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From David Fox <David....@humedica.com>
Subject Re: NullPointerException when RunRemoteAsyncAE tries to unload (UIMA AS and UIMA C++)
Date Fri, 23 Sep 2016 13:41:03 GMT
I was able to install that, and I’m not getting the NullPointerException.
The example annotator still runs successfully, but now I get
---------------------------------------------------------------------------

Attempting to deploy descriptors/Deploy_MeetingAnnotator.xml ...
Waiting for Uima C++ service to connect...
Waiting for Uima C++ service to connect...
Waiting for Uima C++ service to report init status...
deployCppService.cpp91 Start receiving messages

Startinging GetMetaData instance

Starting Annotator instance 0

deployCppService.cpp UIMA C++ Service MeetingAnnotator at
tcp://localhost:61616 Ready to process...

Uima C++ service at MeetingAnnotator Ready to process...
UIMA AS Service Initialization Complete
........Completed 8 documents; 17165 characters
Time Elapsed : 3705 ms
0 8 apr_socket_recv command=SHUTDOWN

deployCppService.cpp Shutdown started.

Stopping GetMetaData instance

Stopping Annotator instance 0

deployCppService.cpp Shutdown done.

UimacppServiceManagement service reports shutdown DONE
UimacppShutdownHook sending quiesce message
java.net.SocketException: Socket is closed
        at java.net.Socket.getInputStream(Socket.java:903)
        at 
org.apache.uima.aae.controller.UimacppServiceManagement.quiesceAndStop(Uima
cppServiceManagement.java:88)
        at 
org.apache.uima.aae.controller.UimacppServiceManagement.quiesceAndShutdown(
UimacppServiceManagement.java:397)
        at 
org.apache.uima.aae.controller.UimacppShutdownHook.run(UimacppServiceContro
ller.java:1105)
UimacppShutdownHook destroy C++ process

―――――

I’ve attached the uima.log

On 9/22/16, 3:54 PM, "Jaroslaw Cwiklik" <uimaee@gmail.com> wrote:

