The Tool Desk
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Start with df -h and df -i to identify the full filesystem and distinguish consumed bytes from exhausted inodes. Then rank directories with a filesystem-aware du command, drill into the largest path, and investigate exceptions such as deleted files still held open, systemd journal data, Docker storage, logs, caches, and backups. This workflow finds the cause without deleting files blindly.
Use this order when a Linux VPS says it is full
Disk alerts usually point to one of three conditions: a filesystem has no free blocks, a filesystem has run out of inodes, or space belongs to a deleted file that a running process still has open. The commands below separate those cases before you remove anything.
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df -h,df -i, anddf -T. - Use
duwith-xto rank directories on the affected filesystem. - Open the largest directory and repeat the measurement until you reach a specific application, log, cache, backup, or data directory.
- If the total from
duis much smaller than the used figure fromdf, check open deleted files withlsof +L1. - Check the systemd journal and, where applicable, Docker’s storage report.
Keep an SSH session open while you work. Use sudo so permission errors do not hide the directory that is actually consuming space.
Confirm which filesystem is full
Check allocated space and free space
df -hdf -h reports each mounted filesystem in human-readable units. Pay attention to the Mounted on column. A separate /var, /home, or /boot partition can be full while the root filesystem still has room. Conversely, a directory such as /var may simply be a directory on /, not a separate filesystem.
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The percentage in Use% is the immediate capacity signal. A filesystem at or near 100 percent can make package installation, logging, database writes, and even SSH-related operations fail.
Check inodes, not just gigabytes
df -iEvery file consumes at least one inode, regardless of whether it is large. A session, mail-queue, cache, or temporary-file directory containing millions of tiny files can exhaust inodes while df -h still reports free gigabytes. In df -i, inspect IUse% and IFree. A nearly full inode percentage means you need to find and reduce the file count, not merely search for one large file.
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See filesystem types and mount boundaries
df -TThis adds the filesystem type and helps reveal separate mount points. It also gives you the boundaries to respect when comparing df and du. Investigate the mount that shows the problem rather than assuming every path under / belongs to the same storage volume.
Interpret the first three checks together
| Observation | Likely condition | Next action |
|---|---|---|
df -h is near 100 percent and df -i is healthy |
Blocks are consumed by ordinary file data, reserved space, or an open deleted file | Rank directories with filesystem-aware du, then check lsof +L1 if totals do not match |
df -i is near 100 percent but df -h has room |
Too many small files | Locate high-file-count application, queue, session, or cache directories and clean them using that application’s retention procedure |
Only a non-root mount such as /var or /boot is full |
The separate filesystem, not the apparent root directory, is the constraint | Run du against that mount point and inspect its contents |
Rank directories with du, while staying on one filesystem
Measure the top level
sudo du -xh --max-depth=1 / | sort -hdu totals space used by files reachable under a path. Here, -h makes the values readable, --max-depth=1 shows each immediate child of /, and sort -h puts the smallest values first so the largest entries appear at the bottom. Read the last lines and select the largest directory that is on the full filesystem.
The -x option is important on servers: it keeps the walk on one filesystem. Without it, mounted disks, bind mounts, network filesystems, and other mount points can be counted as though they were part of the directory you are examining. That can make the result look much larger than the filesystem reported by df. For a reliable comparison, use -x and match the path to the mount point identified by df -T.
Drill down one directory at a time
If /var is the largest entry, run:
sudo du -xh --max-depth=1 -x /var | sort -hContinue with the largest child, for example /var/log, /var/lib, or an application-specific directory. A useful sequence is:
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sudo du -xh --max-depth=1 -x /var/log | sort -h
sudo du -xh --max-depth=1 -x /var/lib | sort -h
sudo du -xh --max-depth=1 -x /home | sort -hUse the same depth and filesystem boundary at every level. Permission-denied messages mean the command could not inspect part of the tree; rerun it with sudo rather than treating the incomplete total as evidence that the directory is small.
