I'm researching graph databases for a work project. Since our data is highly connected, it appears that a graph database would be a good option for us.
One of the first graph DB options I've run into is neo4j, and for the most part, I like it. However, I have one question about neo4j to which I cannot find the answer: Can I get neo4j to store the entire graph in-memory? If so, how does one configure this?
The application I'm designing needs to be lightning-fast. I can't afford to wait for the db to go to disk to retrieve the data I'm searching for. I need the entire DB to be held in-memory to reduce the query time.
Is there a way to hold the entire neo4j DB in-memory?
Thanks!
Further to Bruno Peres' answer, if you want to run a regular server instance, Neo4j will load the entire graph into memory when resources are sufficient. This does indeed improve performance.
The Manual has a chapter on configuring memory.
The page cache portion holds graph data and indexes - this is configured via the dbms.memory.pagecache.size property in neo4j.conf. If it is large enough, the whole graph will be stored in memory.
The heap space portion is for query execution, state management, etc. This is set via the dbms.memory.heap.initial_size and
dbms.memory.heap.max_size properties. Generally these two properties should be set to the same value, so that the whole heap is allocated on startup.
If the sole purpose of the server is to run Neo4j, you can allocate most of the memory to the heap and page cache, leaving enough left over for operating system tasks.
Holding Very Large Graphs In Memory
At Graph Connect in San Francisco, 2016, Neo4j's CTO, Jim Webber, in his typical entertaining fashion, gave details on servers that have a very large amount of high performance memory - capable of holding an entire large graph in memory. He seemed suitably impressed by them. I forget the name of the machines, but if you're interested, the video archive should have details.
Neo4j isn't designed to hold the entire graph in main memory. This leaves you with a couple of options. You can either play around with the config parameters (as Jasper Blues already explained in more details) OR you can configure Neo4j to use RAMDisk.
The first option probably won't give you the best performance as only the cache is held in memory.
The challenge with the second approach is that everything is in-memory which means that the system isn't durable and the writes are inefficient.
You can take a look at Memgraph (DISCLAIMER: I'm the co-founder and CTO). Memgraph is a high-performance, in-memory transactional graph database and it's openCypher and Bolt compatible. The data is first stored in main memory before being written to disk. In other words, you can choose to make a tradeoff between write speed and safety.
Related
I've been reading Neo4j's Operational Manual on Cache Sharding, and posts all over the web, however I can hardly find any detailed example on how to configure HAProxy for cache sharding(yes the one on Operation Manual is rather brief) on a real-world graph, which may contain multiple node labels.
Has anyone ever done this before? Would be lovely if you could share your experience.
Moreover, I'm a bit confused on the mechanism of the way to shard the graph using HAProxy. How do sub-graphs get cached on certain slaves, merely by providing rules in HAProxy? It surprised me to learn that cache sharding isn't handled by Neo4j.
The goal is to send queries hitting the same region of your graph always to the same instance. This of course means that the request data indicates the region. What to use as "region indicator" is heavily depending on the structure and shape of your graph.
In a lot of cases of customer facing applications people successfully used the current user id and set it as additional http header which is then evaluated by haproxy.
I want to run as many instances of Neo4J (using the Enterprise version) on a single VM as possible. What are the real minimum RAM requirements to fire up an instance?
Right now TaskManager is telling me that Java.exe is taking about 70,000K (70 Meg). Does that sound right?
I'm not worried about the performance, I just want to stuff as many instances as possible on a single box so people can do some low demand search of their graph.
One thing is what is recommended and second "it depends".
Neo4j is able to run on the Raspberry Pi. But you shouldn't expect great performance. Also I'm using AWS t2.micro for testing and it's enough.
The size is bound to fluctuate as the graph is loaded into memory to perform traversals and when it is paged back to the disk (When memory is running out).
If I may offer up a suggestion, you could run only one database instance and have unconnected graphs for each of your users. This would very likely be far more efficient in terms of server resources.
For example, If you have say (:Item) nodes which make up a graph for each user,
you could have them instead label them as (:Item-User1) with a unique prefix or postfix for each user.
Thus when you want to alter the query to run for each user you could just add that unique element and search the graph.
The Idea is to have a separate sub-graph for each user which is unconnected to other user's sub-graphs. Instead of having a separate database instance for each Individual user. As long as each user's sub-graph is unconnected from other user's sub-graphs there should be no security vulnerability where a user is given access to another user's data.
This way you could potentially have infinite number of users (within reason. quite possibly in the millions of users) each with their own sub graphs, with potentially no loss in performance, instead of the handful of database instances you could spin up on a single VM, which are likely to be competing for resources and choking out.
For neo4j 3.x, the documented minimum memory requirement is 2GB.
I'd like to use a neo4j database in a docker container with Odroid XU4. The database is not big, approximately 20.000 nodes will be in it. The Odroid has only 2G memory, and I'd like to have a samba server, some nodejs applications and at least one PgSQL database too, so the system is short on memory. I read in the neo4j manual that 2G memory is the minimum, but I read by docker examples that it is used with 512M, so I am a little confused about this. What is the minimum memory I can use the neo4j docker image with?
