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Troubleshooting Full Disk Issues on Linux Servers

Audience: System Administrators, Home Lab Users, DevOps
Last Updated: July 2025
Author: LeValle Bradix

Symptoms

You may encounter one or more of the following:

  • No space left on device errors
  • Failed systemd services or application crashes
  • Inability to write files or restart processes
  • Cron jobs or backup tasks failing
  • System becomes unresponsive or fails to boot

Immediate Checks

  1. Check overall disk usage: 

    df -h

  2. Find large directories: 

    sudo du -sh /* 2>/dev/null | sort -h

  3. Check inside /var (commonly problematic): 

    sudo du -sh /var/* | sort -h

  4. Look for large log files: 

    sudo find /var/log -type f -size +50M

Safe Cleanup Actions

Always verify before deleting. Use ls -lh to inspect.

Rotate or delete logs:

sudo journalctl --vacuum-size=100M
sudo rm -f /var/log/*.gz /var/log/*.[0-9]

Clean apt/yum cache:

  • Debian/Ubuntu:
    sudo apt clean
  • RHEL/Fedora: 
    sudo dnf clean all

Clear thumbnail or temp files (desktop systems):

rm -rf ~/.cache/thumbnails/*
sudo rm -rf /tmp/*

Root Cause Analysis

  • Did a service generate excessive logs? (/var/log/syslog, journald)
  • Did backups or cron jobs write to the wrong location?
  • Are containers, VMs, or snapshots eating space?
  • Was logrotate or a cleanup script misconfigured?

Preventive Measures

  • Enable log rotation:

    sudo nano /etc/logrotate.conf

  • Schedule a monthly disk usage audit via cron:

    crontab -e
# Add:
0 7 1 * * df -h | mail -s "Monthly Disk Report" your@email.com

  • Monitor disk usage with tools like:

    • ncdu
    • glances
    • netdata or grafana

When to Escalate or Reboot

  • Root (/) partition is full and blocking critical services
  • You can't delete anything safely
  • Disk hardware is failing (use smartctl, dmesg)

Quick Fix Checklist

  • df -h run, issue confirmed
  • Large folders identified via du -sh
  • Logs or cache cleaned
  • Root cause documented
  • Prevention in place

Pro Tip: Keep /var/log, /tmp, and /home on separate partitions when possible to isolate failures.