[Beowulf] Station wagon full of tapes

Chris Dagdigian dag at sonsorol.org
Tue May 26 11:27:53 EDT 2009


The flip side to your arguments is that I may not want my tax dollars  
spent on allowing the NIH to operate peta-scale data repositories. I  
can't be more specific than this -- my most recent exposure to a large  
government life science directorate revealed that they were spending  
$500K/year on EMC maintenance costs for a few tens-of-TBs worth of  
disk arrays that were going on 6 years old!

I think my main interest in utility storage providers is that they can  
offer geographical redundancy and large capacity at efficiencies that  
can't be matched locally by individual institutions or even local  
groups of institutions. When I look at the full costs of hosting,  
operating and replicating the data in a local facility the numbers  
from the "utility" providers start to look more attractive.

It will be interesting to see how this all shakes out. The rate at  
which raw disk cost is shrinking in price is amazing and may choke off  
the profit for the utility providers who have invested heavily in  
building out.

My $.02 of course!






On May 26, 2009, at 11:16 AM, Robert G. Brown wrote:

> On Tue, 26 May 2009, Chris Dagdigian wrote:
>
>>
>> I deal quite often with the "next-gen" DNA sequencing instruments  
>> that produce 1TB/day in TIFF images that are then distilled down to  
>> the DNA basecalls before the short reads are subjected to  
>> alignment. Then the resulting longer sequences are usually aligned  
>> again against a reference genome.
>>
>> Lots of data, lots of computation.
>>
>> The 1 Terabyte of TIFF images typically reduces down to about 200  
>> GB in intermediate data which is further distilled down into a few  
>> hundred KB of actual sequence data. The entire process is  
>> interesting and it is a massive Bio/IT challenge as these types of  
>> terabyte-scale data producing lab instruments are popping up  
>> everywhere (the cost of one of these instruments is now easily  
>> within reach of a single grant-funded researcher at a facility of  
>> any size...). We are only a few technology revolutions away from  
>> these boxes showing up in your point of care primary physician's  
>> office (well not really, probably a backend service lab that your  
>> physician outsources to ...)
>>
>> Anyway the new data ingestion service that Amazon offers is, I  
>> think, going to be a big deal in our field.
>
> Sure, but why wouldn't it be cheaper for e.g. NSF or NIH to fund an
> exact clone of the service Amazon plans to offer and provide it for  
> free
> to its supported research groups (or rather, do bookkeeping but it is
> all internal bookkeeping, moving money from one pocket to another).
>
> Amazon has to make a profit.  Granting agencies don't have to pay the
> profit that Amazon has to make.  Amazon has to take substantial  
> risks to
> make its profit.  Granting agencies have no risk.
>
> All of the things you assert for DNA sequencing are true for high  
> energy
> physics.  Enormous datasets, lots of computation.  HEP's INTERNATIONAL
> solution is ATLAS, not Amazon.
>
> Supporting commercial access into such a DB a la >>google<< but for
> genomic data, sure, but that's not really cluster computing, that's a
> large shared DB.  I could see that as a spin off data service of  
> Amazon
> or Google or a new business altogether, but I'd view it as a niche and
> not really HPC.
>
> Grant funded research involving large scale shared data resources can
> ALWAYS be done more cheaply than by buying the data services from
> profit-making third parties unless there are nonlinear e.g.  
> proprietary
> IP barriers.  This is trebly true given that research facilities are
> typically on a very high speed networks e.g. lambda rail that the
> government is funding anyway, where Amazon or other commercial third
> parties have to rent time on those networks and then resell the rental
> back to the government at a profit or use slower commercial networks  
> and
> with the same sort of throughput markup.
>
> Are there any such barriers here?  I'd have to say that I would be  
> most
> unhappy seeing my own tax dollars going to make Amazon shareholders  
> rich
> when they could be spent more efficiently without a middleman raking  
> in
