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From Eddie Epstein <eaepst...@gmail.com>
Subject Re: UIMACPP and multi-threading
Date Thu, 28 Apr 2016 11:43:37 GMT
Benjamin,

Initial testing with the latest AMQ broker indicates an incompatibility
with the existing UIMACPP release. Along with the problems you have exposed
there is good motivation to get another uimacpp release out relatively
soon. THanks for exposing the GC/threading issue with the JNI and potential
fixes.

Eddie

On Tue, Apr 26, 2016 at 3:47 AM, Benjamin De Boe <
Benjamin.DeBoe@intersystems.com> wrote:

> Hi Eddie,
>
> I'm not familiar with the serializeJNI issue.
> Few sources still recommend implementing finalize(), because it is
> undetermined in which order the GC process will eventually invoke them. We
> also thought it was counterintuitive to see the UimacppEngine being
> finalized before the UimacppAnalysisComponent that wraps it, but that's
> what our extra logs quite consistently seemed to indicate, so that's
> probably just what the word "non-deterministic" means.
>
> This article suggests a few alternatives that may be considered for this
> UIMACPP / JNI issue in the long run:
> http://www.oracle.com/technetwork/java/javamail/finalization-137655.html
>
>
> Thanks,
> benjamin
>
> --
> Benjamin De Boe | Product Manager
> M: +32 495 19 19 27 | T: +32 2 464 97 33
> InterSystems Corporation | http://www.intersystems.com
>
> -----Original Message-----
> From: Eddie Epstein [mailto:eaepstein@gmail.com]
> Sent: Tuesday, April 26, 2016 4:58 AM
> To: user@uima.apache.org
> Cc: Jos Denys <Jos.Denys@intersystems.com>; Chen-Chieh Hsu <
> Chen-Chieh.Hsu@intersystems.com>
> Subject: Re: UIMACPP and multi-threading
>
> Hi,
>
> Not the author of the JNI, but does it make sense that
> UimacppEngine.finalize() could be called while UimacppAnalysisComponent
> maintains a valid engine pointer to UimacppEngine? And once the engine
> pointer has been set to null, UimacppAnalysisComponent.destroy() will not
> call UimacppEngine.destroy(). Leaves me confused how this could happen.
>
> At any rate, do you think finalize is related to the serizalizeJNI problem?
>
> Eddie
>
>
>
>
>
> On Mon, Apr 25, 2016 at 8:27 AM, Benjamin De Boe <
> Benjamin.DeBoe@intersystems.com> wrote:
>
> > After some more debugging, it seems this is probably a garbage
> > collection issue rather than a multi-threading issue, although
> > multiple threads may well increase the likelihood of it happening.
> >
> > We've found that there are two methods on the CPP side for cleaning up
> > the memory used by the CPP engine: destroyJNI() and destructorJNI().
> > destructorJNI() is called from the UimacppEngine:finalize() method and
> > only deletes the pInstance pointer, whereas destroyJNI() does a lot
> > more work in cleaning up what lies beyond and is called through
> > UimacppEngine:destroy(), which in turn is invoked from
> UimacppAnalysisComponent:finalize().
> >
> > Now, the arcane magic in the GC process seems to first finish off the
> > UimacppEngine helper object (calling destructorJNI()) and then the
> > UimacppAnalysisComponent instance that contained the other one, with
> > its
> > destroyJNI() method then running into trouble because pInstance was
> > already deleted in destructorJNI(), causing the access violation we've
> > been struggling with.
> >
> > [logged as https://issues.apache.org/jira/browse/UIMA-4899 ]
> >
> > There are a number of ways how we could work around this (such as just
> > calling destroyJNI() in both cases, exiting early if it's already
> > cleaned up), but of course we'd hope someone of the original UIMACPP
> > team to weigh in and share the reasoning behind those two separate
> > methods and anything we're overlooking in our assessment. Anybody who
> > can recommend what we should do in the short run and how this might
> > translate into a fixed UIMA / UIMACPP release at some point? An
> > out-of-the-box 64-bit UIMACPP release would probably benefit more than
> > just us (cf https://issues.apache.org/jira/browse/UIMA-4900).
> >
> >
> >
> > Thanks,
> > benjamin
> >
> > --
> > Benjamin De Boe | Product Manager
> > M: +32 495 19 19 27 | T: +32 2 464 97 33 InterSystems Corporation |
> > http://www.intersystems.com
> >
> > -----Original Message-----
> > From: Eddie Epstein [mailto:eaepstein@gmail.com]
> > Sent: Thursday, April 7, 2016 1:58 PM
> > To: user@uima.apache.org
> > Subject: Re: UIMACPP and multi-threading
> >
> > Standalone.java certainly does show threading issues with uimacpp's JNI.
