When i was reading about limit method then i found a line that was
A negative limit is similar to a positive limit but closes the cursor
after returning a single batch of results. As such, with a negative
limit, if the limited result set does not fit into a single batch, the
number of documents received will be less than the specified limit.
I can't understand this explanation. So can any one explain this with a suitable Example?
If your query returns 100 elements before applying the limit operation, then you have 10 batches of data for your query ( if you do it via mongo shell). You can iterate through the data via it command until end ( 10 iterations).
If you add limit(30) to your query, you indicate that you want to get only 30 elements. Mongod will keep the connection from the mongo shell open until you have gone through all data.
However, if you set limit(-30), your query result on server still has 30 elements, but mongod only returns the first 10 elements to the shell, and you cannot go through the rest with it command because the connection is closed.
Related
I want to run aggregation on my large data sets. (It's about 361K documents) and Insert them to another collection.
I getting this error:
I tried to increase Max Time but it has maximum and it's not enough for my data sets. I found https://docs.mongodb.com/manual/reference/method/cursor.noCursorTimeout/ but it seems noCursorTimeout only apply on find not aggregation.
please tell me how I can disable cursor timeout or another solution to do this.
I am no MongoDB expert but will interpret what I know.
MongoDB Aggregation Cursors don't have a mechanism to adjust Batch Size or set Cursor Timeouts.
Therefore there is no direct way to alter this and the timeout of an aggregation query solely depends on the cursorTimeoutMillis parameter of the MongoDB or mongos` instance. Its default timeout value is 10 minutes.
Your only option is to change this value by the below command.
use admin
db.runCommand({setParameter:1, cursorTimeoutMillis: 1800000})
However, I strongly advise you against using this command. That's because it's a safety mechanism built into MongoDB. It automatically deletes queries that are running idle for more than 10 minutes, so that there is a lesser load in the MongoDB server. If you change this parameter (say to 30 minutes), MongoDB will allow idle queries to be running in the background for those 30 minutes, which will not only make all the new queries slower to execute, but also increase load and memory on the MongoDB side.
You have a couple of workarounds. Reduct the amount of documents if working on MongoDB Compass or copy and run the commands on Mongo Shell (I had success so far with this method).
From aggregate command doucumentation`:
To indicate a cursor with the default batch size, specify cursor: {}.
However, I haven't found the value of such defaul or how to find it (maybe using a mongo admin command).
How to find such value?
From the docs:
The MongoDB server returns the query results in batches. The amount of data in the batch will not exceed the maximum BSON document size.
New in version 3.4: Operations of type find(), aggregate(), listIndexes, and listCollections return a maximum of 16 megabytes per batch. batchSize() can enforce a smaller limit, but not a larger one.
find() and aggregate() operations have an initial batch size of 101 documents by default. Subsequent getMore operations issued against the resulting cursor have no default batch size, so they are limited only by the 16 megabyte message size.
So, the default for the first batch is 101 documents, the batch size for subsequent getMore() calls is undetermined but cannot exceed 16 megabytes.
If I'm not entirely wrong, I think it's 101 for aggregation pipeline.
See here
For my thesis I'm currently investigating the speed (down to milliseconds) of Elasticsearch and MongoDB.
I've noticed that, compared to MongoDB, Elasticsearch is very consistent when it comes to the speed at which it returns data and the total items found. Where other MongoDB takes a longer time to return data the more results are found, Elasticsearch's response time is almost always the same, regardless of the total amount of requests sent.
My hypothesis is that in Elasticsearch, when using the size operator, the number of documents that are actually looked up and retrieved after the search in the indexes is finished is exactly the amount set in the size operator. Where in MongoDB this is not the case, in MongoDB all documents that matched in the index are retrieved, and only the top X amount is eventually returned to the client based on the cursor's batch_size and eventually the max limit() that is set.
I have no way, other than to spend hours looking through the source code, to figure out if this hypothesis is correct, or if something else is going on that I must have missed.
Thanks for taking the time to read this, any responses are appreciated and will help me further my research.
To make it a bit clearer how Elasticsearch actually retrieves results: It uses query then fetch.
So if you search for N results, the first phase will query all the shards involved and return a list of their N results containing the score and the ID — not other information. In the second phase you fetch the top N global results by their ID. So you will retrieve more scores and IDs than you need, but you will only fetch the actual results.
We are troubled by eventually occurring cursor not found exceptions for some Morphia Queries asList and I've found a hint on SO, that this might be quite memory consumptive.
