[R-sig-hpc] distributed R on EC2, designing the software stack

[Saptarshi Guha]

Hello,
I've been testing R across clusters and will execute some more in
depth tests over the weekend.
However, it depends on what Instance Types you use (types and cost:
http://aws.amazon.com/ec2/instance-types/)

I used a cluster of 15 "standard large instance", for less than  1 hr,
which cost me $6. Intra EC2 bandwidth is free (in the same region),
and downloading a GB from outside of the EC2 is ~$0.1 per GB. So, yes,
depending on the budget (i'm a grad student and it is turning out to
be expensive) it can easily run into hundreds of dollars on a monthly
basis if used regularly.

Keep in mind that if you have a web service running on an instance and
check the website (e.g cluster status monitoring) from outside the EC2
an expense is incurred. Also as soon as the instance is up and running
you're being charged. Do not forget to terminate them!

I'll be tabulating my performance and expenditure in the coming week.

Hope it helps
Saptarshi Guha



On Sat, May 2, 2009 at 2:03 PM, malcolm Crouch
<malcolm.croucher at gmail.com> wrote:
>
> Hi ,
>
>
> i have looked at the pricing for Amazon , however am wondering from a
> practical point of view what roughly your monthly costs are ?
>
> I am interested in using this service as I dont have access to a cluster but
> need to do a feasilibilty study ... therefore some ideas on costing would be
> useful.
>
> Regards
>
> Malcolm
> On Wed, Apr 29, 2009 at 9:36 PM, Saptarshi Guha <saptarshi.guha at gmail.com>
> wrote:
>>
>> Hello,
>> Yes, I was playing with EC2 and Rhipe last night. Just got permission
>> to increase my instances to 100!
>> The details (what I know)
>> RHIPE is based on Hadoop and R. Cloudera has a very easy to use AMI
>> for small and large (32/64bit) instances. It is easy enough to install
>> the cloudera AMI.
>> However It does not come with R.
>>
>> Last night, I modified their scripts to yum install R (using yum we
>> get R-2.6) on each machine - as such this results in ~21MB downloads
>> on the machines[1], which is not expensive but is not the best way do
>> things.
>>
>> Once booted, each machine installs R, Rserve and one machine (the
>> master) installs RHIPE.
>> I did it with 1 master and 1 tasktracker and RHIPE worked. I intend to
>> check with 30+ instances to see how things scale.
>>
>> I have emailed cloudera asking them to bundle R with their Hadoop AMI
>> - so that users incur a minimal expense.
>>
>> I will be placing EC2 instructions to use RHIPE shortly this week.
>> Given the reasonable cost of EC2, it would be a great way for users to
>> test out distributed computing with R. Maybe as part of the R
>> community we could host a linux AMI? Again, cost is the issue
>> here(rather not pay for users downloading things)
>>
>> Regards
>> Saptarshi Guha
>> [1] Not quite sure how the AMI's work - if 10 AMIs belong to one
>> group, does EC2 boot up one and replicate the booted instance? If so,
>> then there is only one download, if not each machine downloads.
>>
>>
>> On Wed, Apr 29, 2009 at 3:24 PM, Whit Armstrong
>> <armstrong.whit at gmail.com> wrote:
>> > you should contact Robert Grossman who just gave a presentation on
>> > this topic at R/Finance in Chicago.
>> >
>> > link: http://rinfinance.quantmod.com/speakers/
>> >
>> > -Whit
>> >
>> >
>> > On Wed, Apr 29, 2009 at 3:06 PM, Stephen J. Barr
>> > <stephenjbarr at gmail.com> wrote:
>> >> Greetings,
>> >>
>> >> I am trying to get into distributed computing with R, but do not have
>> >> access to a cluster. Therefore, I am trying to get distributed R
>> >> running on Amazon's EC2. ( http://aws.amazon.com/ec2/ )
>> >>
>> >> For those of you who don't know, EC2 allows you to instantiate large
>> >> numbers of computers, bundled with whatever OS and software
>> >> configuration you want. From my survey of things, there are a lot of
>> >> different options available for distributed computing. For my needs, I
>> >> would just like to run simple Monte Carlo simulations, and other
>> >> things that don't require a ton of inter-node communication.
>> >>
>> >> What I would like to do is put together a public AMI and a howto
>> >> guide, such that it would be very easy for anyone to instantiate an
>> >> N-node cluster and start with parallel computing. I would like to have
>> >> a discussion/brainstorm over what the exact software stack should be.
>> >>
>> >> My initial thoughts were:
>> >>
>> >> 1) R 2.9.0 + OpenMPI + RMpi + Snowfall/sfCluster
>> >>   - will Amazon's network work with OpenMPI. Perhaps it would be
>> >> better to use PVM or something that is more tolerant to non-optimal
>> >> network
>> >>
>> >> 2)  R 2.9.0 + "socket based communication" + Snowfall/sfCluster
>> >>  - is this scalable
>> >>
>> >> 3)  R 2.9.0 + twisted + NetWorkSpaces
>> >>   - not sure of Amazon's network supports broadcast mode, which is
>> >> required by twisted
>> >>
>> >> 4) Biocep-R
>> >>   - this looks like it has the functionality to do what I want, but a
>> >> lot of other stuff as well.
>> >>
>> >> 5) RHIPE
>> >>   - Hadoop is well supported by EC2. Perhaps this is the way to go.
>> >> Seems like a very new package :)
>> >>
>> >> What are people's thoughts on what would be a good software stack with
>> >> the constraint that it should be simple and run on EC2?
>> >>
>> >> Thanks,
>> >> -stephen
>> >> ==========================================
>> >> Stephen J. Barr
>> >> University of Washington
>> >> WEB: www.econsteve.com
>> >>
>> >> _______________________________________________
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>> >>
>> >
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>
>
>
> --
> Malcolm A.B Croucher
>