nvme-cleanup-strategies

Purpose

Comprehensive guide for safely cleaning up disk space on Linux systems with NVMe SSDs, targeting developer environments with Docker, Node.js/pnpm, Python tools, and application caches.

Key Findings

Common Storage Consumers in Developer Environments

Docker artifacts - Images, build cache, and volumes can consume 100GB+
Language package managers - uv (Python), pnpm/npm (Node.js) maintain global caches
Application caches - JetBrains, Chrome, Whisper AI models, etc.
Trash directory - Often forgotten, can accumulate 50GB+
Project dependencies - node_modules directories across projects

Safe Cleanup Priority Levels

High Priority (Safe, High Impact):

Empty trash
Docker build cache and unused images
Package manager caches (uv, pnpm, npm)
Application caches (browser, IDE)
Old downloads

Medium Priority (Requires Review):

Docker volumes
AI model caches (if not actively used)
Project build artifacts
Large unused projects

Low Priority (Risky, Manual Review):

System logs (journalctl)
Project source code

Cleanup Commands & Strategies

1. Empty Trash (Immediate ~61GB Recovery)

# Check trash size first
du -sh ~/.local/share/Trash

# Empty trash
rm -rf ~/.local/share/Trash/*

Impact: Can reclaim 50-100GB+ depending on accumulated deletions.

2. Docker Cleanup (~170GB Potential)

# Show Docker disk usage
docker system df

# Remove unused containers, networks, images, and build cache
docker system prune -a --volumes

# More targeted cleanup:
docker image prune -a     # Remove unused images only
docker builder prune -a   # Remove build cache only
docker volume prune       # Remove unused volumes

Impact:

Build cache: ~78GB
Unused images: ~86GB
Volumes: Variable, check before removing

Important: Ensure Docker is running before executing cleanup commands.

3. Python uv Cache Cleanup (~65GB)

# Check uv cache size
du -sh ~/.cache/uv

# Clean uv cache (safe - will re-download as needed)
uv cache clean

# Or manually remove
rm -rf ~/.cache/uv

Impact: ~65GB immediate recovery. Cache rebuilds automatically when needed.

4. pnpm Package Manager Cleanup (~8GB Store)

# Prune unreferenced packages
pnpm store prune

# Check store size
du -sh ~/.local/share/pnpm/store

# Check cache
du -sh ~/.cache/pnpm
rm -rf ~/.cache/pnpm  # Safe to remove

Impact:

Store pruning: Variable (removes orphaned packages)
Cache: ~236MB+

Important: Unlike npm, pnpm uses symlinks. Never delete the entire store directory without pnpm store prune as it will break existing node_modules across all projects.

5. npm Cache Cleanup

# Verify and clean npm cache
npm cache verify
npm cache clean --force

Impact: Variable, typically a few GB.

6. Browser & Application Caches

# Chrome cache (~5GB)
rm -rf ~/.cache/google-chrome

# GitHub Copilot cache (~6GB)
rm -rf ~/.cache/github-copilot

# Whisper AI models (~5GB - only if not used)
rm -rf ~/.cache/whisper

# HuggingFace models (~3GB - only if not used)
rm -rf ~/.cache/huggingface

# JetBrains cache (~16GB)
rm -rf ~/.cache/JetBrains

Impact: 10-30GB total. Caches rebuild automatically when needed.

Warning: Only remove AI model caches (whisper, huggingface) if you’re not actively using them, as redownloading can be time-consuming.

7. Playwright & Puppeteer Browsers

# Playwright browsers (~2GB)
rm -rf ~/.cache/ms-playwright

# Puppeteer browsers (~1.1GB)
rm -rf ~/.cache/puppeteer

Impact: ~3GB. Browsers reinstall when needed.

8. System Journal Logs

# Check journal size
journalctl --disk-usage

# Keep only last 3 days
sudo journalctl --vacuum-time=3d

# Or limit to size (e.g., 500MB)
sudo journalctl --vacuum-size=500M

Impact: Variable, typically 1-5GB. Safe to reduce.

