I have a query (link below) I must execute once per day or once per week in my application to find groups of connected users. In the query I check all possible groups for each user of the application (not all users are evaluated but could be a lot). For the moment I'm only making performance tests in localhost using Gremlin Server, since my application is not live yet.
The problem is that when testing this query simulating many users the query reaches the time limit a request can take that is configured in Gremlin Server by default, another problem is that the query does not take full CPU usage since it seems a single query is designed to use a single thread or a reduced amount of CPU processing in some way.
So I have 2 solutions in mind, divide the query in one chunk per user or use OLAP:
Solution 1:
Send a query to get the users first and then send one query per user, then remove duplicates in the server code, this should work in my case and since I can send all the queries at the same time I can use all resources available and bypass the time limits.
Solution 2:
Use OLAP. I guess OLAP does not have a time limit. The problem: My idea is to use Amazon Neptune and OLAP is not supported there as far as I know.
In this question about it:
Gremlin OLAP queries on AWS Neptune
David says:
Update: Since GA (June 2018), Neptune supports multiple queries in a single request/transaction
What does it mean "multiple queries in a single request"?
How my solution 1 compares with OLAP?
Should I look for another database service that supports OLAP instead of Neptune? Which one could be? I don't want an option that implies learning to setup my own "Neptune like" server, I have limited time.
My query in case you want to take a look:
https://gremlify.com/69cb606uzaj
This is a bit of a complicated question.
The problem is that when testing this query simulating many users the query reaches the time limit a request can take that is configured in Gremlin Server by default,
I'll assume there is a reason you can't change the default value, but for those who might be reading this answer the timeout is configurable both at the server (with evaluationTimeout in the server yaml) and per request both for scripts and bytecode based requests.
another problem is that the query does not take full CPU usage since it seems a single query is designed to use a single thread or a reduced amount of CPU processing in some way.
If you're testing with TinkerGraph in Gremlin Server then know that TinkerGraph is really simple. It doesn't do anything internally to run any aspect of a traversal in parallel (without TinkerGraphComputer which is OLAP related).
So I have 2 solutions in mind, divide the query in one chunk per user or use OLAP:
Either approach has the potential to work. In the first solution you suggest a form of poor man's OLAP where you must devise your own methods for doing this parallel processing (i.e. manage thread pools, synchronize state, etc). I think that this approach is a common first step that folks take to deal with this sort of problem. I'd wonder if you need to be as fine grained as one user per request. I would think that sending several at a time would be acceptable but only testing in your actual environment would yield the answer to that. The nice thing about this solution is that it will typically work on any graph system, including Neptune.
Using your second solution with OLAP is trickier. You have the obvious problem that Neptune does not directly support it, but going to a different provider that does will not instantly solve your problem. While OLAP rids you of having to worry about how to optimally parallelize your workload, it doesn't mean that you can instantly take that Gremlin query you want to run, throw it into Spark and get an instant win. For example, and I take this from the TinkerPop Reference Documentation:
In OLAP, where the atomic unit of computing is the vertex and its local
"star graph," it is important that the anonymous traversal does not leave the
confines of the vertex’s star graph. In other words, it can not traverse to an
adjacent vertex’s properties or edges.
In your query, there are already a places where you "leave the star graph" so you would immediately find problems there to solve. Usually that limitation can be worked around for OLAP purposes but it's not as simple as adding withComputer() to your traversal and getting a win in this case.
Going further down this path of using OLAP with a graph other than Neptune, you would probably want to at least consider if this complex traversal could be better written as a custom VertexProgram which might better bind your use case to the the capabilities of BSP than what the more generic TraversalVertexProgram does when processing arbitrary Gremlin. For that matter, a mix of Gremlin OLAP, a custom VertexProgram and some standard map/reduce style processing might ultimately lead to the most elegant and efficient answer.
An idea I've been considering for graphs that don't support OLAP has been to subgraph() (with Java) the portion of the graph that is relevant to your algorithm and then execute it locally in TinkerGraph! I think that might make sense in some use cases where the algorithm has some limits that can be defined ahead of time to form the subgraph, where those limits can be easily filtered and where the resulting subgraph is not so large that it takes an obscene amount of time to construct. It would be even better if the subgraph had some use beyond a single algorithm - almost behaving like a cache graph. I have no idea if that is useful to you but it's a thought. Here's a recent blog post I wrote that talks about writing VertexPrograms. Perhaps you will find it interesting.
