How to compact VirtualBox's VDI file size?

I've a VirtualBox VM which configured a very large hard disk size (bigger than host). By my mistake, a program on the VM generated lots of log files and the VDI file size keeps growing until there is no space on the host.

Now I've deleted the log files but the VDI file size are not getting smaller after using VBoxManage.exe modifyhd "C:\Virts\mybox-i386.vdi" compact

Is there a way to really compact the VDI file size? Thanks!

You have to do the following steps:

1. Run defrag in the guest (Windows only)
2. Nullify free space:

With a Linux Guest run this:

dd if=/dev/zero of=/var/tmp/bigemptyfile bs=4096k ; rm /var/tmp/bigemptyfile


Or:

telinit 1
mount -o remount,ro /dev/sda1
zerofree -v /dev/sda1


sdelete.exe c: -z


(replace C: with the drive letter of the VDI)

3. Shutdown the guest VM

4. Now run VBoxManage's modifymedium command with the --compact option:

With a Linux Host run this:

vboxmanage modifymedium --compact /path/to/thedisk.vdi


With a Windows Host run this:

VBoxManage.exe modifymedium --compact c:\path\to\thedisk.vdi


With a Mac Host run this:

VBoxManage modifymedium --compact /path/to/thedisk.vdi


This reduces the vdi size.

• For the next person, my command ended up looking like this: "C:\Program Files\Oracle\VirtualBox\VBoxManage.exe" modifyhd "C:\Users\daniel\VirtualBox VMs\....\thedisk.vdi" --compact – Daniel Dec 13 '13 at 17:57
• According to the zerofree Linux utility manpage (manpages.ubuntu.com/manpages/natty/man8/zerofree.8.html), zerofree should be better than dd for this job. dd would not been recommended because "it is slow", "it makes the disk image (temporarily) grow to its maximal extent", "it (temporarily) uses all free space on the disk, so other concurrent write actions may fail". Zerofree is available on Ubuntu Linux via apt, or you can compile it yourself. – Dakatine Feb 20 '14 at 13:16
• It's fun that the the manpage of zerofree states that with dd other concurrent writes will fail, but zerofree needs the filesystem to be mounted read-only! *duh* – Madarco Feb 25 '14 at 12:04
• Tip: Put the two commands on one line like so: dd ...; rm /bigfile, this will minimize the time with a full disk in case you're not waiting for the dd to complete. – jlh May 14 '14 at 17:45
• @Dakatine Using VirtualBox 4.3.10, the disk image file did not grow to its maximal extent. VirtualBox is clever enough to not bother writing all zero blocks to the physical disk. – jlh May 14 '14 at 17:50

I'm on a Windows 7 host with Windows guests, Here is a batch file I wrote to Compact all of the VDIs in a folder tree

echo off
mode con:cols=140 lines=200
cls
:: see https://forums.virtualbox.org/viewtopic.php?p=29272#p29272
:: How can I reduce the size of a dynamic VDI on disk?
:: but that page says to use sdelete -s which is suboptimal.
:: use -z as per http://technet.microsoft.com/en-us/sysinternals/bb897443.aspx

:: First run the sdelete -z c: inside the VMs that zero-out all the free space
:: THEN run this batch file

Title Compacting Free space on Virtual Machine VMs

:: http://ss64.com/nt/for_r.html
:: http://stackoverflow.com/questions/8836368/windows-batch-file-how-to-loop-through-files-in-a-directory/8836401#8836401

Setlocal EnableDelayedExpansion
:: http://ss64.com/nt/delayedexpansion.html ...
:: Notice that within the for loop we use !variable! instead of %variable%.

For /R %CD% %%G IN (*.vdi) DO (
set ohai=%%G
set lastfive=!ohai:~-5!
:: Skip snapshots which are named {guid}.vdi
if NOT !lastfive!==}.vdi (
echo .
echo Compacting %%G
"C:\Program Files\Oracle\VirtualBox\VboxManage.exe" modifyhd "%%G" --compact )
)

pause
exit


I left the links in the comments so you can (sort of) tell how it works.

edit

Well, after all that, I tried the CloneVDI tool and it did a good job in much less time and in one click.