9. Downloads Folder Review

# Check downloads size
du -sh ~/Downloads

# Review and delete manually
ls -lhS ~/Downloads | head -20  # Show largest files

Impact: Variable. Manual review recommended.

10. Find Large node_modules Directories

# Find all node_modules directories and their sizes
find ~ -name "node_modules" -type d -prune -exec du -sh {} \; 2>/dev/null | sort -hr

# Remove specific project's node_modules (can reinstall with pnpm install)
rm -rf /path/to/project/node_modules

Impact: Variable. Each node_modules can be 100MB-1GB+. Safe to remove as they can be reinstalled.

Recommended Cleanup Workflow

Quick Win (15 minutes, ~150GB+)

# 1. Empty trash
rm -rf ~/.local/share/Trash/*

# 2. Clean Docker
docker system prune -a --volumes

# 3. Clean Python uv cache
uv cache clean

# 4. Clean pnpm
pnpm store prune

# 5. Clean npm
npm cache clean --force

# 6. Clean browser cache
rm -rf ~/.cache/google-chrome

# 7. Trim system logs
sudo journalctl --vacuum-time=7d

Deep Clean (1 hour, additional ~50GB)

Review and clean AI model caches (whisper, huggingface)
Clean JetBrains cache (rebuilds on next launch)
Find and remove old project node_modules
Review Downloads folder
Audit large projects for old branches/build artifacts

NVMe SSD Specific Considerations

TRIM Support

Ensure TRIM is enabled for optimal SSD performance:

# Check if TRIM is enabled
sudo systemctl status fstrim.timer

# Enable weekly TRIM
sudo systemctl enable fstrim.timer
sudo systemctl start fstrim.timer

Secure Erase (Data Sanitization)

For complete drive wipe only (backup data first!):

# Check drive capabilities
nvme id-ctrl /dev/nvme0 -H | grep -E 'Format |Crypto Erase|Sanitize'

# Use nvme-sanitize (most thorough, NVMe 1.3+)
sudo nvme sanitize /dev/nvme0 -a 0x02

# Or nvme-format (faster, less thorough)
sudo nvme format /dev/nvme0 -s 1

Important Warnings:

Never use on USB-connected drives (can brick device)
Avoid “Overwrite” action on SSDs (reduces endurance)
Self-Encrypting Drives (OPAL): Crypto erase changes encryption key, making all data unrecoverable
Always backup before any secure erase operation

Tools

nvme-cli: NVMe-specific utilities for format and sanitize operations
hdparm: Legacy tool for SATA SSDs (not for NVMe)
Parted Magic: Bootable secure erase utility ($15, comprehensive GUI)
Vendor tools: Samsung Magician, Dell BIOS Data Wipe, etc.

Monitoring & Prevention

Regular Maintenance

# Weekly: Check disk usage
df -h /

# Monthly: Review largest directories
du -h --max-depth=1 ~ | sort -hr | head -20

# Quarterly: Deep clean caches and Docker
docker system prune -a --volumes
pnpm store prune

Automated Cleanup

Consider adding to crontab or systemd timer:

#!/bin/bash
docker system prune -f
pnpm store prune
npm cache clean --force
journalctl --vacuum-time=7d
rm -rf ~/.cache/google-chrome

Storage Monitoring Tools

# Install ncdu for interactive disk usage
sudo apt install ncdu

# Use to explore large directories
ncdu ~
ncdu /

Package Manager Cache Comparison

Tool	Cache Location	Safe to Delete	Prune Command
uv (Python)	`~/.cache/uv`	Yes	`uv cache clean`
pnpm	`~/.local/share/pnpm/store`	Prune only	`pnpm store prune`
npm	`~/.cache/npm`	Yes	`npm cache clean --force`
pip	`~/.cache/pip`	Yes	`pip cache purge`

Key Difference: pnpm uses symlinks, so never delete the entire store directory manually. Always use pnpm store prune to safely remove orphaned packages.