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I am just wondering whether there would be a significant speed performance advantage relatively on a given set of machines when using JavaCV as opposed to the C/C++ implementation of OpenCV.
Please correct me if I am wrong, but my understanding is that the c/c++ implementation of opencv is closer to the machine where as the Java implementation of OpenCV, JavaC, would have a slight speed performance disadvantage (in milliseconds) as there would be a virtual machine converting your source code to bytecode which then gets converted to machine code. Whereas, with c/c++, it gets converted straight to machine code and thus doesn't carry that intermediary step of the virtual machine overhead.
Please don't kill me here if I made mistakes; I am just learning and would welcome constructive criticism.
Thank you
I'd like to add a couple of things to #ejbs's answer.
First of all, you concerned 2 separate issues:
Java vs. C++ performance
OpenCV vs JavaCV
Java vs. C++ performance is a long, long story. On one hand, C++ programs are compiled to a highly optimized native code. They start quickly and run fast all the time without pausing for garbage collection or other VM duties (as Java do). On other hand, once compiled, program in C++ can't change, no matter on what machine they are run, while Java bytecode is compiled "just-in-time" and is always optimized for processor architecture they run on. In modern world, with so many different devices (and processor architectures) this may be really significant. Moreover, some JVMs (e.g. Oracle Hotspot) can optimize even the code that is already compiled to native code! VM collect data about program execution and from time to time tries to rewrite code in such a way that it is optimized for this specific execution. So in such complicated circumstances the only real way to compare performance of implementations in different programming languages is to just run them and see the result.
OpenCV vs. JavaCV is another story. First you need to understand stack of technologies behind these libraries.
OpenCV was originally created in 1999 in Intel research labs and was written in C. Since that time, it changed the maintainer several times, became open source and reached 3rd version (upcoming release). At the moment, core of the library is written in C++ with popular interface in Python and a number of wrappers in other programming languages.
JavaCV is one of such wrappers. So in most cases when you run program with JavaCV you actually use OpenCV too, just call it via another interface. But JavaCV provides more than just one-to-one wrapper around OpenCV. In fact, it bundles the whole number of image processing libraries, including FFmpeg, OpenKinect and others. (Note, that in C++ you can bind these libraries too).
So, in general it doesn't matter what you are using - OpenCV or JavaCV, you will get just about same performance. It more depends on your main task - is it Java or C++ which is better suited for your needs.
There's one more important point about performance. Using OpenCV (directly or via wrapper) you will sometimes find that OpenCV functions overcome other implementations by several orders. This is because of heavy use of low-level optimizations in its core. For example, OpenCV's filter2D function is SIMD-accelerated and thus can process several sets of data in parallel. And when it comes to computer vision, such optimizations of common functions may easily lead to significant speedup.
JavaCV interfaces to OpenCV, so when you call something OpenCV related there would be some overhead but in general most of the heavy work will still be on the C++ side and therefore there won't be a very large performance penalty.
You would have to do performance benchmarks to find out more.
PS. I'm pretty new here but I'm rather sure that this is not a suitable question for StackOverflow.
i would like to add a few more insights on java as an interface to c++ libraries...
A)developing:
1)while java may be easier to manage large scale projects and compiles extremely fast, it is very very hard, and next to impossible to debug native code from java...
when code crush on native side...or memory leaks( something that happens a lot... ) you feel kind of helpless...
2)unless you build the bindings yourself( not an easy task even with using swig or whatever... ) you are dependent on the good will/health/time of the bindings builder....
so in this case i would prefer the official "desktop java " bindings over javacv...
B)performance.
1) while bindings may be optimized( memory transfer using neobuffer ) as in the javacv case there is still a very very small jni overhead for each native function call -
this is meaningless in our case since most opencv functions consume X100000++ cpu cycles compared to this jni overhead...
2) The BIG-PROBLEM ---- stop the world GARBAGE COLLECTIOR( GC )
java uses a garbage collector that halts all cpu's threads making it UNSUITABLE for REAL-TIME application's , there are work-around's iv'e heard of like redesigning your app not to produce garbage, use a spaciel gc, or use realtime java( cost money... ) they all seem to be extra-work( and all you wanted is a nice easy path to opencv.... )
conclusion - if you want to create a professional real time app - then go with c++
unless you have a huge modular project to manage - just stick with c++ and precompiled headers( make things compile faster... )
while java is a pleasure to work with , when it comes to native binding's HELL breaks loose...i know iv'e been there....
