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From Conrad Crampton <conrad.cramp...@SecData.com>
Subject Re: Classloader and removal of native libraries <SOLVED>
Date Fri, 11 Aug 2017 13:46:43 GMT
Hi Aljoscha,
“Hope that helps”…

I have dug through the javacpp source code to find how the Loader class uses the temp cache
location for the native libraries and in my open method in my RichMapFunction I am now setting
the System.property to a random location so if the job restarts and calls open again, it uses
a random temp location as in your example.

So thank you so much, got me on the right path. Now I’ve got a problem with out of memory
errors arrghh (I will start another thread on this as I don’t want to soil this one with
a different topic)

Thanks again

From: Aljoscha Krettek <aljoscha@apache.org>
Date: Thursday, 10 August 2017 at 15:57
To: Conrad Crampton <conrad.crampton@SecData.com>
Cc: "user@flink.apache.org" <user@flink.apache.org>
Subject: Re: Classloader and removal of native libraries

Hi Conrad,

I'm afraid you're running in the same problem that we already encountered with loading the
native RocksDB library: https://github.com/apache/flink/blob/219ae33d36e67e3e74f493cf4956a290bc966a5d/flink-contrib/flink-statebackend-rocksdb/src/main/java/org/apache/flink/contrib/streaming/state/RocksDBStateBackend.java#L519

The code section has a good description of what is going on. We're using NativeLibraryLoader
[1], which comes with RocksDB  to try and load the native library from a different temporary
location if loading it the normal way fails. (The relocation of the lib to a temp dir is in
the NativeLibraryLoader, not on our side. We're just providing a temp path for NativeLibraryLoader
to work with.)

Hope that helps,

[1] https://github.com/facebook/rocksdb/blob/master/java/src/main/java/org/rocksdb/NativeLibraryLoader.java

On 10. Aug 2017, at 15:36, Conrad Crampton <conrad.crampton@SecData.com<mailto:conrad.crampton@SecData.com>>

First time posting here so ‘hi’.
I have been using Flink (1.31 now) for a couple of months now and loving it. My deployment
is to JobManager running as a long running session on Yarn.
I have a problem where I have a Flink streaming job that involves loading native libraries
as part of one of the mappers (inheriting from RichMapFunction) loading (in the open method)
a previously trained machine learning model (using Deeplearning4j). The problem lies with
when loading the model, it also loads some native libraries using javacpp Loader class (which
from looking at the source code determines a location for native libraries and from a hierarchy
of availability of a System property, the users home dir (with .javacpp) or temp dir).
Anyway the actual problem lies is if an exception is thrown in the Flink job, the jobmanager
tries to restart it, however it would appear that when it failed in the first place, references
to the objects and therefore the classes aren’t released by the classloader as I get an

        at org.nd4j.linalg.cpu.nativecpu.ops.NativeOpExecutioner.<init>(NativeOpExecutioner.java:43)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
        at java.lang.Class.newInstance(Class.java:442)
        at org.nd4j.linalg.factory.Nd4j.initWithBackend(Nd4j.java:5784)
        at org.nd4j.linalg.factory.Nd4j.initContext(Nd4j.java:5694)
        at org.nd4j.linalg.factory.Nd4j.<clinit>(Nd4j.java:184)
        at org.deeplearning4j.util.ModelSerializer.restoreMultiLayerNetwork(ModelSerializer.java:188)
        at org.deeplearning4j.util.ModelSerializer.restoreMultiLayerNetwork(ModelSerializer.java:138)
        at com.secdata.gi.detect.map.DGAClassifierMapFunction.open(DGAClassifierMapFunction.java:54)
        at org.apache.flink.api.common.functions.util.FunctionUtils.openFunction(FunctionUtils.java:36)
        at org.apache.flink.streaming.api.operators.AbstractUdfStreamOperator.open(AbstractUdfStreamOperator.java:111)
        at org.apache.flink.streaming.runtime.tasks.StreamTask.openAllOperators(StreamTask.java:376)
        at org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:253)
        at org.apache.flink.runtime.taskmanager.Task.run(Task.java:702)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: ND4J is probably missing dependencies. For more information,
please refer to: http://nd4j.org/getstarted.html
        at org.nd4j.nativeblas.NativeOpsHolder.<init>(NativeOpsHolder.java:51)
        at org.nd4j.nativeblas.NativeOpsHolder.<clinit>(NativeOpsHolder.java:19)
        ... 18 more
Caused by: java.lang.UnsatisfiedLinkError: no jnind4jcpu in java.library.path
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1865)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1122)
        at org.bytedeco.javacpp.Loader.loadLibrary(Loader.java:963)
        at org.bytedeco.javacpp.Loader.load(Loader.java:764)
        at org.bytedeco.javacpp.Loader.load(Loader.java:671)
        at org.nd4j.nativeblas.Nd4jCpu.<clinit>(Nd4jCpu.java:10)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:348)
        at org.bytedeco.javacpp.Loader.load(Loader.java:726)
        at org.bytedeco.javacpp.Loader.load(Loader.java:671)
        at org.nd4j.nativeblas.Nd4jCpu$NativeOps.<clinit>(Nd4jCpu.java:62)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:264)
        at org.nd4j.nativeblas.NativeOpsHolder.<init>(NativeOpsHolder.java:29)
        ... 19 more
Caused by: java.lang.UnsatisfiedLinkError: Native Library /home/yarn/.javacpp/cache/blob_a87e49f9a475a9dc4296f6afbc3ae171dc821d19/org/nd4j/nativeblas/linux-x86_64/libjnind4jcpu.so
already loaded in another classloader
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1903)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1822)
        at java.lang.Runtime.load0(Runtime.java:809)
        at java.lang.System.load(System.java:1086)
        at org.bytedeco.javacpp.Loader.loadLibrary(Loader.java:943)

I’m no expert in class loading at all but have tried a number of ways to overcome this based
on the docs and dynamic classloading

1.       Putting the jars that contain the native libraries in the flink/lib directory so
they are always loaded on JobManager startup and removing them from the deployed flink job
2.       Some code in the open / close methods of my mapper to try and dispose of the native
NativeLibrary lib = NativeLibrary.getInstance(Loader.getCacheDir() + "/cache/nd4j-native-0.8.0-"
+ Loader.getPlatform() +  ".jar/org/nd4j/nativeblas/" + Loader.getPlatform() + "/libjnind4jcpu.so");
this.model = null;

if (null != lib) {
    System.out.println("found lib - removing");
This sort of works in finding the library (on my mac running locally) but as from the stacktrace
above, on deployment to yarn some random value is placed after the /cache dir which I don’t
know how to get a handle on to be able to construc the correct library location (and just
using the library name as the jni docs suggest for NativeLibrary.getInstance fails to find
the library)

Neither of the above approaches work, so when my job fails I can’t cancel and resubmit as
it just fails with the same stack trace. The only way I can get it to run again is the cancel
all other jobs running on JobManager, killing the JM yarn session, creating a new Yarn session
JM, resubmitting flink job – which is a real pain. Ideally I would like to stop the exception
in the first place, but as I can’t figure out how to get logging appearing in my yarn logs
either (for debug) I’m at a bit of a loss!

Any pointers, suggestions please??

Many thanks

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