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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!

Karan
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DeepNightTwo
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10 Answers10

647

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
    

    With a Windows Guest, download SDelete from Sysinternals and run this:

     sdelete.exe c: -z
    

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

  1. Shutdown the guest VM

  2. 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
    

    VBoxManage is located here: /Applications/VirtualBox.app/Contents/MacOS/VBoxManage

This reduces the vdi size.

magicandre1981
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  • @user248749 FYI, `dd` with no argument copies one *block* at a time, not one byte. Using a larger block size can speed things up, but [the effect is pretty minor](http://unix.stackexchange.com/questions/9432/is-there-a-way-to-determine-the-optimal-value-for-the-bs-parameter-to-dd/9492#9492). – Gilles 'SO- stop being evil' Aug 27 '13 at 00:15
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    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
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    According to the zerofree Linux utility manpage (http://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
  • @Dakatine I never got it working. Add a working command to the post. – magicandre1981 Feb 20 '14 at 19:35
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    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
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    What is `/bigemptyfile`? A special path recognized by `dd`? – Frozen Flame Apr 30 '14 at 06:24
  • https://en.wikipedia.org/wiki//dev/zero this is simple a large file with zeros – magicandre1981 Apr 30 '14 at 18:13
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    @FrozenFlame /bigemptyfile is just an arbitrary name that magicandre1981 used for the temporary file, you can name it anything you want. `sudo dd if=/dev/zero of=/zero.fill bs=4096k` is functionally exactly the same, it will just write to a file named `zero.fill` instead (you'd need to change the `rm` command to remove this file instead of `/bigemptyfile` though) – Jason Larke May 05 '14 at 05:01
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    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
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    @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
  • this dd trick doesn't work for ext3 guest filesystem, but works well for ext4 – Reinaldo Gil Jul 07 '14 at 01:14
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    Is it normal to have this error? dd: error writing ‘/bigemptyfile’: No space left on device – Vincent Nov 12 '14 at 13:16
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    @Vincent That's the point of this procedure. You're writing zeros to a new file until it fills entire free space, then you delete that file. – gronostaj May 12 '15 at 21:29
  • On Linux, you can defrag [this way](http://askubuntu.com/a/221107/29219): using gparted, shrinking then moving the partition (see the link for more information) – Anthony O. May 29 '15 at 14:39
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    OSX Host - Win8.1 VM - When I try to optimize my C drive, it tells me that optimization is unavailable. - how can I defrag my virtual C drive? – Robert Achmann Sep 24 '15 at 02:34
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    @RobertAchmann post a picture of the defrag UI of Win8.1 – magicandre1981 Sep 24 '15 at 04:02
  • I will in the morning, but both the analyze and optimize buttons are greyed out - and beside the drive in the list it says optimization is not available. but it looks as though you can schedule optimization to occur... – Robert Achmann Sep 24 '15 at 04:07
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    @RobertAchmann ignore it and run sdelete now. – magicandre1981 Sep 24 '15 at 04:09
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    If you experience `/ is busy` on `mount` command, then reboot your guest in recovery mode. – Vasilly.Prokopyev Nov 30 '15 at 14:22
  • Note that the zerofree man page says the "filesystem has to be unmounted or mounted read-only", so changing the run level with telinit then remounting the device read-only is wasted effort. Just unmount, zerofree, shut down, compact. – Urhixidur Mar 23 '16 at 19:33
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    The `dd` operation will take a while, you can see its progress installing `pv` and using `sudo dd if=/dev/zero | pv | sudo dd of=/bigemptyfile bs=4096k`. Source: http://askubuntu.com/questions/215505/how-do-you-monitor-the-progress-of-dd – Katu May 18 '16 at 09:00
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    Awesome! Down to 15Gb from 27Gb – JohnTortugo Jun 08 '16 at 23:18
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    `sdelete` requires a target as argument. Example `sdelete.exe c: -z` – Francesco Frassinelli Jul 08 '16 at 07:30
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    ok there was an update, before it used the current drive. I'll add it. – magicandre1981 Jul 08 '16 at 15:30
  • I suggested an edit to this post but it seems it has been somehow rejected. Anyway, the command is `VBoxManage` also on Linux, not `vboxmanage`. – Andrea Lazzarotto Aug 15 '16 at 21:08
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    @Andrea Lazzarotto actually both VBoxManage and vboxmanage exist on my Linux box with VirtualBox 5.0.24 installed. – PolyTekPatrick Aug 17 '16 at 15:37
  • Ah! That's weird, I am pretty confident it was not working for me when I first tried to edit the answer. Maybe I was using the Ubuntu version. I am now using the version from their website so I cannot really check. – Andrea Lazzarotto Aug 17 '16 at 15:39
  • `telinit 1` didn't work for me in Ubuntu, so I rebooted holding down the left shift to get the grub menu, I booted in recovery mode and in the recovery menu I selected the root shell. After that the `mount` and the `zerofree` commands worked like a charm. VM reduced from 25 GB to the expected 11 GB. – f.ardelian Aug 19 '16 at 19:39
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    As a reference I had to delete my snapshots in order for this to make any difference. – Marcus Sep 04 '16 at 16:28
  • @VlastimilBurian thanks for the edit about the new options – magicandre1981 Nov 27 '16 at 20:32
  • @magicandre1981 No problem, as I use VirtualBox daily, I have just contributed to your good answer. – Vlastimil Burián Nov 28 '16 at 01:38
