So for some research work, I need to analyze a ton of raw movement data (currently almost a gig of data, and growing) and spit out quantitative information and plots.
I wrote most of it using Groovy (with JFreeChart for charting) and when performance became an issue, I rewrote the core parts in Java.
The problem is that analysis and plotting takes about a minute, whereas loading all of the data takes about 5-10 minutes. As you can imagine, this gets really annoying when I want to make small changes to plots and see the output.
I have a couple ideas on fixing this:
Load all of the data into a SQLite database.
Pros: It'll be fast. I'll be able to run SQL to get aggregate data if I need to.
Cons: I have to write all that code. Also, for some of the plots, I need access to each point of data, so loading a couple hundred thousand files, some parts may still be slow.
Java RMI to return the object. All the data gets loaded into one root object, which, when serialized, is about 200 megs. I'm not sure how long it would take to transfer a 200meg object through RMI. (same client).
I'd have to run the server and load all the data but that's not a big deal.
Major pro: this should take the least amount of time to write
Run a server that loads the data and executes a groovy script on command within the server vm. Overall, this seems like the best idea (for implementation time vs performance as well as other long term benefits)
What I'd like to know is have other people tackled this problem?
Post-analysis (3/29/2011): A couple months after writing this question, I ended up having to learn R to run some statistics. Using R was far, far easier and faster for data analysis and aggregation than what I was doing.
Eventually, I ended up using Java to run preliminary aggregation, and then ran everything else in R. R was also much easier to make beautiful charts than using JFreeChart.
Databases are very scalable, if you are going to have massive amounts of data. In MS SQL we currently group/sum/filter about 30GB of data in 4 minutes (somewhere around 17 million records I think).
If the data is not going to grow very much, then I'd try out approach #2. You can make a simple test application that creates a 200-400mb object with random data and test the performance of transferring it before deciding if you want to go that route.
Before you make a decision its probably worth understanding what is going on with your JVM as well as your physical system resources.
There are several factors that could be at play here:
jvm heap size
garbage collection algorithms
how much physical memory you have
how you load the data - is it from a file that is fragmented all over the disk?
do you even need to load all of the data at once - can it be done it batches
if you are doing it in batches you can vary the batch size and see what happens
if your system has multiple cores perhaps you could look at using more than one thread at a time to process/load data
if using multiple cores already and disk I/O is the bottleneck, perhaps you could try loading from different disks at the same time
You should also look at http://java.sun.com/javase/technologies/hotspot/vmoptions.jsp if you aren't familiar with the settings for the VM.
If your data have a relational properties, there are nothing more natural than storing it at some SQL database. There you can solve your biggest problem -- performance, costing "just" to write your appropriate SQL code.
Seems very plain to me.
I'd look into analysis using R. It's a statistical language with graphing capabilities. It could put you ahead, especially if that's the kind of analysis you intend to do. Why write all that code?
I would recommend running a profiler to see what part of the loading process is taking the most time and if there's a possible quick win optimization. You can download an evaluation license of JProfiler or YourKit.
Ah, yes: large data structures in Java. Good luck with that, surviving "death by garbage collection" and all. What java seems to do best is wrapping a UI around some other processing engine, although it does free developers from most memory management tasks -- for a price. If it were me, I would most likely do the heavy crunching in Perl (having had to recode several chunks of a batch system in perl instead of java in a past job for performance reasons), then spit the results back to your existing graphing code.
However, given your suggested choices, you probably want to go with the SQL DB route. Just make sure that it really is faster for a few sample queries, watch the query-plan data and all that (assuming your system will log or interactively show such details)
Edit,(to Jim Ferrans) re: java big-N faster than perl (comment below): the benchmarks you referenced are primarily little "arithmetic" loops, rather than something that does a few hundred MB of IO and stores it in a Map / %hash / Dictionary / associative-array for later revisiting. Java I/O might have gotten better, but I suspect all the abstractness still makes it comparitively slow, and I know the GC is a killer. I haven't checked this lately, I don't process multi-GB data files on a daily basis at my current job, like I used to.
Feeding the trolls (12/21): I measured Perl to be faster than Java for doing a bunch of sequential string processing. In fact, depending on which machine I used, Perl was between 3 and 25 times faster than Java for this kind of work (batch + string). Of course, the particular thrash-test I put together did not involve any numeric work, which I suspect Java would have done a bit better, nor did it involve caching a lot of data in a Map/hash, which I suspect Perl would have done a bit better. Note that Java did much better at using large numbers of threads, though.
