Thanks Dan

I did think it slightly unusual that so many volumes are created and stay
attached. I look forward to heard from you!

If you do have any advice on what you think would be the most appropriate
way for R to terminate an instance once a job is done, I'd also appreciate
it enormously.

Thanks,
Quin



On 12 August 2011 18:46, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Fri, Aug 12, 2011 at 12:32 AM, Quin Wills <qilin@quinwills.net> wrote:
> > Thanks for the advice Dan.
> >
> > The reason I like to use S3 is that I like to run jobs, log out and
> > have them automatically
> > shut down when done. At the moment I'm just running the following
> function for
> > automated shutdown of my instances from within my R script:
> >
> > shutdown <- function(time=0) return(system(paste("echo 'sudo halt' |
> > at now + ",time," min",sep="")))
> >
> > Even if I set my instance's shutdown behaviour to "terminate" (in the
> > AWS management console),
> > those EBS volumes seem to persist when I automate termination this way.
>
> Hi,
>
> I just tried running the Bioconductor AMI as a different user and I
> notice that those volumes are created and stay "attached" to the
> instance even after the instance is terminated. I'm not sure why they
> are created in the first place; I'll look into that and report back to
> you. You can safely detach and delete them after your instance is
> halted. You can do that in the EC2 web console, with EC2 command-line
> tools, or calling the EC2 API from a programming language. I can send
> you an example of the latter if you are interested.
>
>
> >
> > Do you perhaps have a recommendation on how better to make sure my
> > instance shuts
> > down once the job is done? Ideally it would be great if it could fire
> > off a quick
> > email too, but this doesn't seem so easy to do unless I create my own
> > AMI I think.
> >
>
> You might look into Amazon's Simple Email Service.
> http://aws.amazon.com/ses/
>
> Dan
>
>
> > Thanks a ton,
> > Quin
> >
> >
> >>>On Thu, Aug 11, 2011 at 6:11 AM, Quin Wills <qilin at quinwills.net>
> wrote:
> >>> Hello Bioconductor AMI gurus
> >>>
> >>> Delighted that Bioconductor has an AMI with pre-loaded bells and
> whistles.
> >>> I'm hardly an AWS guru (yet?), and in particular feel like all the dots
> >>> aren't connecting in my brain regarding EBS.
> >>>
> >>> So I see that the Bioconductor AMI automatically initiates 1 x 20GiB
> root
> >>> EBS volume, and 3 x 30 GiB extra volumes, correct?
> >>> What if I don't want
> >>> these? Presumably just detaching and deleting them in the AWS
> management
> >>> console is one way to do it? Is this the only (reasonably easy) way?
> >>
> >>
> >>The AMI "lives" on these EBS volumes so you don't want to delete them.
> >>You may find you don't even own them.
> >>
> >>
> >>
> >>> For the moment I'm just using AWS for CPU-intensive work that I need to
> >>> speed up. I have an S3 bucket and am using the omegahat RAmazonS3
> library to
> >>> access and save data on a semi-permanent basis. Does this seem like a
> >>> reasonable tactic? For the moment, the sizes of the data objects in my
> S3
> >>> bucket are manageable.
> >>
> >>If it works for you, it is reasonable. The reason we don't use S3 is
> >>that we find it slow, plus it is a two-step process to push files to
> >>S3 from your AMI, then pull them from S3 to your local machine, as
> >>opposed to using scp to copy files directly in one step.
> >>
> >>But if you find that S3 works for you, there's no reason not to use it.
> >>Dan
> >>
> >>> Perhaps there's a link to an idiots guide on "EBS vs S3" options and
> >>> suggestions when using the Bioconductor AMI?
> >>>
> >>> Thanks in advance for any wisdom,
> >>> Quin
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>



-- 

Quin Wills
Live the kind of life that when you die half the world mourns the loss of a
great sentience, whilst the other half are just grateful that it's over.

Brasenose College
Oxford
OX1 4AJ
tel: +44 (0)7951 335 714
inet: www.quinwills.net

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