A Quarto book providing guidance, best practices, and recommendations for users of Sasquatch, a High Performance Computing (HPC) cluster.
Note: This is an archival portfolio project — a snapshot of documentation built for a previous organization. Content may not reflect current Slurm syntax or HPC best practices.
This guide covers the full lifecycle of HPC usage, from initial onboarding through advanced job optimization. It is structured for users at all experience levels:
- New to HPC entirely? Start with the Introduction to HPC Clusters section.
- Familiar with HPC but new to Sasquatch? Start with the Quick Start Guide.
| Part | Content |
|---|---|
| HPC Quick Start Guide | Onboarding, quick start, examples, FAQ |
| Sasquatch | Cluster overview, access, storage, policies |
| Slurm | Job scheduler, submission, monitoring, scaling |
| Software | Modules, containers, R, Mamba, installation |
| Posit | Posit Workbench and Connect |
| Working Smarter | Optimization, parallelism, GPUs, Nextflow, SSH, Git, IDEs |
| RSC Resources | Support, training sessions, Linux cheat sheet |
- Quarto CLI (any recent release)
- R (≥ 4.0 recommended)
- R packages listed in
DESCRIPTION
# Option 1: using renv (recommended for reproducibility)
install.packages("renv")
renv::restore()
# Option 2: install packages from DESCRIPTION manually
install.packages(c(
"knitr", "rmarkdown", "quarto",
"dplyr", "ggplot2", "readr", "tibble",
"tidyr", "purrr", "stringr", "kableExtra"
))quarto renderOutput is written to _book/.
quarto previewOpens the book in a browser and reloads automatically as you edit .qmd files.
_quarto.yml # Book configuration (structure, theme, format)
_variables.yml # Shared variables (paths, links used across chapters)
DESCRIPTION # R package metadata and declared dependencies
index.qmd # Preface / book home page
*.qmd # Chapter source files
images/ # Screenshots and figures referenced by chapters
styles.css # Custom HTML styling
_book/ # Rendered HTML output (generated, not committed)
.quarto/ # Quarto build cache (generated, not committed)
| Property | Value |
|---|---|
| Engine | knitr (R) |
| Output format | HTML |
| HTML theme | cosmo |
| Quarto extensions | None |
| Code evaluation | Disabled (eval: false) — code is shown but not run at render time |
| Category | Packages |
|---|---|
| Core rendering | knitr, rmarkdown, quarto |
| Data wrangling | dplyr, readr, tibble, tidyr, purrr, stringr |
| Visualization | ggplot2 |
| Table formatting | kableExtra |