Deleting files doesn't free disk space

During work to improve BleachBit's method of wiping free disk space, I noticed a relatively obscure way in which deleted files do not fully free the disk space they occupied. The process is basically to create an empty partition, fill it with 2000 files each 4096 bytes each, and then delete the files. If the files are in the root of the partition, then the file system keeps 45 more blocks allocated. If the 2000 files are created in a sub directory that is deleted after the 2000 files are deleted, then all the used blocks are freed.

The following code demonstrates the issue.

#uncomment ONE of the TWO following lines
echo "********* initializing"
rm /tmp/fs.ext3
mkdir /tmp/mountpoint
dd if=/dev/zero of=/tmp/fs.ext3 bs=1M count=10
mkfs.ext3 -F /tmp/fs.ext3
sudo mount -o loop /tmp/fs.ext3 /tmp/mountpoint
df /tmp/mountpoint
df -i /tmp/mountpoint
du /tmp/mountpoint
echo "********* creating many small files"
mkdir /tmp/mountpoint/${SUB}
for i in {1..2000}; do dd if=/dev/zero of=/tmp/mountpoint/${SUB}file$i bs=1K count=4 &>/dev/null; done
df /tmp/mountpoint
df -i /tmp/mountpoint
du /tmp/mountpoint
echo "******** cleaning"
for i in {1..2000}; do rm /tmp/mountpoint/${SUB}file$i ; done
rmdir /tmp/mountpoint/sub
df /tmp/mountpoint
df -i /tmp/mountpoint
du /tmp/mountpoint
echo "******** unmount"
sudo umount /tmp/mountpoint
dumpe2fs /tmp/fs.ext3

In both cases, the file system starts with 1121 used blocks. In both cases creating the files results in the use of 9166-9167 blocks. After deleting the files from the root folder, the file system uses 1116 blocks, while after deleting the files from the subdirectory, the file system uses 1121 blocks.

Unmounting and remounting the file system (simulating a reboot) does not affect the used blocks.

This was tested with Ubuntu 13.04, Linux 3.8, and ext3.

By the way, another reason deleting a file may not free its space is if an active process has it open: use the lsof program to find the process or simply reboot. Of course, you should also check the trash can or run BleachBit to clean the trash and other disk space hogs.