I am building an application that requires a lot of data constantly being extracted from a local MongoDB to be put into Neo4j. Seeing as I am also having many users access the Neo4j database, from both a Django webserver and other places, I decided on using the REST interface for Neo4j.
The problem I am having is that, even with batch insertion, the Neo4j server is active over 50% of the time with just trying the insert all the data from the mongoDB. As far as I can see there might be some waiting time because of the HTTP requests but I have been trying to tweak but have only gotten so far.
The question is, if I write a Java plugin (http://docs.neo4j.org/chunked/stable/server-plugins.html) that can handle inserting the mongoDB extractions directly, will I then go around the REST API? Or will the java plugin commands just convert to regular REST API requests? Furthermore, will there be a performance boost by using the plugin?
The last question is how do I optimize the speed of the REST API (So far I am performing around 1500 read/write operations which includes many "get_or_create_in_index" operations)? Is there a sweet spot where the number of queries appended to one HTTP requests will keep Neo4j busy until the next HTTP request arrives?
Update:
I am using Neo4j version 2.0
The data that I am extracting consists of bluetooth observations, where the phone that is running the app i created scans all nearby phones. This single observation is then saved as a document in MongoDB and consists of the users id, the time of the scan and a list of the phones/users that he has seen in that scan.
In Neo4j I model all the users as nodes and I also model an observation between two users as a node so that it will look like this:
(user1)-[observed]->(observation_node)-[observed]->(user2)
Furthermore I index all user nodes.
When moving the observation from mongoDB to Neo4j, I do the following for each document:
Check in the index if the user doing the scan already has a node assigned, else create one
Then for each observed user in the scan: A) Check in index if the observed user has a node else create one B) Create an observation node and relationships between the users and the observation node, if this doesn't already exist C) Make a relationship between the observation node and a timeline node (the timeline just consists of a tree of nodes so that I can quickly find observations at a certain time)
As it can be seen I am doing quite a few lookups in the user index (3), some normal read (2-3) and potentially many writes for each observation.
Each bluetooth scan average around 5-30 observations and I batch 100 scans in a single HTTP request. This means that each request usually contains 5000-10000 updates.
What version are you using?
The unmanaged extension would use the underlying Java-API so it much faster, also you can decide on the format & protocol of the data that you push to it.
It is sensible to batch writes, so that you don't incurr tx overhead per each tiny write. E.g. aggregating 10-50k updates in one operation helps a lot.
What is the concrete shape of the updates you do? Can you edit your question to reflect that?
Some resources for this:
http://maxdemarzi.com/2013/09/05/scaling-writes/
http://maxdemarzi.com/2013/12/31/the-power-of-open-source-software/
Related
My team’s been thrown into the deep end and have been asked to build a federated search of customers over a variety of large datasets which hold varying degrees of differing data about each individuals (and no matching identifiers) and I was wondering how to go about implementing it.
I was thinking Apache Nifi would be a good fit to query our various databases, merge the result, deduplicate the entries via an external tool and then push this result into a database which is then queried for use in an Elasticsearch instance for the applications use.
So roughly speaking something like this:-
For examples sake the following data then exists in the result database from the first flow :-

Then running https://github.com/dedupeio/dedupe over this database table which will add cluster ids to aid the record linkage, e.g.:-

Second flow would then query the result database and feed this result into Elasticsearch instance for use by the applications API for querying which would use the cluster id to link the duplicates.
Couple questions:-
How would I trigger dedupe to run on the merged content was pushed to the database?
The corollary question - how would the second flow know when to fetch results for pushing into Elasticsearch? Periodic polling?
I also haven’t considered any CDC process here as the databases will be getting constantly updated which I'd need to handle, so really interested if anybody had solved a similar problem or used different approach (happy to consider other technologies too).
Thanks!
For de-duplicating...
You will probably need to write a custom processor, or use ExecuteScript. Since it looks like a Python library, I'm guessing writing a script for ExecuteScript, unless there is a Java library.
For triggering the second flow...
Do you need that intermediate DB table for something else?
If you do need it, then you can send the success relationship of PutDatabaseRecord as the input to the follow-on ExecuteSQL.
If you don't need it, then you can just go MergeContent -> Dedupe -> ElasticSearch.
I'm the owner of the Blockchain2graph project that reads data from Bitcoin core rest API and insert Blocks, Addresses and Transactions as Graph objects in Neo4j.
After some imports, the process is slowing down until the memory is full. I don't want to use CSV imports. My problem is not performance, my goal is to insert things without the application stopping because of memory (even if it takes quite a lot of time)
I'm using spring-boot-starter-data-neo4j.
In my code, I try to make session.clear from times to times but it doesn't seem to have an impact. After restarting tomcat8, things go fast again.
As your project is about mass inserts, I wouldn't use an OGM like Spring Data Neo4j for writing the data.
You don't want a session to keep your data around on the client.
Instead, use Cypher directly sending updates you get from the BlockChain API directly as a batch per request, see my blog post for some examples (some of which we also use in SDN/Neo4j-OGM under the hood).