• You would think on this sort of site there would be some kind of syntax highlighting for DOS but no. It looks much prettier in Notepad++ – CAD bloke Jan 9 '15 at 10:26
• @CAD_bloke that would require a parsing engine and when you consider the number of different languages posted on SE you are looking at a HUGE project. Just think how many versions and dialects of DOS there are for example and that's before you even get to Linux etc. – Caltor Sep 17 '15 at 9:58
• Very good point. Ironically it is highlighted on the stack exchange iOS app. – CAD bloke Sep 17 '15 at 10:32
• Yeah CloneVDI is much better and faster way for personal use – VarunAgw Nov 14 '15 at 9:51
• The download of the CloneVDI tool is attached on page 1 of that forum's thread: forums.virtualbox.org/viewtopic.php?f=6&t=22422 – Peter Wippermann May 5 at 14:04

Debian guest on Windows host using discard/TRIM.

This isn't a direct answer per se, as I'm addressing the problem, not the question. Instead of periodically compacting the image, this solution uses discard to automatically remove unused blocks in the host's VM disk image.

This solution requires a guest filesystem that supports continuous TRIM. The Arch Linux wiki has a list of filesystems supporting TRIM operations.

FDE and cryptoroot are specifically not covered, as there are security concerns and none of the other solutions to this question would allow compacting either. The Arch Linux wiki has information about TRIM and dm-crypt devices.

In theory, this will work for all Linux guests on VBox hosts using VDI storage.

Host configuration

With VBox exited and no VMs running, add discard support to your disks by setting both discard and nonrotational for each disk in the config file for the VM. At this time discard is not in the GUI, but nonrotational is exposed as the "Solid-state Drive" checkbox. (ref: vbox forums, discard support)

<AttachedDevice discard="true" nonrotational="true" type="HardDisk" [..other options..] >


Boot the VM up, and verify that TRIM support is enabled:

sudo hdparm -I /dev/sda | grep TRIM


Guest Configuration

If LVM is in use, change the discard setting in /etc/lvm/lvm.conf. (ref: debian wiki, lvm.conf example)

devices {
...
}


In fstab, add the discard option to the filesystems you wish to auto-discard (ref: debian wiki, fstab example)

UUID=8db6787f-1e82-42d8-b39f-8b7491a0523c   /   ext4    discard,errors=remount-ro   0   1
UUID=70bfca92-8454-4777-9d87-a7face32b7e7   /build  ext4    discard,errors=remount-ro,noatime   0   1


Remount the filesystems to have them pick up their new options.

sudo mount -o remount /
sudo mount -o remount /build


Manually trim free blocks now with fstrim. fstrim uses the mounted filesystem, not the block device backing it. Instead of setting continuous discard in fstab, this could be done on a weekly cron. (The weekly cron is recommended for physical SSDs which may have questionable support for TRIM, but this is not relevant here since underlying SSDs are handled by the host OS. see: ssd trim warning).

fstrim /
fstrim /build


At this point, the size of the filesystems inside the VM and the size of the VM images should be pretty close in value.

Tested with:

• Guest1: Debian 8.7, kernel: linux 4.8 grsec from backports, filesystem: ext4
• Guest2: Debian 9 RC2, kernel: linux 4.9, filesystem: ext4
• Host1: VBox 5.1.14, Win7, image fmt: VDI
• Host2: VBox 5.1.14, Win8.1, image fmt: VDI

I use this for my VDI image mounted to virtual Debian in Windows VirtualBox. It isn't a general solution, but it should at least give you a gist of what I do.