Java and OpenCL both support Heterogeneous Computing; systems with multiple architecture working cooperatively in parallel(Task and data parallel ).
portability is the main goal in both the cases, and both have achieved this goal to a large extent. In fact still OpenCl cannot be run on FPGAs and DSPs, as the tools are not available. JVM can be developed for GPUs FPGA, ARM etc.
Both generate intermediate code.
Despite so many similarities why and when should one prefer OpenCL over Java for Heterogeneous Computing?
EDITED
Please be specific to my question: Despite so many similarities why and when should one prefer OpenCL over Java for Heterogeneous Computing? Why at all I chose OpenCL instead of Java?
If you say openCl has better performance then my immediate question will be why it is so(since both generate intermediate code that need to be converted into binaries for specific h/w).
OpenCL is normally used for processing large amounts of parallel operations(calculations etc). This is where OpenCL thrives and the throughput of your program is really increased by it.
Java is a general purpose language for writing applications running on various platforms/devices.
They have a different purpose as tools but you can use OpenCL from your Java program using JOCL. I also used a tool from AMD called Aparapi. because I wanted my application to carry out some calculations, a job that my ASUS AMD 6970 card seemed to get done faster than my 6 core AMD 1090T Phenom Black Edition.
Just for you to know what Aparapi is(taken from the google code site):
Aparapi allows Java developers to take advantage of the compute power
of GPU and APU devices by executing data parallel code fragments on
the GPU rather than being confined to the local CPU. It does this by
converting Java bytecode to OpenCL at runtime and executing on the
GPU, if for any reason Aparapi can't execute on the GPU it will
execute in a Java thread pool.
Despite so many similarities why and when should one prefer OpenCL
over Java for Heterogeneous Computing?
One would choose OpenCL for parallel processing tasks that would otherwise take a lot of time to be executed on the CPU. The disadvantage in this case would be the extra heat and power consumption costs. Bear also in mind that some tasks would execute faster on a CPU. It all depends on the application that most of the time would require trials on both types of chips in order to decide which one does the job best.
Why at all I chose OpenCL instead of Java?
One would choose OpenCL over Java for parallel processing oriented tasks. OpenCL is a tool built for this purpose. OpenCL is not something you would use for building enterprise or desktop applications. Java is a programming language for almost any domain running on many platforms. If one would know that using OpenCL would save them 24 hours of calculations over Java; of course Java would be sidelined and OpenCL would be the way to go or simply OpenCL could be used through a Java application.
If you say openCl has better performance then my immediate question
will be why it is so(since both generate intermediate code that need
to be converted into binaries for specific h/w).
It has better performance on specific applications since GPU have more cores than a CPU. Their frequency though is quite low so this means that they are better on parallel tasks rather than sequential. You have to bear in mind that OpenCL is used for basic calculations and not for building full flavor applications...at least as far as I know.
I am building a trading portfolio management system that is responsible for production, optimization, and simulation of non-high frequency trading portfolios (dealing with 1min or 3min bars of data, not tick data).
I plan on employing Amazon web services to take on the entire load of the application.
I have four choices that I am considering as language.
Java
C++
C#
Python
Here is the scope of the extremes of the project scope. This isn't how it will be, maybe ever, but it's within the scope of the requirements:
Weekly simulation of 10,000,000 trading systems.
(Each trading system is expected to have its own data mining methods, including feature selection algorithms which are extremely computationally-expensive. Imagine 500-5000 features using wrappers. These are not run often by any means, but it's still a consideration)
Real-time production of portfolio w/ 100,000 trading strategies
Taking in 1 min or 3 min data from every stock/futures market around the globe (approx 100,000)
Portfolio optimization of portfolios with up to 100,000 strategies. (rather intensive algorithm)
Speed is a concern, but I believe that Java can handle the load.
I just want to make sure that Java CAN handle the above requirements comfortably. I don't want to do the project in C++, but I will if it's required.