> > The multithread testing thru the JNI, like the one I did a few days
> > ago, was clearly not sufficient to declare it thread safe.
> >
> > Our local uimacpp development with regards thread safety was focused
> > on multithread testing for the development of uimacpp's native AMQ
> > service wrapper.
> >
> > If you do fix the JNI threading issues please consider contributing
> > them back to ASF!
> > Eddie
> >
> > On Tue, Apr 5, 2016 at 8:54 AM, Jos Denys <Jos.Denys@intersystems.com>
> > wrote:
> >
> > > Hi Eddie,
> > >
> > > I worked on the CPP-side, and what I noticed was that the JNI
> > > Interface always passes an instance pointer :
> > >
> > > JNIEXPORT void JNICALL JAVA_PREFIX(resetJNI) (JNIEnv* jeEnv, jobject
> > > joJTaf) {
> > >   try {
> > >     UIMA_TPRINT("entering resetDocument()");
> > >
> > >     uima::JNIInstance* pInstance = JNIUtils::getCppInstance(jeEnv,
> > > joJTaf);
> > >
> > >
> > > Now the strange thing, and finally what caused the acces violation
> > > error, was that the pInstance pointer was the same for the 3 threads
> > > that
> > > (simultaneously) did the UIMA processing, so it looks like the same
> > > CAS was passed for 3 different analysis worker threads.
> > >
> > > Any idea why and how this can happen ?
> > >
> > > Thanks for your feedback,
> > > Jos Denys,
> > > InterSystems Benelux.
> > >
> > >
> > > De : Benjamin De Boe
> > > Envoyé : mardi 5 avril 2016 09:33
> > > À : user@uima.apache.org
> > > Cc : Jos Denys <Jos.Denys@intersystems.com>; Chen-Chieh Hsu <
> > > Chen-Chieh.Hsu@intersystems.com> Objet : RE: UIMACPP and
> > > multi-threading
> > >
> > >
> > > Hi Eddie,
> > >
> > >
> > >
> > > Thanks for your prompt response.
> > >
> > > In our experiment, we have one initial thread instantiating a
> > > CasPool and then passing it on to newly spawned threads that each
> > > have their own DaveDetector instance and fetch a new CAS from the
> shared pool.
> > > The UimacppEngine objects' cppEnginePointer variable differs per
> > > thread, but on the C++ side, it looks like all threads are pointing
> > > to the same memory address for the CAS they operate on. Given the
> > > actions
> > > UimacppEngine:process() performs and its cas being process
> > > registered as a protected field rather than a local variable, it's
> > > no wonder it causes trouble.
> > >
> > >
> > >
> > > I can imagine UIMA-AS follows a path that's perhaps slightly
> > > different (and apparently safe, given your test case), but I'm
> > > wondering what we're doing wrong that we need to fiddle with
> > > synchronized keywords on the framework classes to ensure we avoid the
> crash.
> > >
> > > Here's our test program. When the CAS pool is small enough (i.e. 5),
> > > things work fine. When it is larger than the number of documents we
> > > want to process (23), it also works. When it is somewhere in between
> > > (i.e. 20), we get the crash.
> > >
> > >
> > >
> > > package com.intersys.uima.test;
> > >
> > >
> > >
> > > import java.io.File;
> > >
> > > import java.net.URL;
> > >
> > > import java.net.URLClassLoader;
> > >
> > > import org.apache.uima.UIMAFramework;
> > >
> > > import org.apache.uima.analysis_engine.AnalysisEngine;
> > >
> > > import org.apache.uima.cas.CAS;
> > >
> > > import org.apache.uima.resource.ResourceSpecifier;
> > >
> > > import org.apache.uima.util.CasCreationUtils;
> > >
> > > import org.apache.uima.util.CasPool;
> > >
> > > import org.apache.uima.util.Level;
> > >
> > > import org.apache.uima.util.XMLInputSource;
> > >
> > >
> > >
> > > /**
> > >
> > > *
> > >
> > > * @author bdeboe
> > >
> > > */
> > >
> > > public class Standalone implements Runnable {
> > >
> > >
> > >
> > >     private String text;
> > >
> > >     private AnalysisEngine ae;
> > >
> > >     private CasPool pool;
> > >
> > >
> > >
> > >     public Standalone(String txt, AnalysisEngine ae, CasPool pool) {
> > >
> > >         this.text = txt;
> > >
> > >         this.ae = ae;
> > >
> > >         this.pool = pool;
> > >
> > >     }
> > >
> > >
> > >
> > >     public static void main(String[] args) throws Exception {
> > >
> > >
> > >
> > >         String descPath = ((args != null) && (args.length > 0))
?