  • For a WindowsServer/7 guest on linux host, I used ccleaner to nullify empty space and then used your answer to compact vdi file. Worked great! – Alfabravo Jan 17 '17 at 17:16
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    Great answer! This works well. I just wanted to point out that you don't need `sudo` when writing zeros to disk on a Linux guest. Just write to /tmp/bigemptyfile instead of /bigemptyfile: `dd if=/dev/zero | pv | dd of=/tmp/bigemptyfile bs=4096k; rm /tmp/bigemptyfile` – sbleon Sep 27 '17 at 17:00
  • @sbleon ok, edit the answer and add this change. I don't use linux that much – magicandre1981 Sep 28 '17 at 14:56
  • @sbleon thanks, I've approved your edit. thanks for pointing this out – magicandre1981 Sep 28 '17 at 15:16
  • @AndreaLazzarotto as PolyTekPatrick already mentioned there are both versions ( `vboxmanage` and `VBoxManage` ) of the tool. Even more, they are just symlinks to a real executable: command `ls -o $( which vboxmanage VBoxManage )` produces `lrwxrwxrwx 1 root 4 Sep 13 16:37 /usr/bin/VBoxManage -> VBox` and `lrwxrwxrwx 1 root 4 Sep 13 16:37 /usr/bin/vboxmanage -> VBox` . – Victor Yarema Oct 10 '17 at 10:19
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    @Victor, when I left my previous comment (and we are talking about more than a year ago) there was no lowercase version on my Ubuntu system. Only the uppercase one was present. – Andrea Lazzarotto Oct 10 '17 at 13:41
  • @AndreaLazzarotto, copy that. I didn't want to say that you are wrong. I know that things change. I just wanted to add some up to date info (including command example) for anyone that may come here for answers. Your comment was useful at that moment. Thanks. – Victor Yarema Oct 10 '17 at 14:10
  • If you create a file full of zeroes till ALL of the space is taken, won't the file grow to its absolute maximum size? My disk size is 100Gb, whereas the actual size is 15Gb. I know it should be around 9, If I run the command, will I have to wait for `dd` to write 85Gb?!? – Merc Nov 25 '17 at 05:47
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    Excellent! From 187GB to 46GB! I am confirming that this procedure works on Ubuntu 17.10 as host OS and Windows 10 as guest OS. – Bosko Mijin Jan 10 '18 at 16:03
  • A similar `dd` command suggested here; https://askubuntu.com/a/903178/516133 – Lee Jan 12 '18 at 12:23
  • Had to remove my shared folder first. Worked great after that. – mgershen Apr 29 '18 at 10:09
  • Can somebody explain why defrag is needed? – vehsakul Oct 18 '18 at 16:52
  • zerofree: Worked with Win10 host, Ubuntu 18.04 guest and Ubuntu 18.04 live CD/iso. Please note you need plenty of **free disk space on the host**, otherwise VM stops working! – Tobias Weibel Nov 02 '18 at 07:31
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    It's worth noting that Windows 10 guests will not defrag a disk tagged as an SSD. The rest of this worked for me. Thanks. – Mooseman Mar 27 '19 at 11:25
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    Be honest, I do not know why this is accepted answer. If I have 500GB VDI, only used about 100GB in win guest. The VDI is about 150GB. The sdelete will actually enlarge the VDI to 500GB. And after compact it only shrink down about 480GB. So it actually make the VDI larger. Just clone the 150GB VDI and run compact on it will shrink down to 120GB. I really want to middle finger the guy who did not test this on recent NTFS at all. Wasting lots of time and energy. This works on linux guest only! – Wang Apr 08 '19 at 01:06
  • `VBoxManage: error: Cannot register the hard disk '/path/to/thedisk.vdi' {eee104d7-cd65-402f-b816-a3be4ac30eb3} because a hard disk '/path/to/thedisk.vdi' with UUID {eee104d7-cd65-402f-b816-a3be4ac30eb3} already exists` `VBoxManage: error: Details: code NS_ERROR_INVALID_ARG (0x80070057), component VirtualBoxWrap, interface IVirtualBox, callee nsISupports` `VBoxManage: error: Context: "OpenMedium(Bstr(pszFilenameOrUuid).raw(), enmDevType, enmAccessMode, fForceNewUuidOnOpen, pMedium.asOutParam())" at line 179 of file VBoxManageDisk.cpp` – Ed Randall Jun 10 '19 at 11:59
  • @EdRandall submit the issue in their bug tracker. I stopped using Virtualbox for some times – magicandre1981 Jun 10 '19 at 13:43
  • @Vasilly.ProkopyevI hadd to `swapoff -a` in addition to booting in recovery mode and disabling systemd services. – Dan M. Aug 29 '19 at 16:40
  • That bigemptyfile hung my VM, eating all the space leaving nothing for OS. Horrible advice. – Oleg Mihailik Oct 28 '19 at 10:49
  • As what @Marcus inferred, a good addition to this answer would be Step 0: For best results, delete all snapshots of the machine before performing the following steps. – Tfb9 Dec 20 '19 at 03:26
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    If running the command in the accepted answer produces an unhelpful error message like this VBoxManage.exe: error: Cannot register the hard disk 'thedisk.vdi' {aaaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeeee} because a hard disk 'thedisk.vdi' with UUID {aaaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeeee} already exists Simply run the command by the UUID instead of the filename: VBoxManage.exe modifyhd {aaaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeeee} --compact – DustWolf Feb 27 '20 at 10:09
  • Should I use SDelete if the host uses an SSD (if the VDI is on an SSD)? – aswine Apr 17 '20 at 00:36
  • @aswine I always use it, but he older version 1.6.1, sdlete 2 has a bug – magicandre1981 Apr 17 '20 at 13:26
  • Do not run defrag if the virtual machine has snapshots. It might move data that would otherwise not have changed, which results in a bigger differential. – Bachsau Feb 23 '21 at 20:18
  • must be rm -f /var/tmp/bigemptyfile – Pavel Tankov Jun 24 '21 at 07:40
  • FYI: this does *not* work on encrypted media (probably neither virtualbox's encryption, nor the guest os' encryption). I was confused why it did not work until I realized that it relies on the zeros on disk and with encryption you (often?) don't have zeros on disk. – Boris Jun 29 '21 at 15:42
  • after running defrag and sdelete.exe on my Win7 VM, I created a clone of it. The VM clone has the same VDI file size reduction I obtained later using modifymedium on the original VM – wlf Aug 12 '21 at 02:07
  • @Merc Then zerofree is probably a best option – golimar Oct 20 '22 at 05:02
  • @Marcus is right, with a Windows guest I had to delete all my snapshots THEN run `modifymedium` on the VDI. – kontextify Mar 27 '23 at 05:59
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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 {
...
    issue_discards = 1
}

