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A Linux VPS reporting 100% disk usage needs diagnosis before deletion. The full condition may mean exhausted data blocks or exhausted inodes, and the affected filesystem may be something other than /. Start with df -hT and df -i, identify the mount and failure symptom, then trace usage with filesystem-bounded tools. Clean only confirmed-safe journals, logs, caches, or unused container data. If legitimate data keeps returning, resize the VPS volume rather than repeatedly deleting files.
1. Confirm what is actually full
Log in through your normal administrative method and establish the scope before changing anything. A write failure, package-manager error, service crash, or No space left on device message can result from either byte exhaustion or inode exhaustion. The two conditions require different remedies.
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df -hTRead the output row by row. Note the filesystem whose percentage is 100%, its mounted path, filesystem type, total size, used space, and available space. Do not assume the root filesystem is the problem: a separate /var, database, home, or attached-data mount can fill independently. Your investigation must stay on the affected mount.
Check inode usage separately
df -iInodes are the filesystem records used to represent files and directories. Millions of tiny files can consume every inode while the filesystem still has free bytes. Conversely, a few large files can exhaust blocks while inode use remains low. Record both percentages before deleting anything.
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Record the operational symptom
- No space left on device: writes, uploads, temporary files, or database operations are failing.
- Package errors: the package manager cannot download, unpack, or create its working files.
- Service crashes: a daemon may be unable to append logs, create sockets, write state, or extend a database.
- Intermittent failures: a filesystem may be close enough to full that bursts of activity consume its remaining free space.
Keep the original df output and timestamp. It provides a baseline for judging whether a cleanup actually released space.
2. Locate the directories consuming the space
Once you know the affected mount, measure directories without crossing into unrelated filesystems. Crossing a mounted database volume, network share, or container mount can make a directory appear responsible when its contents belong elsewhere.
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sudo du -xhd1 /Replace / with the mount point you recorded if it is different. The -x option keeps the scan on one filesystem, -h makes sizes readable, and -d1 limits the first pass to immediate children. Sort the resulting directories mentally or by size, then run the same command inside the largest directory. For example, if /var dominates, inspect /var and then its largest children rather than scanning the entire server repeatedly.
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sudo ncdu -x /ncdu presents an interactive size view while honoring the same filesystem boundary. Navigate into the largest branches and inspect names before deciding whether anything is disposable. Treat delete keys as destructive: measure first, identify the owning service or package, and remove data only through a supported cleanup method.
Interpret apparent discrepancies
du counts directory entries that are visible in the tree it scans. It can therefore miss blocks held by deleted files, and it can report a different scope if you accidentally cross mounts or omit a directory. Compare the mount path in df -hT with the path passed to du; they must describe the same filesystem.
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3. Inspect journals and application logs
Logs are useful evidence, but unbounded retention can consume a small VPS volume. Investigate system journals, ordinary log files, rotated archives, web-server logs, database logs, and application-specific directories.
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Measure the systemd journal
sudo journalctl --disk-usageThe systemd manual describes this operation as: “Shows the current disk usage of all journal files.” The result is the amount occupied by journal files, not necessarily the amount that can be removed immediately. Active journal files may still be receiving entries.
Review ordinary log locations
- Inspect
/var/logand its subdirectories for current files and rotated archives. - Check the application’s own log directory, especially for debug logging accidentally left enabled.
- Review web-server access and error logs, which can grow rapidly under scans or traffic spikes.
- Check database logs and diagnostic dumps; use the database’s retention controls instead of deleting files that are still part of an active logging sequence.
- Look for compressed or date-suffixed archives that have no retention requirement.
Use the service’s supported rotation and retention mechanism whenever one exists. Deleting a file behind a running process may not release space if the process still has it open, and it can also break an application’s expected file ownership or permissions.
