Robomongo : Exceeded memory limit for $group

Question

I`m using a script to remove duplicates on mongo, it worked in a collection with 10 items that I used as a test but when I used for the real collection with 6 million documents, I get an error.

This is the script which I ran in Robomongo (now known as Robo 3T):

var bulk = db.getCollection('RAW_COLLECTION').initializeOrderedBulkOp();
var count = 0;

db.getCollection('RAW_COLLECTION').aggregate([
  // Group on unique value storing _id values to array and count 
  { "$group": {
    "_id": { RegisterNumber: "$RegisterNumber", Region: "$Region" },
    "ids": { "$push": "$_id" },
    "count": { "$sum": 1 }      
  }},
  // Only return things that matched more than once. i.e a duplicate
  { "$match": { "count": { "$gt": 1 } } }
]).forEach(function(doc) {
  var keep = doc.ids.shift();     // takes the first _id from the array

  bulk.find({ "_id": { "$in": doc.ids }}).remove(); // remove all remaining _id matches
  count++;

  if ( count % 500 == 0 ) {  // only actually write per 500 operations
      bulk.execute();
      bulk = db.getCollection('RAW_COLLECTION').initializeOrderedBulkOp();  // re-init after execute
  }
});

// Clear any queued operations
if ( count % 500 != 0 )
    bulk.execute();

This is the error message:

Error: command failed: {
    "errmsg" : "exception: Exceeded memory limit for $group, but didn't allow external sort. Pass allowDiskUse:true to opt in.",
    "code" : 16945,
    "ok" : 0
} : aggregate failed :
_getErrorWithCode@src/mongo/shell/utils.js:23:13
doassert@src/mongo/shell/assert.js:13:14
assert.commandWorked@src/mongo/shell/assert.js:266:5
DBCollection.prototype.aggregate@src/mongo/shell/collection.js:1215:5
@(shell):1:1

So I need to set allowDiskUse:true to work? Where do I do that in the script and is there any problem doing this?

Answer 1

{ allowDiskUse: true } 

Should be placed right after the aggregation pipeline.

In you code this should go like this:

db.getCollection('RAW_COLLECTION').aggregate([
  // Group on unique value storing _id values to array and count 
  { "$group": {
    "_id": { RegisterNumber: "$RegisterNumber", Region: "$Region" },
    "ids": { "$push": "$_id" },
    "count": { "$sum": 1 }      
  }},
  // Only return things that matched more than once. i.e a duplicate
  { "$match": { "count": { "$gt": 1 } } }
], { allowDiskUse: true } )

Note: Using { allowDiskUse: true } may introduce issues related to performance as aggregation pipeline will access data from temporary files on disk. Also depends on disk performance and the size of your working set. Test performance for your use case