Search for individual large files after identifying the area
Directory totals tell you where to look. Once you have narrowed the location, list files within that area using a targeted command rather than scanning the entire server repeatedly:
sudo find /var/log -xdev -type f -printf '%s %pn' | sort -n | tail -20This prints the 20 largest regular files under /var/log by byte count. The -xdev option prevents crossing into another filesystem. Output is in bytes, so use it for ranking and then inspect the owning service and rotation policy before removing anything.
Browse the result interactively with ncdu
ncdu provides a keyboard-driven view of the same directory tree and is useful over SSH. Install it with your distribution’s package manager, then scan the affected filesystem:
sudo ncdu -x /Use the arrow keys to move, Enter to open a directory, and the parent-directory key shown by the program to move back. The -x option keeps the scan on one filesystem, which makes its total easier to reconcile with df. Because it is designed for remote shells, it remains practical on a VPS without a graphical interface.
Do not press d until you have confirmed that the selected item is safe to remove and that no service needs it. ncdu deletes immediately; it does not provide a recycle bin. Prefer an application’s cleanup command, log-rotation mechanism, or package-manager procedure when one exists.
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When df and du disagree: find deleted files still held open
Recognize the mismatch
df measures blocks allocated by the filesystem, while du walks directory entries that are still visible. If df reports substantially more used space than the sum you can find with du, a process may still have an unlinked file open. Large logs are a common example: an administrator deletes or rotates the pathname, but the logging process continues writing through its open file descriptor.
Deleting a file does not release its blocks while a process still has the file open. The pathname disappears, so du cannot count it, but the filesystem must retain the data until the last file descriptor closes.
List open files whose directory link count is zero
sudo lsof +L1The +L1 filter asks lsof to show open files with a link count below one, which identifies files that have been deleted but remain open. Look for a large size, the owning process, its process ID, and the filesystem on which the file resides. Some distributions may require installing the lsof package first.
Release the space safely
The space returns only when the owning process closes the descriptor. Use the service’s documented log-reopen, reload, or rotation mechanism whenever possible. If that is not available, schedule a controlled restart during an appropriate maintenance window and verify that the service returns healthy. A blanket process kill can interrupt unrelated work or cause data loss, so do not use it as the first response.
Truncating a live log is sometimes suggested as an emergency measure, but its safety depends on the application and logging setup. Confirm the service behavior and your recovery plan before changing an open file. After the process closes or reopens the file, run df -h again to verify that the blocks were released.
Measure and limit the systemd journal
See journal usage
journalctl --disk-usageThis reports the disk space occupied by systemd journal files. Journal data is often under /var/log/journal or /run/log/journal, but use the command’s result rather than assuming a path.
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Rotate before vacuuming recent archives
sudo journalctl --rotate
sudo journalctl --vacuum-size=200M--rotate closes the current journal file and starts a new one, allowing the vacuum operation to include entries that were recently active. --vacuum-size=200M removes archived files until archived journal data is within approximately 200 MB. You can use a time policy instead:
sudo journalctl --rotate
sudo journalctl --vacuum-time=7dVacuuming removes archived journal files only; it does not delete the active journal file. If the filesystem is critically full, rotation may itself need some free space, so first remove or relocate a known-safe non-journal item if the command cannot create a new file.
Make the limit persistent
Temporary vacuuming will not prevent the journal from growing again. Set an appropriate persistent limit in /etc/systemd/journald.conf, using the journal size and retention settings documented for your distribution. After editing, reload or restart the journald service according to that distribution’s procedure, then confirm the effective usage with journalctl --disk-usage. Choose a limit that leaves room for troubleshooting logs rather than reducing retention to zero.
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If Docker is installed, its images, writable container layers, volumes, and build cache can consume space under Docker’s data root. Start with a summary:
docker system dfFor a per-object breakdown, use:
docker system df -vReview this output with the images, containers, and volumes that your applications still need. Cleanup commands have different scopes:
| Command | Removes | Important retention behavior |
|---|---|---|
docker system prune |
Stopped containers, unused networks, dangling images, and build cache | Volumes are kept unless --volumes is supplied; unused tagged images are kept unless -a is supplied |
docker system prune -a |
The items above plus unused images, including unused tagged images | Review image usage carefully before confirming |
docker system prune --volumes |
Prunable items plus eligible unused volumes | Data in an unused volume can be application data, so verify ownership first |
docker volume prune |
Unused Docker volumes | Named unused volumes are not removed by plain docker system prune |
Do not run a destructive prune command as an unexplained emergency shortcut. Capture docker system df -v, identify what is disposable, and confirm that stopped containers or volumes are not part of a rollback plan.
