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Start by identifying whether the filesystem is out of data blocks or inodes: run df -hT and df -i. Then isolate the affected mount with filesystem-bounded du or ncdu, clean only confirmed-safe logs, journals, caches, or unused container data, and investigate open deleted files if df and du disagree. If the data is legitimate and keeps returning, expand the VPS volume rather than repeatedly deleting files.
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What a 100% disk reading actually means
A Linux VPS reports a disk as full for two different resource limits. The usual case is exhausted data blocks: there is no room for more file contents, temporary files, package downloads, database writes, or log entries. The other case is exhausted inodes, the filesystem records used to represent files and directories. A server can have free gigabytes but still fail to create a file when every inode is consumed.
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Both conditions can produce errors such as No space left on device, failed deployments, package-manager errors, crashed services, and incomplete writes. Do not begin by deleting random files. First establish which mount is full and which resource is exhausted.
First response: confirm the affected filesystem
- Check space by filesystem and type. Run
df -hT. The-hoption makes sizes readable, while-Tshows the filesystem type. Note the mount whoseUse%is 100%; it may be/,/var, a database volume, a Docker data volume, or another mount. A full root filesystem is not the only possible failure. - Check inode consumption separately. Run
df -i. IfIUse%is 100% while byte usage is comparatively low, you have an inode problem and must find excessive numbers of small files rather than merely looking for the largest files. - Record the symptom and timing. Write down whether the failure is a write error, a service crash, a package installation failure, a failed backup, or a deployment that stopped. This helps identify the application that was creating data and prevents you from removing files that are still needed.
- Check the mount before every cleanup command. A directory such as
/var/libmay be on a separate filesystem. Clean the filesystem that is actually full, and do not assume that freeing space under/homewill help a full/varvolume.
Keep a privileged shell available, but avoid starting new services or running large package operations until you have recovered working space. Some emergency commands need a small amount of free space to create temporary files.
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Find what is consuming the bytes
Use a filesystem-bounded scan so that a mounted backup disk, network share, or container volume does not distort the result.
Start with a one-level directory summary
For a full root filesystem, run:
sudo du -xhd1 /
The -x option stays on the filesystem containing the path, -h uses readable units, and -d1 summarizes one directory level. On another mount, replace / with that mount point, for example sudo du -xhd1 /var. Sort or inspect the output and recurse into the largest directory:
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sudo du -xhd1 /varsudo du -xhd1 /var/lib
Repeat only where the previous result shows meaningful usage. This narrowing approach is faster and less disruptive than scanning every path repeatedly.
Use an interactive view when the tree is complicated
If it is installed, ncdu -x / provides an interactive, filesystem-bounded view. Navigate into the largest directories, but treat deletion prompts as dangerous: the tool can show a path clearly without proving that its contents are safe to remove. Use it to investigate, then apply the owning application’s cleanup procedure.
Inspect the usual high-growth locations
/var/logand application-specific log directories, including web-server and database logs./var/log/journalfor systemd journal files.- Package-manager caches under
/var/cacheand related package directories. - Container storage such as
/var/lib/dockeror the data root configured for another runtime. - Backup, export, upload, and temporary directories created by your applications.
- Database data, write-ahead logs, binary logs, and snapshots, which must be managed through database retention controls rather than manual deletion.
Large files are not automatically expendable. A database file, container layer, or current log may be essential even when it is the largest item on the disk.
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Measure and reduce systemd journal usage safely
Measure journal files directly:
sudo journalctl --disk-usage
The systemd manual describes this command as: “Shows the current disk usage of all journal files.” It reports both active and archived journal files, so the number may not equal the size of only the archived files that can be vacuumed.
Rotate, then vacuum archived journals
If your retention policy permits removing older entries, run:
sudo journalctl --rotate
sudo journalctl --vacuum-size=200M
--rotate closes the current active journal and starts a new file. Vacuum operations remove archived files; active files can remain, which explains why a subsequent usage report may still be higher than 200 MB. A size limit is a cleanup decision, not a guarantee that total journal usage will never exceed that number.
Choose retention deliberately
Before vacuuming, determine how long you need logs for incident response, security investigations, compliance, or debugging. If a service has its own log rotation, use that mechanism instead of deleting files in its directory. Removing a current log file can leave the process writing to an unlinked inode, creating the very df/du mismatch discussed below.
