NoClassDefFoundError: org.jblas.NativeBlas?

[prismofeverything]

Running the following code on a clean project throws this error (Mac OSX 10.6.8):

(require '[clatrix.core :as m])
(m/pp (m/* (m/rand 2 5) (m/rand 5 2)))

Could not initialize class org.jblas.NativeBlas
[Thrown class java.lang.NoClassDefFoundError]

Backtrace:
0: SimpleBlas.java:245 org.jblas.SimpleBlas.gemm
1: DoubleMatrix.java:1674 org.jblas.DoubleMatrix.mmuli
2: DoubleMatrix.java:3005 org.jblas.DoubleMatrix.mmul
3: core.clj:630 clatrix.core/*

Any ideas?

[prismofeverything]

Actually, simply cloning the clatrix repo and running lein test gives me this:

java.lang.UnsatisfiedLinkError: Couldn't find the resource libjblas_arch_flavor.jnilib/
/bin/
/lib/static/Mac OS X/x86_64/
/lib/static/Mac OS X/x86_64/
/lib/dynamic/Mac OS X/x86_64/
/lib/dynamic/Mac OS X/x86_64/
/lib/Mac OS X/x86_64/
/Mac OS X/x86_64/
.

    at org.jblas.util.LibraryLoader.loadLibrary(LibraryLoader.java:100)
    at org.jblas.util.ArchFlavor.<clinit>(ArchFlavor.java:50)
    at org.jblas.util.LibraryLoader.loadLibrary(LibraryLoader.java:75)
    at org.jblas.NativeBlas.<clinit>(NativeBlas.java:84)
    at org.jblas.SimpleBlas.gemm(SimpleBlas.java:245)
    at org.jblas.DoubleMatrix.mmuli(DoubleMatrix.java:1674)
    at org.jblas.DoubleMatrix.mmul(DoubleMatrix.java:3005)
    at clatrix.core$_STAR_.invoke(core.clj:615)
    at clatrix.core_test$eval1153.invoke(core_test.clj:16)

I have atlas installed, is this a path issue? Is libjblas_arch_flavor.jnilib/ a directory or a file, (it seems like it would be a file) and if so, is that trailing slash messing it up?

[Quantisan]

I'm getting the same error when running lein expectations but runs fine when lein repl

[cbilson]

I get a similar error as well, in a project that uses clatrix:

$ lein repl                                                                                                                                                                
nREPL server started on port 57272                                                                                                                                                  
REPL-y 0.1.0-beta10                                                                                                                                                                 
Clojure 1.4.0                                                                                                                                                                       
...
user=> (require '[clatrix.core :as m])                                                                                                                                              
nil                                                                                                                                                                                 
user=> (m/rnorm 5 5)                                                                                                                                                                
#<Matrix [5 5]>                                                                                                                                                                     
user=> (m/* (m/rnorm 5 5) (m/rnorm 5 5))                                                                                                                                            
-- org.jblas ERROR Couldn't load copied link file: java.lang.UnsatisfiedLinkError: /private/var/folders/p4/ykgp4h_973q9z3j0v_m1r8jc0000gn/T/jblas55269708383826120libjblas_arch_fla\
vor.jnilib:  Library not loaded: /usr/local/lib/libgfortran.3.dylib   Referenced from: /private/var/folders/p4/ykgp4h_973q9z3j0v_m1r8jc0000gn/T/jblas55269708383826120libjblas_arch\
_flavor.jnilib   Reason: image not found.                                                                                                                                           

UnsatisfiedLinkError org.jblas.util.ArchFlavor.SSELevel()I  org.jblas.util.ArchFlavor.SSELevel (ArchFlavor.java:-2)                                                                 

user=> quit                                                                                                                                                                         
Bye for now!$

Is this just a jblas issue that I should talk to them about, or is there some workaround?

[Quantisan]

I found a solution. If you download and unzip the pre-built jblas native libraries, find the files that it's complaining about, then just copy it into native directory within the project. It works for me on OS X 10.8.2. Note that I already have gfortran and apple developer command line tools installed.

[ejackson]

This seems to be an OSX issue. On linux, using the standard package, I don't observe the problem :(

[Quantisan]

Yes, I looked at jblas source and this happens because of an extra IF statement for OSX which loads ArchFlavor.

[cbilson]

Thanks for the help guys! I was able to get my project working by putting the two files it wanted out of the prebuilt jblas jar (lib/static/Mac OS X/x86_64/libjblas_arch_flavor.jnilib and sse3/libjblas.jnilib) into some place on my project's class path (I just put them in resources for now.)

[cbilson]

@Quantisan: Where did you see the code in jblas that has an extra IF statement for OSX? I glanced at ArchFlavor and LibraryLoader and it looks right based on the paths in the resources folder. Is it somewhere in the native code?

If you know where the problem is, maybe we can make a pull request for jblas?

It looks like it may actually preferable to have these libraries on the path somewhere (https://github.com/mikiobraun/jblas/blob/master/src/main/java/org/jblas/util/ArchFlavor.java#L47-49) anyway so maybe we should mention this in the clatrix readme?

[Quantisan]

@cbilson It works for me when I did lein run before. So I'm thinking it might be leiningen not expanding native folder during lein test. I don't know exactly where's the problem so couldn't patch it.

[ejackson]

@cbilson: Can you please update the docs with the solution you found and then we can close the issue ?

[Quantisan]

jblas 1.2.2 fixed this issue

[ejackson]

Great, thanks Paul.