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Inspect the usual non-Docker suspects
Unrotated or unexpectedly verbose logs
Begin with /var/log and identify which service owns a large file. Check that service’s log-rotation configuration and whether compression is occurring. Do not remove an active log by pathname without understanding how the daemon handles file descriptors; use the service’s rotation or reopen mechanism, especially when the df/du mismatch indicates an open deleted file.
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Package managers retain downloaded packages for reinstall and rollback. A cache can be cleaned using the package manager’s own cache command, but the exact command differs between Debian/Ubuntu and RHEL-family distributions. Confirm the package manager and review what it proposes before accepting a cleanup.
Old kernels
Multiple kernels may be installed under /boot. Keep the running kernel and at least one known-good fallback. Remove older kernels only through the distribution’s package-management tooling, never by manually deleting files from /boot while that kernel might be needed for recovery.
Backups, archives, and user data
Look in /var/backups, /root, application upload directories, database dump locations, and home directories. Before deleting an archive, establish where the next valid backup is stored and whether retention requirements apply. Moving a backup to another filesystem can free the affected mount without destroying the only copy, but verify the transfer before removing the original.
Millions of small files
When inodes are exhausted, a single-file size search will miss the cause. Focus on session stores, mail queues, temporary directories, cache trees, and application-generated per-request files. Use the application’s expiry or queue-draining procedure, and monitor inode usage afterward with df -i. Avoid recursive deletion commands until you have confirmed the path, owner, age policy, and service impact.
Recover from “No space left on device” without making the outage worse
- Preserve access. Keep the current SSH connection open and avoid starting upgrades, compactions, or builds that need temporary space.
- Identify the mount. Run
df -h,df -i, anddf -T; note whether blocks or inodes are exhausted. - Create a small safety margin. Remove or move one clearly disposable item on the affected filesystem, such as an obsolete cache or already-verified temporary archive. Do not touch
/proc,/sys, or arbitrary system files. - Find the owner. Use the
du -xdrill-down, then inspectlsof +L1, journal usage, Docker usage, logs, caches, and backups as applicable. - Apply the narrowest fix. Rotate a log, vacuum archived journals, remove confirmed-unused Docker objects, or use the application’s own retention command.
- Verify service health. Re-run
df -handdf -i, check the affected service, and confirm that logging and scheduled jobs resume.
If every visible directory is small but df remains full, return to sudo lsof +L1. If inodes remain at 100 percent after deleting data, the deletion may have targeted the wrong mount or a process may be recreating files; identify the creating service before repeating cleanup.
Keep the VPS from filling again
- Set and test log rotation for every service that writes locally.
- Define journal size or time limits in
/etc/systemd/journald.confand review the resulting usage. - Give Docker images, build cache, containers, and volumes an explicit retention policy; do not rely on emergency pruning.
- Schedule checks for both
df -handdf -i. Byte capacity and inode capacity can fail independently. - Monitor separate mounts individually, especially
/var,/boot, and application data volumes. - Keep backups outside the VPS or on a separate filesystem and test restoration before deleting local copies.
- Record which files and services were changed during an incident so the same growth pattern can be fixed rather than repeatedly cleaned.
A compact diagnostic command set
These commands form a safe starting sequence. Replace / with the affected mount point when df identifies a separate filesystem:
df -h
df -i
df -T
sudo du -xh --max-depth=1 -x / | sort -h
sudo ncdu -x /
sudo lsof +L1
journalctl --disk-usage
docker system df
docker system df -vRun only the commands relevant to software installed on the VPS. Measurement is non-destructive; cleanup is not. Treat every deletion, prune, vacuum, or service restart as a change that needs an identified owner and a recovery path.
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