Review application and web-server logs
After checking the journal, inspect /var/log and each service’s configured log directory. Look for an unbounded debug log, repeated authentication failures, a crashed worker writing a stack trace in a loop, or rotated archives that never expire.
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- Confirm that log rotation is enabled and that its timer or cron job actually runs.
- Check compression and retention counts; a rotation rule that creates archives without deleting old ones only postpones the problem.
- Use the application’s reload or reopen command after a supported rotation procedure.
- For databases, follow the database vendor’s archive and write-ahead-log retention process. Never remove database log segments by filename guessing.
- For web servers, check access logs, error logs, per-site logs, and any reverse-proxy or application-worker logs.
If one service is growing rapidly, fix its cause—such as a failing upstream, a verbose log level, or a retry loop—after recovering enough space to keep the service stable.
Clean package caches and container data without damaging workloads
Package-manager caches
Inspect package-cache directories and use the package manager’s supported cache-cleaning command for your distribution. A cache can usually be regenerated, but an installed package, a repository metadata file in active use, or a locally stored package needed for an offline recovery may not be disposable. Verify what the command removes before confirming it.
Container images, layers, and logs
Container runtimes can consume space in their data root through old images, stopped containers, writable layers, build caches, and JSON or equivalent container logs. Identify the runtime’s own disk-usage report, then remove only unused objects with its supported prune or cleanup command. Confirm that an image is not needed for rollback and that a stopped container does not contain the only copy of application data.
Do not delete files directly from /var/lib/docker or another runtime data root while the daemon is operating. Manual removal can corrupt metadata, break running containers, or make future cleanup commands unreliable. Keep persistent databases and uploads on deliberate volumes with backups, not inside disposable layers.
When df is full but du cannot find the space
A process can keep an open file after the directory entry has been deleted. The blocks remain allocated until that process closes the file, so df counts the space while du cannot see a pathname for it.
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List open deleted files with:
sudo lsof +L1
Look for a large deleted log or temporary file and note the owning process, user, and file descriptor. Do not truncate or kill a process blindly. Determine whether the service can be reloaded, whether a controlled restart is required, and whether a high-availability or maintenance window is available. Restart or otherwise recycle the owning service using its supported procedure; once the descriptor closes, the kernel releases the blocks. Re-run df -hT and du to confirm recovery.
If a restart is not immediately safe, first free a small amount of space elsewhere, schedule the service action, and monitor the process. A deleted-open file can continue growing while you investigate.
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When df -i shows 100% inode use, search for directories containing millions of small files. Common examples include mail queues, web-session directories, thumbnail or package caches, temporary upload fragments, application work trees, and failed job output.
Use bounded counts to locate concentration without crossing mounts. For example, inspect likely directories with a depth-limited file count and then narrow further:
sudo find /var -xdev -type f | wc -l
This command gives a broad count; repeat it for specific subdirectories rather than launching an unrestricted scan across unrelated filesystems. Once you identify the owner, use the application’s queue-expiry, session-cleanup, cache-pruning, or job-retention feature. Deleting individual files from a live queue or session store can leave inconsistent state even if it frees inodes.
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After cleanup, run df -i again. Byte usage and inode usage are independent, so a successful inode cleanup may barely change the gigabyte figure shown by df -hT.
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Random freezes, missing sound and display glitches usually trace back to one bad driver. Find and replace yours safely.Free scan · under a minuteDecide between cleanup and expanding the VPS disk
Cleanup is appropriate when the usage is accidental, obsolete, or a one-time surge. Capacity expansion is appropriate when the data is legitimate, recurring, and required by the workload. Compare the choices before taking an irreversible action.
| Decision factor | Cleanup of logs, caches, or unused data | Disk or volume expansion |
|---|---|---|
| Reversibility | Removing a cache is often reversible by regeneration; deleting logs, images, or data may not be. | Usually reversible only by shrinking or restoring a backup, which many filesystems and providers do not support in place. |
| Operational risk | Risk comes from deleting active, required, or compliance-relevant data. | Risk comes from snapshot, partition, filesystem, and provider operations; an error can make the volume unavailable. |
| Time to relief | Can be immediate when a large safe target is identified. | Depends on provider provisioning, partition growth, filesystem growth, and any required reboot or maintenance window. |
| Persistence | Temporary unless retention and monitoring are corrected. | Addresses a genuinely undersized volume but does not stop unbounded logs or caches. |
| Backup requirement | Back up or preserve anything that may be needed before destructive deletion. | Take a provider snapshot or tested backup before resizing. |
| Constraints | Depends on what the application can safely expire. | Provider limits, partition layout, filesystem support, region, plan, and available capacity vary. |
| Recurring cost | Usually no added storage charge, but it requires maintenance. | Creates an ongoing storage cost and may affect the VPS plan or attached-volume limits. |
Safe expansion sequence
- Confirm that growth is legitimate and recurring rather than a runaway log, leak, or failed cleanup job.
