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If Linux still reports a full filesystem after you delete files, stop deleting at random and reconcile the accounting first. df reports blocks allocated by the filesystem, while du totals files that are still reachable through directory entries. A deleted file held open by a running process can therefore consume space that du cannot see. Inodes, journal retention, reserved blocks, snapshots, and container layers can also make the numbers appear contradictory.
The safe sequence is: identify the filesystem, check both blocks and inodes, compare df with a filesystem-limited du scan, find open deleted files, then investigate journals and filesystem-specific layers. Change retention or restart a service only after you know which object owns the space.
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Do not begin with another broad cleanup command. First establish which path, mount, and resource are exhausted.
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Run
df -hT /path, replacing/pathwith the directory where applications report failures. The-hoption makes sizes readable;-Tshows the filesystem type. Record the filesystem device, mount point, total, used, available, and percentage.#1 Best Overall
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Check inode capacity separately with
df -i /path. A filesystem can have free byte capacity but no free inodes, preventing creation of any more files. -
Use the mount point shown by
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A percentage near 100 percent is not by itself proof that one visible directory contains all the used bytes. Filesystem allocation, inode slots, reserved space, and layers such as snapshots are separate accounting domains.
Why df and du disagree
df measures allocated filesystem blocks
df asks the filesystem how many data blocks and file slots are used and available. It includes allocation that is not represented by a currently visible filename, and POSIX permits the available value to be negative when reserved or otherwise unavailable space is included. In that situation the displayed percentage can even exceed 100 percent.
du measures reachable directory entries
du walks directory trees and adds the blocks charged to files it can reach. It does not count an unlinked file whose directory name has been removed, and it can cross into other mounted filesystems unless you restrict the walk.
For a meaningful comparison, run:
sudo du -xhd1 /mountpointThe -x option keeps the walk on one filesystem. Sort or inspect the largest entries, then repeat the command on that directory to drill down. The two totals are not expected to be identical because they answer different questions; a large gap is a diagnostic clue rather than a calculation error.
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1. Capture a baseline before changing anything
Save the output of these commands to a text file or maintenance ticket:
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df -hT /path
df -i /path
sudo du -xhd1 /mountpoint
sudo lsof +L1Keeping the baseline lets you verify whether a restart, vacuum, or deletion actually released capacity.
2. Find the largest visible directories
Run sudo du -xhd1 /mountpoint and inspect the largest rows. Run the same command inside the largest directory until you reach a specific log, cache, upload area, or database directory. Do not delete a large path merely because its name looks unfamiliar: first confirm its owner, mount boundary, and whether the application still needs it.
3. Look for deleted files that are still open
When df is much higher than the filesystem-limited du total, run:
sudo lsof +L1If your distribution or lsof version does not support that form, use:
sudo lsof | grep deletedLook for a row with a process ID, command, user, and a deleted pathname. The pathname is gone from the directory tree, but the process still has a file descriptor referring to the inode. Red Hat describes the behavior precisely: unlinking removes the directory entry, yet an open file remains accessible to the process and continues to occupy disk space. Alibaba Cloud documentation likewise notes that deleted files still holding space do not appear in ordinary df or du inspection.
4. Map the file to the responsible service
Use the PID from lsof to identify the service. On a systemd host, check the service status and its logs; on another system, use the platform’s process manager. Confirm that the process really owns the deleted file and that it is safe to interrupt. A deleted database file, socket, or temporary file may be part of an active transaction even when its name looks disposable.
5. Close the descriptor in the narrowest safe way
Prefer a graceful reload or restart of the specific service that owns the descriptor, scheduled in an appropriate maintenance window. After it stops or closes the file, run df -hT again. The blocks should become available without any further deletion.
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Do not kill a process before confirming its role. Rebooting releases every open descriptor, but it is a broad action that interrupts unrelated workloads and can hide the underlying service problem. If a restart does not reduce usage, repeat lsof; another process may hold a different deleted file, or the reported usage may have another cause.
Open deleted files: what happened and how to prevent a repeat
On Linux, removing a filename unlinks a directory entry. The inode and data blocks remain until the last process reference is closed. This allows a daemon to keep writing to a log after an administrator has removed the log’s name. Rotation tools normally rename the old file and signal the daemon to reopen it; a daemon that never reopens can accumulate hidden space indefinitely.
Use service-aware log rotation
After releasing the current descriptor, fix the rotation policy rather than repeatedly deleting logs. Verify that the service supports a reload or reopen signal, that the rotation job runs under the correct user, and that compression and retention limits are applied to files the service has actually closed. Monitor both df and the service’s log directory after the next rotation.
When a graceful restart is not possible
Escalate through the service’s documented maintenance procedure. Terminating a process that owns a database, queue, or stateful transaction can cause data loss or recovery work. If capacity is at an emergency threshold, move noncritical, already-closed data to planned storage first, then perform the controlled restart.
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Check systemd journal consumption
Journald can consume substantial space even when ordinary application directories look small. Measure its current footprint with:
journalctl --disk-usageReview the effective settings in journald.conf, including SystemMaxUse=, RuntimeMaxUse=, SystemKeepFree=, and RuntimeKeepFree=. The current systemd manual documents default keep-free values of 10 percent for persistent system storage and 15 percent for runtime storage; each calculated default is capped at 4 GiB.
Keep-free settings reserve headroom for other applications; they are not a promise that existing archives will disappear as soon as the filesystem fills. The manual notes that journald may stop adding data without immediately removing archives when the filesystem later becomes constrained.