> > > args[0]
> > > : "C:\\InterSystems\\UIMA\\bin\\DaveDetector.xml";
> > >
> > >        int casPoolSize = ((args != null) && (args.length > 1)) ?
> > > Integer.valueOf(args[1]) : 20;
> > >
> > >
> > >
> > >         XMLInputSource in = new XMLInputSource(descPath);
> > >
> > >         ResourceSpecifier specifier
> > >
> > >                 =
> > > UIMAFramework.getXMLParser().parseResourceSpecifier(in);
> > >
> > >         AnalysisEngine ae =
> > > UIMAFramework.produceAnalysisEngine(specifier);
> > >
> > >
> > >
> > >         String[] text = new String[23];
> > >
> > >         // populating the array…
> > >
> > >         text[22] = "…";
> > >
> > >
> > >
> > >         CasPool pool = (casPoolSize > 0) ? new CasPool(casPoolSize,
> ae) :
> > > null;
> > >
> > >         for (int i = 0; i < text.length; i++) {
> > >
> > >             Standalone task = new Standalone(text[i],
> > > UIMAFramework.produceAnalysisEngine(specifier), (casPoolSize > 0) ?
> > > pool
> > :
> > > null);
> > >
> > >             Thread t = new Thread(task);
> > >
> > >             t.start();
> > >
> > >         }
> > >
> > >     }
> > >
> > >
> > >
> > >     @Override
> > >
> > >     public void run() {
> > >
> > >
> > >
> > >         CAS cas  = null;
> > >
> > >         try {
> > >
> > >             if (pool != null) {
> > >
> > >                 cas = pool.getCas();
> > >
> > >             } else {
> > >
> > >                 cas =
> > > CasCreationUtils.createCas(ae.getAnalysisEngineMetaData());
> > >
> > >             }
> > >
> > >
> > >
> > >             cas.setDocumentText(text);
> > >
> > >             ae.process(cas);
> > >
> > >
> > >
> > >             System.out.println("Done processing text");
> > >
> > >
> > >
> > >         } catch (Exception e) {
> > >
> > >             e.printStackTrace();
> > >
> > >         } finally {
> > >
> > >             if (pool != null) pool.releaseCas(cas);
> > >
> > >         }
> > >
> > >     }
> > >
> > > }
> > >
> > >
> > >
> > >
> > >
> > > Probably also of note: we sometimes get a simple exception on
> > > destroyJNI() (pasted below), rather than the outright total process
> > > crash described earlier. We assume this is just “luck” in that the
> > > different threads are invoking a not-so-critical section.
> > >
> > >
> > >
> > > Apr 05, 2016 9:25:25 AM
> > > org.apache.uima.uimacpp.UimacppAnalysisComponent
> > > logJTafException
> > >
> > > SEVERE: The following internal exception was caught: 5,002
> > > (UIMA_ERR_ENGINE_UNEXPECTED_EXCEPTION)
> > >
> > > Apr 05, 2016 9:25:25 AM
> > > org.apache.uima.uimacpp.UimacppAnalysisComponent
> > > logJTafException(431)
> > >
> > > SEVERE:
> > >
> > > Error number  : 5002
> > >
> > > Recoverable   : No
> > >
> > > Error         : Unexpected error
> > >
> > > (5002)
> > >
> > > org.apache.uima.uimacpp.InternalTafException:
> > >
> > > Error number  : 5002
> > >
> > > Recoverable   : No
> > >
> > > Error         : Unexpected error
> > >
> > > (5002)
> > >
> > >         at org.apache.uima.uimacpp.UimacppEngine.destroyJNI(Native
> > > Method)
> > >
> > >         at
> > > org.apache.uima.uimacpp.UimacppEngine.destroy(UimacppEngine.java:304
> > > )
> > >
> > >         at
> > > org.apache.uima.uimacpp.UimacppAnalysisComponent.destroy(UimacppAnal
> > > ys
> > > isComponent.java:338)
> > >
> > >         at
> > > org.apache.uima.uimacpp.UimacppAnalysisComponent.finalize(UimacppAna
> > > ly
> > > sisComponent.java:354)
> > >
> > >         at java.lang.System$2.invokeFinalize(System.java:1270)
> > >
> > >         at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:98)
> > >
> > >         at java.lang.ref.Finalizer.access$100(Finalizer.java:34)
> > >
> > >         at
> > > java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:210)
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Many thanks for your feedback,
> > >
> > >
> > >
> > > benjamin
> > >
> > >
> > >
> > >
> > >
> > > --
> > >
> > > Benjamin De Boe | Product Manager
> > >
> > > M: +32 495 19 19 27 | T: +32 2 464 97 33
> > >
> > > InterSystems Corporation | http://www.intersystems.com
> > >
> > >
> > >
> > > -----Original Message-----
> > >
> > > From: Eddie Epstein [mailto:eaepstein@gmail.com]
> > >
> > > Sent: Tuesday, April 5, 2016 12:47 AM
> > >
> > > To: user@uima.apache.org<mailto:user@uima.apache.org>
> > >
> > > Subject: Re: UIMACPP and multi-threading
> > >
> > >
> > >
> > > Hi Benjamin,
> > >
> > >
> > >
> > > UIMACPP is thread safe, as is the JNI interface. To confirm, I just
> > > created a UIMA-AS service with 10 instances of DaveDetector, and fed
> > > the service
> > >
> > > 800 CASes with up to 10 concurrent CASes at any time.
