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Boot your Linux VM in single user mode.
(Please see software manufacturer documentation how to perform this operations.)

Follow the steps bellow:

init 1                                                                        - switch to level 1
mount -n -o remount,ro -t ext3 /dev/hda1 /         - remount the disk as read only
fsck.ext3 -f /dev/hda1                                            - file system check for errors
zerofree /dev/hda1                                                - fill emptu space with zero bytes
mount -o remount,rw -t ext3 /dev/hda1 /             - remount in read/write mode
shutdown -h now

For now you can compact your Virtual Machine
1. In Parallels Desktop version 3:
- Click Hard Disk 1 - Advanced -click Compact

2. In Parallels Desktop version 4:
Start Parallels Image Tools from Applications/Parallels
Select Disk to compact pointing to Virtual Machine pvm


Click to harddisk0.hdd (or whatever the name is)


Click to the next harddisk0.hdd file (It is correct - there are 2 files inside each other)



Click "Choose" button
Click "Continue"
Select "Compact Disk"
Click "Start"