Related
I'm learning a bit more about hadoop and its applications, and I understand it is geared toward massive datasets and large files. Let's say I had an application in which I was processing a relatively small number of files (say 100k), which isn't a huge number for something like hadoop/hdfs. However, it does take a macro amount of time to run on a single machine, so I'd like to distribute the process.
The problem can be broken down into a map reduce style problem (e.g. each of the files can be processed independently and then I can aggregate the results). I'm open to using infrastructure such as Amazon EC2, but I'm not so sure about what technologies to be exploring for actually aggregating the results of the process. Seems like hadoop might be a bit overkill here.
Can anyone provide guidance on this type of problem?
First off, you may want to reconsider your assumption that you can't combine files. Even images can be combined- you just need to figure out how to do that in a way that allows you to break them out again in your mappers. Combining them with some sort of sentinel value or magic number between them might make it possible to turn them into one giant file.
Other options include HBase, where you could store the images in cells. HBase also has a built-in TableMapper and TableReducer, and can store the results of your processing alongside the raw data in a semi-structured way.
EDIT: As for the "is Hadoop overkill" question, you need to consider the following:
Hadoop adds at least one machine of overhead (the HDFS NameNode). You typically dont want to store data or run jobs on that machine, since it is a SPOF.
Hadoop is best suited for processing data in batch, with relatively high latency. As #Raihan mentions, there are several other FOSS distributed compute architectures that may server your needs better if you need realtime or low-latency results.
100k files isn't so very few. Even if they are 100k each, that's 10GB of data.
Other than the above, Hadoop is a relatively low-overhead way of approaching distributed computing problems. It has a huge, helpful community behind it, so you can get help quickly if you need it. And it is focused on running on cheap hardware and a free OS, so there really isnt any significant overhead.
In short, I'd try it before you discard it for something else.
I am developing a application for benchmarking purposes, for which I require to create large number of http connection in a short time, I created a program in java to test how much threads is java able to create, it turns out in my 2GB single core machine, the limit is variable between 5000 and 6000 with 1 GB of memory given to JVM after which it hits outofmemoryerror with heap limit reached.
It is suggested that erlang will be able to generate much more concurrent processes, I am willing to learn erlang if it is capable of solving the problem , can erlang be able to generate somewhere around 100000 processes which are essentially http requests waiting for responses, in a matter of few seconds without reaching any limit like memory error etc.,
According famous Richard Jones blog you can handle 100k connection almost out of the box. You have to increase process limit, see +P parameter and it needs little bit memory management trickery e.g. gc or hibernate. To achieve significantly more you have to do more hacking with C.
It can handle pretty much anything you throw at it. Erlang processes are extremely light weight.
See http://www.sics.se/~joe/apachevsyaws.html for a benchmark in concurrency between Yaws and Apache. It gives you a good idea of what's possible.
I thought an interesting thing for this is that a guy was able to get a million comet connections with mochiweb http://www.metabrew.com/article/a-million-user-comet-application-with-mochiweb-part-1
As previously stated, a lot is a good answer. And also given your requirement is to write a tsunami client, you can/should distribute code over to several erlang nodes.
Even better, you might want to check out Tsung. It is a distributed load testing application written in erlang.
And if you don't want to use it, I am pretty sure there's code you want to read in there.
What's a good method for assigning work to a set of remote machines? Consider an example where the task is very CPU and RAM intensive, but doesn't actually process a large dataset. The language of choice would be Java. I was thinking Hadoop would be a good option, but the dataset passed between remote machines is fairly small, and Hadoop seems to focus mainly on the distribution of data rather than distribution of work.
What are some good technologies that can help?
EDIT: I'm mainly interested in load balancing. There will be a series of jobs with a small (< 3MB) dataset, but significant processing and memory needs.
MPI would probably be a good choice, there's even a JAVA implementation.
MPI may be part of your answer, but looking at the question, I'm not sure if it addresses the portion of the problem you care about.
MPI provides a communication layer between processing components. It is low level requiring you to do a fair amount of work, but from what I saw in an introduction presentation, it also comes with some common matrix data manipulation functions.
In your question, you seem to be more interested in the load balancing/job processing aspects of the problem. If that really is your focus, maybe a small program hosted in a Servlet or an RMI server might be sufficient. Let each program go to the server for their next unit of work and then submit the results back (you might even be able to use a database/file share, but pay attention to locking issues). In other words, a pull mechanism versus a push mechanism.
