At what seems to be random times, the mongod primary never seems to finish some queries.
Some cursors had been running for 6+ hours. It has only happened on the primary.

The log always has these entries when this occurs:

[conn123812] warning: virtual size (129449MB) - mapped size (123342MB) is large. could indicate a memory leak

[initandlisten] connection accepted from 172.16.49.98:40540 #123818
[conn123816] end connection 172.16.49.98:40539
[conn123817] Assertion failure cc->_pinValue < 100 db/clientcursor.h 309
[conn123817] killcursors exception: assertion db/clientcursor.h:309 1ms

And as we can see in the log, the queries that work seem to take forever:
[conn123170] query x.scores nscanned:1015 scanAndOrder:1 nreturned:306 reslen:12260 302422ms

The server resources doesn't seem to be exhausted and restarting the server gets everything back to normal again.