4. Reclaim journal space deliberately
Only reduce journal retention after confirming the host’s operational, audit, and troubleshooting requirements. If the policy permits cleanup, rotate active files and then vacuum archived files.
sudo journalctl --rotate
sudo journalctl --vacuum-size=200M--rotate acts on active journal files, while vacuum operations remove archived files. Consequently, the usage reported after the commands can still include active files. A 200 MB limit is an example target, not a universal policy; choose a size that preserves the history your administrators need. Recheck the filesystem with df -hT and measure the journal again.
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5. Check package caches and container storage
Package-manager caches
Package managers retain downloaded packages and metadata so reinstallations and upgrades can be faster. On a constrained VPS, these caches may be a significant but replaceable consumer. Identify the cache through your distribution’s package-manager tools and remove only data that the tool marks as safe to clean. Do not manually erase package database files or lock files.
Container data
Container runtimes commonly store images, writable layers, volumes, build cache, and logs below a data root such as /var/lib/docker (or an equivalent path for another runtime). First determine which category is large. Remove unused images, stopped containers, and build cache only with the runtime’s supported prune or cleanup commands. Never guess at files inside live container layers or volumes: those may contain application state or databases.
Verify the result
After each cleanup category, run df -hT and, when useful, repeat the relevant du scan. Making one controlled change at a time preserves a clear cause-and-effect record and prevents an emergency cleanup from hiding a second growth source.
6. Fix the df/du mismatch
If df -hT reports a full filesystem but visible files from du do not account for the used blocks, inspect open deleted files. A process can keep a deleted log or temporary file allocated until it closes the file descriptor; the directory entry disappears, but the blocks remain charged to the filesystem.
List deleted files still held open
sudo lsof +L1Look for large entries on the affected mount. Note the process ID, executable, user, file size, and path shown as deleted. Confirm that the process really owns the space before taking action; unrelated deleted files on another mount will not solve the current problem.
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Release the blocks in a controlled window
- Identify the owning service and check whether it supports a log reopen, graceful reload, or other non-disruptive operation.
- Schedule a maintenance window if a restart is required, especially for a web server, database, queue, or stateful application.
- Restart or otherwise recycle the owning service using your normal service-management procedure so the file descriptor closes.
- Run
df -hTagain and verify that the expected space returned. - Investigate why rotation or truncation left a large deleted file open, then correct that configuration rather than relying on restarts.
Do not truncate arbitrary files listed by lsof while a service is writing. An unsafe operation can corrupt logs, disrupt application state, or fail to release the allocation you intended to remove.
7. Diagnose inode exhaustion
When df -i reaches 100% while byte usage is comparatively low, search for directories containing enormous numbers of small files. Common locations include mail queues, session directories, application caches, temporary trees, upload staging areas, and development work directories.
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Compare directory counts on the affected mount and narrow the search one branch at a time. Use filesystem-bounded tools so another mount does not distort the result. For a suspicious directory, inspect filename patterns, age, ownership, and whether an application still references the files.
Clean through the supported retention path
- Ask the mail, session, or queue service to expire completed entries.
- Configure application cache and temporary-file retention instead of deleting active working files.
- Remove abandoned work-tree artifacts only after confirming they are not needed for a build, deployment, or recovery.
- Recheck
df -iafter each controlled cleanup.