This approach is fairly simple to implement and gives you the advantage of scaling up by just running more distributed clients. Load balancing isn't too important if you intend to allow your process to take full control of the machine. You can experiment with running multiple clients on a machine that has multiple cores to see if you can improve overall through-put for the node. A multi-threaded client would be more efficient, but can increase complexity depending on the structure of the code you are using to solve the problem.
have written a stochastic simulation in Java, which loads data from a few CSV files on disk (totaling about 100MB) and writes results to another output file (not much data, just a boolean and a few numbers). There is also a parameters file, and for different parameters the distribution of simulation outputs would be expected to change. To determine the correct/best input parameters I need to run multiple simulations, across multiple input parameter configurations, and look at the distributions of the outputs in each group. Each simulation takes 0.1-10 min depending on parameters and randomness.
I've been reading about Hadoop and wondering if it can help me running lots of simulations; I may have access to about 8 networked desktop machines in the near future. If I understand correctly, the map function could run my simulation and spit out the result, and the reducer might be the identity.
The thing I'm worried about is HDFS, which seems to meant for huge files, not a smattering of small CSV files, (none of which would big enough to even make up the minimum recommended block size of 64MB). Furthermore, each simulation would only need an identical copy of each of the CSV files.
Is Hadoop the wrong tool for me?
I see a number of answers here that basically are saying, "no, you shouldn't use Hadoop for simulations because it wasn't built for simulations." I believe this is a rather short sighted view and would be akin to someone saying in 1985, "you can't use a PC for word processing, PCs are for spreadsheets!"
Hadoop is a fantastic framework for construction of a simulation engine. I've been using it for this purpose for months and have had great success with small data / large computation problems. Here's the top 5 reasons I migrated to Hadoop for simulation (using R as my language for simulations, btw):
Access: I can lease Hadoop clusters through either Amazon Elastic Map Reduce and I don't have to invest any time and energy into the administration of a cluster. This meant I could actually start doing simulations on a distributed framework without having to get administrative approval in my org!
Administration: Hadoop handles job control issues, like node failure, invisibly. I don't have to code for these conditions. If a node fails, Hadoop makes sure the sims scheduled for that node gets run on another node.
Upgradeable: Being a rather generic map reduce engine with a great distributed file system if you later have problems that involve large data if you're used to using Hadoop you don't have to migrate to a new solution. So Hadoop gives you a simulation platform that will also scale to a large data platform for (nearly) free!
Support: Being open source and used by so many companies, the number of resources, both on line and off, for Hadoop are numerous. Many of those resources are written with the assumption of "big data" but they are still useful for learning to think in a map reduce way.
Portability: I have built analysis on top of proprietary engines using proprietary tools which took considerable learning to get working. When I later changed jobs and found myself at a firm without that same proprietary stack I had to learn a new set of tools and a new simulation stack. Never again. I traded in SAS for R and our old grid framework for Hadoop. Both are open source and I know that I can land at any job in the future and immediately have tools at my fingertips to start kicking ass.
Hadoop can be made to perform your simulation if you already have a Hadoop cluster, but it's not the best tool for the kind of application you are describing. Hadoop is built to make working on big data possible, and you don't have big data -- you have big computation.
I like Gearman (http://gearman.org/) for this sort of thing.
While you might be able to get by using MapReduce with Hadoop, it seems like what you're doing might be better suited for a grid/job scheduler such as Condor or Sun Grid Engine. Hadoop is more suited for doing something where you take a single (very large) input, split it into chunks for your worker machines to process, and then reduce it to produce an output.
Since you are already using Java, I suggest taking a look at GridGain which, I think, is particularly well suited to your problem.
Simply said, though Hadoop may solve your problem here, its not the right tool for your purpose.
Question in nutshell
What is the best way to get Python and Java to play nice with each other?
More detailed explanation
I have a somewhat complicated situation. I'll try my best to explain both in pictures and words. Here's the current system architecture:
We have an agent-based modeling simulation written in Java. It has options of either writing locally to CSV files, or remotely via a connection to a Java server to an HDF5 file. Each simulation run spits out over a gigabyte of data, and we run the simulation dozens of times. We need to be able to aggregate over multiple runs of the same scenario (with different random seeds) in order to see some trends (e.g. min, max, median, mean). As you can imagine, trying to move around all these CSV files is a nightmare; there are multiple files produced per run, and like I said some of them are enormous. That's the reason we've been trying to move towards an HDF5 solution, where all the data for a study is stored in one place, rather than scattered across dozens of plain text files. Furthermore, since it is a binary file format, it should be able to get significant space savings as compared to uncompressed CSVS.
As the diagram shows, the current post-processing we do of the raw output data from simulation also takes place in Java, and reads in the CSV files produced by local output. This post-processing module uses JFreeChart to create some charts and graphs related to the simulation.
