[SERVER-18454] Slow Read Performance - MongoDB 3 with WiredTiger Storage Engine. Created: 13/May/15  Updated: 14/May/15  Resolved: 14/May/15

Status: Closed
Project: Core Server
Component/s: Performance
Affects Version/s: None
Fix Version/s: None

Type: Question Priority: Major - P3
Reporter: Peter John King Assignee: Sam Kleinman (Inactive)
Resolution: Done Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Participants:

 Description   

We have a 3x3 MongoDB Cluster in Amazon EC2, we are querying from an Azure Worker Role and an Azure Web Worker Role.

We have about 10M documents stored, there are only 2 main collections:

  • controls
  • controlIssues

The _id for controls is a string GUID.
The _id for controlIssues is a compound of: the control string guid and a guid for itself.

Therefore are indexes are as follows (below is our createDb() function for creating our sharded collections and index):

var createDb = function() {
    var client = db.getMongo();
 
    // Create collections.
    var controlIt = client.getDB("controlIt");
    controlIt.createCollection("controls");
    controlIt.createCollection("controlIssues");
    controlIt.createCollection("controlIssueMetaData");
    controlIt.createCollection("controlIssueReasons");
    controlIt.createCollection("issueStates");
 
    // Sharding.
    sh.enableSharding("controlIt");
    sh.shardCollection("controlIt.controls", { _id: 1 }, { "unique": true });
    sh.shardCollection("controlIt.controlIssues", { _id: 1 }, { "unique": true });
 
    // Indexes on controls collection.
    db.controls.ensureIndex({ "name": 1 }, { "background": true });
    db.controls.ensureIndex({ "description": 1 }, { "background": true, "sparse": true });
    db.controls.ensureIndex({ "active": 1 }, { "background": true, "sparse": true });
 
    // Indexes on controlIssues collection.
    db.controlIssues.ensureIndex({ "state.id": 1 }, { "background": true });
    db.controlIssues.ensureIndex({ "state.treatAsClosed": 1 }, { "background": true, "sparse": true });
    db.controlIssues.ensureIndex({ "attributes.id": 1 }, { "background": true, "sparse": true });
    db.controlIssues.ensureIndex({ "attributes.value": 1 }, { "background": true, "sparse": true });
}

Below is an example "control", simple JSON:

{
    "_id": "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea",
    "typeId": -1,
    "surrogateKey": "-600",
    "name": "Sample SM Control D",
    "shortName": "Sample SM Control D Short name",
    "description": "Sample SM Control D Description",
    "itemsForInvestigation": 0,
    "escalationId": -1,
    "effectiveStartDate": { "$date": "2015-02-18T00:00:00.000Z" },
    "subscribingUserIds": [1,2,4,94],
    "active": true,
    "activeForNotifications": true,
    "owner": 1,
    "ownerDelegate": 94,
    "owningTeamId": 7,
    "ragThreshold": 
    {
        "red": 
        {
            "shortName": "R",
            "ragCode": "1",
            "lower": 100.01000,
            "upper": 10000.00000
        },
        "amber": 
            {
                "shortName": "A",
                "ragCode": "2",
                "lower": 0.01000,
                "upper": 100.00000
            },
        "green": 
            {
                "shortName": "G",
                "ragCode": "3",
                "lower": 0.00000,
                "upper": 0.00000
            }
    }
}

Below is a "controlIssue" example, JSON:

{
    "_id": {
        "controlId": "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea",
        "id": "8dff48e4-7b6f-4cf2-ba1e-dea889432e24"
    },
    "state": {
        "id": "NEW",
        "date": {
            "$date": "2015-02-18T00:00:00.000Z"
        },
        "treatAsClosed": false
    },
    "stateHistory": [
        {
            "date": {
                "$date": "2015-02-18T00:00:00.000Z"
            },
            "id": "NEW"
        },
        {
            "date": {
                "$date": "2015-02-19T00:00:00.000Z"
            },
            "id": "CLOSED"
        }
    ],
    "attributes": [
        {
            "id": "-1",
            "value": "Test01"
        },
        {
            "id": "109",
            "value": "Test1"
        },
        {
            "id": "110",
            "value": "Name"
        },
        {
            "id": "111",
            "value": "LastName"
        }
    ],
    "commentary": [
        {
            "reasonId": "UNDER_INVESTIGATION",
            "text": "Something entered by user",
            "userId": 123,
            "date": {
                "$date": "2015-02-19T00:00:00.000Z"
            }
        }
    ]
}

As you can see, there is a parent child relationship between control and controlIssue, control being the parent.

Here is a query that takes a long time to run and obviously it shouldn't:

db.controlIssues.find({ "_id.controlId": "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea" }).limit(100)

Here is the explain of the above:

{
	"clusteredType" : "ParallelSort",
	"shards" : {
		"ciShard_0/CI-0.acr-group.9122.mongodbdns.com:27000,CI-1.acr-group.9122.mongodbdns.com:27000,CI-5.acr-group.9122.mongodbdns.com:27000" : [
			{
				"queryPlanner" : {
					"plannerVersion" : 1,
					"namespace" : "controlIt.controlIssues",
					"indexFilterSet" : false,
					"parsedQuery" : {
						"_id.controlId" : {
							"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
						}
					},
					"winningPlan" : {
						"stage" : "LIMIT",
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"direction" : "forward"
							}
						}
					},
					"rejectedPlans" : [ ]
				},
				"executionStats" : {
					"executionSuccess" : true,
					"nReturned" : 0,
					"executionTimeMillis" : 2205,
					"totalKeysExamined" : 0,
					"totalDocsExamined" : 3519658,
					"executionStages" : {
						"stage" : "LIMIT",
						"nReturned" : 0,
						"executionTimeMillisEstimate" : 1930,
						"works" : 3519660,
						"advanced" : 0,
						"needTime" : 3519659,
						"needFetch" : 0,
						"saveState" : 27497,
						"restoreState" : 27497,
						"isEOF" : 1,
						"invalidates" : 0,
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"nReturned" : 0,
							"executionTimeMillisEstimate" : 1920,
							"works" : 3519660,
							"advanced" : 0,
							"needTime" : 3519659,
							"needFetch" : 0,
							"saveState" : 27497,
							"restoreState" : 27497,
							"isEOF" : 1,
							"invalidates" : 0,
							"chunkSkips" : 0,
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"nReturned" : 0,
								"executionTimeMillisEstimate" : 1840,
								"works" : 3519659,
								"advanced" : 0,
								"needTime" : 3519659,
								"needFetch" : 0,
								"saveState" : 27497,
								"restoreState" : 27497,
								"isEOF" : 1,
								"invalidates" : 0,
								"direction" : "forward",
								"docsExamined" : 3519658
							}
						}
					},
					"allPlansExecution" : [ ]
				},
				"serverInfo" : {
					"host" : "CI-0",
					"port" : 27000,
					"version" : "3.0.2",
					"gitVersion" : "6201872043ecbbc0a4cc169b5482dcf385fc464f"
				}
			}
		],
		"ciShard_1/CI-12.acr-group.9122.mongodbdns.com:27000,CI-3.acr-group.9122.mongodbdns.com:27000,CI-6.acr-group.9122.mongodbdns.com:27000" : [
			{
				"queryPlanner" : {
					"plannerVersion" : 1,
					"namespace" : "controlIt.controlIssues",
					"indexFilterSet" : false,
					"parsedQuery" : {
						"_id.controlId" : {
							"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
						}
					},
					"winningPlan" : {
						"stage" : "LIMIT",
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"direction" : "forward"
							}
						}
					},
					"rejectedPlans" : [ ]
				},
				"executionStats" : {
					"executionSuccess" : true,
					"nReturned" : 0,
					"executionTimeMillis" : 2350,
					"totalKeysExamined" : 0,
					"totalDocsExamined" : 3459816,
					"executionStages" : {
						"stage" : "LIMIT",
						"nReturned" : 0,
						"executionTimeMillisEstimate" : 2080,
						"works" : 3459818,
						"advanced" : 0,
						"needTime" : 3459817,
						"needFetch" : 0,
						"saveState" : 27029,
						"restoreState" : 27029,
						"isEOF" : 1,
						"invalidates" : 0,
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"nReturned" : 0,
							"executionTimeMillisEstimate" : 2060,
							"works" : 3459818,
							"advanced" : 0,
							"needTime" : 3459817,
							"needFetch" : 0,
							"saveState" : 27029,
							"restoreState" : 27029,
							"isEOF" : 1,
							"invalidates" : 0,
							"chunkSkips" : 0,
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"nReturned" : 0,
								"executionTimeMillisEstimate" : 2000,
								"works" : 3459817,
								"advanced" : 0,
								"needTime" : 3459817,
								"needFetch" : 0,
								"saveState" : 27029,
								"restoreState" : 27029,
								"isEOF" : 1,
								"invalidates" : 0,
								"direction" : "forward",
								"docsExamined" : 3459816
							}
						}
					},
					"allPlansExecution" : [ ]
				},
				"serverInfo" : {
					"host" : "CI-12",
					"port" : 27000,
					"version" : "3.0.2",
					"gitVersion" : "6201872043ecbbc0a4cc169b5482dcf385fc464f"
				}
			}
		],
		"ciShard_2/CI-2.acr-group.9122.mongodbdns.com:27000,CI-4.acr-group.9122.mongodbdns.com:27000,CI-7.acr-group.9122.mongodbdns.com:27001" : [
			{
				"queryPlanner" : {
					"plannerVersion" : 1,
					"namespace" : "controlIt.controlIssues",
					"indexFilterSet" : false,
					"parsedQuery" : {
						"_id.controlId" : {
							"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
						}
					},
					"winningPlan" : {
						"stage" : "LIMIT",
						"limitAmount" : 0,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"direction" : "forward"
							}
						}
					},
					"rejectedPlans" : [ ]
				},
				"executionStats" : {
					"executionSuccess" : true,
					"nReturned" : 100,
					"executionTimeMillis" : 62,
					"totalKeysExamined" : 0,
					"totalDocsExamined" : 100100,
					"executionStages" : {
						"stage" : "LIMIT",
						"nReturned" : 100,
						"executionTimeMillisEstimate" : 40,
						"works" : 100102,
						"advanced" : 100,
						"needTime" : 100001,
						"needFetch" : 0,
						"saveState" : 782,
						"restoreState" : 782,
						"isEOF" : 1,
						"invalidates" : 0,
						"limitAmount" : 0,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"nReturned" : 100,
							"executionTimeMillisEstimate" : 40,
							"works" : 100101,
							"advanced" : 100,
							"needTime" : 100001,
							"needFetch" : 0,
							"saveState" : 782,
							"restoreState" : 782,
							"isEOF" : 0,
							"invalidates" : 0,
							"chunkSkips" : 0,
							"inputStage" : {
								"stage" : "COLLSCAN",
								"filter" : {
									"_id.controlId" : {
										"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
									}
								},
								"nReturned" : 100,
								"executionTimeMillisEstimate" : 40,
								"works" : 100101,
								"advanced" : 100,
								"needTime" : 100001,
								"needFetch" : 0,
								"saveState" : 782,
								"restoreState" : 782,
								"isEOF" : 0,
								"invalidates" : 0,
								"direction" : "forward",
								"docsExamined" : 100100
							}
						}
					},
					"allPlansExecution" : [ ]
				},
				"serverInfo" : {
					"host" : "CI-2",
					"port" : 27000,
					"version" : "3.0.2",
					"gitVersion" : "6201872043ecbbc0a4cc169b5482dcf385fc464f"
				}
			}
		]
	},
	"n" : 100,
	"nscanned" : 0,
	"nscannedObjects" : 7079574,
	"millisShardTotal" : 4617,
	"millisShardAvg" : 1539,
	"numQueries" : 3,
	"numShards" : 3,
	"executionTimeMillis" : 2351
}