All that said about OLAP, I think that your first solution seems fine to start with. You don't have a multi-billion edge graph yet and can probably afford to take this approach for now.
What does it mean "multiple queries in a single request"?
I believe that this just means that you can send a script like:
g.addV().iterate()
g.addV().iterate()
g.V()
where multiple Gremlin commands can be executed within the scope of a single transaction where each command must be "separated by newline ('\n'), spaces (' '), semicolon ('; '), or nothing (for example: g.addV(‘person’).next()g.V() is valid)". I think that only the last command returns a value. It doesn't seem like that particular feature would be helpful in your case. I would look more to batch users within a particular request where possible.
If you a looking for a native OLAP graph engine, perhaps take look at AnzoGraphDB which scales and performs much better for that style of more complex querying than anything else we know of. It's an MPP engine, so every core works on the query in parallel. Depending on how much data you need it to act on, the free version (single node only, RAM limited) may well be all you need and can be used commercially. You can find it in the AWS Marketplace or on Docker Hub.
Disclaimer: I work for Cambridge Semantics Inc.
Related
I have a user search feature in my app where the searcher don't want to see some results, he does this by "blocking" a tag, when blocking a tag all users that are "subscribed" to that tag will be ignored in his search results.
I'm writing the query to filter the search results and I found 2 ways of getting the same:
First:
g.V(1991)
.out("blocked").fold().as("blockedTags")
.V().hasLabel("user")
.not(
where(
out("subscribed").where(
within("blockedTags")
)
)
)
Second:
g.V(1991).as("user")
.V().hasLabel("user")
.not(
where(
out("subscribed")
.in("blocked")
.as("user")
)
)
Gremlify: https://gremlify.com/xnqhvtzo6b
One uses within() and the other performs 2 steps out() and in(), I want to know which one is faster so I can decide which one to use, these 2 options are possible in many queries of my application.
EDIT:
I ran both queries in the gremlin console with profile() step at the end but the >TOTAL field gives random time numbers from 0.300ms to 1.220ms for both queries, because of this I don't know how to compare the performance of 2 queries.
I will offer a general answer here that is largely derived from the comments on the question itself. It really isn't possible to profile() one graph and then project those results on another. They will each have different capabilities and performance characteristics. If you need to know which of two approaches to a query is better, then you must test both traversals on the graph system you intend to target.
I'd also be wary of going too far in a particular development direction without doing ongoing testing on the target graph. Just as you wouldn't do all your development on MySQL only to switch to Oracle when it was time to go to production, you really shouldn't try to build your entire application against a graph you don't intend to use. There are subtle differences in these systems that could make a significant differences to you.
As to the differences in profile() times on TinkerGraph, there is bound to be timing differences on the JVM for what I'm guessing is a test on a small dataset that resides in memory. Or perhaps for TinkerGraph there is no significant difference between the two approaches. Consider trying to execute the queries a few thousand times and average the time taken and compare that. Gremlin Console has a clock() function that helps with that. Of course, as I alluded to earlier what you learn there is no guarantee that you have the right solution on Neptune.
If you'd like a bit of analysis about your queries I could offer a few words (though I don't base this thinking on Neptune specifically). How each performs depends a lot on your graph structure, but I think I'd be the first query to be faster because it captures "blocked" vertices with:
.out("blocked").fold()
and re-use it over and over for however many V().hasLabel('user') there are. That's just a gut feeling though. I'm guessing the blocked list will be relatively small for a single user so traversing the opposing way with:
out("subscribed").in("blocked")
would just be more expensive as you would have to traverse a lot more "blocked" edges that don't terminate with the initial vertex.
My application is not live yet, so I'm testing the performance of my Gremlin queries before it gets into production.
To test I'm using a query that adds edges from one vertex to 300 other vertices. It does more things but that's the simple description. I added this mentioned workload of 300 just for testing.
If I run the query 300 times one after the other it takes almost 3 minutes to finish and 90.000 edges are created (300 x 300).
I'm worried because if I have like 60.000 users using my application at the same time they probably are going to be creating 90.000 edges in 2 minutes using this query and 60.000 users at the same time is not much in my case.
If I have 1 million users at the same time I'm going to be needing many servers at full capacity, that is out of my budget.
Then I noticed that when my test is executing the CPU doesn't show much activity, I don't know why, I don't know how the DB works internally.
