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Research Computing and Data Workshops
Introductory Sequence
Introduction to Linux
Workshop Outline
What is Linux?
Shell Specifics
Accessing the Palmetto Cluster
Navigating Files and Directories
Working With Files and Directories
File Permissions and Atrributes
Pipes and Redirection
Finding Things
Utilities and Useful Information
Workshop Conclusion
Introduction to Palmetto
Introduction
Accessing the Palmetto Cluster
The structure of the Palmetto Cluster
Storage on Palmetto
Running an interactive job on Palmetto
Transferring files to and from Palmetto
Web-based access to the Palmetto Cluster
Running a batch job
R
Introduction to R
Introduction to R
Basics of R
Data Structures
Vectors, Matrices, Lists and Data Frames
Control Structure
Functions
Parallel Computing in R
Basic plotting with R
Ploting with ggplot
R in Palmetto
Machine Learning using R
Introduction to Machine Learning
Introduction to Caret
Data Partition with caret
Evaluation Metrics with caret
Training Machine Learning model using Regression Method
Classification with decision boundaries
Nearest Neighbours Classification
Training Machine Learning model using Tree-based model
Training Machine Learning model using Ensemble approach
Unsupervised Learning
Neural Network
Python
Introduction to Python Programming
Introduction to Python I
Introduction to Python II
Introduction to Python III
Matplotlib
Machine Learning using Python
TL;DR
Preparing data
Data partition: training and testing
Model Pipelines in Sklearn
Deep Learning in Python
Introduction to Deep Learning
Deep Learning Library Framework
Recap on ANN
Introduction to Keras
Training Deep Learning Regression model with Keras
Training Deep Learning Classification model with Keras
Convolution Neural Network for image classification
Recurrent Neural Network for Timeseries forecasting
Big Data Analytics in Python
Introduction to Apache Spark
Launching the Spark cluster
1. Where are the notebooks
Deep Learning
Deep Learning in Pytorch
PyTorch Quickstart
PyTorch Basics
Pytorch GPU support
Regression and Classification with Fully Connected Neural Networks
High Dimensional Data
Datasets and data loading
Building the network
Computer Vision and Convolutional Neural Networks
Advanced Deep Learning in Pytorch
EMNIST Baseline
Move reused code into python script files
Model fine-tuning
Pytorch Lightning
Training Techniques
Attention, Transformers, and LLMs: a hands-on introduction in Pytorch
Preparing data for LLM training
Small Language Models: an introduction to autoregressive language modeling
Attention is all you need
Other LLM Topics
Advanced Palmetto Usage
Containerization on Palmetto (under development)
Introduction to CloudLab
Docker Containers on CloudLab
Singularity/Apptainers on Palmetto
Advanced Scheduling (under development)
1. What is Spark?
Software Development Life Cycle
Introduction to Version Control with Git and GitLab
Version Control Overview
Git Version Control
Git Commands
Installing Git
Practice With a Local Repository
GitLab
Collaboration and Conflicts
More Resources
Index
