Free space after removing ibdata1 file My ibdata1 file was taking up a lot of space so I followed the steps explqined on How to shrink/purge ibdata1 file in MySQL

However after deleting the ibdata file and recreating the DB I'm still not able to see any free space.

df -h shows 98% usage, du -sh shows usage of 774Mb

I've looked at the deleted files that are held open by certain processes using the lsof command and while there are a number of entries as below, restarting mysql makes no difference.

mysqld    5216 5219    mysql    6u      REG              253,1         0   25417110 /tmp/ib4eLfA1 (deleted)
mysqld    5216 5219    mysql    7u      REG              253,1         0   25417243 /tmp/ibcoRi27 (deleted)
mysqld    5216 5219    mysql   11u      REG              253,1         0   25417290 /tmp/ibhr6Thb (deleted)
mysqld    5216 5220    mysql    4u      REG              253,1         0   25417100 /tmp/ibs0uz9U (deleted)


Is there any way to force the system to check / rest free space?
It will not answer your question directly, but I wanted to notice you about this ibdata issue in general. Unfortunately, there is no magic solution to decrease the ibdata file size... It is the central point of the InnoDB engine, removing it (even when database is shutdown properly) will cause data inconsistency/corruption. 

The only way to restart from a healthy state (with a small ibdata) is to reinstall a brand new MySQL instance and load the data from your origin, and PLEASE use innodb_file_per_table to avoid having all you data in one single file (MySQL doc here).

To load you current data into your new instance, you can use mysqldump if your dataset is small (few GB) or use "Transporting tablespace" procedures to cleanly import table by table your dataset (example on Percona Blog here).

You can also read this article form Percona Blog which explain many things regarding these ibdata issues.

Max.