> > >
> > >
> > >
> > > It is not the case with DaveDetector, but at annotator
> > > initialization some analytics will store info in thread local
> > > storage, and expect the same thread be used to call the annotator
> > > process method. UIMA-AS and DUCC guarantee that an instantiated AE
> > > is always called on the same
> > thread.
> > >
> > >
> > >
> > > Eddie
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Mon, Apr 4, 2016 at 10:56 AM, Benjamin De Boe <
> > > Benjamin.DeBoe@intersystems.com<mailto:Benjamin.DeBoe@intersystems.c
> > > om
> > > >>
> > > wrote:
> > >
> > >
> > >
> > > > Hi,
> > >
> > > >
> > >
> > > > We're working with a UIMACPP annotator (wrapping our existing NLP
> > >
> > > > library) and are running in what appears to be thread safety
> > > > issues,
> > >
> > > > which we can reproduce with the DaveDetector demo AE.
> > >
> > > > When separate threads are accessing separate instances of the
> > >
> > > > org.apache.uima.uimacpp.UimacppAnalysisComponent wrapper class on
> > > > the
> > >
> > > > Java side, it appears they are invoking the same object on the C++
> > >
> > > > side, which results in quite a mess (access violations and process
> > >
> > > > crashes) when different threads concurrently invoke resetJNI() and
> > >
> > > > fillCASJNI() on the
> > > > org.apache.uima.uimacpp.UimacppAnalysisComponent
> > >
> > > > object. When using a small CAS pool on the Java side, the problem
> > > > does
> > >
> > > > not seem to occur, but it resurfaces if the CAS pool grows bigger
> > > > and
> > >
> > > > memory settings are not increased accordingly. However, if this
> > > > were a
> > >
> > > > pure memory issue, we had hoped to see more telling errors and
> > > > just
> > >
> > > > guessing how big memory should be for larger deployments isn't
> > > > very
> > > appealing an option either.
> > >
> > > > Adding the synchronized keyword to the relevant method of the
> > > > wrapper
> > >
> > > > class on the Java side also avoids the issue, at the obvious cost
> > > > of
> > >
> > > > performance. Moving to UIMA-AS is not an option for us, currently.
> > >
> > > >
> > >
> > > > Given that the documentation is not explicit about it, we're
> > > > hoping to
> > >
> > > > get an unambiguous answer from this list: is UIMACPP actually
> > > > supposed
> > >
> > > > to be thread-safe? We saw old and resolved JIRA's that addressed
> > >
> > > > thread-safety issues for UIMACPP, so we assumed it was the case,
> > > > but
> > >
> > > > reality seems to point in the opposite direction.
> > >
> > > >
> > >
> > > >
> > >
> > > > Thanks in advance for your feedback,
> > >
> > > >
> > >
> > > > benjamin
> > >
> > > >
> > >
> > > >
> > >
> > > > --
> > >
> > > > Benjamin De Boe | Product Manager
> > >
> > > > M: +32 495 19 19 27 | T: +32 2 464 97 33 InterSystems Corporation
> > > > |
> > >
> > > > http://www.intersystems.com
> > >
> > > >
> > >
> > > >
> > >
> >
>

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