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 .license file even if they don't actually use the file so that cloud usages get counted (license count is critical for us for grant renewal purposes). Ideas on a clean way to do this? 

N.

On Nov 12, 2011, at 11:10 AM, Thomas Ballinger <thomasballinger@gmail.com> wrote:

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 with Freesurfer, particularly due to the predictable long running time (lessening the benefits of job distribution) and ability of a recon-all job to efficiently use all of a ec2 small instance's cpu. I think starcluster is pretty awesome, and I would love to push people in that direction, but it won't be quite as push-button, and the benefits may be minimal for small use cases.  That's not to say there aren't plenty of folks who would rather use Nolan's solution (me for one :))

Tom


On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols <bnniii@uw.edu> wrote:

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 7:32 AM, "Satrajit Ghosh" <satra@mit.edu> wrote:
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:

example: (another neurodebian ami)

cheers,

satra

On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols <bnniii@uw.edu> wrote:
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 for installing tools from the NeuroDebian repository.
I've also been playing around with using s3fs, which allows Amazon's
S3 to be mounted as a drive and accessed directly as the
"subjects_dir".

The AMI can be launched here:
https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e

I did not include the .license for FS as I wasn't sure about licensing
issues, but I would be happy to publish an AMI with a built-in license
if I get the go ahead. For now you will need to start a cluster and
your license to each instance.

A few details:

Ubuntu 10.04 x86
built from StarClusters ami-8cf913e5
us-east-1 region
See the StarCluster details at http://web.mit.edu/stardev/cluster/
Customizing StarCluster
(http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html)
s3fs (http://code.google.com/p/s3fs/)
Freesurfer 5.1 32-bit
NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.)

Thanks again for starting this thread, and let me know if I can help
in any way. It would be great to see "cloud" resources be readily
accessibly to the community with minimal effort to get a cluster with
freesurfer and tools available via neurodebian up and running.

Cheers,

Nolan
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