The Problem
As I alluded to earlier, the CSVs are really untenable and are not scaling well as we generate more and more data from simulation. Furthermore, the post-processing code is doing more than it should have to do, essentially performing the work of a very, very poor man's relational database (making joins across 'tables' (csv files) based on foreign keys (the unique agent IDs). It is also difficult in this system to visualize the data in other ways (e.g. Prefuse, Processing, JMonkeyEngine getting some subset of the raw data to play with in MatLab or SPSS).
Solution?
My group decided we really need a way of filtering and querying the data we have, as well as performing cross table joins. Given this is a write-once, read-many situation, we really don't need the overhead of a real relational database; instead we just need some way to put a nicer front end on the HDF5 files. I found a few papers about this, such as one describing how to use [XQuery as the query language on HDF5 files][3], but the paper describes having to write a compiler to convert from XQuery/XPath into the native HDF5 calls, way beyond our needs.
Enter [PyTables][4]. It seems to do exactly what we need (provides two different ways of querying data, either through Python list comprehension or through [in-kernel (C level) searches][5].
The proposed architecture I envision is this:
What I'm not really sure how to do is to link together the python code that will be written for querying, with the Java code that serves up the HDF5 files, and the Java code that does the post processing of the data. Obviously I will want to rewrite much of the post-processing code that is implicitly doing queries and instead let the excellent PyTables do this much more elegantly.
Java/Python options
A simple google search turns up a few options for [communicating between Java and Python][7], but I am so new to the topic that I'm looking for some actual expertise and criticism of the proposed architecture. It seems like the Python process should be running on same machine as the Datahose so that the large .h5 files do not have to be transferred over the network, but rather the much smaller, filtered views of it would be transmitted to the clients. [Pyro][8] seems to be an interesting choice - does anyone have experience with that?
This is an epic question, and there are lots of considerations. Since you didn't mention any specific performance or architectural constraints, I'll try and offer the best well-rounded suggestions.
The initial plan of using PyTables as an intermediary layer between your other elements and the datafiles seems solid. However, one design constraint that wasn't mentioned is one of the most critical of all data processing: Which of these data processing tasks can be done in batch processing style and which data processing tasks are more of a live stream.
This differentiation between "we know exactly our input and output and can just do the processing" (batch) and "we know our input and what needs to be available for something else to ask" (live) makes all the difference to an architectural question. Looking at your diagram, there are several relationships that imply the different processing styles.
Additionally, on your diagram you have components of different types all using the same symbols. It makes it a little bit difficult to analyze the expected performance and efficiency.
Another contraint that's significant is your IT infrastructure. Do you have high speed network available storage? If you do, intermediary files become a brilliant, simple, and fast way of sharing data between the elements of your infrastructure for all batch processing needs. You mentioned running your PyTables-using-application on the same server that's running the Java simulation. However, that means that server will experience load for both writing and reading the data. (That is to say, the simulation environment could be affected by the needs of unrelated software when they query the data.)
To answer your questions directly:
PyTables looks like a nice match.
There are many ways for Python and Java to communicate, but consider a language agnostic communication method so these components can be changed later if necessarily. This is just as simple as finding libraries that support both Java and Python and trying them. The API you choose to implement with whatever library should be the same anyway. (XML-RPC would be fine for prototyping, as it's in the standard library, Google's Protocol Buffers or Facebook's Thrift make good production choices. But don't underestimate how great and simple just "writing things to intermediary files" can be if data is predictable and batchable.
To help with the design process more and flesh out your needs:
It's easy to look at a small piece of the puzzle, make some reasonable assumptions, and jump into solution evaluation. But it's even better to look at the problem holistically with a clear understanding of your constraints. May I suggest this process:
Create two diagrams of your current architecture, physical and logical.
On the physical diagram, create boxes for each physical server and diagram the physical connections between each.
Be certain to label the resources available to each server and the type and resources available to each connection.
Include physical hardware that isn't involved in your current setup if it might be useful. (If you have a SAN available, but aren't using it, include it in case the solution might want to.)
On the logical diagram, create boxes for every application that is running in your current architecture.
Include relevant libraries as boxes inside the application boxes. (This is important, because your future solution diagram currently has PyTables as a box, but it's just a library and can't do anything on it's own.)
Draw on disk resources (like the HDF5 and CSV files) as cylinders.
Connect the applications with arrows to other applications and resources as necessary. Always draw the arrow from the "actor" to the "target". So if an app writes and HDF5 file, they arrow goes from the app to the file. If an app reads a CSV file, the arrow goes from the app to the file.
Every arrow must be labeled with the communication mechanism. Unlabeled arrows show a relationship, but they don't show what relationship and so they won't help you make decisions or communicate constraints.