The reason C# is on there is because I thought it was a good alternative to Java, even though I don't like Windows at all and would prefer Java if all things are the same.
Python - I've read somethings on PyPy and pyscho that claim python can be optimized with JIT compiling to run at near C-like speeds... That's pretty much the only reason it is on this list, besides that fact that Python is a great language and would probably be the most enjoyable language to code in, which is not a factor at all for this project, but a perk.
To sum up:
real time production
weekly simulations of a large number of systems
weekly/monthly optimizations of portfolios
large numbers of connections to collect data from
There is no dealing with millisecond or even second based trades. The only consideration is if Java can possibly deal with this kind of load when spread out of a necessary amount of EC2 servers.
Thank you guys so much for your wisdom.
Pick the language you are most familiar with. If you know them all equally and speed is a real concern, pick C.
While I am a huge fan of Python and personaly I'm not a great lover of Java, in this case I have to concede that Java is the right way to go.
For many projects Python's performance just isn't a problem, but in your case even minor performance penalties will add up extremely quickly. I know this isn't a real-time simulation, but even for batch processing it's still a factor to take into consideration. If it turns out the load is too big for one virtual server, an implementation that's twice as fast will halve your virtual server costs.
For many projects I'd also argue that Python will allow you to develop a solution faster, but here I'm not sure that would be the case. Java has world-class development tools and top-drawer enterprise grade frameworks for parallell processing and cross-server deployment and while Python has solutions in this area, Java clearly has the edge. You also have architectural options with Java that Python can't match, such as Javaspaces.
I would argue that C and C++ impose too much of a development overhead for a project like this. They're viable inthat if you are very familiar with those languages I'm sure it would be doable, but other than the potential for higher performance, they have nothing else to bring to the table.
C# is just a rewrite of Java. That's not a bad thing if you're a Windows developer and if you prefer Windows I'd use C# rather than Java, but if you don't care about Windows there's no reason to care about C#.
I would pick Java for this task. In terms of RAM, the difference between Java and C++ is that in Java, each Object has an overhead of 8 Bytes (using the Sun 32-bit JVM or the Sun 64-bit JVM with compressed pointers). So if you have millions of objects flying around, this can make a difference. In terms of speed, Java and C++ are almost equal at that scale.
So the more important thing for me is the development time. If you make a mistake in C++, you get a segmentation fault (and sometimes you don't even get that), while in Java you get a nice Exception with a stack trace. I have always preferred this.
In C++ you can have collections of primitive types, which Java hasn't. You would have to use external libraries to get them.
If you have real-time requirements, the Java garbage collector may be a nuisance, since it takes some minutes to collect a 20 GB heap, even on machines with 24 cores. But if you don't create too many temporary objects during runtime, that should be fine, too. It's just that your program can make that garbage collection pause whenever you don't expect it.
Why only one language for your system? If I were you, I will build the entire system in Python, but C or C++ will be used for performance-critical components. In this way, you will have a very flexible and extendable system with fast-enough performance. You can find even tools to generate wrappers automatically (e.g. SWIG, Cython). Python and C/C++/Java/Fortran are not competing each other; they are complementing.
Write it in your preferred language. To me that sounds like python. When you start running the system you can profile it and see where the bottlenecks are. Once you do some basic optimisations if it's still not acceptable you can rewrite portions in C.
A consideration could be writing this in iron python to take advantage of the clr and dlr in .net. Then you can leverage .net 4 and parallel extensions. If anything will give you performance increases it'll be some flavour of threading which .net does extremely well.
Edit:
Just wanted to make this part clear. From the description, it sounds like parallel processing / multithreading is where the majority of the performance gains are going to come from.
It is useful to look at the inner loop of your numerical code. After all you will spend most of your CPU-time inside this loop.
If the inner loop is a matrix operation, then I suggest python and scipy, but of the inner loop if not a matrix operation, then I would worry about python being slow. (Or maybe I would wrap c++ in python using swig or boost::python)
The benefit of python is that it is easy to debug, and you save a lot of time by not having to compile all the time. This is especially useful for a project where you spend a lot of time programming deep internals.
