When we are running large Map Reduce jobs, we have noticed that an index building operation seems to happen as phase 2 of 3 phases. When this happens, it seems to prevent the database from being used. That is, the indexing is not happening in the background and also not during insertions into the temporary MR collections.

See output snippet from the currentOp command. This index building seemed to happen during the execution of a Map/Reduce job after the Map phase ended and before the Reduce phase began.

{
"opid" : 853796039,
"active" : true,
"lockType" : "write",
"waitingForLock" : false,
"secs_running" : 229,
"op" : "insert",
"ns" : "sociocast.system.indexes",
"client" : "0.0.0.0:0",
"desc" : "conn",
"msg" : "index: (2/3) btree bottom up 4200477/18418261 22%"
},