Commands in Debian:

root@debian:~# lsblk  # show partitions

NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sdb 8:16 0 128G 0 disk
└─sdb1 8:17 0 128G 0 part /mnt/web  # THIS IS THE PARTITION OF INTEREST!
sda 8:0 0 64G 0 disk
├─sda1 8:1 0 61,4G 0 part /
├─sda2 8:2 0 1K 0 part
└─sda5 8:5 0 2,7G 0 part
[SWAP] sr0 11:0 1 56,3M 0 rom

root@debian:~# service mysql stop  # terminate all operations with partition
root@debian:~# service apache2 stop  # terminate all operations with partition
root@debian:~# umount /mnt/web  # unplug partition
root@debian:~# apt-get install zerofree  # install tool for filling in zeros to empty space
root@debian:~# zerofree -v /dev/sdb1  # fill with zeros
root@debian:~# poweroff  # shut down machine


Commands in Windows:

C:\Program Files\Oracle\VirtualBox>VBoxManage.exe modifyhd --compact "D:\VirtualBox VMs\web.vdi"  # convert zeros to empty space


Hope it helps :)

For MacOS Guest do this:

1. Nullify free space in guest system:

diskutil secureErase freespace 0 "/Volumes/Macintosh HD"


(replace /Volumes/Macintosh HD with your drive name)

2. Shutdown the guest VM

3. Run this command to reduce VDI disk image size

VBoxManage modifyhd /path/to/thedisk.vdi --compact


OR

VBoxManage modifymedium /path/to/thedisk.vdi --compact


IMPORTANT NOTE FOR LEGACY (~1997-2007) OPERATING SYSTEMS

In general, the techniques in the answers previously given are valid; HOWEVER, there is a very important special case.

For a period of some years-- perhaps 1997-2007 or so-- 32-bit operating systems were still the norm, but hard disks larger than 2GB were already in use. As a result, when attempting to consume all free space by writing a file of zeroes (which should always be done as root, to include root's privileged free space, which no one else can touch), you may see:

File too large

No space left on device.

If this occurs, you have most likely hit a 2GB file size limitation. This was common at the time because many file operations returned results in signed 32-bit integers, so that negative values could report error codes. This effectively meant that offset results were limited to 2^31 bytes without special measures.

The workaround is straightforward: keep creating separate, differently-named zeroing files until the disk actually runs out of space.

If you are an instructor wishing to demonstrate this situation for a class, a 4GB disk image with an old copy of Red Hat Linux 7.0 is sufficient.

• Addl. historic info: Linux large file support starts in glibc 2.2 + linux 2.4.0. Windows large file support starts in NTFS, though older versions like Win2k will have other disk limits (48-bit LBA → 128 GiB max disk, etc). – Andrew Domaszek Apr 21 at 16:10

I don't want to enable TRIM support in OS, because every data deletion will force data compacting in VDI file, making guest system unusable when VDI file is on classic rotational disc. For me better is to perform compacting by hand e.g. once per month.

During normal compacting, VDI file content is copied to new file. This requires some (sometimes big) free space on host disc.

I've solution similar to pointed by Andrew Domaszek. It works very well even with NTFS (Windows10).

To do this:

• create new virtual machine which boots with GParted Live CD (you can use your favorite Linux distro).
• Edit machine settings and set SATA disc controller
• Add existing VDI files which you want to compact
• Change VDI based discs to be visible as SSD with TRIM support:

VBoxManage storageattach "gpared live" --storagectl "SATA" --port 0 --discard on --nonrotational on
VBoxManage storageattach "gpared live" --storagectl "SATA" --port 1 --discard on --nonrotational on

• start machine

• In Linux root shell, mount NTFS partition mount /dev/sda2 /mnt
• zero free space dd if=/dev/zero of=/mnt/bigfile
• rm /mnt/bigfile
• force compacting VDI without creating new file: fstrim -v /mnt

A very neat trick to supplement the accepted answer is that you can get away without doing any compacting at all after zeroing guest space, by using a compressed file system on the host (e.g. selecting to compress the folder of virtual drives on NTFS properties on a Windows host). This in fact has the benefit to save a lot more space because operating systems tend to hold a lot of repetitive text or binary files (e.g. a 30GB guest drive that had 15GB of space zeroed can turn to 4GB on the host drive).

Caveats include that drive access on the real hardware may increase and there is a slight increase in CPU usage.