I would go with pypy. If not, http://lolcode.com/.
I am curious about performance of Java numerical algorithms, say for example matrix matrix double precision multiplication, using the latest JIT machines as compared for example to hand tuned SSE C++/assembler or Fortran counterparts.
I have looked on the web but most of the results come from almost 10 years ago and I understand Java progressed quite a lot since then.
If you have experience using Java for numerically intensive applications can you share your experience. Also how well does Java perform in kernels where the loops are relatively short and the memory access is not very uniform but still within the limits of L1 cache? If such kernel is executed multiple times in succession, can JVM optimize it during runtime?
Thanks
I have written some reasonably large and performance sensitive numerical code in Java (crunching large arrays of doubles usually).
I've found Java to be "good enough" for fast numerical calculations. Especially when you consider that you are usually not CPU-bound anyway - memory latency and cache awareness will probably be your biggest problem for large datasets.
However, you can still beat Java with hand-optimized C/C++ code that takes advantage of specific vectorised instructions etc. or highly customised memory layouts. So for the very fastest code, you could consider writing the core algorithm in C/C++ and calling it from Java using JNI.
Personally, I find that creating a native code dependency is usually more trouble than it is worth so I tend to stick to the pure Java approach.
This is coming from a .NET side of things, but I'm 90% sure that it's the case for Java too. While the JIT will make some use of SSE instructions where it can, it currently does not auto-vectorize your code when dealing with, for example, matrix multiplications. Hand vectorized C++ using compiler intrinsics/inline assembly will definitely be faster here.
One of the weakest points in java is (native) matrix operations. This is due to the nature of Java matrices:
You can not declare a matrix to be rectangular, ie. each row can have a different number of columns.
A matrix is technically not a "matrix of doubles (or ints, ...)", but an array of arrays of ... . The big difference is that since arrays are Java objects you can assign the same array object to more than 1 row.
These two properties make a lot of standard matrix optimizations impossible for the compiler.
You might get better performance by using a Java library which emulates matrices on a single long array. However you have the overhead of method calls for all access.
C++ will definitely be faster. You can even have some hand-optimized libraries for your purposes that contain assembly codes for each of the major CPUs out there. You can't get better than that.
Afterwards, you can use JNI to call to it from Java, if needed.
Java is not meant for high performance arithmetic calculations like this. If you are depending on these, I'd recommend picking a proper, low-level language to implement that. Or, alternatively, you can write the performance-specific part in a low level language, and then connect it to a Java front-end using JNI or some other IPC method.
This is a link to the programming language shootout page for java vs c++, which will give you a comparison of java's speed on several compute intensive algorithms. It will also show you what highest performance java code looks like. For the most part, for these few specific benchmarks, java took more time (but not more than 2 or 3 times) to run.
Seconding that your best bet is to test it for yourself, as performance will vary somewhat depending on what you're doing exactly. I find it difficult to believe Shane C. Mason's answer that Java performance will be the same as C++ or Fortran performance, as even C++ and Fortran are not really comparable for some scientific computing algorithms.
I have a computational fluid dynamics code that I wrote using C++ and the same code essentially translated into Fortran. I'm not really sure why yet, but the Fortran version is about twice as fast as the C++ version. I would guess that with features like bounds-checking and garbage collection, Java would be slower than both, but I would not know until I tested.
This can be so dependent on what you are doing in the C++ code.
For example, are you using the GPU? Edit I forgot about jogl, so Java can compete here.
Are you parallelized using STM or shared-memory, then Java can't compete.
For a link on analysis of parallel matrix multiplication: http://www.cs.utexas.edu/users/plapack/papers/ipps98/ipps98.html
Do you have enough memory to do the calculations in memory, so the garbage collector won't be needed, and have you fine-tuned the garbage collector for optimal performance? Then, Java can be competitive, perhaps.
Are you using multicores, and is the C++ optimized to take advantage of this architecture? Then Java won't be able to compete.
Are you using several computers tied together, then Java won't be able to compete.
Are you using any combination of these, then it will depend on the particular implementation.
Java is not designed to compete with a hand-tuned C++ program, but, the time it takes to do the tuning, are you doing enough calculations where it will matter? Java will be able to give some reasonable speed but with less work than hand-tuning, but not much of an improvement over just doing C++ code.
