[BioC] EBS volumes with the Bioconductor AMI: how to change default behaviour
dtenenba at fhcrc.org
Fri Aug 12 19:46:00 CEST 2011
On Fri, Aug 12, 2011 at 12:32 AM, Quin Wills <qilin at 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.
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.
> Thanks a ton,
>>>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.
>>> 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,
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor