On 08/20/2014 10:37 AM, Lazarevich, Alexander wrote:
Thanks for the reply Zeke. 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?
Running large amounts of data in the freesurfer virtual image is about as far from an efficient use of time as you can get. I think advising them to restart their entire processing run on the RHEL6 machines might be the way to go.
Another option is to advise them to perhaps rerun 1 or 2 "anchor" cases which were already run on Ubuntu and then rerun them the RHEL6 machines. The results might be identical, in which case they may be able to simply transition to the Red Hat machines instead of starting over on them.
Understandably the switch may concern them... As you know, we strongly advise people to stick with the same platform/version so as to avoid those effects on analysis results. **However, and I make the following statement in a completely unofficial capacity, the warning of running everything on the same platform is more of a Linux vs. MacOS issue, as opposed to a Linux distro vs. Linux distro issue.**
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?
No. If anything the opposite is true. Freesurfer is built on and supported for CentOS machines which are much closer to RedHat than Ubuntu. The users are probably requesting Ubuntu installs so as to keep a consistent platform for their study.
I would run a couple anchor cases on Ubuntu and RedHat, compare results, and then decide if I was going to start over or simply transition.
-Zeke
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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