Now I'd like to know a bit more about the background: can sombody explain (in English), what a Cursor (in MongoDB) actually is? Why can it kept open or be not found?
The documentation defines a cursor as:
A pointer to the result set of a query. Clients can iterate through a cursor to retrieve results. By default, cursors timeout after 10 minutes of inactivity
But this is not very telling. Maybe it could be helpful to define a batch for query results, because the documentation also states:
The MongoDB server returns the query results in batches. Batch size will not exceed the maximum BSON document size. For most queries, the first batch returns 101 documents or just enough documents to exceed 1 megabyte. Subsequent batch size is 4 megabytes. [...] For queries that include a sort operation without an index, the server must load all the documents in memory to perform the sort before returning any results.
Note: in our queries in question we don't use sort statements at all, but also no limit and offset.
Here's a comparison between toArray() and cursors after a find() in the Node.js MongoDB driver. Common code:
var MongoClient = require('mongodb').MongoClient,
assert = require('assert');
MongoClient.connect('mongodb://localhost:27017/crunchbase', function (err, db) {
assert.equal(err, null);
console.log('Successfully connected to MongoDB.');
const query = { category_code: "biotech" };
// toArray() vs. cursor code goes here
});
Here's the toArray() code that goes in the section above.
db.collection('companies').find(query).toArray(function (err, docs) {
assert.equal(err, null);
assert.notEqual(docs.length, 0);
docs.forEach(doc => {
console.log(`${doc.name} is a ${doc.category_code} company.`);
});
db.close();
});
Per the documentation,
The caller is responsible for making sure that there
is enough memory to store the results.
Here's the cursor-based approach, using the cursor.forEach() method:
const cursor = db.collection('companies').find(query);
cursor.forEach(
function (doc) {
console.log(`${doc.name} is a ${doc.category_code} company.`);
},
function (err) {
assert.equal(err, null);
return db.close();
}
);
});
With the forEach() approach, instead of fetching all data in memory, we're streaming the data to our application. find() creates a cursor immediately because it doesn't actually make a request to the database until we try to use some of the documents it will provide. The point of cursor is to describe our query. The second parameter to cursor.forEach shows what to do when an error occurs.
In the initial version of the above code, it was toArray() which forced the database call. It meant we needed ALL the documents and wanted them to be in an array.
Note that MongoDB returns data in batches. The image below shows requests from cursors (from application) to MongoDB:
forEach scales better than toArray because we can process documents as they come in until we reach the end. Contrast it with toArray - where we wait for ALL the documents to be retrieved and the entire array is built. This means we're not getting any advantage from the fact that the driver and the database system are working together to batch results to your application. Batching is meant to provide efficiency in terms of memory overhead and the execution time. Take advantage of it in your application, if you can.
I am by no mean a mongodb expert but I just want to add some observations from working in a medium sized mongo system for the last year. Also thanks to #xameeramir for the excellent walkthough about how cursors work in general.
The causes of a "cursor lost" exception may be several. One that I have noticed is explained in this answer.
The cursor lives server side. It is not distributed over a replica set but exists on the instance that is primary at the time of creation. This means that if another instance takes over as primary the cursor will be lost to the client. If the old primary is still up and around it may still be there but for no use. I guess it is garbaged collected away after a while. So if your mongo replica set is unstable or you have a shaky network in front of it you are out of luck when doing any long running queries.
If the full content of what the cursor wants to return does not fit in memory on the server the query may be very slow. RAM on your servers needs to be larger than the largest query you run.
All this can partly be avoided by designing better. For a use case with large long running queries you may be better of with several smaller database collections instead of a big one.
The collection's find method returns a cursor - this points to the set of documents (called as result set) that are matched to the query filter. The result set is the actual documents that are returned by the query, but this is on the database server.
To the client program, for example the mongo shell, you get a cursor. You can think the cursor is like an API or a program to work with the result set. The cursor has many methods which can be run to perform some actions on the result set. Some of the methods affect the result set data and some provide the status or info about the result set.
As the cursor maintains information about the result set, some information can change as you use the result set data by applying other cursor methods. You use these methods and information to suit your application, i.e., how and what you want to do with the queried data.
Working on the result set using the cursor and some of its commonly used methods and features from mongo shell:
The count() method returns the count of the number of documents in the result set, initially - as the result of the query. It is always constant at any point in the life of the cursor. This is information. This information remains same even after the cursor is closed or exhausted.