Below is our sh.status():

--- Sharding Status --- 
  sharding version: {
	"_id" : 1,
	"minCompatibleVersion" : 5,
	"currentVersion" : 6,
	"clusterId" : ObjectId("553a4a3173a8b2c25c74b403")
}
  shards:
	{  "_id" : "ciShard_0",  "host" : "ciShard_0/CI-0.acr-group.9122.mongodbdns.com:27000,CI-1.acr-group.9122.mongodbdns.com:27000,CI-5.acr-group.9122.mongodbdns.com:27000" }
	{  "_id" : "ciShard_1",  "host" : "ciShard_1/CI-12.acr-group.9122.mongodbdns.com:27000,CI-3.acr-group.9122.mongodbdns.com:27000,CI-6.acr-group.9122.mongodbdns.com:27000" }
	{  "_id" : "ciShard_2",  "host" : "ciShard_2/CI-2.acr-group.9122.mongodbdns.com:27000,CI-4.acr-group.9122.mongodbdns.com:27000,CI-7.acr-group.9122.mongodbdns.com:27001" }
  databases:
	{  "_id" : "admin",  "partitioned" : false,  "primary" : "config" }
	{  "_id" : "controlIt",  "partitioned" : true,  "primary" : "ciShard_2" }
		controlIt.controlIssues
			shard key: { "_id" : 1 }
			chunks:
				ciShard_2	175
				ciShard_1	176
				ciShard_0	177
			too many chunks to print, use verbose if you want to force print
		controlIt.controls
			shard key: { "_id" : 1 }
			chunks:
				ciShard_1	1
				ciShard_2	1
				ciShard_0	1
			{ "_id" : { "$minKey" : 1 } } -->> { "_id" : "e1542af1-308c-4bca-a28e-5a78c8a25a94" } on : ciShard_1 Timestamp(3, 0) 
			{ "_id" : "e1542af1-308c-4bca-a28e-5a78c8a25a94" } -->> { "_id" : "fb495ea8-bed8-440c-8b87-22926adf83c8" } on : ciShard_2 Timestamp(3, 1) 
			{ "_id" : "fb495ea8-bed8-440c-8b87-22926adf83c8" } -->> { "_id" : { "$maxKey" : 1 } } on : ciShard_0 Timestamp(2, 0) 
	{  "_id" : "test",  "partitioned" : false,  "primary" : "ciShard_1" }
	{  "_id" : "ControlItDb",  "partitioned" : false,  "primary" : "ciShard_0" }



 Comments   
Comment by Sam Kleinman (Inactive) [ 14/May/15 ]

I'm glad to hear that your issue is resolved. I'm going to go ahead and close this issue, but if you encounter another issue in the future, please feel free to open another ticket, or reach out to one of our support channels.

Cheers,
sam

Comment by Peter John King [ 14/May/15 ]

Sam,

Yes it did, the database was the last think to check, we didn't think it was the issue and investigated other possibilities first.
Once we exhausted everything and checked the database we were at the end of our tether and submitted the JIRA ticket.
Soon after though, as you can see, the light-bulb moment hit and I realised the index was the problem, once I added that, the calls were ok.

Comment by Sam Kleinman (Inactive) [ 13/May/15 ]

Did adding the index on _id.controlId fully resolve your issue, or are there remaining performance issues?

Comment by Peter John King [ 13/May/15 ]

This ticket can be downgraded.

Comment by Peter John King [ 13/May/15 ]

We believe it's a missing index on the _id.controlId field.

