Navigating the Filesystem

Overview

Questions

• How is the Sagehen HPC filesystem organized?
• What are the different storage spaces and what are they for?
• How do I check my storage quota?

Objectives

• Understand the different storage locations on Sagehen
• Distinguish between persistent and temporary storage
• Check storage quotas and usage
• Navigate the filesystem using fundamental Linux commands

Sagehen HPC’s Storage Architecture

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Sagehen uses a BeeGFS parallel filesystem connected via 100 Gb Infiniband. It has multiple storage systems, each designed for specific purposes.

Sagehen HPC’s storage hierarchy: persistent gold tiers at the top, encrypted storage for RESTRICTED data in the middle, and fast temporary tiers at the bottom.

Storage Location Overview

Location	Quota	Backup	Persistence	Speed	Use Case
/rhome/<myusername>	~100 GB	Daily	Persistent	Medium	Code, config, small results
/bigdata/lab/<labname>	1 TB/lab	Daily	Persistent	Medium	Lab datasets, shared files
/scratch/...	None	No	Temporary	Fast (SSD)	Large intermediate files
/tmpfs	~1 GB/job	No	Temporary	Fastest (RAM)	Ultra-fast I/O during jobs

Note: /rhome and /bigdata share a combined 1 TB lab quota.

Your Home Directory: /rhome/<myusername>

This is your personal space on Sagehen.

• Size: Approximately 100 GB
• Backup: Yes, daily backups
• When to use: Source code, configuration files, small result files
• When NOT to use: Large datasets, temporary files from jobs

BASH

# Navigate to your home directory
cd ~

# See where you are
pwd

# List files with details
ls -lah

Callout

The Tilde Shortcut

In bash, ~ always refers to your home directory:

BASH

cd ~              # Go to home
cd ~/workshop-0   # Go to workshop-0 in home
cp file.txt ~     # Copy file to home

Lab Storage: /bigdata/lab/<labname>

If you’re part of a research lab, you may have access to shared lab storage.

• Size: 1 TB per lab group (shared among all lab members)
• Backup: Yes, daily backups
• When to use: Large datasets, results shared with collaborators

BASH

# Check if you have lab storage
ls /bigdata/lab

If you don’t see your lab listed, contact its-hpc@pomona.edu.

Scratch Storage

High-speed temporary SSD storage designed for jobs that need fast I/O.

• Location: /scratch/$SLURM_JOB_USER/$SLURM_JOB_ID
• Lifetime: Deleted when job completes (non-persistent)
• When to use: Large temporary files created during job execution

RAM Disk: /tmpfs

Ultra-fast memory-backed storage.

• Lifetime: Deleted when job ends
• Size: Limited (~1-2 GB per job)
• When to use: Only for jobs with extreme I/O needs

Essential Navigation Commands

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BASH

# Print working directory (where am I?)
pwd

# List files in current directory
ls

# List with human-readable sizes and hidden files
ls -lah

# Change to home directory
cd

# Change to a specific directory
cd /rhome/<myusername>

# Change to previous directory
cd -

# Change up one level
cd ..

Checking Your Storage Usage

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Callout

BeeGFS Quota Check

On Sagehen’s BeeGFS filesystem, the standard du command does not work correctly for quota checks. Use the provided script instead:

BASH

quota_check.sh

This will display your current usage against your quota.

Output of quota_check.sh: the lab’s shared pool usage on top, your per-user usage below.

If you’re approaching your quota, consider:

1. Compressing old results: tar czf archive.tar.gz data/
2. Removing unnecessary files
3. Moving data to lab storage: mv results /bigdata/lab/<labname>/
4. Contacting its-hpc@pomona.edu for additional storage

Challenge

Challenge 1: Explore Sagehen HPC’s Storage

Connect to Sagehen and explore the filesystem.

Steps:

1. Check your home directory: cd ~ && pwd
2. List its contents: ls -lah
3. Check for lab storage: ls /bigdata/lab
4. Run the quota check: quota_check.sh

Questions:

• What is the full path to your home directory?
• Do you have access to lab storage?
• How much of your quota is used?

Show me the solution

• Your home directory should be /rhome/<myusername>
• Lab storage appears under /bigdata/lab/ if your lab has been set up
• quota_check.sh shows your current usage vs. your quota limit

If you’re using close to 100 GB, consider cleaning up old files. Contact its-hpc@pomona.edu if you need more space.

Key Points

• Sagehen uses BeeGFS over 100 Gb Infiniband for its parallel filesystem
• Your home directory /rhome/<myusername> is persistent and backed up (~100 GB)
• Lab storage /bigdata/lab/<labname> provides 1 TB shared among lab members
• Scratch (/scratch) is SSD-based and deleted when your job completes
• RAM disk (/tmpfs) is the fastest but most ephemeral storage
• Use quota_check.sh to check your storage usage (not du)
• Essential navigation: pwd, ls, cd, cd ~, cd ..