> a 50 to 100% markup on the service.  Of course I'm easily irked --  
> when
> I think of all the money spent on Windows by the US government it  
> makes
> my blood boil.
>
> I'd want to see a solid CBA proving that this is the cheapest way to
> proceed before dumping tons of tax money into it, if I were king of  
> the
> world (or just in charge of a major granting agency).
>
>   rgb
>
>>
>> For the following reasons:
>>
>> - Bio people are being buried in data
>> - Once we process the data to get the derived results, the primary  
>> data just needs to go somewhere cheap
>> - Amazon and other internet-scale people can do peta-scale or exa- 
>> scale storage far better & cheaper than any of my customers
>> - These instruments are popping up in wet labs across campus with  
>> weak/anemic network links to IT core facilities and data centers
>> - Scientists in many cases are required to share data that is grant  
>> funded
>> - Amazon has some neat "downloader pays" models that make it easier  
>> for researchers to affordably offer up peta-scale data sets for  
>> sharing
>>
>> I suspect that very large amount of scientific data will be making  
>> a 1-way trip into the cloud. The data will stay there "forever" as  
>> a deep store. In the ocasional cases where the data needs to be re- 
>> processed or re-analyized it would be not unreasonable to fire up  
>> some cloud server nodes to do the re-work in-situ.
>>
>> The disk ingest service was the final piece. I can see this  
>> happening in life science environments:
>>
>> - Massive data generated in the wet lab
>> - Captured to local storage (10 - 40TB) with small HPC component
>> - Data is processed locally into derived and distilled forms
>> - Derived data replicated to campus/lab facilities for online  
>> primary storage
>> - Derived data (and possibly the full raw data) is compressed,  
>> placed onto drives and ingested into Amazon for long term storage
>> - If re-analysis is ever needed, have existing EC2 AMIs preloaded  
>> with the necessary software
>>
>> Basically it comes down to the fact that Amazon may be able to  
>> offer big-yet-slow storage in the terabyte to petabyte range at  
>> levels of cost and geographical redundancy that would be extremely  
>> difficult to match with local resources at a small non-specialized  
>> organization.
>>
>> My $.02 of course
>>
>> -Chris
>>
>>
>>
>>
>>
>>
>> On May 26, 2009, at 8:58 AM, Jeff Layton wrote:
>>
>>> Gerry Creager wrote:
>>>> There was an interesting brainstorming session at Rocks-A-Palooza  
>>>> a couple of weeks ago.  Someone wants to offer Amazon resources.   
>>>> Problem remains for me: How can I get sufficient cloud resources  
>>>> for computing (I'll hammer on dataset transport in a moment) that  
>>>> will handle reasonable weather models with their small message  
>>>> MPI chatter, and lots of file I/O? I've been assured that  
>>>> Amazon's ready to accommodate that.
>>> This is one of the problems - clouds aren't ready for this kind of
>>> usage model yet. They only have GigE and usually it's  
>>> oversubscribed.
>>> When you say file IO, they hear capacity, not performance (either
>>> throughput or IOPS). And as you point out, the pipe to/from the
>>> cloud is not ready for lots of data.
>>>> However, getting data into S3 for availability, when a daily  
>>>> multi-gigabyte dataset is used for initiation, and another is  
>>>> created as output, is going to be expensive, and likely slow.  I  
>>>> think there are other approaches that have to be evaluated.  I am  
>>>> not sure the cloud is ready for MPI play on a significant basis,  
>>>> just yet.
>>> I haven't seen the cloud ready yet for anything other than  
>>> embarrassingly
>>> parallel codes (i.e. since node, small IO requirements). Has  
>>> anyone seen
>>> differently? (as an example of what might work, CloudBurst seems  
>>> to be
>>> gaining some traction - doing sequencing in the cloud. The only  
>>> problem
>>> is that sequencing can generate a great deal of data pretty  
>>> rapidly).
>>> Jeff
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>
> Robert G. Brown	                       http://www.phy.duke.edu/~rgb/
> Duke University Dept. of Physics, Box 90305
> Durham, N.C. 27708-0305
> Phone: 1-919-660-2567  Fax: 919-660-2525     email:rgb at phy.duke.edu
>

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