You may want to see if there is an improvement over Haskell or Erlang, for example, over your C++, as these languages are better designed for this type of work.
Are these kind of computations you're interested in - Fast Fourier Transform, Jacobi Successive Over Relaxation, Monte Carlo Integration, Sparse Matrix Mult, Dense LU Matrix Factorisation?
They make up the SciMark 2.0 composite benchmark which you can launch as an applet on your machine.
There are also ANSI C versions of the programs, and an Intel document (pdf) on optimizing and recompiling SciMark for C++.
Similarly you could use The Java Grande Forum Benchmark Suite and the comparison C programs.
Java uses a Just in Time (JIT) compiler to convert the bytecode to native machine language - so the first time it runs through a code block it will be slower but once the segment is 'warmed up' the performance will be equivalent. In short - the numerical performance is pretty good.
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We are computing something whose runtime is bound by matrix operations. (Some details below if interested.) This experience prompted the following question:
Do folk have experience with the performance of Java libraries for matrix math (e.g., multiply, inverse, etc.)? For example:
JAMA
COLT
Apache commons math
I searched and found nothing.
Details of our speed comparison:
We are using Intel FORTRAN (ifort (IFORT) 10.1 20070913). We have reimplemented it in Java (1.6) using Apache commons math 1.2 matrix ops, and it agrees to all of its digits of accuracy. (We have reasons for wanting it in Java.) (Java doubles, Fortran real*8). Fortran: 6 minutes, Java 33 minutes, same machine. jvisualm profiling shows much time spent in RealMatrixImpl.{getEntry,isValidCoordinate} (which appear to be gone in unreleased Apache commons math 2.0, but 2.0 is no faster). Fortran is using Atlas BLAS routines (dpotrf, etc.).
Obviously this could depend on our code in each language, but we believe most of the time is in equivalent matrix operations.
In several other computations that do not involve libraries, Java has not been much slower, and sometimes much faster.
I'm the author of Java Matrix Benchmark (JMatBench) and I'll give my thoughts on this discussion.
There are significant difference between Java libraries and while there is no clear winner across the whole range of operations, there are a few clear leaders as can be seen in the latest performance results (October 2013).
If you are working with "large" matrices and can use native libraries, then the clear winner (about 3.5x faster) is MTJ with system optimised netlib. If you need a pure Java solution then MTJ, OjAlgo, EJML and Parallel Colt are good choices. For small matrices EJML is the clear winner.
The libraries I did not mention showed significant performance issues or were missing key features.
Just to add my 2 cents. I've compared some of these libraries. I attempted to matrix multiply a 3000 by 3000 matrix of doubles with itself. The results are as follows.
Using multithreaded ATLAS with C/C++, Octave, Python and R, the time taken was around 4 seconds.
Using Jama with Java, the time taken was 50 seconds.
Using Colt and Parallel Colt with Java, the time taken was 150 seconds!
Using JBLAS with Java, the time taken was again around 4 seconds as JBLAS uses multithreaded ATLAS.
So for me it was clear that the Java libraries didn't perform too well. However if someone has to code in Java, then the best option is JBLAS. Jama, Colt and Parallel Colt are not fast.
I'm the main author of jblas and wanted to point out that I've released Version 1.0 in late December 2009. I worked a lot on the packaging, meaning that you can now just download a "fat jar" with ATLAS and JNI libraries for Windows, Linux, Mac OS X, 32 and 64 bit (except for Windows). This way you will get the native performance just by adding the jar file to your classpath. Check it out at http://jblas.org!
I just compared Apache Commons Math with jlapack.
Test: singular value decomposition of a random 1024x1024 matrix.
Machine: Intel(R) Core(TM)2 Duo CPU E6750 # 2.66GHz, linux x64
Octave code: A=rand(1024); tic;[U,S,V]=svd(A);toc
results execution time
---------------------------------------------------------
Octave 36.34 sec
JDK 1.7u2 64bit
jlapack dgesvd 37.78 sec
apache commons math SVD 42.24 sec
JDK 1.6u30 64bit
jlapack dgesvd 48.68 sec
apache commons math SVD 50.59 sec
Native routines
Lapack* invoked from C: 37.64 sec
Intel MKL 6.89 sec(!)
