For example, move into one of the directories inside practice_exercises, then navigate back to where you started. 

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        cd practice_exercises/wrf/test/em_real
        cd ../../..

     You should now be back in the */glade/derecho/scratch/$USER/* directory.

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Listing Directory Content
=========================

For a list of files and directories in your current directory, use ``ls``, which includes various options.

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#.   Running the following lists all files and directories in your current directory.

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        ls
     
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#.   To list files/directories in "long format", which includes information like the file's size, owner, permissions, etc., use the following.

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        ls -ls

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#.   To list file/directories in another directory, you could use something like this example, which prints the contents of your home directory.

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        ls /glade/u/home/$USER

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#.   Hidden files, such as environment files (e.g., *.bashrc*), are often found in your home directory. Change to your home directory, then list all files, including hidden ones. 

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        cd
        ls -a

     Notice that no directory was specified with *cd* in this case. This shortcut works only when navigating to your home directory — otherwise, you'll always need to specify a directory.

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Renaming, Moving, or Copying Files and Directories
==================================================

To copy a file, use the ``cp`` command. Try copying a file into your */glade/derecho/scratch/$USER/* directory. 

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#.   First verify that you're in the right place.

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        cd /glade/derecho/scratch/$USER/
        cp practice_exercises/wrf/test/em_real/namelist.input .

     Notice the full path was needed to locate the file, followed by a "." at the end. This command copies the *namelist.input* file from its current location (*practice_exercises/wrf/test/em_real/*) to the current directory - the (".") meaning "here."

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#.   You can also move the file to a location other than "here."

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        cp practice_exercises/wrf/test/em_real/namelist.input    practice_exercises

     There should now be a copy of *namelist.input* in the *practice_exercises/* directory. Use *ls* to verify.

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        ls practice_exercises

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#.   To move or rename a file, use *mv*. Rename *namelist.input* in your current directory.

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        mv namelist.input copied_namelist.input

     List the files in the directory (type ``ls``) to the file name changed to *copied_namelist.input*.

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#.   Now move that file to another directory.

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        mv copied_namelist.input practice_exercises

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#.   List the contents in the *practice_exercises/* directory (``ls practice_exercises``). Along with other files/directories, you should see both *namelist.input* and *copied_namelist.input*.

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Other Common Unix Commands
==========================

.. csv-table::
   :header: Command, Syntax, Usage
   :escape: \

   **mkdir** |br| **rmdir**, ``mkdir new_directory_name``, To make (mkdir) or remove (rmdir) directories
   **rm**, ``rm file``, Remove files
   **more**, ``more file``, Prints the first part of a file\, as much as will fit on one screen. Double-tap the space bar to see more or type "q" to quit.
   **cat**, ``cat file``, Prints the entire file to the screen
   **head**, ``head file``, Prints the file's first few lines to the screen
   **tail**, ``tail file``, Prints the file's last few lines to the screen
   **grep**, ``grep word file`` |br| ``grep -i word file`` |br| ``grep -i word *``, Find lines within the specified file that match the patterns used in the command |br| Add "-i" to make the search case–insensitive |br| Use "*" to search all files in the current (or specified) directory
   **pwd**, ``pwd``, Prints the path of your current directory
   **ln -sf**, ``ln -sf path/file``, Creates a symbolic (*-s*) link to a file. After\, the file appears in both locations\, but physically resides in only its original directory. *–f* ensures that if the target already exists\, it is unlinked first so the new link can be created correctly.

For additional resources, check out some of these pages:

*   `Stanford's Basic Unix Commands <http://mally.stanford.edu/~sr/computing/basic-unix.html>`_
*   `Wikipedia's List of POSIX/Unix Commands <http://en.wikipedia.org/wiki/List_of_Unix_utilities>`_
*   `Colorado State University's VI Commands <http://www.cs.colostate.edu/helpdocs/vi.html>`_

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**You can now go back to Case Studies to run the Initial Exercise.**

.. rst-class:: horizbuttons-primary-m

* `Return to Practice Exercises <./practices.html>`_

.. toctree::
   :maxdepth: 4
   :hidden:

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