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

[Saptarshi Guha]

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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