Once you've got these diagrams done, make a few copies of them, and then right on top of them start to do data-flow doodles. With a copy of the diagram for each "end point" application that needs your original data, start at the simulation and end at the end point with a pretty much solid flowing arrow. Any time your data arrow flows across a communication/protocol arrow, make notes of how the data changes (if any).
At this point, if you and your team all agree on what's on paper, then you've explained your current architecture in a manner that should be easily communicable to anyone. (Not just helpers here on stackoverflow, but also to bosses and project managers and other purse holders.)
To start planning your solution, look at your dataflow diagrams and work your way backwards from endpoint to startpoint and create a nested list that contains every app and intermediary format on the way back to the start. Then, list requirements for every application. Be sure to feature:
What data formats or methods can this application use to communicate.
What data does it actually want. (Is this always the same or does it change on a whim depending on other requirements?)
How often does it need it.
Approximately how much resources does the application need.
What does the application do now that it doesn't do that well.
What can this application do now that would help, but it isn't doing.
If you do a good job with this list, you can see how this will help define what protocols and solutions you choose. You look at the situations where the data crosses a communication line, and you compare the requirements list for both sides of the communication.
You've already described one particular situation where you have quite a bit of java post-processing code that is doing "joins" on tables of data in CSV files, thats a "do now but doesn't do that well". So you look at the other side of that communication to see if the other side can do that thing well. At this point, the other side is the CSV file and before that, the simulation, so no, there's nothing that can do that better in the current architecture.
So you've proposed a new Python application that uses the PyTables library to make that process better. Sounds good so far! But in your next diagram, you added a bunch of other things that talk to "PyTables". Now we've extended past the understanding of the group here at StackOverflow, because we don't know the requirements of those other applications. But if you make the requirements list like mentioned above, you'll know exactly what to consider. Maybe your Python application using PyTables to provide querying on the HDF5 files can support all of these applications. Maybe it will only support one or two of them. Maybe it will provide live querying to the post-processor, but periodically write intermediary files for the other applications. We can't tell, but with planning, you can.
Some final guidelines:
Keep things simple! The enemy here is complexity. The more complex your solution, the more difficult the solution to implement and the more likely it is to fail. Use the least number operations, use the least complex operations. Sometimes just one application to handle the queries for all the other parts of your architecture is the simplest. Sometimes an application to handle "live" queries and a separate application to handle "batch requests" is better.
Keep things simple! It's a big deal! Don't write anything that can already be done for you. (This is why intermediary files can be so great, the OS handles all the difficult parts.) Also, you mention that a relational database is too much overhead, but consider that a relational database also comes with a very expressive and well-known query language, the network communication protocol that goes with it, and you don't have to develop anything to use it! Whatever solution you come up with has to be better than using the off-the-shelf solution that's going to work, for certain, very well, or it's not the best solution.
Refer to your physical layer documentation frequently so you understand the resource use of your considerations. A slow network link or putting too much on one server can both rule out otherwise good solutions.
Save those docs. Whatever you decide, the documentation you generated in the process is valuable. Wiki-them or file them away so you can whip them out again when the topic come s up.
And the answer to the direct question, "How to get Python and Java to play nice together?" is simply "use a language agnostic communication method." The truth of the matter is that Python and Java are both not important to your describe problem-set. What's important is the data that's flowing through it. Anything that can easily and effectively share data is going to be just fine.
Do not make this more complex than it needs to be.
Your Java process can -- simply -- spawn a separate subprocess to run your PyTables queries. Let the Operating System do what OS's do best.
Your Java application can simply fork a process which has the necessary parameters as command-line options. Then your Java can move on to the next thing while Python runs in the background.
This has HUGE advantages in terms of concurrent performance. Your Python "backend" runs concurrently with your Java simulation "front end".
You could try Jython, a Python interpreter for the JVM which can import Java classes.
Jython project homepage
Unfortunately, that's all I know on the subject.
Not sure if this is good etiquette. I couldn't fit all my comments into a normal comment, and the post has no activity for 8 months.
Just wanted to see how this was going for you? We have a very very very similar situation where I work - only the simulation is written in C and the storage format is binary files. Every time a boss wants a different summary we have to make/modify handwritten code to do summaries. Our binary files are about 10 GB in size and there is one of these for every year of the simulation, so as you can imagine, things get hairy when we want to run it with different seeds and such.
I've just discovered pyTables and had a similar idea to yours. I was hoping to change our storage format to hdf5 and then run our summary reports/queries using pytables. Part of this involves joining tables from each year. Have you had much luck doing these types of "joins" using pytables?