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Quick Reference

This page contains Linux commands commonly used on Oscar, basic module commands, and definitions for common terms used within this documentation.

Common Linux Commands

Command
Related Word/Phrase
Description
cd
Change Directory
Moves the user into the specified directory
cd .. to move one directory up
cd by itself to move to home directory
cd- to move to previous directory
cd <directory-path> to move to a directory (can be an absolute path or relative path)
cp <old_file_path> <new_directory_path>
Copy
Copies the file into the specified directory
clear
Clear
Clears the terminal
cat <filename>
Concatenate
Lists the contents of a file
ls
List
Lists contents within the current directory
grep <string_to_match> <filename>
Globally Search for a Regular Expression and Print Matching Lines
Searches for the string / regular expression within the specified file and prints the line(s) with the result
pwd
Present Working Directory
Displays the path of the current directory that you are in
man <command>
Manual
Displays the manual instruction for the given command
mv <file_name> <new_directory>
Move
Moves a file into a new directory
mv <old_file_name> <new_file_name> to rename a file
mkdir <directory_name>
Make Directory
Creates a new directory
rm <directory_name>
Remove
Deletes directories and the contents within them
rmdir <directory_name>
Remove Directory
Removes the specified directory (must be empty)
touch
Touch
Creates a blank new file

Modules

Command
Description
module list
Lists all modules that are currently loaded in your software environment.
module avail
Lists all available modules on the system. Note that a module can have multiple versions.
module help <name>
Prints additional information about the given software.
module load <name>
Adds a module to your current environment. If you load using just the name of a module, you will get the default version. To load a specific version, load the module using its full name with the version: "module load gcc/6.2"
module unload <name>
Removes a module from your current environment.

Common Acronyms and Terms

Term
Description
Anaconda / Conda
A distribution of Python and R used for scientific computing that is meant to simplify package management and deployment. Conda is used for installing packages and managing their dependencies.
Association
Within Oscar, an association refers to a combination of four factors: Cluster, Account, User, and Partition. Associations are used to control job submissions for users.
Batch Jobs
Put simply, batch jobs are scheduled programs that are assigned to run on a computer without further user interaction.
CCV
Brown University's Center for Computation and Visualization. Provides software, expertise, and other services for Brown's research community. See our website for more information.
CESM
Stands for Community Earth System Model. "CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states." (Source)
CIFS
Stands for Common Internet File System. CIFS is a network protocol used for providing shared access to files and devices on the same network. Users who are unable to use SMB for file-sharing should try CIFS as an alternative.
Condo
PIs can purchase condos that have a significant amount of computing resources which can be shared with others.
CUDA
"CUDA is an extension of the C language, as well as a runtime library, to facilitate general-purpose programming of NVIDIA GPUs." (Source)
HPC
Stands for High Performance Computing. HPC is the ability to process data and perform highly complex calculations at an accelerated rate. Oscar is the service that CCV offers to the Brown community for their High Performance Computing needs.
Job Array
A job array is a collection of jobs that all run the same program but on different values of a parameter.
Jupyter Notebook
"The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text."
Interactive Jobs
Jobs that allow the user to interact in real time with applications within Oscar, often from the command line. This differs from batch jobs in that each command to be run must be put in one at a time.
Modules
Modules are software components that can easily be loaded or unloaded into Oscar. For instance, a user can load the Python 3 module using a module load command.
MPI
Stands for Message Passing Interface. MPI is a system that aims to be the standard for portable and efficient message passing. Message passing is a technique often used in object-oriented programming and parallel programming
Partition
Partitions are essentially groupings of nodes that allocate resources for specific types of tasks. On Oscar, partitions are based on job submissions through the Slurm workload manager.
PI
Stands for Principal Investigator. Mainly used to refer to the individual responsible for conducting and administrating a research grant. Within Oscar, PIs have their own data directories that can be shared to students. PIs may also purchase condos.
PuTTY
A client for SSH for Windows and Unix that emulates a terminal
Python
An object-oriented, high-level, and popular programming language
Slurm
A workload manager used within Oscar to schedule jobs
SSH
Stands for Secure Shell Protocol. Used to communicate securely between computers and often used within a command-line interface (CLI) for connections to remote servers
SMB
The Server Message Block (SMB) protocol is a network protocol that allows users to communicate with remote computers for file-sharing and other uses. It is one of the versions of the Common Internet File System (CIFS). Within Oscar, SMB is mainly used for file transfer.
VNC
Stands for Virtual Network Computing. VNC is a desktop sharing system that allows you to remotely control another desktop. On Oscar, it is used to allow a desktop interface for applications.
Quality of Service (QOS)
The job limits that are linked to a given association. For instance, Priority Accounts will generally have a higher quality of service than Exploratory Accounts.