I have similar troubles with the disk space. The system is on a 32GB SD card. I'd like to save database data there and backup on an external hard drive, so I could spend max 16GB for the neo4j. The data certainly does not require that kind of space, I am not sure why neo4j needs it (according to the manual again).
First you can use http://neo4j.com/hardware-sizing-calculator/ to get rough estimate for memory and disk usage.
Second option is to do some math. You can use information on page 12 in http://graphaware.com/assets/bachman-msc-thesis.pdf
You should keep in mind it's good to have all data in the memory for the performance reasons.
From my point of view you shouldn't have problem with the memory, but you can't expect great performance.
It's better to try it by yourself before you ask here ;)
Apache Samza uses RocksDB as the storage engine for local storage. This allows for stateful stream processing and here's a very good overview.
My use case:
I have multiple streams of events that I wish to process taken from a system such as Apache Kafka.
These events create state - the state I wish to track is based on previous messages received.
I wish to generate new stream events based on the calculated state.
The input stream events are highly connected and a graph such as OrientDB / Neo4J is the ideal medium for querying the data to create the new stream events.
My question:
Is it possible to use a non-KV store as the local storage for Samza? Has anyone ever done this with OrientDB / Neo4J and is anyone aware of an example?
I've been evaluating Samza and I'm by no means an expert, but I'd recommend you to read the official documentation, and even read through the source code—other than the fact that it's in Scala, it's remarkably approachable.
In this particular case, toward the bottom of the documentation's page on State Management you have this:
Other storage engines
Samza’s fault-tolerance mechanism (sending a local store’s writes to a replicated changelog) is completely decoupled from the storage engine’s data structures and query APIs. While a key-value storage engine is good for general-purpose processing, you can easily add your own storage engines for other types of queries by implementing the StorageEngine interface. Samza’s model is especially amenable to embedded storage engines, which run as a library in the same process as the stream task.
Some ideas for other storage engines that could be useful: a persistent heap (for running top-N queries), approximate algorithms such as bloom filters and hyperloglog, or full-text indexes such as Lucene. (Patches accepted!)
I actually read through the code for the default StorageEngine implementation about two weeks ago to gain a better sense of how it works. I definitely don't know enough to say much intelligently about it, but I can point you at it:
https://github.com/apache/samza/tree/master/samza-kv-rocksdb/src/main/scala/org/apache/samza/storage/kv
https://github.com/apache/samza/tree/master/samza-kv/src/main/scala/org/apache/samza/storage/kv
The major implementation concerns seem to be:
Logging all changes to a topic so that the store's state can be restored if a task fails.
Restoring the store's state in a performant manner
Batching writes and caching frequent reads in order to save on trips to the raw store.
Reporting metrics about the use of the store.
Do the input stream events define one global graph, or multiple graphs for each matching Kafka/Samza partition? That is important as Samza state is local not global.
If it's one global graph, you can update/query a separate graph system from the Samza task process method. Titan on Cassandra would one such graph system.
If it's multiple separate graphs, you can use the current RocksDB KV store to mimic graph database operations. Titan on Cassandra does just that - uses Cassandra KV store to store and query the graph. Graphs are stored either via matrix (set [i,j] to 1 if connected) or edge list. For each node, use it as the key and store its set of neighbors as the value.
I am new to Neo4j and graph databases. Saying that, I have around 40000 independent graphs uploaded into a neo4j database using Batch insertion, so far everything went well. My current database folder size is 180Gb, the problem is querying, which is too slow. Just to count number of nodes, it takes forever. I am using a server with 1TB ram and 40 cores, therefore I would like to load the entire database into memory and perform queries on it.
I have looked into the configurations but not sure what changes I should make to cache the entire database into memory. So please suggest me the properties I should modify.
I also noticed that most of the time Neo4j is using only one or two cores, How can I increase it?
I am using the free version for a university research project therefore I am unable to use High-Performance Cache is there an alternative in free version?
My Solution:
I added more graphs to my database and now my database size is 400GB with more than a billion nodes. I took Stefan's comments and used java APIs to access my database and moved my database to RAM disk. It takes to 3 hours to walk through all the nodes and collect information from each node.
RAM disk and Java APIs gave a big boost in performance.
Counting nodes in a graph is a global operation that obviously needs to touch each and every node. If caches are not populated (or not configured according to your dataset) the drive of your hard disc is the most influencing factor.
To speed up things, be sure to have caches configured efficiently, see http://neo4j.com/docs/stable/configuration-caches.html.
With current versions of Neo4j, a Cypher query traverses the graph in single threaded mode. Since most graph applications out there are concurrently used by multiple users, this model saturates the available cores.
If you want to run a single query multithreaded, you need to use Java API.
In general Neo4j community edition has some limitation in scaling for more than 4 cores (due to a more performant lock manager implementation in Enterprise edition). Also the HPC (high performance cache) in Enterprise edition reduces the impact of full garbage collections significantly.
What Neo4j version are you using?
Please share your current config (conf/* and data/graph.db/messages.log) you can use the personal edition of Neo4j enterprise.
What kinds of use cases do you want to run?
Counting all nodes is probably not your main operation (there are ways in the Java API that make it faster).
For efficient multi-core usage, run multiple clients or write java-code that utilizes more cores during traversal with ThreadPools.