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Reduce journals without damaging active files
Use journald’s documented vacuum operations and your distribution’s retention policy, for example a size- or time-based journalctl --vacuum-... command approved for your system. Do not remove active journal files with rm. After vacuuming, check journalctl --disk-usage and df -hT, then set persistent limits so the same growth does not recur.
When the real problem is inode exhaustion
If df -i /path shows 100 percent inode use, deleting a few large files will not solve the failure. Millions of tiny cache files, mail fragments, temporary files, or per-request artifacts can consume every inode while many data blocks remain free.
Find directories containing many small files
Use the filesystem-limited du walk to locate high-count working areas, then inspect application-specific cache and spool directories. Count files with tools appropriate to your shell and distribution, and identify the owner before removal. Consolidating records into fewer files, expiring stale entries, or changing the application’s spool policy addresses inode pressure more effectively than deleting one large archive.
Clean inode usage safely
- Stop or pause the producer if it will recreate files while you clean.
- Delete only files covered by a documented retention rule.
- Preserve directory structure and permissions expected by the service.
- Recheck
df -iafter cleanup; byte usage and inode usage can move independently.
Investigate mounts, containers, snapshots, and metadata
If no open deleted files explain the gap, inspect the storage layout shown by df -T and the relevant mount information. A generic du / result can cross into other mounts, omit storage hidden beneath a mount point, or fail to represent copy-on-write metadata.
Separate mount points
A full /var filesystem is different from a full root filesystem even when both are visible under one directory tree. Run df -hT for the exact path used by the failing application and repeat the directory scan with -x on that mount only.
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Container overlay filesystems
Container writable layers and overlay filesystems may account for changes in a host-specific location rather than where the container’s path appears. Identify which layer and mount are full using the container runtime’s supported inspection commands. Never delete files directly from an overlay storage directory simply because they are large; the runtime may need their metadata to start or remove containers correctly.
Snapshots and copy-on-write filesystems
Snapshots can retain old blocks after the visible file has been changed or deleted. Their space accounting is filesystem-specific, and ordinary du output may not include snapshot metadata. Use the tools documented for the identified filesystem to list snapshots and their referenced space. Delete a snapshot only after confirming its backup, rollback, or replication role.
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Reserved blocks and filesystem metadata
Some filesystems reserve blocks for system operation, and metadata can consume capacity outside the totals you expect from visible files. Do not change reservation settings until df -T identifies the filesystem and you understand the operational effect. Reducing a reservation may make more space available to ordinary users while removing emergency headroom for the system.
Choose a remedy by the failure mode
| Remedy | Releases already allocated blocks? | Requires service restart? | Data-loss risk | Addresses bytes or inodes | Filesystem scope |
|---|---|---|---|---|---|
| Close or restart the owner of an open deleted file | Yes, when the last descriptor closes | Usually yes; a graceful reload may suffice | Depends on the service and shutdown procedure | Bytes | Any Linux filesystem |
| Journald vacuum using documented policy | Yes, for archives eligible under the policy | No, when performed through journald controls | Retained logs are intentionally removed | Bytes | Persistent or runtime journal storage |
| Lower future journal limits or set keep-free values | No immediate release is guaranteed | No, after configuration reload or restart as required by the distribution | Future history may be shorter | Bytes and reserved headroom | Journald storage |
| Remove or consolidate tiny files | Yes | Often no, but stop writers when necessary | Potential loss if retention is misunderstood | Primarily inodes, also bytes | Any filesystem |
| Delete a snapshot through filesystem tools | Usually, after snapshot references are released | No general requirement | Rollback or backup point may be lost | Bytes and metadata | Filesystem-specific, such as copy-on-write systems |
| Expand the correct filesystem or move planned data | Adds capacity rather than reclaiming old blocks | Depends on storage layout | Low when performed with a tested change plan | Bytes; inode capacity may also need planning | Filesystem and volume-manager specific |
What not to delete
/procand/sysentries: these are virtual interfaces, not ordinary files to purge.- Database directories: removing a large data, journal, or write-ahead-log file can destroy recoverability even if a process currently has it open.
- Container storage layers: use the runtime’s cleanup and retention commands, not manual deletion inside its private directories.
- Active journal files: use journald retention and vacuum controls.
- Unknown mount points: identify the filesystem and owner before changing reservation, snapshot, or quota settings.
When cleanup is not enough: plan capacity
After reconciling df, du, open descriptors, journals, inodes, and filesystem-specific layers, decide whether the workload has genuinely outgrown the filesystem. If the used blocks remain high and the available margin is too small for normal bursts, expand the correct filesystem or move data to planned storage. Verify the result with both df -hT and df -i; adding byte capacity does not automatically add inode capacity on every storage design.
Record the service, mount point, filesystem type, retention policy, and expected growth rate in the change plan. Capacity work is safer when it follows accounting rather than replacing it.
A practical decision checklist
-
Is
df -ifull? If yes, find and consolidate excessive small files before chasing large files. -
Is
dffar higher thandu -x? Runsudo lsof +L1and map every result to a service. -
Does journald account for the gap or ongoing growth? Check
journalctl --disk-usageand the four retention controls, then use documented vacuum procedures.Recommended Free Tools
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Do the numbers still not reconcile? Recheck mount boundaries and inspect overlay storage, snapshots, reserved blocks, and metadata with filesystem-specific tools.
-
Is capacity genuinely exhausted after reconciliation? Expand the identified filesystem or move data under a planned maintenance procedure.
The key distinction is whether you need to release blocks already allocated, prevent future growth, or add capacity. A service restart can release hidden blocks; a retention setting may only limit future growth; inode cleanup solves a different resource entirely. Treating those as interchangeable is what makes a successful deletion appear to have done nothing.
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