Friday, May 5, 2017

Spark OutOfMemoryErrors.

Spark can deal with data sets that are much larger than the available physical memory. So, you never have problems with OutOfMemoryErrors, right? Well, no. It depends what you're doing.

When asked how to avoid OOMEs, the first thing people generally say is increase the number of partitions so that there is never too much data in memory at one time. However, this doesn't always work and you're better off having a look at the root cause.

This very week was one of those times. I was getting FetchFailedException. "This error is almost guaranteed to be caused by memory issues on your executors" (from here). Increasing the number of partitions didn't help.

The problem was that I had to find similar entities and declare there was a relationship between them. Foolishly, I tried to do a Cartesian product of all entities that were similar. This is fine 99.99% of the time but scales very badly - O(n2) - for outlying data points where n is large.

The symptoms were that everything was running tickety-boo until the very end where the last few partitions were taking tens of minutes and then the fatal FetchFailedException was thrown.

These pairs were going to be passed to GraphX's Connected Components algorithm so instead of creating a complete graph (which is what the Cartesian product of the entities would give you) you need to a different graph topology. This is not as simple as it sounds as you have to be a little clever in choosing an alternative. For instance, a graph that is just a line will take ages for GraphX to process if it is sufficiently large. For me, my driver ran out of memory after tens of thousands of Pregel supersteps.

A more efficient approach is a star topology that has branches of length 1. This graph is very quickly explored by Pregel/ConnectedComponents and has the same effect as a complete graph or a line since all vertices are part of the same connected component and we don't care at this point how they got there.

The result was the whole graph was processed in about 20 minutes.

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