Thanks for the reply Zeke.
I understand what you are saying about the VM. So my question is now, how do we help our users to optimize FreeSurfer for their large scale data sets?
We have a couple of Red Hat Enterprise Linux 6 64bit machines with the newest FreeSurfer installed (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz), and these machines are very powerful. (16 x 3.3GHz cores, 128GB of memory, 1888 Bus speed, Nvidia Quadro K5000 video, etc.) We have encouraged our users to use these machines, but they have hesitated because I think a lot of their data has already been processed on the XUbuntu VM and they are worried about switching the FreeSurfer platforms in the middle of their research. I wonder if it makes sense for them to restart their entire processing run on the RHEL6 machines. If the processing is that much faster, then they may save time in the long run?
But then our users have also requested a fresh Ubuntu install with FreeSurfer installed on top? (not a VM) Is there anything about Ubutnu OS that is better suited for FreeSurfer than Red Hat Enterprise 6 or 7?
Alex
-----Original Message----- From: Z K [mailto:zkaufman@nmr.mgh.harvard.edu] Sent: Tuesday, August 19, 2014 4:28 PM To: Freesurfer support list; Lazarevich, Alexander Subject: Re: [Freesurfer] FreeSurfer platform/performance questions
Hello Alex,
I created the FreeSurfer VM and you are correct that the Virtual Box host is 32bit. I cant remember exactly why I did it that way, but I suspect it may have been in an effort to reduce overall size, as the gzipped size of the .vdi file is 9gigs. Also, it was created more as matter of convenience to allow users with PCs the means for viewing and processing data, but it is not optimized for processing large scale data sets.
There is no 64bit VM currently available. However, it would not be too difficult to make one. Simply download any of the available 64bit host images (http://virtualboxes.org/images/), open it in VirtualBox, install 64bit freesurfer within the image, and then export the disk image which will now have freesurfer installed on it.
I could take on this task but I can not guarantee I will get to it in the immediate future.
-Zeke
On 08/18/2014 12:07 PM, Lazarevich, Alexander wrote:
One of the packages we have recently installed upon request is FreeSurfer. We have installed freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer -Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz on our Red Hat Enterprise Linux 6 workstations, as well as on our Windows 7 Enterprise 64bit workstations. We have also installed Oracle's VirtualBox on a Windows 7 Enterprise 64bit machine, and run the VM freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer -Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz inside that virtual environment.
The researchers who requested FreeSurfer are all part of the same group, and they are trying to complete a very large research project which requires FreeSurfer to process large amounts of data. They have normally been running FreeSurfer on the VM in the XUbuntu VirtualBox environment on their own average desktop PC's. However, they are concerned about their processing time with FreeSurfer, so they are hoping to take advantage of the Vislab computing resources to decrease the processing time in FreeSurfer.
We are running into the following problems/concerns:
1)The FreeSurfer VM (Xubuntu) that runs in VirtualBox is a 32bit host. Is there a 64bit VM available? That 32bit host can only access 4GB of memory, whereas they would like to be able to access more of the workstations 128GB of memory.
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