Why Deleting Large Files Doesn’t Free Disk Space on Linux and How to Fix It

Problem Description

A server’s root partition reached 100% usage after an 80 GB file was deleted with rm -f, yet the space was not released.

Cause Analysis

In Linux, deleting a file only removes its directory entry (unlink). If a process still has the file open, the inode remains in use, so the data blocks are not freed and df still reports full usage.

File storage consists of metadata (pointers) and data blocks. When a file is deleted, the metadata is cleared, but the data blocks stay allocated until no process holds the file.

Remediation Steps

Use lsof | grep deleted to list deleted files still held open, then terminate the offending processes (carefully, as killing processes may affect services).

Stop or restart the application that was using the deleted file so the OS can reclaim the space.

Reboot the system as a last resort.

For log files that are continuously written, truncate the file (e.g., echo " " > /home/wangshibo.log or cat /dev/null > /home/wangshibo.log) to free space without stopping the process.

Example of Truncating a Log File

echo " " > /home/wangshibo.log</code>
<code>cat /dev/null > /home/wangshibo.log</code>
<code>> /home/wangshibo.log

Additional Disk‑Space Issue

Sometimes df -h shows ample free space, but creating or writing files fails with “no space left on device”. This is often due to deleted files still occupying space.

Typical workflow:

Run df -lh to identify the problematic partition.

Locate the partition (e.g., /data).

List deleted but still‑open files: lsof -n /data | grep deleted.

Kill the processes holding those files:

lsof -n /data | grep deleted | awk '{print $2}' | xargs kill -9

.

Verify no deleted files remain with another lsof check.

Reserved Space on ext Filesystems

Ext2/3/4 reserve a default of 5 % of the filesystem for privileged processes. This can appear as wasted space. Adjust with tune2fs -m 2 /dev/vda1 to set the reservation to 2 % (not recommended to set to 0%).

tune2fs -m 2 /dev/vda1</code>
<code>Setting reserved blocks percentage to 2% (209704 blocks)

After running the command, the root partition freed about 1 GB, confirming the reservation change.