So I thought that maybe a more real situation could be to call my queries all at the same time because that is what's going to happen with the real users, when I tried test that I got ConcurrentModificationException.
Is far as I understand this error happens because an edge or vertex is being read or written in 2 queries at the same time, this is something that could happen a lot in my application because all the user vertices are changing connections to the same 4 vertices all the time, this "collisions" are going to be happening all the time.
I'm testing in local using gremlin server 3.4.8 connecting using sockets with Node.js. My plan is to use AWS Neptune as my database when it goes to production.
What can I do to recover hope? There must be very important things about this subject that I don't know because I don't know how graph databases work internally.
Edit
I implemented a logic to retry the queries requests when receiving an error using the "Exponential Backoff" approach. It fixed the ConcurrentModificationException
but there are a lot of problems in Gremlin Server when sending multiple queries at the same time that shows how multi-threading is totally unsupported and unstable in Gremlin Server and we should try multi-threading in other Gremlin compatible databases as the response says. I experienced random inconsistencies in the data returned by the queries and errors like NegativeArraySize and other random stuff coming from the database, be warned of this to not waste time thinking that your code could be bugged like it happened to me.
While TinkerPop and Gremlin try to provide a vendor agnostic experience, they really only do so at their interface level. So while you might be able to run the same query in JanusGraph, Neptune, CosmosDB, etc, you will likely find that there are differences in performance depending on the nature of the query and the degree to which the graph in question is capable of optimizing that query.
For your case, consider TinkerGraph as you are running your tests there locally. TinkerGraph is an in-memory graph without transaction capability and is not proven thread safe for writes. If you apply a heavy write workload to it, I could envision ConcurrentModificationException easy to generate. Now consider JanusGraph. If you had tested your heavy write workload with that, you might have found that you were struck with tons of TemporaryLockingException errors if your schema had required a unique property key and would have to modify your code to do transactional retries with exponential backoff.
The point here is that if your target graph is Neptune and you have a traversal you've tested for correctness and now are concerned about performance, it's probably time to load test on Neptune to see if any problems arise there.
I'm worried because if I have like 60.000 users using my application at the same time they probably are going to be creating 90.000 edges in 2 minutes using this query and 60.000 users at the same time is not much in my case. If I have 1 million users at the same time I'm going to be needing many servers at full capacity, that is out of my budget.
You will want to develop a realistic testing plan. Is 60,000 users all pressing "submit" to trigger this query at the exact same time really what's going to happen? Or is it more likely that you have 100,000 users with some doing reads and perhaps every half second three of them happens to click the "submit".
Your graph growth rate seems fairly high and the expected usage you've described here will put your graph in the category of billions of edges quite quickly (not to mention whatever other writes you might have). Have you tested your read workloads on a graph with billions of edges? Have you tested that explicitly on Neptune? Have you thought about how you will maintain a multi-billion edge graph (e.g. changing the schema when a new feature is needed, ensuring that it is growing correctly, etc.)?
All of these questions are rhetorical and just designed to make you think about your direction. Good luck!
Although there is already an accepted answer I want to suggest another approach to deal with this problem.
Idea is to figure out whether you really need to do synchronous writes on the Graph. I'm suggesting that when you receive a request, just use the attributes in this request to fetch the sub-graph / neighbors, and continue with the business logic.
Simultaneously put the event in an SQS or something to have the writes taken care of by an Asynchronous system - say AWS Lambda. Because in SQS + Lambda you can decide the write concurrency to your systems' comfort (low enough that your query does NOT cause above exception).
Further suggestion: You have abnormally high write blast radius - your query should NOT touch that many nodes while writing. You can try converting some of the edges to vertices in order to reduce the radius. Then while inserting a node you'll just have to make one edge to the vertex which was previously an edge instead of making hundreds of edges to all the vertices this node is related to. I hope this makes sense.
We've developed a system with a search screen that looks a little something like this:
(source: nsourceservices.com)
As you can see, there is some fairly serious search functionality. You can use any combination of statuses, channels, languages, campaign types, and then narrow it down by name and so on as well.
Then, once you've searched and the leads pop up at the bottom, you can sort the headers.
The query uses ROWNUM to do a paging scheme, so we only return something like 70 rows at a time.
The Problem
Even though we're only returning 70 rows, an awful lot of IO and sorting is going on. This makes sense of course.