Deleting a few large files will not help inode exhaustion unless those files also represent the inode pressure. The objective is to reduce the file count safely.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.8. Decide between cleanup and more capacity
Cleanup is appropriate when the usage is accidental, stale, or replaceable. Capacity expansion is appropriate when the data is legitimate, required, and recurring. Use these axes to choose deliberately:
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| Decision axis | Targeted cleanup | Disk or volume expansion |
|---|---|---|
| Reversibility | Removing caches or old logs is often difficult to undo; retention changes can be reversed for future files. | Adding capacity generally preserves existing data, but partition and filesystem changes still need a recovery plan. |
| Operational risk | Risk comes from deleting required logs, images, queues, or application state. | Risk comes from provider operations, partition layout, filesystem support, and possible downtime. |
| Time to relief | Can release space immediately when a safe, large consumer is identified. | Depends on provider provisioning, resizing, partition growth, and filesystem expansion. |
| Persistence | Temporary if the workload continues producing the same data. | Durable for the current growth rate, but not a substitute for retention controls. |
| Backup requirement | Take a tested backup or snapshot before destructive cleanup. | Take a provider snapshot or backup before resizing and filesystem changes. |
| Constraints | Limited by what can be safely removed and by application support. | Provider limits, pricing, supported filesystems, partitioning scheme, and maintenance windows vary. |
| Recurring cost | Usually no new capacity charge, but administration and monitoring continue. | Higher recurring storage cost may apply to the larger VPS disk or attached volume. |
9. Expand a VPS disk safely
If investigation shows that the data is legitimate and recurring, expansion is the correct engineering fix. Provider procedures are not interchangeable: commands, downtime, filesystem support, volume limits, and pricing differ.
- Confirm the target volume and its current partition and filesystem layout.
- Take a provider snapshot or verify a tested backup that can restore the server.
- Resize the VPS disk or attach a larger volume using the provider’s documented procedure.
- Verify that the operating system sees the enlarged block device.
- Grow the partition if the volume uses a partition table and the provider did not do so automatically.
- Grow the filesystem with the method appropriate to its filesystem type and layout.
- Run
df -hTand, if inode pressure was part of the incident,df -ito confirm the new capacity. - Record the new size, partition map, filesystem type, and recovery steps in the server documentation.
Do not publish or apply one provider’s resize command as if it were universal. A wrong device name or filesystem command can make an otherwise recoverable incident worse.
10. Make the fix durable
Bound systemd journal growth
Set journald limits in accordance with your retention requirements. The relevant controls are SystemMaxUse=, RuntimeMaxUse=, SystemKeepFree=, and RuntimeKeepFree=. The systemd documentation states that the first pair defaults to 10% of the filesystem, capped at 4 GiB, while the keep-free pair defaults to 15%, also capped at 4 GiB. Those defaults are safeguards, not a guarantee that a small VPS will retain enough history for your needs; choose explicit limits after considering incident response and audit obligations.
Verify application rotation
Keep application log rotation enabled, confirm that files actually rotate, and check that old archives expire. A configuration that declares rotation but cannot run its scheduler, lacks permissions, or writes to a different directory will not control growth.
Control container logs and images
Configure bounded log retention for the container runtime and review image, build-cache, stopped-container, and volume growth. Schedule supported pruning of objects that are no longer referenced. Exclude persistent application data from automated deletion.
Monitor both bytes and inodes
Alert before either resource reaches 100%. Byte alerts catch large logs, backups, and layers; inode alerts catch small-file explosions. Include each important mount in monitoring rather than watching only /, and test that alerts arrive during a controlled threshold check.
Review recurring consumers
- Temporary files and session directories.
- Package caches.
- Backups and database exports.
- Rotated logs and journal history.
- Container images, layers, volumes, and build cache.
Assign an owner and retention period to each category. A monthly review can reveal a trend before it becomes an outage.
Quick Recap
11. A concise incident runbook
- Run
df -hT; record the full mount and symptom. - Run
df -i; distinguish block exhaustion from inode exhaustion. - Run
sudo du -xhd1on the affected mount or usesudo ncdu -x; recurse into the largest directory. - Measure journals with
sudo journalctl --disk-usageand inspect system, application, web, and database logs. - Rotate and vacuum journals only within policy; use supported package-manager and container-runtime cleanup for replaceable data.
- If
dfanddudisagree, runsudo lsof +L1and recycle the owning service in a controlled window. - If inodes are exhausted, remove millions of small files through the owning application’s cleanup process.
- Recheck both
df -hTanddf -iafter every change. - Snapshot or back up before destructive work or resizing.
- Expand the volume when legitimate recurring data has outgrown the VPS, then apply retention limits and monitoring.
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