This project is maintained by CCML-UCONN

Getting Started

  1. Logging Into the Computing Clusters
  2. Basic UNIX
  3. Python

Basic UNIX


  1. Basic Comamands
  2. Wildcards
  3. Advanced Commands
  4. Text Editors
  5. Exercises

Basic Commands

These are some of the basic commands that you will be using in the shell on a daily basis.

ase-gui <file_name>

Graphical user interface for the Atomic Simulation Environment (ASE). This is the tool you will be using for viewing or setting up your structures.

cd ..

Move up one directory.

cd <directory_name>

Changes directory to the one provided. If no directory is given, the default is to return you to your home directory (/home/username/)

cp <source_file_with_path> <destination_path>

Copies files or directories from the source_file_with_path to the destination_path

cp -r <source_file_with_path> <destination_path>

Copy recursively. Useful for copying multiple files and directories (copies contents of the subdirectories).

cp -u <source_file_with_path> <destination_path>

Update. Copies only if the source file is newer than the destination file or the destination file does not exist.

mkdir <directory_name>

Create new a new directory.

mv <source_file> <destination_file>

Move or rename file.

ls <directory_name>

Lists the files and directories contained within the directory. Leave blank for present directory.

ls -t

List files in chronological order.

ls -la

List all files even those starting with a dot ‘.’ which are generally not listed.

ls | more

If the number of files in a directory is too large to fit in a single screen this command lists files and directories page after page on spacebar keystroke.


Provides the “present working directory,” i.e. the current folder.

rm <file>

Remove files. This is always permanent.

rm -r <file_or_directory_with_path>

Remove file or the directory and its contents recursively.

rmdir <directory_name>

Remove an empty directory. Use rm -r to remove recursively, such as if directory contains files (be careful).

less <file_name>


more <file_name>

Print out contents of a text file or files within the shell.

grep [keyword] <file_name>

Search “keyword” in each File.

man <command>

This is the most powerful command on this page. It prints out the manual of the command, including options and syntax.

scp [options] username1@source_host:directory1/filename1 username2@destination_host:directory2/filename2

Securely transfer files between two Unix computers. Most of the time you are transferring files between your local computer and HPC clusters.

from the cluster to your computer

scp username@hostname:directory1/filename1 directory2/filename2

from the cluster to your computer

scp directory2/filename2 username@hostname:directory1/filename1

use scp -r if your are transferring a directory.


Wildcards can be used to perform commands on multiple files simultaneously.


Single character. Example: ag neb?.traj neb??.traj will use ag to open all files containing one or two characters between neb and .traj


Any number of characters. Example: ls *.traj will list all .traj files.

Advanced Commands for File Streaming


sed command in UNIX is stands for stream editor and it can perform lot’s of function on file like, searching, find and replace, insertion or deletion.


awk is a scripting language used for manipulating data and generating reports

 env|sed -n '/USER/p'|awk -F '=' '{print $2}'

The above line reads output from the command env, from the output, sed -n '/USER/p' finds the line contains the keyword “USER”, awk -F '=' '{print $2}' splits the line using “=” as the separator, and prints the second element. | is the separator for pipelines of multiple commands, the next command takes the output of the previous command as the input.

Text Editors

There are several text editors available. Popular ones include vim and nano.


  1. Login to HPC-Storrs
  2. Go to your scratch directory and create a new folder called “trail”
  3. Go to the new folder “trail”, and copy a file named “Numb” from “/home/liz18025/Group/share/doc/exercises” to the current directory.
  4. Rename the copied file as “MyNumb”
  5. Now open “MyNumb” with any text-editor: a. change the title(first line) from “Numb” to “Not Numb”; b. insert a new line after the title with your UCONN NetID; c. delete the last two lines of this file.
  6. grep all lines that contains “numb” in the file “MyNumb”
  7. Send the path of the current directory to me through Slack or Email.