This has always caused some minor spikes to the Disk Queue. It started slowing down more when we hit 3 million leads, and now that we're getting closer to 5, the Disk Queue pegs for up to a second or two straight sometimes.
That would actually still be workable, but this system has another area with a time-sensitive process, lets say for simplicity that it's a web service, that needs to serve up responses very quickly or it will cause a timeout on the other end. The Disk Queue spikes are causing that part to bog down, which is causing timeouts downstream. The end result is actually dropped phone calls in our automated VoiceXML-based IVR, and that's very bad for us.
What We've Tried
We've tried:
Maintenance tasks that reduce the number of leads in the system to the bare minimum.
Added the obvious indexes to help.
Ran the index tuning wizard in profiler and applied most of its suggestions. One of them was going to more or less reproduce the entire table inside an index so I tweaked it by hand to do a bit less than that.
Added more RAM to the server. It was a little low but now it always has something like 8 gigs idle, and the SQL server is configured to use no more than 8 gigs, however it never uses more than 2 or 3. I found that odd. Why isn't it just putting the whole table in RAM? It's only 5 million leads and there's plenty of room.
Poured over query execution plans. I can see that at this point the indexes seem to be mostly doing their job -- about 90% of the work is happening during the sorting stage.
Considered partitioning the Leads table out to a different physical drive, but we don't have the resources for that, and it seems like it shouldn't be necessary.
In Closing...
Part of me feels like the server should be able to handle this. Five million records is not so many given the power of that server, which is a decent quad core with 16 gigs of ram. However, I can see how the sorting part is causing millions of rows to be touched just to return a handful.
So what have you done in situations like this? My instinct is that we should maybe slash some functionality, but if there's a way to keep this intact that will save me a war with the business unit.
Thanks in advance!
Database bottlenecks can frequently be improved by improving your SQL queries. Without knowing what those look like, consider creating an operational data store or a data warehouse that you populate on a scheduled basis.
Sometimes flattening out your complex relational databases is the way to go. It can make queries run significantly faster, and make it a lot easier to optimize your queries, since the model is very flat. That may also make it easier to determine if you need to scale your database server up or out. A capacity and growth analysis may help to make that call.
Transactional/highly normalized databases are not usually as scalable as an ODS or data warehouse.
Edit: Your ORM may have optimizations as well that it may support, that may be worth looking into, rather than just looking into how to optimize the queries that it's sending to your database. Perhaps bypassing your ORM altogether for the reports could be one way to have full control over your queries in order to gain better performance.
Consider how your ORM is creating the queries.
If you're having poor search performance perhaps you could try using stored procedures to return your results and, if necessary, multiple stored procedures specifically tailored to which search criteria are in use.
determine which ad-hoc queries will most likely be run or limit the search criteria with stored procedures.. can you summarize data?.. treat this
app like a data warehouse.
create indexes on each column involved in the search to avoid table scans.
create fragments on expressions.
periodically reorg the data and update statistics as more leads are loaded.
put the temporary files created by queries (result sets) in ramdisk.
consider migrating to a high-performance RDBMS engine like Informix OnLine.
Initiate another thread to start displaying N rows from the result set while the query
continues to execute.
I have a huge directed graph: It consists of 1.6 million nodes and 30 million edges. I want the users to be able to find all the shortest connections (including incoming and outgoing edges) between two nodes of the graph (via a web interface). At the moment I have stored the graph in a PostgreSQL database. But that solution is not very efficient and elegant, I basically need to store all the edges of the graph twice (see my question PostgreSQL: How to optimize my database for storing and querying a huge graph).
It was suggested to me to use a GraphDB like neo4j or AllegroGraph. However the free version of AllegroGraph is limited to 50 million nodes and also has a very high-level API (RDF), which seems too powerful and complex for my problem. Neo4j on the other hand has only a very low level API (and the python interface is not mature yet). Both of them seem to be more suited for problems, where nodes and edges are frequently added or removed to a graph. For a simple search on a graph, these GraphDBs seem to be too complex.
One idea I had would be to "misuse" a search engine like Lucene for the job, since I'm basically only searching connections in a graph.
Another idea would be, to have a server process, storing the whole graph (500MB to 1GB) in memory. The clients could then query the server process and could transverse the graph very quickly, since the graph is stored in memory. Is there an easy possibility to write such a server (preferably in Python) using some existing framework?
Which technology would you use to store and query such a huge readonly graph?
