If your Linux VPS reports “No space left on device,” start by identifying the affected filesystem, then determine whether it is out of storage blocks or inodes. Use df for the filesystem-level view, du or ncdu to locate large directories, and lsof +L1 to find deleted files that are still held open. This sequence also explains the common case where df says the disk is full but du cannot find the missing gigabytes.
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Start with a safe, read-only triage
Connect over SSH and avoid deleting anything until you know which mount is full and what owns the data. Most investigation commands only read metadata, so you can run them even when an application is failing because of low space.
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df -h. - Check inode consumption with
df -i. - Check filesystem types and mount layout with
df -T. - Use
duorncduon the affected mount, staying on that filesystem. - If the totals do not match, inspect open-but-deleted files with
sudo lsof +L1.
Use sudo consistently. Without root access, du and lsof may be unable to read private directories and will under-report usage.
1. Confirm which filesystem is full
Read block usage with df -h
df -hThe output is one row per mounted filesystem. Focus on the Use%, Used, Avail and Mounted on columns. A VPS can have separate mounts for /, /var, /home or /boot; a nearly empty root filesystem does not help if a dedicated /var partition is full.
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Check whether inodes, not bytes, are exhausted
df -iInodes are the filesystem records used to track files and directories. Millions of tiny session files, mail-queue entries or application cache files can consume every inode while df -h still shows free gigabytes. When IUse% reaches 100%, creating a new file can fail with “No space left on device” even though byte usage looks safe.
Inspect filesystem types and mount boundaries
df -TThis command adds the filesystem type and helps you see which mount point is actually full. Record the mount point before running du; investigating / when the problem is a separate /var mount produces confusing totals.
2. Rank directories by size with du
Once you know the affected mount, summarize its immediate children and sort the result numerically:
sudo du -xh --max-depth=1 / | sort -hRead the final lines: they are the largest directories. If /var is largest, repeat the same pattern there:
sudo du -xh --max-depth=1 /var | sort -hContinue into the largest child, such as /var/log, /var/lib or /var/cache, until you reach the files or service-specific directory responsible.
Why the flags matter
-hprints human-readable units.--max-depth=1gives one summary per immediate child instead of flooding the terminal with every file.-xkeeps the calculation on one filesystem. It prevents mounted disks, bind mounts and virtual filesystems from being counted as though they belonged to the mount you are measuring.
For a server, keep -x as the default. Some guides omit it, but crossing into another mount can make du appear much larger than the corresponding df row. Compare the final du total with the matching mount point in df; they should be reasonably close when no deleted-open files are involved.
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Measure a non-root mount directly
If df -T shows that /var is a separate filesystem, scan that path rather than scanning the whole root tree:
sudo du -xh -x --max-depth=1 /var | sort -hDo not treat a large virtual path as ordinary disk data. Directories such as /proc and /sys expose kernel state, not persistent files to remove.
3. Browse the result interactively with ncdu
ncdu provides a keyboard-driven view that is useful over SSH. Install it using your distribution’s package manager, then scan the affected mount:
sudo ncdu -x /Use the arrow keys to move through directories and press Enter to open one. The -x option has the same single-filesystem purpose as it does with du. ncdu was designed primarily for remote shells, so it is practical when a VPS has no graphical tools.
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4. When df is much larger than du
A large gap between filesystem usage reported by df and visible files reported by du often means a process still has a deleted file open. This commonly happens with a log: an administrator removes the directory entry, but the logging process keeps the file descriptor and its disk blocks remain allocated.
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Find deleted files that are still open
sudo lsof +L1The +L1 filter lists open files whose link count is zero. Look for a large SIZE/OFF value and note the process ID, command and pathname. The pathname may include “(deleted)”.
Release the space safely
Deleting the name is not enough; the process must close the descriptor. Use the service’s documented log-reopen or reload mechanism first. If it cannot reopen logs, perform a controlled restart of the owning service during an appropriate maintenance window. Avoid blanket killing of processes, which can interrupt unrelated workloads or corrupt active operations.
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Some administrators suggest truncating a live log in place with truncate -s 0. Treat that as a service-specific option to verify before use: truncation can destroy information needed for incident analysis, and behavior depends on how the process writes the file. After a reload or restart, run df -h again to confirm that the space returned.
