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While I couldn't agree more with the general point of the article, I have some small additional comments. Just as a bit of background, I think that Chris would
by davidmr 13y ago
While I couldn't agree more with the general point of the article, I have some small additional comments.
Just as a bit of background, I think that Chris would very much agree that I am not the intended recipient of this advice, and so my comments probably aren't keeping in the spirit of the article. I've spent the last 10+ years exclusively in very large HPC environments where the average size of the problem set is somewhere between 500TB and 10PB, and usually much closer to the latter than the former.
I think that, for the types of problems Chris mentions, for small data sets, hadoop is as silly a solution as he claims, and for the large map-reduce problem set of the (divide and conquer using simple arithmetic) of 5TB+, he's clearly in the right. Periodically I peruse job postings to see what is out there, and I'm personally ashamed at what many people call "big data", but just because your problem set doesn't fit the traditional model of big data (incidentally, I'm having trouble thinking of a canonical example of big data. perhaps genome sequencing? astronomical survey data?), doesn't mean that a) hadoop is not the right solution, and b) it's best done on a box with a hard drive and a postgres install, pandas/scipy, whatever.
We'll be generous and say that 4TB can do 150MB/s. A single run through the data at maximum efficiency will cost you ~8 hours. Since we've restricted ourselves to a single box, we're also not going to be able to keep the data in memory for subsequent calculations/simulations/whatever.
Take for example a 4TB data set. It is defined such that it would fit on a 4TB hard drive, but if your problem set involves reading the entire set of data and not just the indexes of a well-ordered schema, you're still going to have a bad time if you want it done quickly, or have a parameterization model that requires each permutation to be applied through the entire sequence of the data rather than chunks you can properly load into memory and then move on, you're going to have a really bad time.
I suppose all of this is to say that the amount of required parallelization of a problem isn't necessarily related to the size of the problem set as is mentioned most in the article, but also the inherent CPU and IO characteristics of the problem. Some small problems are great for large-scale map-reduce clusters, some huge problems are horrible for even bigger-scale map-reduce clusters (think fluid dynamics or something that requires each subdivision of the problem space to communicate with its neighbors).
I've had a quote printed on my door for years: Supercomputers are an expensive tool for turning CPU-bound problems into IO-bound problems.
- jedbrown 13y ago"Big Data starts at 1.5 PB [because that's what fits in memory on Blue Waters]" -- Bill Gropp On today's top HPC installations, it currently takes about an hour to read or write the contents of memory from/to global storage. If the workflow has broad dependencies (PDEs are especially bad, but lots of network analysis also fits the bill), it's much better to use more parallelism to run for a shorter period of time with the working set in memory. If you can't fit your working set in memory on the largest machine available, chances are you should either find time on a bigger machine or you can't afford to do the analysis. (The largest scientific allocations are in the 10s of millions of core hours per year, which would be burned in a few reads and writes on a million-core machine.) Also note that MapReduce is not very expressive. When IBM's Watson team was getting started, some people suggested using MapReduce/Hadoop, but the team quickly concluded it was way too slow/constraining and instead opted for an in-memory database with MPI for communication.
- w_t_payne 13y ago1.5 PB is pretty huge for most people outside of supercomputing. The biggest dataset I ever worked with fell some way short of that (It was approaching 1PB, I think, although we were not too sure how much data we had exactly, and it might have been slightly over, depending on how you measured). Even handling small(er) working sets could be a challenge in organisation, since we only had a small compute cluster (& associated infrastructure) to work with.
- dekhn 13y ago"Supercomputing" has never really been about big data. I used to work in supercomputing (NERSC) and have used most of the major machines in the field in the past. The supercomputer centers claim they're moving lots of data around, but it you look closely, it's almost entirely message passing during a calculation. And in most cases, the calculations they are doing are just wasted resources- simulating a protein over one long trajectory. Supercomputers, as compared to high throughput clusters, are just wasted money.
- 13y ago