Navigating Storage Locations

Last updated on 2026-08-27 | Edit this page

Estimated time: 15 minutes

Overview

Questions

  • What storage locations are available on Sagehen HPC?
  • How do /rhome and /bigdata differ from /scratch and /tmpfs?
  • What are the capacity limits for each storage location?
  • When should you use each storage location?

Objectives

  • Identify the four storage locations and their purposes
  • Understand which storage is persistent and which is temporary
  • Choose the right storage location for different types of data
  • Check storage quotas using quota_check.sh

Storage Locations on Sagehen HPC

Sagehen provides four storage locations, each designed for different use cases. Access them through the Files menu in the left navigation.

/rhome (Home Directory)

  • Path: /rhome/<myusername>
  • Purpose: Personal files, configuration, source code, small datasets
  • Persistent: Yes – files are preserved across sessions
  • Quota: Shared 1 TB lab quota with /bigdata (BeeGFS filesystem)
  • Access: Files > Home Directory

/bigdata (Shared Research Storage)

  • Path: /bigdata/lab/<labname>
  • Purpose: Large research datasets shared across lab members
  • Persistent: Yes – files are preserved across sessions
  • Quota: Shared 1 TB lab quota with /rhome (BeeGFS filesystem)
  • Access: Files > bigdata

/scratch (Fast Temporary Storage)

  • Path: /scratch
  • Speed: SSD (very fast)
  • Purpose: Intermediate computation results, temporary working files
  • Persistent: No – files are deleted when the job completes
  • Quota: Large, but temporary only
  • Access: Files > scratch

/tmpfs (In-Memory Storage)

  • Path: /tmpfs (per-node, not shared across nodes)
  • Speed: RAM-backed (fastest possible)
  • Purpose: Extremely fast I/O during active jobs
  • Persistent: No – files are deleted when the job completes
  • Capacity: Limited by node RAM
  • Access: Only available within running SLURM jobs
Callout

Choose Your Storage Wisely

Use /rhome for personal files and configuration. Store large research datasets in /bigdata for durability and sharing with collaborators. Use /scratch for temporary files needed during active jobs – but remember, scratch is non-persistent SSD and files are deleted when the job completes. Never rely on /scratch or /tmpfs for permanent storage!

Checking Your Quota

Because /rhome and /bigdata share a BeeGFS filesystem, the standard du command does not report usage correctly. Use the provided script instead:

BASH 

quota_check.sh

Run this from the Web Terminal or a shell session to see your current usage against the 1 TB lab quota.

Summary Table

Location Persistent Speed Shared Best For
/rhome Yes Standard Per-user Config, code, small files
/bigdata Yes Standard Per-lab Research data, results
/scratch No (job) SSD Yes Temp computation files
/tmpfs No (job) RAM Per-node High-speed I/O in jobs
Challenge

Challenge: Match the Storage Location

For each scenario below, choose the best storage location (/rhome, /bigdata, /scratch, or /tmpfs):

  1. You need to store a 200 GB genomics reference dataset that your whole lab uses.
  2. You are writing a Python script for your analysis pipeline.
  3. Your SLURM job produces 50 GB of intermediate files that are only needed during computation.
  4. You need the fastest possible I/O for reading millions of small temporary files during a single job.
  5. You want to keep your .bashrc and SSH configuration files.
  1. /bigdata – Large, shared dataset that needs to persist and be accessible to the whole lab.
  2. /rhome – Small personal file (source code) that should persist across sessions.
  3. /scratch – Intermediate files only needed during the job; deleted when the job completes.
  4. /tmpfs – RAM-backed storage provides the fastest I/O for temporary files within a single job.
  5. /rhome – Personal configuration files belong in your home directory.
Key Points
  • Sagehen has four storage locations: /rhome, /bigdata, /scratch, and /tmpfs
  • /rhome and /bigdata are persistent and share a 1 TB lab quota on BeeGFS
  • /scratch is non-persistent SSD storage deleted when the job completes
  • /tmpfs is RAM-backed storage deleted when the job completes
  • Use quota_check.sh to check usage – du does not work correctly on BeeGFS
  • Choose storage based on persistence needs, speed requirements, and sharing