Here is the new explain plan of the very same query that was mentioned above:

"clusteredType" : "ParallelSort",
	"shards" : {
		"ciShard_0/CI-0.acr-group.9122.mongodbdns.com:27000,CI-1.acr-group.9122.mongodbdns.com:27000,CI-5.acr-group.9122.mongodbdns.com:27000" : [
			{
				"queryPlanner" : {
					"plannerVersion" : 1,
					"namespace" : "controlIt.controlIssues",
					"indexFilterSet" : false,
					"parsedQuery" : {
						"_id.controlId" : {
							"$eq" : "9e5b2f2b-a1a0-4b51-b261-16c61cff53ea"
						}
					},
					"winningPlan" : {
						"stage" : "LIMIT",
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"inputStage" : {
								"stage" : "FETCH",
								"inputStage" : {
									"stage" : "IXSCAN",
									"keyPattern" : {
										"_id.controlId" : 1
									},
									"indexName" : "_id.controlId_1",
									"isMultiKey" : false,
									"direction" : "forward",
									"indexBounds" : {
										"_id.controlId" : [
											"[\"9e5b2f2b-a1a0-4b51-b261-16c61cff53ea\", \"9e5b2f2b-a1a0-4b51-b261-16c61cff53ea\"]"
										]
									}
								}
							}
						}
					},
					"rejectedPlans" : [ ]
				},
				"executionStats" : {
					"executionSuccess" : true,
					"nReturned" : 0,
					"executionTimeMillis" : 0,
					"totalKeysExamined" : 0,
					"totalDocsExamined" : 0,
					"executionStages" : {
						"stage" : "LIMIT",
						"nReturned" : 0,
						"executionTimeMillisEstimate" : 0,
						"works" : 1,
						"advanced" : 0,
						"needTime" : 0,
						"needFetch" : 0,
						"saveState" : 0,
						"restoreState" : 0,
						"isEOF" : 1,
						"invalidates" : 0,
						"limitAmount" : 100,
						"inputStage" : {
							"stage" : "SHARDING_FILTER",
							"nReturned" : 0,
							"executionTimeMillisEstimate" : 0,
							"works" : 1,
							"advanced" : 0,
							"needTime" : 0,
							"needFetch" : 0,
							"saveState" : 0,
							"restoreState" : 0,
							"isEOF" : 1,
							"invalidates" : 0,
							"chunkSkips" : 0,
							"inputStage" : {
								"stage" : "FETCH",
								"nReturned" : 0,
								"executionTimeMillisEstimate" : 0,
								"works" : 1,
								"advanced" : 0,
								"needTime" : 0,
								"needFetch" : 0,
								"saveState" : 0,
								"restoreState" : 0,
								"isEOF" : 1,
								"invalidates" : 0,
								"docsExamined" : 0,
								"alreadyHasObj" : 0,
								"inputStage" : {
									"stage" : "IXSCAN",
									"nReturned" : 0,
									"executionTimeMillisEstimate" : 0,
									"works" : 1,
									"advanced" : 0,
									"needTime" : 0,
									"needFetch" : 0,
									"saveState" : 0,
									"restoreState" : 0,
									"isEOF" : 1,
									"invalidates" : 0,
									"keyPattern" : {
										"_id.controlId" : 1
									},
									"indexName" : "_id.controlId_1",
									"isMultiKey" : false,
									"direction" : "forward",
									"indexBounds" : {
										"_id.controlId" : [
											"[\"9e5b2f2b-a1a0-4b51-b261-16c61cff53ea\", \"9e5b2f2b-a1a0-4b51-b261-16c61cff53ea\"]"
										]
									},
									"keysExamined" : 0,
									"dupsTested" : 0,
									"dupsDropped" : 0,
									"seenInvalidated" : 0,
									"matchTested" : 0
								}
							}
						}
					},
					"allPlansExecution" : [ ]
				},
				"serverInfo" : {
					"host" : "CI-0",
					"port" : 27000,
					"version" : "3.0.2",
					"gitVersion" : "6201872043ecbbc0a4cc169b5482dcf385fc464f"
				}
			}
		],
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