You can still use SDN for individual entity handling (CRUD) that's what OGMs are good for in my book to reduce the boilerplate.
But for more complex read operations that have aggregation, filtering, projection and path matches I'd still use Cypher on an annotated repository method, returning rows that can be mapped to a list of DTOs.
I'm currently create a program that imports all groups and feeds from Facebook which the user wants.
I used to use the Graph API with OAuth and this works very well.
But I came to the point that I realized that one request can't handle the import of 1000 groups plus the feeds.
So I'm looking for a solution that imports this data in the background (like a cron job) into a database.
Requirements
Runs in background
Runs under Linux
Restful
Questions
What's you experience about that?
Would hadoop the right solution?
You can use neo4j.
Neo4j is a graph database, reliable and fast for managing and querying highly connected data
http://www.neo4j.org/
1) Decide structure of nodes, relationships, and there properties and accordingly
You need to create API that will get data from facebook and store it in Neo4j.
I have used neo4j in 3 big projects, and it is best for graph data.
2) Create a cron jon that will get data from facebook and store into the neo4j.
I think implementing mysql for graph database is not a good idea. for large data neo4j is the good option.
Interestingly you designed the appropriate solution yourself already. So in fact you need following components:
a relational database, since you want to request data in a structured, quick way
-> from experiences I would pressure the fact to have a fully normalized data model (in your case with tables users, groups, users2groups), also have 4-Byte surrogate keys over larger keys from facebook (for back referencing you can store their keys as attributes, but internal relations are more efficient on surrogate keys)
-> establish indexes based on hashes rather than strings (eg. crc32(lower(STRING))) - an example select would than be this: select somethinguseful from users where name=SEARCHSTRING and hash=crc32(lower(SEARCHSTRING))
-> never,ever establish unique columns based on strings with length > 8 Byte; unique bulk inserts can be done based on hashes+string checking via insert...select
-> once you got that settled you could also look into sparse matrices (see wikipedia) and bitmaps to get your users2groups optimized (however I have learned that this is an extra that should not hinder you to come up with a first version soon)
a cron job that is run periodically
-> ideally along the caps, facebook is giving you (so if they rule you to not request more often than once per second, stick to that - not more, but also try to come as close as possible to the cap) -> invest some time in getting the management of this settled, if different types of requests need to be fired (request for user records <> requests for group records, but maybe hit by the same cap)
-> most of the optimization can only be done with development - so if I were you I would stick to any high level programming language that does not bother to much with var type juggling and that also comes along with a broad support for associative arrays such as PHP and I would programm that thing myself
-> I made good experiences with setting up the cron job as web page with deactivated output buffering (for php look at ob_end_flush(void)) - easy to test and the cron job can be triggered via curl; if you channel status outputs via an own function (eg with time stamps) this could then also become flexible to either run viw browser or via command line -> which means efficient testing + efficient production running
your user ui, which only requests your database and never, ever, never the external system api
lots of memory, to keep your performance high (optimal: all your data+index data fits into database memory/cache dedicated to the database)
-> if you use mysql as database you should look into innodb_flush_log_at_trx_commit=0, and innodb_buffer_pool_size (just google, if interested)
Hadoop is a file system layer - it could help you with availability. However I would put this into the category of "sparse matrix", which is nothing that stops you from coming up with a solution. From my experience availability is not a primary constraint in data exposure projects.
-------------------------- UPDATE -------------------
I like neo4j from the other answer. So I wondered what I can learn for my future projects. My experiences with mysql is that RAM is usually the biggest constraint. So increasing your RAM to be able to load the full database can gain you performance improvements by a factor of 2-1000 - depending on from where you are coming from. Everything else such as index improvements and structure somehow follows. So if I would need to make up a performance prioritization list, it would be something like this:
MYSQL + enough RAM dedicated to the database to load all data
NEO4J + enough RAM dedicated to the database to load all data
I would still prefer MYSQL. It stores records efficiently, but needs to run joins for deriving relations (which neo4j does not require to that extend). Join-costs are usually low with the right indexes and according to http://docs.neo4j.org/chunked/milestone/configuration-caches.html neo4j does need to add extra management data to the property separation. For big data projects those management data sums up and in full load to memory set ups requires you buy more memory. Performance wise these both options are ultimate. Further, much further down the line you would find this:
NEO4J + not enough RAM dedicated to the database to load all data
MYSQL + not enough RAM dedicated to the database to load all data
In worst case MYSQL will even put indexes to disk (at least partly), which can result in massive read delay. In comparison with NEO4J you could perform a ' direct jump from node to node' exercise, which should - at least in theory - be faster.
Here is what we came up with. By using 3 value status column.
0 = Not indexed
1 = Updated
2 = Indexed
There will be 2 jobs...
Job 1 will select top X records where status = 0 and pop them into a queue like RabitMQ.
Then a consumer will bulk insert those records to ES and update the status of DB records to 1.
