Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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" 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 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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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" 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 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 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 conta
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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 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" 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 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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 > 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 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" 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 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 e
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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 > 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 >> 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 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" 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 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 : > 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 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 >> 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 >>> 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 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" 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 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 mric
