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 to not include a .license file with it, so as to force the download of this file (so that freesurfer usage will be tracked). A user need only do this once for however many times they use the cloud instance.
N. On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote: > 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 > disk that comes with the instance. I had disk-write errors because the > the main partition ran out of space. > > Anyway, ec2 rocks with Freesurfer. > - > > Joshua Lee > > Graduate Student > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > 530.747.3805 > > > 2011/11/12 Nolan Nichols <bnn...@uw.edu> > 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 stands, the starcluster FS AMI > does not > have a .license file and requires one to be uploaded manually. > > Nolan > > 2011/11/12 Thomas Ballinger <thomasballin...@gmail.com>: > > > 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 > <p...@netfilter.com.br> > >> > >> 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.com/br/artist/netfilter/id365306441 > >> > >> > >> > >> > >> On Sat, Nov 12, 2011 at 15:28, Nick Schmansky > <ni...@nmr.mgh.harvard.edu> > >> wrote: > >>> > >>> 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 > >>> <thomasballin...@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 > <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. > >>>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> _______________________________________________ > >>> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