My conclusion is that jlapack called from JDK 1.7 is very close to the native
binary performance of lapack. I used the lapack binary library coming with linux distro and invoked the dgesvd routine to get the U,S and VT matrices as well. All tests were done using double precision on exactly the same matrix each run (except Octave).
Disclaimer - I'm not an expert in linear algebra, not affiliated to any of the libraries above and this is not a rigorous benchmark.
It's a 'home-made' test, as I was interested comparing the performance increase of JDK 1.7 to 1.6 as well as commons math SVD to jlapack.
I can't really comment on specific libraries, but in principle there's little reason for such operations to be slower in Java. Hotspot generally does the kinds of things you'd expect a compiler to do: it compiles basic math operations on Java variables to corresponding machine instructions (it uses SSE instructions, but only one per operation); accesses to elements of an array are compiled to use "raw" MOV instructions as you'd expect; it makes decisions on how to allocate variables to registers when it can; it re-orders instructions to take advantage of processor architecture... A possible exception is that as I mentioned, Hotspot will only perform one operation per SSE instruction; in principle you could have a fantastically optimised matrix library that performed multiple operations per instruction, although I don't know if, say, your particular FORTRAN library does so or if such a library even exists. If it does, there's currently no way for Java (or at least, Hotspot) to compete with that (though you could of course write your own native library with those optimisations to call from Java).
So what does all this mean? Well:
in principle, it is worth hunting around for a better-performing library, though unfortunately I can't recomend one
if performance is really critical to you, I would consider just coding your own matrix operations, because you may then be able perform certain optimisations that a library generally can't, or that a particular library your using doesn't (if you have a multiprocessor machine, find out if the library is actually multithreaded)
A hindrance to matrix operations is often data locality issues that arise when you need to traverse both row by row and column by column, e.g. in matrix multiplication, since you have to store the data in an order that optimises one or the other. But if you hand-write the code, you can sometimes combine operations to optimise data locality (e.g. if you're multiplying a matrix by its transformation, you can turn a column traversal into a row traversal if you write a dedicated function instead of combining two library functions). As usual in life, a library will give you non-optimal performance in exchange for faster development; you need to decide just how important performance is to you.
Jeigen https://github.com/hughperkins/jeigen
wraps Eigen C++ library http://eigen.tuxfamily.org , which is one of the fastest free C++ libraries available
relatively terse syntax, eg 'mmul', 'sub'
handles both dense and sparse matrices
A quick test, by multiplying two dense matrices, ie:
import static jeigen.MatrixUtil.*;
int K = 100;
int N = 100000;
DenseMatrix A = rand(N, K);
DenseMatrix B = rand(K, N);
Timer timer = new Timer();
DenseMatrix C = B.mmul(A);
timer.printTimeCheckMilliseconds();
Results:
Jama: 4090 ms
Jblas: 1594 ms
Ojalgo: 2381 ms (using two threads)
Jeigen: 2514 ms
Compared to jama, everything is faster :-P
Compared to jblas, Jeigen is not quite as fast, but it handles sparse matrices.
Compared to ojalgo, Jeigen takes about the same amount of elapsed time, but only using one core, so Jeigen uses half the total cpu. Jeigen has a terser syntax, ie 'mmul' versus 'multiplyRight'
There's a benchmark of various matrix packages available in java up on
http://code.google.com/p/java-matrix-benchmark/ for a few different hardware configurations. But it's no substitute for doing your own benchmark.
Performance is going to vary with the type of hardware you've got (cpu, cores, memory, L1-3 cache, bus speed), the size of the matrices and the algorithms you intend to use. Different libraries have different takes on concurrency for different algorithms, so there's no single answer. You may also find that the overhead of translating to the form expected by a native library negates the performance advantage for your use case (some of the java libraries have more flexible options regarding matrix storage, which can be used for further performance optimizations).
