latest
Quickstart
About
Cluster Usage: Rules and Guidelines
General Etiquette
Rules
1. Do not store sensative information on the cluster
2. Do not abuse cluster resources
Guidelines
1. Avoid running scripts directly
2. Avoid running jobs on the head node
3. Use globus to transfer large files onto the cluster
4. Run jobs in an appropriate partition
5. Avoid allocating unnecessary recources
6. Avoid running unnessary jobs
7. Avoid queueing an extreme number of jobs
8. Be aware of software licenses
Connecting to Buddy
Get an Account
Connect Through Open Ondemand
Connect Through SSH
General
Open OnDemand
Access and Login
Interactive Applications
Queue
Number of Hours
Number of Cores
Version
Additonal Modules
Other Options
File Browser
Top Menu
Navigation Menu
File Context Menu
File Editor
File Options
Editor Options
Terminal Access
Job Management
View Options
Job Context Menu
Job Composer
Overview
Creating Job From Template
Modifying Job Options
Saving and Managing Templates
Using the Terminal
Background
Accessing the Terminal
Web browser Access
SSH Access
Terminal Basics
Navigation
Creating and Deleting Files and Directories
Copy, Move, and Rename
Common Commands and Features
File Viewing/Editing and Pipes
Viewing
Editing with nano
Editing with vim
Pipes
Shortcuts
Searching
grep
find
File Permissions and Information
Listing file info
Changing file permissions
Compressing and Uncompressing
Downloading Files
wget
sftp
git
Tips and Tricks
Basic Bash Scripting
Hello World
Basic Logic
Variables
Branching and Conditions
Loops
Providing Input
Troubleshooting
Slurm
Terminology
Tasks
Partitions
Cores
Commands
Sbatch Parameters
Common sbatch parameters
Common toolchains
Component versions in
foss
toolchain
Component versions in
intel
toolchain
Component versions in
foss
toolchain (deprecated versions)
Component versions in
intel
toolchain (deprecated versions)
Data Storage
Home Folder
Project Space
Scratch Storage
Data Transfer
Using SFTP or SCP
Using Github
Using Globus
1. Make an Account and Obtain a Golbus ID
2. Log in with Globus ID
3. Connect to Buddy
Account and Software Requests
General Account Request
Classroom Account Request
Software Request
Tips and Tricks
Slurm
Use
%j-PROJECT.out
for output files
Create general scripts
Python
Use the
-u
flag
Software
Overview
ANSYS
COMSOL
Anaconda
Example Script
Gaussian
Example Script
Jupyter/Python
R/RStudio
Stacks
Advanced
Overview
Advanced Slurm
Array Jobs
Using Git and Github
Machine Learning
OMPI
Other HPC Resources
OURRstore
buddy-documentation
R/RStudio
Edit on GitHub
R/RStudio
Read the Docs
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latest
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epub
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