db version v3.2.16
git version: 056bf45128114e44c5358c7a8776fb582363e094
OpenSSL version: OpenSSL 1.0.2g  1 Mar 2016
allocator: tcmalloc
modules: none
build environment:
    distmod: ubuntu1404
    distarch: x86_64
    target_arch: x86_64

Relevant logs are in log.txt

At the time of incident I was running mongoexport on big collection (~10gb 15mln docs)
I suppose that mongoexport have slowed database to the level, when "group reduce init 2" exceeded its 2 second timeout.

invariant(_scope->exec("$arr = [];", "group reduce init 2", false, true, false /*assertOnError*/, 2 * 1000));

Maybe it would be better to fail single query instead of halting entire instance.