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 <bnn...@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" <sa...@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: >> http://docs.fabfile.org/en/1.3.2/index.html >> >> example: (another neurodebian ami) >> https://github.com/wholeslide/ipython_in_a_box/blob/master/fabfile.py >> >> cheers, >> >> satra >> >> On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols <bnn...@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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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