For updates, since we have control of our data... The SQL stored proc that updates that particular record will set it's status to 2. Job2 will select top x records where status = 2 and pop them on RabitMQ. Then a consumer will bulk insert those records to ES and update the status of DB records to 1.
Of course we may need an intermediate status for "queued" so none of the jobs pick up the same record again but the same job should not run if it hasn't completed. The chances of a queued record being updated are slim to none. Since updates only happen at end of day usually the next day.
So I know there's rivers (but being deprecated and probably not flexible like ETL)
I would like to bulk insert records from my SQL server to Elasticsearch.
Write a scheduled batch job of some sort either ETL or any other tool doesn't matter.
select from table where id > lastIdInsertedToElasticSearch this will allow to load the latest records into Elasticsearch at scheduled interval.
But what if a record is updated in the SQL server? What would be a good pattern to track updated records in the SQL server and then push the updated records in ES? I know ES has document versions when putting the same Id. But can't seem to be able to visualize a pattern.
So IMHO, batch inserts are good for building or re-building the index. So for the first time, you can run batch jobs that run SQL queries and perform bulk updates. Rivers, as you correctly pointed out, don't provide a lot of flexibility in terms of transformation.
If the entries in your SQL data store are created by you (i.e. some codebase in your control), it would be better that the same code base updates documents in Elasticsearch, may be not directly but by notifying some other service or with the help of queues to not waste time in responding to requests (if that's the kind of setup you have).
We have a pretty similar use case of Elasticsearch. We provide search inside our app, which performs search across different categories of data. Some of this data is actually created by the users of our app through our app - so we handle this easily. Our app writes that data to our SQL data store and pushes the same data in RabbitMQ for indexing/updating in Elasticsearch. On the other side of RabbitMQ, we have a consumer written in Python that basically replaces the entire document in Elasticsearch. So the corresponding rows in our SQL datastore and documents in Elasticsearch share the ID which enables us to update the document.
Another case is where there are a few types of data that we perform search on comes from some 3rd party service which exposes the data over their HTTP API. The data creation is in our control but we don't have an automated mechanism of updating the entries in Elasticsearch. In this case, we basically run a cron job that takes care of this. We have managed to tune the cron's schedule because we also have a limited number of API queries quota. But in this case, our data is not really updated so much per day. So this kind of system works for us.
Disclaimer: I co-developed this solution.
I needed something like the jdbc-river that could do more complex "roll-ups" of data. After careful consideration of what it would take to modify the jdbc-river to suit my needs, I ended up writing the river-net.
Here are a few of the features:
It gets fairly decent performance (comparable to the jdbc-river. We get upwards of 6k rows/sec)
It can join many tables to create complex nested arrays of documents without creating duplicate child documents
It follows a lot of the same conventions as the jdbc-river.
It also supports reading from files.
It's written in C#
It uses Quartz.Net and supports cron expressions for scheduling.
This project is open source, and we already have a second project (also to be open sourced) that does generic job scheduling with RabbitMQ. We have ported over a lot of this project, and plan to the RabbitMQ river for better performance and stability when indexing into Elasticsearch.
To combat large updates, we aren't hitting tables directly. Instead we use stored procedures that only grab deltas. We also have an option on the sp to reset the delta to reindex everything.
The project is fairly young with only a few commits, but we are open to collaboration and new ideas.
I am working with node.js and mongodb.
I am going to have a database setup and use socket.io to have real-time updates that will have the db queried again as well or push the new update to the client.
I am trying to figure out what is the best way to filter the database?
Some more information in regards to what is being queried and what the real time updates are:
A document in the database will include information such as an address, city, time, number of packages, name, price.
Filters include city/price/name/time (meaning only to see addresses within the same city, or within the same time period)
Real-time info: includes adding a new document to the database which will essentially update the admin on the website with a notification of a new address added.
Method 1: Query the db with the filters being searched?
Method 2: Query the db for all searches and then filter it on the client side (Javascript)?
Method 3: Query the db for all searches then store it in localStorage then query localStorage for what the filters are?
Trying to figure out what is the fastest way for the user to filter it?
Also, if it is different than what is the most cost effective way, then the most cost effective as well (which I am assuming is less db queries)...
It's hard to say because we don't see exact conditions of the filter, but in general:
Mongo can use only 1 index in a query condition. Thus whatever fields are covered by this index can be used in an efficient filtering. Otherwise it might do full table scan which is slow. If you are using an index then you are probably doing the most efficient query. (Mongo can still use another index for sorting though).
Sometimes you will be forced to do processing on client side because Mongo can't do what you want or it takes too many queries.
The least efficient option is to store results somewhere just because IO is slow. This would only benefit you if you use them as cache and do not recalculate.
Also consider overhead and latency of networking. If you have to send lots of data back to the client it will be slower. In general Mongo will do better job filtering stuff than you would do on the client.
According to you if you can filter by addresses within time period then you could have an index that cuts down lots of documents. You most likely need a compound index - multiple fields.