virtualbox.org

Hello everyone,

I am using Virtualbox 4.2.6 to run FreeSurfer. I had previously set the memory for the VM to the recommended amount, however that gave a memory error, so I incresed to just under 80% of the total memory available. However after doing that, I am now getting a disk space error: Sure enough, when I open the virtualuser folder in File Manager and look at Properties, the Free Space is "0 B"!

I have a folder on my HDD that I defined as share, which I mount using the command ..however when I got the diskspace error, the command would have wanted to write in a different folder (somewhere in the freesurfer folder)

From the Properties of my VM, on the Storage space, I only have Storage Tree options, and no option to set a certain amount of HDD space as being available to the VM.

There is no option in VirtualBox to limit the amount of data that can be stored in a shared folders.

Virtual hard disk drives are not the same as shared folders. A virtual hard disk can be limited to a particular size on creation. Partitioning and formatting the drive must be done in the guest OS, and partition size offers another opportunity to limit disk space consumption.

Btw, I have no idea what FreeSurfer is.

Please post a VM log file as a .zip attachment if you want to discuss this further. The VM log file is called "VBox.log" and can be found in the "Logs" subfolder of the VM folder.

Hello, thanks for your reply, and sorry to not have provided a full background: FreeSurfer is a package that does brain imaging analyses, and which runs on Linux. I was running one of its commands when I got the memory error, followed, later, by the disk space error.

Log attached..

So will I have to set up a partition in order for the free space of the virtual drive to no longer show up as zero?

longtalker wrote:So will I have to set up a partition in order for the free space of the virtual drive to no longer show up as zero?

Perhaps not. From the log it looks like you downloaded a prepared Linux VDI image? In that case the disk should be as prepared as it needs to be. Though, it would be helpful to know what flavor of Linux is being used...

Edit:  Just checked the Freesurfer website, it looks like it's based on Ubuntu 32bit. In that case allocating 2GB RAM to the VM is way overkill, and a bad idea since your host only has 2.6GB total available RAM. IMHO you should reduce this to 1GB. What was the recommended amount? You should install the latest Guest Additions for Ubuntu Linux (I see you currently have the 3.2.x GAs installed - and you have the latest Guest Additions ISO mounted in the VM, but have not actually installed them - see user manual for instructions). I would like details of the hard disk: check File|Virtual Media Manager in the VBox manager, and tell me what it says about this disk in terms of capacity, current size, disk type etc.

FreeSurfer support says it needs at least 2GB to run, which is why I allocated that much memory to the VM... Consequently though, my computer is really sluggish when the VM is on.

When I open the Update Manager and click on Install Updates (which presumably includes the GAs), I'm told that there isn't enough disk space...

Re: what you asked - see screenshot. Thanks for your help.

Hmm. It looks like they made the rather unwise move of creating a virtual drive with a logical size only just big enough to hold the data they put on it. The quickest fix for that is to resize the disk using CloneVDI (CloneVDI will make a clone disk which is larger). Resize it to 32GB, then replace the current disk in the VM with the clone vdi. And incidentally it's best to keep the VDI inside the VM folder.

Note that after cloning it is only the disk which will be larger, not the partitions inside. So you need next to boot the VM using a gparted live-cd iso and use it to resize the main partition to fill the drive. After unmounting the gparted cd and rebooting you should then be able to update the GAs... as well as avoid other problems to do with lack of disk space.

Your host cannot really afford 2GB, so you need to get that figure down. I would try 1GB and see if it works. If you really must then try 1.5GB. You may also have to consider shutting down any other memory hungry apps you have running.

This sounds awfully complicated, at least for someone who hasn't used any non-Windows OSs or VMs before. I really just want to be able to run the FreeSurfer commands asap, isn't there an easier way of making them be able to store their output somewhere where there's already space? Perhaps move everything in my shared folder, and then run the command from there? Or will this still not solve the problem of there being 0 KB of disk space overall?

It's hard to believe anyone running FreeSurfer on Windows would have to go through so many technical steps just to have some disk space available inside the VM!

The strange thing is that I've run FreeSurfer commands from inside the VM before, and they worked fine - I just don't recall what was different in those past cases in comparison to now..

longtalker, if I may be blunt on this : The VM that you downloaded was prepared a certain way. It was given a specific disk with a specific size. Just like if you would go and buy a 15 Gb hard disk for your Windows 7 installation.
Basically - they did it wrong.

The issue with doing this wrong is that it always leads to technical steps to "save the day", which are never easy for people who only used windows, but that's just how it is. What mpack described may sound awfully complicated but really, it isn't that much. Other ways involve clearing out logs or temporary files. But that's about it really.
If you want to move data from the VM to another place, yes you can, but we have no idea how this program works, and so we can't really give you any answers on this...

Thanks, in this case I'll just try to work through the steps above when I have the time