Re: Many views in the cas to serialize cause java.lang.NullPointerException in service uima-as

[Jaroslaw Cwiklik]

Just a bit more evidence. The caller of the gerSofaAddr()

public void writeViewsCommons() throws Exception {
  // Get indexes for each SofaFS in the CAS
  int numViews = cas.getBaseSofaCount();

  for (int sofaNum = 1; sofaNum <= numViews; sofaNum++) {
FSIndexRepositoryImpl loopIR = (FSIndexRepositoryImpl)
 cas.getBaseCAS().getSofaIndexRepository(sofaNum);
final int sofaAddr = getSofaAddr(sofaNum);

Not an expert of this code, but it smells like another thread is changing a
CAS which is being serialized.

-jerry

On Fri, Feb 10, 2017 at 4:31 PM, Jaroslaw Cwiklik  wrote:

> Is this a primitive (single-threaded) aggregate or async (multi-threaded)?
> If async, try to simplify and run primitive aggregate with scaleout=1.
>
> The CAS does not seem to be null in this case. The caller of the 
> getSerializedCas()
> checks for null.
>
> The code dies here:
> Caused by: java.lang.NullPointerException
> at org.apache.uima.cas.impl.CasSerializerSupport$CasDocSerializ
> er.getSofaAddr(CasSerializerSupport.java:454)
>
>public int getSofaAddr(int sofaNum) {
>   if (sofaNum != 1 || cas.isInitialSofaCreated()) { //skip if initial
> view && no Sofa yet
> // all
> non-initial-views must have a sofa
>* return ((CASImpl)cas.getView(sofaNum)).getSofaRef();*
>   }
>   return 0;
> }
>
> Looks to me that getView(sofaNum) is returning null. Is it possible that
> two threads are operating on the same CAS maybe? One removing a view while
> another trying to serialize. Have no idea what else could it be.
>
> -jerry
>
>
>
> On Fri, Feb 10, 2017 at 8:45 AM, nelson rivera 
> wrote:
>
>> Hi,  The first thing I did was these tests,i made a simple test case
>> that create a Cas with 17 views and then serialize using
>> XmiCasSerializer.serialize(newJCas.getCas(), fis) and serializes
>> correctly.
>> Also i made other test, initialize the same AE but of local way with
>> UIMA API and process the same input documents and the processing is
>> correct and then serialize the CAS, without problem.
>>
>> The error is with AE deployed in uima-as and consuming it.
>>
>> 2017-02-09 17:30 GMT-05:00, Marshall Schor :
>> > one thing that would help track this down is a small isolated test case.
>> >
>> > Do you think uima-as is needed? I'm wondering if a simple test case
>> which
>> > generated 17 views and then tried to serialize would show the failure...
>> >
>> > If you could supply a small test case that showed the failure so we
>> could
>> > reproduce it, that would enable a rapid resolution.
>> >
>> > -Marshall
>> >
>> >
>> > On 2/9/2017 3:58 PM, Marshall Schor wrote:
>> >>  The line throwing the null pointer exception is :
>> >>
>> >> cas.getView(sofaNum).getSofaRef()
>> >>
>> >> So the NPE is either the cas is null, or the getView(sofaNum) is
>> returning
>> >> null.
>> >>
>> >> I'm not sure what the best way is to debug this...
>> >>
>> >> -Marshall
>> >>
>> >>
>> >>
>> >>
>> >> On 2/9/2017 12:42 PM, nelson rivera wrote:
>> >>> I have a aggregate service uima-as, at the end of aggregate the cas to
>> >>> return is composed of as many views as the number of input files, each
>> >>> view with annotations of processing.
>> >>> With a number of input documents less than 15 the processing is
>> >>> successful always,
>> >>> but if the number of documents is greater than 15, i get a
>> >>> NullPointerException at the aggregate service trying to serialize the
>> >>> cas, not in the processing of AE aggregate.
>> >>> the logs of aggregate service:
>> >>>
>> >>> 11:51:38.815 - 42:
>> >>> cu.datys.xinetica.uima.core.MergerInViewCasMultipler.hasNext(285):
>> >>> INFO: HasNext false
>> >>> 11:51:38.875 - 44:
>> >>> org.apache.uima.uimacpp.UimacppAnalysisComponent.log(396): INFO: :
>> >>> XClusterAnalyzer::process --- OK
>> >>> 11:51:39.145 - 45:
>> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineContro
>> ller_impl.replyToClient:
>> >>> WARNING: Service: XClusterAnalyzerAggregate Runtime Exception
>> >>> 11:51:39.145 - 45:
>> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineContro
>> ller_impl.replyToClient:
>> >>> WARNING:
>> >>> org.apache.uima.aae.error.AsynchAEException:
>> >>> org.apache.uima.UIMARuntimeException
>> >>> at
>> >>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.getSer
>> ializedCas(JmsOutputChannel.java:1265)
>> >>> at
>> >>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.sendRe
>> ply(JmsOutputChannel.java:800)
>> >>> at
>> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineContro
>> ller_impl.sendReplyToRemoteClient(AggregateAnalysisEngineCon
>> troller_impl.java:2173)
>> >>> at
>> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineContro
>> ller_impl.replyToClient(AggregateAnalysisEngineController_impl.java:2342)
>> >>> at
>> >>> 

Re: Many views in the cas to serialize cause java.lang.NullPointerException in service uima-as

[Jaroslaw Cwiklik]

Is this a primitive (single-threaded) aggregate or async (multi-threaded)?
If async, try to simplify and run primitive aggregate with scaleout=1.