Generally though, JAMA, Jampack and COLT are getting old, and do not represent the state of the current performance available in Java for linear algebra. More modern libraries make more effective use of multiple cores and cpu caches. JAMA was a reference implementation, and pretty much implements textbook algorithms with little regard to performance. COLT and IBM Ninja were the first java libraries to show that performance was possible in java, even if they lagged 50% behind native libraries.
I'm the author of la4j (Linear Algebra for Java) library and here is my point. I've been working on la4j for 3 years (the latest release is 0.4.0 [01 Jun 2013]) and only now I can start doing performace analysis and optimizations since I've just covered the minimal required functional. So, la4j isn't as fast as I wanted but I'm spending loads of my time to change it.
I'm currently in the middle of porting new version of la4j to JMatBench platform. I hope new version will show better performance then previous one since there are several improvement I made in la4j such as much faster internal matrix format, unsafe accessors and fast blocking algorithm for matrix multiplications.
Have you taken a look at the Intel Math Kernel Library? It claims to outperform even ATLAS. MKL can be used in Java through JNI wrappers.
Linalg code that relies heavily on Pentiums and later processors' vector computing capabilities (starting with the MMX extensions, like LAPACK and now Atlas BLAS) is not "fantastically optimized", but simply industry-standard. To replicate that perfomance in Java you are going to need native libraries. I have had the same performance problem as you describe (mainly, to be able to compute Choleski decompositions) and have found nothing really efficient: Jama is pure Java, since it is supposed to be just a template and reference kit for implementers to follow... which never happened. You know Apache math commons... As for COLT, I have still to test it but it seems to rely heavily on Ninja improvements, most of which were reached by building an ad-hoc Java compiler, so I doubt it's going to help.
At that point, I think we "just" need a collective effort to build a native Jama implementation...
Building on Varkhan's post that Pentium-specific native code would do better:
jBLAS: An alpha-stage project with JNI wrappers for Atlas: http://www.jblas.org.
Author's blog post: http://mikiobraun.blogspot.com/2008/10/matrices-jni-directbuffers-and-number.html.
MTJ: Another such project: http://code.google.com/p/matrix-toolkits-java/
We have used COLT for some pretty large serious financial calculations and have been very happy with it. In our heavily profiled code we have almost never had to replace a COLT implementation with one of our own.
In their own testing (obviously not independent) I think they claim within a factor of 2 of the Intel hand-optimised assembler routines. The trick to using it well is making sure that you understand their design philosophy, and avoid extraneous object allocation.
I have found that if you are creating a lot of high dimensional Matrices, you can make Jama about 20% faster if you change it to use a single dimensional array instead of a two dimensional array. This is because Java doesn't support multi-dimensional arrays as efficiently. ie. it creates an array of arrays.
Colt does this already, but I have found it is more complicated and more powerful than Jama which may explain why simple functions are slower with Colt.
The answer really depends on that you are doing. Jama doesn't support a fraction of the things Colt can do which make make more of a difference.
You may want to check out the jblas project. It's a relatively new Java library that uses BLAS, LAPACK and ATLAS for high-performance matrix operations.
The developer has posted some benchmarks in which jblas comes off favourably against MTJ and Colt.
For 3d graphics applications the lwjgl.util vector implementation out-performed above mentioned jblas by a factor of about 3.
I have done 1 million matrix multiplications of a vec4 with a 4x4 matrix.
lwjgl finished in about 18ms, jblas required about 60ms.
(I assume, that the JNI approach is not very suitable for fast successive application of relatively small multiplications. Since the translation/mapping may take more time than the actual execution of the multiplication.)
There's also UJMP
There are many different freely available java linear algebra libraries. http://www.ujmp.org/java-matrix/benchmark/
Unfortunately that benchmark only gives you info about matrix multiplication (with transposing the test does not allow the different libraries to exploit their respective design features).
What you should look at is how these linear algebra libraries perform when asked to compute various matrix decompositions.
http://ojalgo.org/matrix_compare.html
Matrix Tookits Java (MTJ) was already mentioned before, but perhaps it's worth mentioning again for anyone else stumbling onto this thread. For those interested, it seems like there's also talk about having MTJ replace the linalg library in the apache commons math 2.0, though I'm not sure how that's progressing lately.
You should add Apache Mahout to your shopping list.