MongoDB - find() calls getting stuck sometimes - Timeout

Question

We are using MongoDb for saving and fetching data.

All calls that are putting data into collections are working fine and are through common method.

All calls that are fetching data from collections are working fine sometimes and are through common method.

But Sometimes, only for one of the collection, i get my calls being stuck for forever, consuming CPU usage. I have to manually kill the threads otherwise it consumes my whole CPU.

Mongo Connection

MongoClient mongo = new MongoClient(hostName , Integer.valueOf(port));
DB mongoDb = mongo.getDB(dbName);

Code To fetch

DBCollection collection = mongoDb.getCollection(collectionName);
DBObject dbObject = new BasicDBObject("_id" , key);
DBCursor cursor = collection.find(dbObject);

Though i have figured out the collection for which it is causing issues, but how can i improve upon this, since it is occurring for this particular collection and sometimes.

EDIT

Code to save

DBCollection collection = mongoDb.getCollection(collectionName);
DBObject query = new BasicDBObject("_id" , key);
DBObject update = new BasicDBObject();
update.put("$set" , JSON.parse(value));
collection.update(query , update , true , false);

Bulk Write / collection

DB mongoDb = controllerFactory.getMongoDB();
        DBCollection collection = mongoDb.getCollection(collectionName);

        BulkWriteOperation bulkWriteOperation = collection.initializeUnorderedBulkOperation();

        Map<String, Object> dataMap = (Map<String, Object>) JSON.parse(value);

        for (Entry<String, Object> entrySet : dataMap.entrySet()) {
            BulkWriteRequestBuilder bulkWriteRequestBuilder = bulkWriteOperation.find(new BasicDBObject("_id" ,
                    entrySet.getKey()));

            DBObject update = new BasicDBObject();
            update.put("$set" , entrySet.getValue());

            bulkWriteRequestBuilder.upsert().update(update);
        }

How can i set timeout for fetch calls..??

Answer 1

Just some possible explanations/thoughts.

In general "query by id" has to be fast since _id is supposed to be indexed, always. The code snippet looks correct, so probably the reason is in mongo itself. This leads me to a couple of suggestions:

Try to connect to mongo directly from the command line and run the "find" from there. The chances are that you'll still be able to observe occasional slowness.

In this case:

• Maybe its about the disks (maybe this particular server is deployed on the slow disk or at least there is a correlation with some slowness of accessing the disk).

• Maybe your have a sharded configuration and one shard is slower than others

• Maybe its a network issue that occurs sporadically. If you run mongo locally/on staging env. with the same collection does this reproduce?

• Maybe (Although I hardly believe that) the query runs in sub un-optimal way. In this case you can use "explain()" as someone has already suggested here.

• If you happen to have replica set, please figure out what is the [Read Preference]. Who knows, maybe you prefer to get this id from the sub-optimal server

Answer 2

The answers posted by others are great, but did not solve my purpose. Actually issue was in my existing code itself , my cursor was waiting in while loop infinite time.

I was missing few checks which has been resolved now.

Answer 3

A different approach is to use the proposed method for MongoDB 3.2 Driver. Keep in mind that you have to update your .jar libraries (if you haven't) to the latest version.

public final MongoClient connectToClient(String hostName, String port) {
    try {
        MongoClient client = new MongoClient(hostName, Integer.valueOf(port));
        return client;
    } catch(MongoClientException e) {
        System.err.println("Cannot connect to Client.");
        return null;
    }
}

public final MongoDatabase connectToDB(String databaseName) {
    try {
        MongoDatabase db = client.getDatabase(databaseName);
        return db;
    } catch(Exception e) {
        System.err.println("Error in connecting to database " + databaseName);
        return null;
    }

public final void closeConnection(MongoClient client) {
    client.close();
}

public final void findDoc(MongoDatabase db, String collectionName) {
    MongoCollection<Document> collection = db.getCollection(collectionName);
    try {
        FindIterable<Document> iterable = collection
                .find(new Document("_id", key));
        Document doc = iterable.first();
        //For an Int64 field named 'special_id'
        long specialId = doc.getLong("special_id");
    } catch(MongoException e) {
        System.err.println("Error in retrieving document.");
    } catch(NullPointerException e) {
        System.err.println("Document with _id " + key + " does not exist.");
    }
}

public final void insertToDB(MongoDatabase db, String collectioName) {
    try {
        db.getCollection(collectionName).insertOne(new Document()
            .append("special_id", 5)
            //Append anything
        );
    catch(MongoException e) {
        System.err.println("Error in inserting new document.");
    }
}

public final void updateDoc(MongoDatabase db, String collectionName, long id) {
    MongoCollection<Document> collection = db.getCollection(collectionName);
    try {
        collection.updateOne(new Document("_id", id),
                             new Document("$set", 
                                     new Document("special_id", 
                                             7)));
    catch(MongoException e) {
        System.err.println("Error in updating new document.");
    }
}

public static void main(String[] args) {
    String hostName = "myHost";
    String port = "myPort";
    String databaseName = "myDB";
    String collectionName = "myCollection";
    MongoClient client = connectToClient(hostName, port);
    if(client != null) {
        MongoDatabase db = connectToDB(databaseName);
        if(db != null) {
            findDoc(db, collectionName);
        }
        client.closeConnection();
    }
}

EDIT: As the others suggested, check from the command line if the procedure of finding the document by its ID is slow too. Then maybe this is a problem with your hard drive. The _id is supposed to be indexed but for better or for worse, re-create the index on the _id field.