The CAS does not seem to be null in this case. The caller of the
getSerializedCas()
checks for null.

The code dies here:
Caused by: java.lang.NullPointerException
at org.apache.uima.cas.impl.CasSerializerSupport$
CasDocSerializer.getSofaAddr(CasSerializerSupport.java:454)

   public int getSofaAddr(int sofaNum) {
  if (sofaNum != 1 || cas.isInitialSofaCreated()) { //skip if initial
view && no Sofa yet
// all
non-initial-views must have a sofa
   * return ((CASImpl)cas.getView(sofaNum)).getSofaRef();*
  }
  return 0;
}

Looks to me that getView(sofaNum) is returning null. Is it possible that
two threads are operating on the same CAS maybe? One removing a view while
another trying to serialize. Have no idea what else could it be.

-jerry



On Fri, Feb 10, 2017 at 8:45 AM, nelson rivera 
wrote:

> Hi,  The first thing I did was these tests,i made a simple test case
> that create a Cas with 17 views and then serialize using
> XmiCasSerializer.serialize(newJCas.getCas(), fis) and serializes
> correctly.
> Also i made other test, initialize the same AE but of local way with
> UIMA API and process the same input documents and the processing is
> correct and then serialize the CAS, without problem.
>
> The error is with AE deployed in uima-as and consuming it.
>
> 2017-02-09 17:30 GMT-05:00, Marshall Schor :
> > one thing that would help track this down is a small isolated test case.
> >
> > Do you think uima-as is needed? I'm wondering if a simple test case which
> > generated 17 views and then tried to serialize would show the failure...
> >
> > If you could supply a small test case that showed the failure so we could
> > reproduce it, that would enable a rapid resolution.
> >
> > -Marshall
> >
> >
> > On 2/9/2017 3:58 PM, Marshall Schor wrote:
> >>  The line throwing the null pointer exception is :
> >>
> >> cas.getView(sofaNum).getSofaRef()
> >>
> >> So the NPE is either the cas is null, or the getView(sofaNum) is
> returning
> >> null.
> >>
> >> I'm not sure what the best way is to debug this...
> >>
> >> -Marshall
> >>
> >>
> >>
> >>
> >> On 2/9/2017 12:42 PM, nelson rivera wrote:
> >>> I have a aggregate service uima-as, at the end of aggregate the cas to
> >>> return is composed of as many views as the number of input files, each
> >>> view with annotations of processing.
> >>> With a number of input documents less than 15 the processing is
> >>> successful always,
> >>> but if the number of documents is greater than 15, i get a
> >>> NullPointerException at the aggregate service trying to serialize the
> >>> cas, not in the processing of AE aggregate.
> >>> the logs of aggregate service:
> >>>
> >>> 11:51:38.815 - 42:
> >>> cu.datys.xinetica.uima.core.MergerInViewCasMultipler.hasNext(285):
> >>> INFO: HasNext false
> >>> 11:51:38.875 - 44:
> >>> org.apache.uima.uimacpp.UimacppAnalysisComponent.log(396): INFO: :
> >>> XClusterAnalyzer::process --- OK
> >>> 11:51:39.145 - 45:
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.replyToClient:
> >>> WARNING: Service: XClusterAnalyzerAggregate Runtime Exception
> >>> 11:51:39.145 - 45:
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.replyToClient:
> >>> WARNING:
> >>> org.apache.uima.aae.error.AsynchAEException:
> >>> org.apache.uima.UIMARuntimeException
> >>> at
> >>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.
> getSerializedCas(JmsOutputChannel.java:1265)
> >>> at
> >>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.
> sendReply(JmsOutputChannel.java:800)
> >>> at
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.
> sendReplyToRemoteClient(AggregateAnalysisEngineController_impl.java:2173)
> >>> at
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.replyToClient(AggregateAnalysisEngineController_impl.java:2342)
> >>> at
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.finalStep(AggregateAnalysisEngineController_impl.java:1862)
> >>> at
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.executeFlowStep(AggregateAnalysisEngineController_impl.java:2489)
> >>> at
> >>> org.apache.uima.aae.controller.AggregateAnalysisEngineControl
> ler_impl.process(AggregateAnalysisEngineController_impl.java:1271)
> >>> at
> >>> org.apache.uima.aae.handler.HandlerBase.invokeProcess(
> HandlerBase.java:118)
> >>> at
> >>> org.apache.uima.aae.handler.input.ProcessResponseHandler.
> cancelTimerAndProcess(ProcessResponseHandler.java:117)
> >>> at
> >>> org.apache.uima.aae.handler.input.ProcessResponseHandler.
> 

Re: Many views in the cas to serialize cause java.lang.NullPointerException in service uima-as

[nelson rivera]

Hi,  The first thing I did was these tests,i made a simple test case
that create a Cas with 17 views and then serialize using
XmiCasSerializer.serialize(newJCas.getCas(), fis) and serializes
correctly.
Also i made other test, initialize the same AE but of local way with
UIMA API and process the same input documents and the processing is
correct and then serialize the CAS, without problem.