LinkedIn have to manage a sizeable graph. It may be instructive to check out this info on their architecture. Note particularly how they cache their entire graph in memory.
There is also OrientDB a open source document-graph dbms with commercial friendly license (Apache 2). Simple API, SQL like language, ACID Transactions and the support for Gremlin graph language.
The SQL has extensions for trees and graphs. Example:
select from Account where friends traverse (1,7) (address.city.country.name = 'New Zealand')
To return all the Accounts with at least one friend that live in New Zealand. And for friend means recursively up to the 7th level of deep.
I have a directed graph for which I (mis)used Lucene.
Each edge was stored as a Document, with the nodes as Fields of the document that I could then search for.
It performs well enough, and query times for fetching in and outbound links from a node would be acceptable to a user using it as a web based tool. But for computationally intensive, batch calculations where I am doing many 100000s queries I am not satisfied with the query times I'm getting. I get the sense that I am definitely misusing Lucene so I'm working on a second Berkeley DB based implementation so that I can do a side by side comparison of the two. If I get a chance to post the results here I will do.
However, my data requirements are much larger than yours at > 3GB, more than could fit in my available memory. As a result the Lucene index I used was on disk, but with Lucene you can use a "RAMDirectory" index in which case the whole thing will be stored in memory, which may well suit your needs.
Correct me if I'm wrong, but since each node is list of the linked nodes, seems to me a DB with a schema is more of a burden than an advantage.
It also sound like Google App Engine would be right up your alley:
It's optimized for reading - and there's memcached if you want it even faster
it's distributed - so the size doesn't affect efficiency
Of course if you somehow rely on Relational DB to find the path, it won't work for you...
And I just noticed that the q is 4 months old
So you have a graph as your data and want to perform a classic graph operation. I can't see what other technology could fit better than a graph database.
How would one go about profiling a few queries that are being run from an ASP.NET application? There is some software where I work that runs extremely slow because of the database (I think). The tables have indexes but it still drags because it's working with so much data. How can I profile to see where I can make a few minor improvements that will hopefully lead to larger speed improvements?
Edit: I'd like to add that the webserver likes to timeout during these long queries.
Sql Server has some excellent tools to help you with this situation. These tools are built into Management Studio (which used to be called Enterprise Manager + Query Analyzer).
Use SQL Profiler to show you the actual queries coming from the web application.
Copy each of the problem queries out (the ones that eat up lots of CPU time or IO). Run the queries with "Display Actual Execution Plan". Hopefully you will see some obvious index that is missing.
You can also run the tuning wizard (the button is right next to "display actual execution plan". It will run the query and make suggestions.
Usually, if you already have indexes and queries are still running slow, you will need to re-write the queries in a different way.
Keeping all of your queries in stored procedures makes this job much easier.
To profile SQL Server, use the SQL Profiler.
And you can use ANTS Profiler from Red Gate to profile your code.
Another .NET profiler which plays nicely with ASP.NET is dotTrace. I have personally used it and found lots of bottlenecks in my code.
I believe you have the answer you need to profile the queries. However, this is the easiest part of performance tuning. Once you know it is the queries and not the network or the app, how do you find and fix the problem?
Performance tuning is a complex thing. But there some places to look at first. You say you are returning lots of data? Are you returning more data than you need? Are you really returning only the columns and records you need? Returning 100 columns by using select * can be much slower than returning the 5 columns you are actually using.
Are your indexes and statistics up-to-date? Look up how to update statisistcs and re-index in BOL if you haven't done this in a awhile. Do you have indexes on all the join fields? How about the fields in the where clause.
Have you used a cursor? Have you used subqueries? How about union-if you are using it can it be changed to union all?
Are your queries sargable (google if unfamiliar with the term.)
Are you using distinct when you could use group by?
Are you getting locks?
There are many other things to look at these are just a starting place.
If there is a particular query or stored procedure I want to tune, I have found turning on statistics before the query to be very useful:
SET STATISTICS TIME ON
SET STATISTICS IO ON
When you turn on statistics in Query Analyzer, the statistics are shown in the Messages tab of the Results pane.
IO statistics have been particularly useful for me, because it lets me know if I might need an index. If I see a high read count from the IO statistics, I might try adding different indexes to the affected tables. As I try an index, I run the query again to see if the read count has gone down. After a few iterations, I can usually find the best index(es) for the tables involved.
Here are links to MSDN for these statistics commands:
SET STATISTICS TIME
SET STATISTICS IO