MapReduce programming is not a good match for all problems. It’s good for simple information requests and problems that can be divided into independent units, but it's not efficient for iterative and interactive analytic tasks. MapReduce is file-intensive. Because the nodes don’t intercommunicate except through sorts and shuffles, iterative algorithms require multiple map-shuffle/sort-reduce phases to complete. This creates multiple files between MapReduce phases and is inefficient for advanced analytic computing.
There’s a widely acknowledged talent gap. It can be difficult to find entry-level programmers who have sufficient Java skills to be productive with MapReduce. That's one reason distribution providers are racing to put relational (SQL) technology on top of Hadoop. It is much easier to find programmers with SQL skills than MapReduce skills. And, Hadoop administration seems part art and part science, requiring low-level knowledge of operating systems, hardware and Hadoop kernel settings.
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