5. Check systemd journal retention
On systems using systemd, the journal can grow independently of ordinary files in /var/log. Measure its current footprint:
journalctl --disk-usageTo remove archived entries by size, run:
sudo journalctl --vacuum-size=200MOr remove archived entries older than seven days:
sudo journalctl --vacuum-time=7dVacuuming removes archived journal files only; it does not remove the active journal file. Rotate first when you need recent entries to become eligible:
sudo journalctl --rotate
sudo journalctl --vacuum-size=200MChoose a size or age that preserves the logs required for debugging and compliance. To prevent the same emergency from recurring, set persistent limits in /etc/systemd/journald.conf, then reload or restart journald according to your distribution’s procedure. A limit is a retention policy, not a substitute for fixing an application that emits runaway errors.
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6. Investigate Docker storage, if Docker is installed
Docker stores image layers, writable container layers, volumes and build cache under its data root. Get a high-level report first:
docker system dfFor object-by-object detail, use:
docker system df -vReview the detailed list before pruning. The scopes differ:
| Command | Removes | What it keeps by default |
|---|---|---|
docker system prune |
Stopped containers, unused networks, dangling images and build cache | Volumes and unused tagged images |
docker system prune --volumes |
The items above plus eligible unused volumes | Volumes still referenced by containers |
docker system prune -a |
The items above plus unused tagged images | Images used by at least one container |
docker volume prune |
Unused named volumes | Volumes referenced by a container |
Prune commands are destructive. Confirm that an image, stopped container, build cache or volume is not needed for rollback, a database, save files or a game-server world before removing it. Plain docker system prune does not remove unused named volumes; handle those separately only after inspection.
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7. Inspect the usual non-container culprits
Unrotated logs
Drill into /var/log with du and look for current logs, rotated archives and unexpectedly large application-specific files. Fix log rotation or the application’s verbosity rather than repeatedly deleting logs. Removing a log that is still open can create the df/du mismatch described above.
Package caches
Package managers can retain downloaded archives in /var/cache. Identify the owning package manager and use its supported cache-cleaning command; do not delete arbitrary files from package databases.
Old kernels
Multiple kernel packages may remain in /boot or the package database after upgrades. Keep the running kernel and at least one known-good fallback. Remove older kernels only through the distribution’s package manager, never by deleting files from /boot manually.
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Backups and administrator files
Check /root, application backup directories and temporary export locations. Backups are often the largest legitimate files on a small VPS. Verify that a copy exists elsewhere and that the retention policy allows removal before deleting one.
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Small-file floods
If inode usage is the problem, size alone will not identify it. Descend with du and count entries in suspected session, cache, queue or mail-spool directories. Clean them with the service’s retention mechanism, and investigate why expiration or queue processing stopped.
8. Recover when applications are already failing
When a full filesystem prevents package installation, logging or temporary-file creation, preserve a small amount of space for diagnostics:
- Stop a nonessential service that is generating data, if you can do so safely.
- Use
df -h,df -i,duandlsof +L1before removing anything. - Release deleted-open files through a log reopen or controlled service restart.
- Vacuum archived journals after rotating them.
- Remove only confirmed disposable caches, failed builds or expired backups.
Never delete from /proc, /sys or arbitrary system directories to create emergency space. If the VPS remains full after safe cleanup, increase the virtual disk or attach a separate volume, then expand the partition and filesystem using procedures appropriate to its filesystem type.
9. Make the result permanent
Finding the largest directory solves today’s outage; retention controls prevent the next one. After recovery:
Do these 3 things before closing this tab:
1Clear out junk files and repair common Windows errors2Scan for outdated or missing drivers - takes under a minute3Repair Windows errors before they cause bigger problems- Set log rotation and confirm that rotated files are compressed and eventually deleted.
- Configure journald size or time limits in
/etc/systemd/journald.conf. - Give Docker images, build cache, containers and volumes explicit ownership and cleanup rules.
- Set expiration for sessions, queues, caches, temporary exports and backups.
- Monitor both filesystem bytes (
df -h) and inode percentage (df -i). - Alert before a mount reaches 100%, leaving room for logs and recovery commands.
- For game servers, include world saves, map backups, workshop downloads and crash dumps in the retention plan; these often live outside the directory you first expect.
A repeatable command checklist
# Filesystem blocks, inodes and types
df -h
df -i
df -T
# Largest directories on one filesystem
sudo du -xh -x --max-depth=1 / | sort -h
sudo du -xh -x --max-depth=1 /var | sort -h
# Interactive view
sudo ncdu -x /
# Deleted files still consuming blocks
sudo lsof +L1
# Journal and Docker reports
journalctl --disk-usage
docker system df
docker system df -vRun the directory scan against the mount that df identified, not automatically against /. Keep the output from the first df run so you can verify that the responsible mount’s used space falls after each corrective action.
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