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.
[Related Page - Anaconda]
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. 
[Related Page - Associations & Quality of Service]
Batch Jobs
Put simply, batch jobs are scheduled programs that are assigned to run on a computer without further user interaction.
[Related Page - Batch Jobs]
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)
[Related Page - Using a CESM module]
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.
[Related Page - CIFS non-AD]
Condo
PIs can purchase condos that have a significant amount of computing resources which can be shared with others.
[Related Page - Account Types]
CUDA
"CUDA is an extension of the C language, as well as a runtime library, to facilitate general-purpose programming of NVIDIA GPUs." (Source)
[Related Page - Intro to CUDA]
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.
[Related Page - Job Arrays]
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."
[Related Page - Jupyter Notebooks on Oscar]
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.
[Related Page - Interactive Jobs]
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.
[Related Page - Using Modules]
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
[Related Page - MPI Jobs]
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.
[Related Page - Slurm Partitions]
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.
[Related Page - Account Types]
PuTTY
A client for SSH for Windows and Unix that emulates a terminal
[Related Page - SSH (Terminal)]
Python
An object-oriented, high-level, and popular programming language
[Related Page - Python on Oscar]
Slurm
A workload manager used within Oscar to schedule jobs
[Related Page - Slurm Partitions]
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
[Related Page  - SSH (Terminal)]
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.
[Related Page - SMB (Local Mount)]
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.
[Related Page - VNC (Virtual Desktop)]
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.
[Related Page - Associations & Quality of Service (QOS)]
​

Short "How to" Videos

Common Acronyms and Terms

Last modified 4mo ago

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

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.

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. [Related Page - Anaconda]
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. [Related Page - Associations & Quality of Service]
Batch Jobs	Put simply, batch jobs are scheduled programs that are assigned to run on a computer without further user interaction. [Related Page - Batch Jobs]
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) [Related Page - Using a CESM module]
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. [Related Page - CIFS non-AD]
Condo	PIs can purchase condos that have a significant amount of computing resources which can be shared with others. [Related Page - Account Types]
CUDA	"CUDA is an extension of the C language, as well as a runtime library, to facilitate general-purpose programming of NVIDIA GPUs." (Source) [Related Page - Intro to CUDA]
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. [Related Page - Job Arrays]
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." [Related Page - Jupyter Notebooks on Oscar]
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. [Related Page - Interactive Jobs]
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. [Related Page - Using Modules]
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 [Related Page - MPI Jobs]
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. [Related Page - Slurm Partitions]
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. [Related Page - Account Types]
PuTTY	A client for SSH for Windows and Unix that emulates a terminal [Related Page - SSH (Terminal)]
Python	An object-oriented, high-level, and popular programming language [Related Page - Python on Oscar]
Slurm	A workload manager used within Oscar to schedule jobs [Related Page - Slurm Partitions]
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 [Related Page - SSH (Terminal)]
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. [Related Page - SMB (Local Mount)]
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. [Related Page - VNC (Virtual Desktop)]
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. [Related Page - Associations & Quality of Service (QOS)]