The error is with AE deployed in uima-as and consuming it.

2017-02-09 17:30 GMT-05:00, Marshall Schor :
> one thing that would help track this down is a small isolated test case.
>
> Do you think uima-as is needed? I'm wondering if a simple test case which
> generated 17 views and then tried to serialize would show the failure...
>
> If you could supply a small test case that showed the failure so we could
> reproduce it, that would enable a rapid resolution.
>
> -Marshall
>
>
> On 2/9/2017 3:58 PM, Marshall Schor wrote:
>>  The line throwing the null pointer exception is :
>>
>> cas.getView(sofaNum).getSofaRef()
>>
>> So the NPE is either the cas is null, or the getView(sofaNum) is returning
>> null.
>>
>> I'm not sure what the best way is to debug this...
>>
>> -Marshall
>>
>>
>>
>>
>> On 2/9/2017 12:42 PM, nelson rivera wrote:
>>> I have a aggregate service uima-as, at the end of aggregate the cas to
>>> return is composed of as many views as the number of input files, each
>>> view with annotations of processing.
>>> With a number of input documents less than 15 the processing is
>>> successful always,
>>> but if the number of documents is greater than 15, i get a
>>> NullPointerException at the aggregate service trying to serialize the
>>> cas, not in the processing of AE aggregate.
>>> the logs of aggregate service:
>>>
>>> 11:51:38.815 - 42:
>>> cu.datys.xinetica.uima.core.MergerInViewCasMultipler.hasNext(285):
>>> INFO: HasNext false
>>> 11:51:38.875 - 44:
>>> org.apache.uima.uimacpp.UimacppAnalysisComponent.log(396): INFO: :
>>> XClusterAnalyzer::process --- OK
>>> 11:51:39.145 - 45:
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.replyToClient:
>>> WARNING: Service: XClusterAnalyzerAggregate Runtime Exception
>>> 11:51:39.145 - 45:
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.replyToClient:
>>> WARNING:
>>> org.apache.uima.aae.error.AsynchAEException:
>>> org.apache.uima.UIMARuntimeException
>>> at
>>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.getSerializedCas(JmsOutputChannel.java:1265)
>>> at
>>> org.apache.uima.adapter.jms.activemq.JmsOutputChannel.sendReply(JmsOutputChannel.java:800)
>>> at
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.sendReplyToRemoteClient(AggregateAnalysisEngineController_impl.java:2173)
>>> at
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.replyToClient(AggregateAnalysisEngineController_impl.java:2342)
>>> at
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.finalStep(AggregateAnalysisEngineController_impl.java:1862)
>>> at
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.executeFlowStep(AggregateAnalysisEngineController_impl.java:2489)
>>> at
>>> org.apache.uima.aae.controller.AggregateAnalysisEngineController_impl.process(AggregateAnalysisEngineController_impl.java:1271)
>>> at
>>> org.apache.uima.aae.handler.HandlerBase.invokeProcess(HandlerBase.java:118)
>>> at
>>> org.apache.uima.aae.handler.input.ProcessResponseHandler.cancelTimerAndProcess(ProcessResponseHandler.java:117)
>>> at
>>> org.apache.uima.aae.handler.input.ProcessResponseHandler.handleProcessResponseWithCASReference(ProcessResponseHandler.java:485)
>>> at
>>> org.apache.uima.aae.handler.input.ProcessResponseHandler.handle(ProcessResponseHandler.java:767)
>>> at
>>> org.apache.uima.aae.handler.HandlerBase.delegate(HandlerBase.java:149)
>>> at
>>> org.apache.uima.aae.handler.input.ProcessRequestHandler_impl.handle(ProcessRequestHandler_impl.java:1113)
>>> at
>>> org.apache.uima.aae.spi.transport.vm.UimaVmMessageListener.onMessage(UimaVmMessageListener.java:107)
>>> at
>>> org.apache.uima.aae.spi.transport.vm.UimaVmMessageDispatcher$1.run(UimaVmMessageDispatcher.java:70)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>> at
>>> org.apache.uima.aae.UimaAsThreadFactory$1.run(UimaAsThreadFactory.java:132)
>>> at java.lang.Thread.run(Thread.java:745)
>>> Caused by: org.apache.uima.UIMARuntimeException
>>> at
>>> org.apache.uima.cas.impl.XmiCasSerializer.serialize(XmiCasSerializer.java:420)
>>> at
>>> org.apache.uima.cas.impl.XmiCasSerializer.serialize(XmiCasSerializer.java:385)
>>> at
>>>