Hi Satra
we did originally consider tracking usage in that way, but it seemed
invasive and a bit creepy to have FreeSurfer keeping track of what you
were up to and reporting back to us, so ultimately we decided not to
Bruce
On Fri,
18 Nov 2011, Satrajit Ghosh wrote:
hi nick,
i really like
hi nick,
i really like pedro's idea of tracking through instance tracking as opposed
to licenses. on a separate project we are setting up the ability to pull up
as many instances as necessary and install whatever software environment
that's needed to run your analysis. we'll try to ensure that eac
Long term, after we put together an 'official' instance of the AMI with
scripts (which might well be an instance that Pedro Paulo created) I
think sftp'ing the .license file to each instance is the way to go.
The .license file need only apply to the user (not each instance or
run).
N.
On Fri, 2
When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to
each instance prior to running an analysis. Not a big deal. I didn't get a
new license for each instance, but copied the same one to multiple
instances.
Joshua
2011/11/18 Pedro Paulo de Magalhães Oliveira Junior
> I have re
I have restored the image: 060244368407/FREESURFER51
I'll create a web service that can log the number of instances spawned. Is
that ok with you?
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netf
Hi PPJ,
I would rather people use FS without licenses than find themselves unable
to use it, so why not leave it for now. Can you put a request that they
first download a license or register on your website? Alternatively, can
you just remove the .license file from the AMI forcing the users to
As requested I removed the AMI image because that image contains a .license
file.
I can republish the image when we find a solution for the licensing issue.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
It would be great if Freesurfer maintained an official AMI. One important
reason to do so is security. If the AMI is maintained by the organization,
then people can feel reassured that their data is not being downloaded to a
compromised instance, not that any on this board would have such malicious
Ok. I'll label as private this AMI that has .license file.
Maybe we can make a tutorial on how to create an AMI instead.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobil
Glad to hear it works well. To revisit the issue of the license (in the
form of the .license file which needs to be in the $FREESURFER_HOME
directory and the request of which is used for usage tracking), I think
the convention to follow for any publicly available AMI freesurfer
instances should be
Thanks again Pedro. I just ran 220 brains through in day or two using the
cloud. Fantastic.
The script people have been talking about would have been useful.
One thing I didn't realize was that I should have moved the freesurfer
subject directory from /usr/local/freesurfer/subjects to the larger di
If only running a small number of instances, I think it is reasonable
to leave the ami w/o a .license file since it is easy enough to scp it
up to the cloud. For running a cluster it would be nice to have a
script, perhaps using Fabric, to upload a .license file to each
instance in a cluster. As it
Perhaps the AMI image could be without a licence file and uploading one
(acquired though normal means) would be required? (I suppose that's the
basic solution we're looking for a clean way around)
2011/11/12 Pedro Paulo de Magalhães Oliveira Junior
> Maybe we can set up a web server in the Mart
Maybe we can set up a web server in the Martinos center and the AMI Image
can authenticate in it.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.c
I'm happy to see the work getting the cloud to be feasible. I still need to
catch up on this thread but one issue that I'd like to sort out is tracking the
license count. Its fine for a new user to use an existing image, but I think
there will need to be a way to remind people to request our .l
Satra, the ipython example looks great. The scripts I posted also use
fabric for running Freesurfer, but don't download Freesurfer due to it
already being installed on Pedro's image. I agree with Satra that
individually administered instances might work better for those wishing to
run a few cases w
Hi Satra,
Fabric does look nice, thanks for pointing it out and for a link to the
ipython_in_a_box example.
That framework might work for what I had in mind for freesurfer and
starcluster, which uses the same idea to keep the initial AMI footprint
smaller/flexible.
Cheers,
Nolan
On Nov 12, 2011
hi nolan,
i think starcluster is a great way to create a cluster on aws. but for
those wanting to create a single instance and install things on an ami
without actually having a large ami, fabric might be a good option.
fabric:
http://docs.fabfile.org/en/1.3.2/index.html
example: (another neurod
Thanks, Pedro!
I am glad to see that you posted a public AMI for freesurfer. And
thanks to Thomas for producin documentation on how to use it.
This thread inspired me share a StarCluster AMI (ami-27f1384e in the
us-east-1 region) that I built for batch FS jobs, which includes the
initial setup fo
I've posted two scripts -- one for starting an instance and one for running
freesurfer -- using Pedro's AMI. They're in Python, and require two
additional Python packages which are easily installable. If people find
this a good starting point, please send me suggestions or code (including
suggesti
thanks Pedro Paulo!
Thomas, yes that script would be useful. A handy 'use case' for a
contributor to add to that wiki page would be to show how to use your
script to process the 40 tutorial subjects we supply on our site.
n.
On Fri, 2011-11-11 at 09:11 -0500, Thomas Ballinger wrote:
> I had p
I had previously worked on a script which, given Amazon EC2 credentials,
would spin up the instance, upload freesurfer data and run it, then send an
email when done - if this would be helpful to anyone I'll bother to finish
it, we use local compute resources so I never quite bothered. Now that
Ped
I've put together the basic tutorial on getting started using Amazon AWS
system:
It's in the same place Nick pointed out:
https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter
Tomorrow I'll post a tutorial.
It's quite simple
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
2011/11/9
Pedro Paulo,
thanks for posting the info. i've added this to the Download wiki page,
and created a stub page for the Amazon Cloud:
https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
i've never set one up so i have no idea how to do it. maybe someone can
flesh-out this page as using the ec2
No. This is for non GPU instances
-- iOS 5.0
Em 09/11/2011, às 22:28, Satrajit Ghosh escreveu:
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> Some weeks ago I was asked about a public image (AMI) to run in the Amazon
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> Some weeks ago I was asked about a public image (AMI) to run in the Amazon
> EC2 infrastructure
>
> If you want to use FreeSurfer in the EC2 infrastructure you can use this
Some weeks ago I was asked about a public image (AMI) to run in the Amazon
EC2 infrastructure
If you want to use FreeSurfer in the EC2 infrastructure you can use this
public AMI: *060244368407/FREESURFER51*
Just for your information this AMI can run a recon-all in 23 hours in an
Amazon AWS Small
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