As you read documents from the result set, the result set gets exhausted. Once completely exhausted you cannot read any more. The hasNext() tells if there are any documents available to be read - returns a boolean true or false. The next() returns a document if available (you first check with hasNext, and then do a next). These two methods are commonly used to iterate over the result set data. Another iteration method is the forEach().
The data is retrieved from the server in batches - which has a default size. With the first batch you read the documents and when all it's documents are read, the following next() method retrieves the next batch of documents, etc., until all documents are read from the result set. This batch size can be configured and you can also get its status.
If you apply the toArray() method on the cursor, then all the remaining documents in the result set are loaded into the memory of your client computer and are available as a JavaScript array. And, the result set data is exhausted. The following hasNext method will return false, and the next will throw an error (once you exhaust the cursor, you cannot read data from it). This method loads all the result set data into your client's memory (the array). This can be memory consuming in case of large result sets.
The itcount() returns the count of remaining documents in the result set and exhausts the cursor.
There are cursor methods like isClosed(), isExhausted(), size() which give status information about the cursor and its underlying result set as you work with your data.
Those are the basic features of cursor and result set. There are many cursor methods, and you can try and see how they work and get a better understanding.
Reference:
mongo shell's cursor
methods
Cursor behavior with Aggregate
method
(the collection's aggregate method also returns a cursor)
Example usage in mongo shell:
Assume the test collection has 200 documents (run the commands in the same sequence).
var cur = db.test.find( { } ).limit(25) creates a result set with 25
documents only.
But, cur.count() will show 200, which is the actual count of
documents by the query's filter.
hasNext() will return true.
next() will return a document.
itcount() will return 24 (and exhausts the cursor).
itcount() again will return 0.
cur.count() will still show 200.
This error also comes when you have a large set of data and are doing batch processing on that data and each batch takes more time, totalling that time be exceeded the default cursor live time.
Then you need to change that default time to tell mongo that will not expire this cursor until processing is done.
Do check No TimeOut Documentation
A cursor is an object returned by calling db.collection.find() and which enables iterating through documents (NoSQL equivalent of a SQL "row") of a MongoDB collection (NoSQL equivalent of "table").
In case your cluster is stable and no members where down or changing state, the most posible reason for not finding the cursor is this:
Default idle cursor timeout is 10min , but in the versions >= 3.6 the cursor is also associated with session which is having default session timeout 30min , so even you set the cursor to not expire with the option noCursorTimeout() you are still limited by the session timeout of 30min. To avoid your cursor to be killed by the session timeout you will need to perioducally check in your code and execute sessionRefresh command:
db.adminCommand({"refreshSessions" : [sessionId]})
to extend the session with another 30min so your cursor to not be killed if you do something with the data before fetching the next batch...
check the docs here for detail how to do it:
https://docs.mongodb.com/manual/reference/method/cursor.noCursorTimeout/
I'm not sure how to put this. Well, recently I worked on a rails project with mongoid, and I had the task of inserting multiple records in Mongodb.
Say insert multiple records of PartPriceRecord in the database. After googling this I came across the collection.insert commands:
PartPriceRecord.collection.insert(multiple_part_price_records)
But on inserting large number of records, MongoDb always seemed to prompt me with error message:
Exceded maximum insert size of 16,000,000 bytes
Googling around I found that the the upper limit for MongoDb for a single document, but surprisingly when I changed my above query to this:
multiple_part_price_records.each do|mppr|
PartPriceRecord.create(mppr)
end
the above errors do not seem to appear any more.
Can anyone explain in depth under the hood what is exactly is the difference between the two?
Thanks
The maximum size for a single, bulk insert is 16M bytes. That's what you're trying to do in your first example.
In your second example, you're inserting each document individually. Therefore, each insert is under the max limit for an insert.
#Kyle explained the difference in his answer quite succinctly (+1'd), but as for a solution to your problem you may want to look at doing batch inserts:
BATCH_SIZE = 200
multiple_part_price_records.each_slice(BATCH_SIZE) do |batch|
PartPriceRecord.collection.insert(batch)
end
This will slice the records into batches of 200 (or whatever size is best for your situation) and insert them within that limit. This will be a lot faster than running save on each one individually which would be sending far more requests to the database.
A few quick things to note about collection.insert:
It does not run validations on your models prior to insertion, you may want to check this prior to insert
It is required to be in a document format unlike save which requires it be a model. You can easily convert to a document by calling as_document on the model.