- Take a provider snapshot or verified backup and confirm that you can restore it.
- Review the provider’s exact resize procedure, supported filesystems, maximum size, downtime expectations, and billing effect.
- Resize the VPS disk or attach a larger volume through that procedure.
- Grow the partition if the partitioning scheme requires it, then grow the filesystem with the command appropriate to that filesystem. Do not copy a command from another provider or assume that a partition and filesystem expand automatically.
- Verify the result with
df -hT, check application health, and confirm that mounts persist after reboot if a configuration file was changed.
Provider commands, filesystem support, pricing, limits, and downtime differ, so there is no universal Linux resize command that is safe for every VPS.
Make the fix durable
Set journald limits
Configure journal retention in journald.conf or an appropriate drop-in after checking your operational and compliance needs. The documented defaults for SystemMaxUse= and RuntimeMaxUse= are 10% of the relevant filesystem, capped at 4 GiB. SystemKeepFree= and RuntimeKeepFree= default to 15%, also capped at 4 GiB. These are defaults, not a substitute for choosing limits that fit your disk and retention policy.
After changing settings, reload or restart journald according to your distribution’s supported procedure, then verify actual usage with journalctl --disk-usage. Keep enough history to diagnose failures without allowing logs to consume the operating system’s working space.
Keep application rotation working
- Set maximum file sizes, retention counts, and compression in the application or system rotation mechanism.
- Verify that the scheduled rotation job runs and that a new log file receives writes after rotation.
- Alert when a single log grows unusually fast instead of waiting for the disk alert.
Control container growth
Set container log limits supported by your runtime, review image and build-cache retention, and schedule pruning of objects that are confirmed unused. Monitor the runtime data root separately from the root filesystem when it is on its own mount.
Monitor both bytes and inodes
Create alerts below 100% for every important mount. Track df -hT-style byte utilization and df -i-style inode utilization; alerting on only one misses the other failure mode. Include trend views so you can distinguish a sudden incident from a steady workload that needs more capacity.
Review temporary files, backups, and database retention
Schedule reviews of temporary directories, export files, local backups, package caches, and database archives. Keep tested backups or snapshots before destructive cleanup and before filesystem resizing. A backup that has never been restored is not proof that recovery will work.
Quick Recap
A concise emergency runbook
- Run
df -hTanddf -i; record the full mount and whether bytes or inodes are exhausted. - Use
sudo du -xhd1 <mount>orncdu -x <mount>to locate the largest branches. - Measure journals with
sudo journalctl --disk-usageand review system, web, application, and database logs. - Apply supported rotation, vacuum, cache cleanup, or container-pruning actions only to confirmed-safe targets.
- If visible files do not explain
df, runsudo lsof +L1and recycle the owning service in a controlled window. - If inodes are full, locate directories with excessive small files and use the owner application’s cleanup process.
- Re-run both
df -hTanddf -i, then verify that failed services, writes, and package operations recover. - If legitimate growth will continue, snapshot or back up the VPS and expand the volume using the provider- and filesystem-specific procedure.
Common mistakes that make a full disk worse
- Deleting by guesswork: removing files from database, container, queue, or runtime directories can destroy state.
- Scanning without
-x: crossing into other mounts leads to the wrong conclusion and wastes time. - Assuming
duis authoritative when files are open and deleted: uselsof +L1for the mismatch case. - Vacuuming without checking retention needs: old journal entries may be required for an incident investigation.
- Restarting a critical service without a plan: recycle the process only through a controlled maintenance or failover procedure.
- Resizing without a backup: provider and filesystem operations can fail, and shrinking is often unsupported.
- Fixing the symptom only once: without rotation, limits, alerts, and retention controls, the same full-disk incident will return.
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