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
Andrew Domaszek
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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.

CAD bloke
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    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 09 '15 at 10:26
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    @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 09:58
  • Very good point. Ironically it **is** highlighted on the stack exchange iOS app. – CAD bloke Sep 17 '15 at 10:32
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    Yeah CloneVDI is much better and faster way for personal use –  Nov 14 '15 at 09:51
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    The download of the CloneVDI tool is attached on page 1 of that forum's thread: https://forums.virtualbox.org/viewtopic.php?f=6&t=22422 – Peter Wippermann May 05 '20 at 14:04
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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
    
Mrskman
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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

instead of what you expect:

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.

breakpoint
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    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 '20 at 16:10
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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 :)

Dejv
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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
phuclv
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niziak
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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.

j riv
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0

Just to add an alternative to the accepted answer: vboxmanage clonehd not only clones but also compacts virtual disks, so if you also need to clone it you can use a similar process and do it in one go (in my case I was moving the VM from an external disk to an internal disk with less space so I needed clone+compact):

  1. run defrag in the guest (Windows only)
  2. zero-out free space in the guest
  3. shutdown the guest VM
  4. vboxmanage clonehd /mnt/externaldisk/VMs/win10.vdi /home/myuser/VMs/win10.vdi
golimar
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Just use the Live CD from this Open Source Project, on Linux Hosts / Guests ( this Live CD has the zerofree utility built in; also read the instructions on the site ) :

https://sourceforge.net/projects/live-cd-with-zerofree-utility/

This will also help in reducing the size of an exported virtual machine appliance as well ( i.e. .ova file ).

As others mentioned, after zerofree is run, use the compact option, to reduce the vdi file size.

P.S. A 32-Bit Version ( i686 architecture ) of this Live CD is available at: https://sourceforge.net/projects/live-cd-with-zerofree-32-bit/

Nathan SR
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