>David, I've deployed uima-as 2.9.0-SNAPSHOT here:
>
>https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apache.org
>_content_repositories_snapshots_org_apache_uima_uima-2Das_2.9.0-2DSNAPSHOT
>_&d=DQIFaQ&c=3XrKki35ZWuh8X2qbeRISQ&r=BYS7q6K6Famz8NiMJzvOgYA-WQSvBt9z6TEb
>aT3nnNM&m=NnQy2jfAk4Dyg-uijgdjHHbg6pxfdvwDkCn3166fVc8&s=y7GSTfzyEzhkYgFGy1
>vLLmDJ82il_hzMP7Y4LQjuBPg&e=
>
>there is a binary tarball (tar.gz) in there.
>
>This is a trunk level uima-as code for the upcoming 2.9.0 uima-as release.
>It has not been thoroughly
>tested or vetted yet.  It has some fixes and improvements since 2.8.1. It
>includes a new AMQ broker
>version 5.14.0. It also has a fix for the problem you've reported.
>
>-jerry
>
>
>On Thu, Sep 22, 2016 at 3:15 PM, Jaroslaw Cwiklik <uimaee@gmail.com>
>wrote:
>
>> Another possibility is to deploy a snapshot in a public maven repo.
>> Hopefully you can get the binary tarball
>> onto your machines somehow. I will to do that know and let you know
>>where
>> to get this.
>>
>> -jerry
>>
>> On Thu, Sep 22, 2016 at 3:01 PM, David Fox <David.Fox@humedica.com>
>>wrote:
>>
>>> Building from svn on our linux machines is a bit tricky, because they
>>>are
>>> cut off from the internet by a firewall, and maven install wants
>>>internet
>>> access to download dependencies.  It looks like there are workarounds
>>>for
>>> that
>>> 
>>>(https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_q
>>>uestions_7233328_how-2Ddo-2Di-2Dconfigu&d=DQIFaQ&c=3XrKki35ZWuh8X2qbeRIS
>>>Q&r=BYS7q6K6Famz8NiMJzvOgYA-WQSvBt9z6TEbaT3nnNM&m=NnQy2jfAk4Dyg-uijgdjHH
>>>bg6pxfdvwDkCn3166fVc8&s=sk4NjHKmY1SCj4WAEH0A59C50xulbEthh1b5K5egbv0&e=
>>> re-maven-for-of
>>> fline-development
>>> 
>>><https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_q
>>>uestions_7233328_how-2Ddo-2Di-2Dconfigure-2Dmaven-2Dfor-2Doffline-2Ddeve
>>>lopment&d=DQIFaQ&c=3XrKki35ZWuh8X2qbeRISQ&r=BYS7q6K6Famz8NiMJzvOgYA-WQSv
>>>Bt9z6TEbaT3nnNM&m=NnQy2jfAk4Dyg-uijgdjHHbg6pxfdvwDkCn3166fVc8&s=pMHCokJs
>>>jTNk_XvWxddISyww6QBt65VZmeVGKLTLK94&e= >
>>> suggests Artifactory), but it may take a day or two
>>> before I can get everything set up.
>>>
>>> I could build it on my dev machine (OS X), but with the binary
>>>install, I
>>> wasn’t able to get the sample UIMA C++ code to build on Mac OS X.  (My
>>> eventual plan is to get linux on my dev machine via virtual box, but
>>>that
>>> means more software to install…)
>>>
>>> So anyway, I’ll try to get this working so I can build from svn before
>>>the
>>> fix, reproduce the problem, and then update and verify the fix.
>>>
>>> Thanks,
>>> David
>>>
>>> On 9/22/16, 1:23 PM, "Jaroslaw Cwiklik" <uimaee@gmail.com> wrote:
>>>
>>> >I think I see the bug. Do you know how to build uima-as from svn?
>>> >
>>> >https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.
>>> apache.org_build
>>> >ing-2Duima.html&d=DQIFaQ&c=3XrKki35ZWuh8X2qbeRISQ&r=BYS7q6K
>>> 6Famz8NiMJzvOgY
>>> >A-WQSvBt9z6TEbaT3nnNM&m=9Hf7csP-1jIlxx_vgB3QA47yh0w3i1-
>>> XbVER8KQmhT8&s=Gin5
>>> >am-lATmbl6WQFmZrKwjxKa3tiL1qz1ykFh0cdWI&e=
>>> >
>>> >I will fix this shortly in the svn trunk. The next release of uima-as
>>> >(2.9.0) is in the
>>> >works. I will get a release candidate out hopefully next week.
>>> >
>>> >-jerry
>>> >
>>> >On Thu, Sep 22, 2016 at 12:08 PM, David Fox <David.Fox@humedica.com>
>>> >wrote:
>>> >
>>> >> Thanks for the quick response
>>> >>
>>> >> Yes, it occurs every time, at the same line in RunRemoteAsyncAE and
>>> >> org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_
>>> >> impl.undeploy(BaseUIMAAsynchronousEngine_impl.java:964)
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> On 9/22/16, 11:15 AM, "Jaroslaw Cwiklik" <uimaee@gmail.com> wrote:
>>> >>
>>> >> >This warning
>>> >> >
>>> >> >WARN  Transport                      - Transport Connection to:
>>>tcp://
>>> >> >127.0.0.1:56261 failed: java.io.EOFException
>>> >> >
>>> >> >is from brokers log or console I suspect. It just means that the
>>> broker
>>> >> >lost a connection to a client. Looks like the client
>>> >> >went away without closing a connection. This is probably a
>>>side-effect
>>> >>of
>>> >> >NPE.
>>> >> >
>>> >> >Is the NPE repeatable? Does it happen each time you run this test?
>>> >>Looking
>>> >> >for a hint if there is a race
>>> >> >condition in the UIMA-AS code.
>>> >> >
>>> >> >
>>> >> >
>>> >> >On Thu, Sep 22, 2016 at 10:54 AM, David Fox
>>><David.Fox@humedica.com>
>>> >> >wrote:
>>> >> >
>>> >> >> I¹m using the UIMA C++ framework 2.4.0 (32-bit) on linux (CentOS
>>> >>6.5),
>>> >> >>and
>>> >> >> following the instructions
>>> >> >>https://urldefense.proofpoint.com/v2/url?u=https-
>>> >> 3A__uima.apache.org_d_&d
>>> >> >>=DQIFaQ&c=3XrKki35ZWuh8X2qbeRISQ&r=BYS7q6K6Famz8NiMJzvOgYA-
>>> >> WQSvBt9z6TEbaT
>>> >> >>3nnNM&m=dFZSJENJkyCDLeCQuBn89fBrTrsdKh4RIWwwPV7r0o8&s=CaIoLZ_7Je-
>>> >> TYsr0ZIP
>>> >> >>xs98mHRestzC4RtgVSp7kJaY&e=
>>> >> >> uimacpp-2.4.0/docs/overview_and_setup.html.  I¹ve successfully
>>> built
>>> >> >> DaveDetector and run it with the standalone C++ pipeline
>>>(runAECpp)
>>> >>and
>>> >> >> within a Java pipeline via JNI.  I¹ve now installed UIMA AS
>>>2.8.1 so
>>> >>I
>>> >> >>can
>>> >> >> follow the instructions under 2.3 Testing Interoperability
with
>>>UIMA
>>> >>AS
>>> >> >>
>>> >> >>
>>> >> >> cd $UIMACPP_HOME/examples/tutorial
>>> >> >> runRemoteAsyncAE.sh tcp://localhost:61616 MeetingAnnotator
\
>>> >> >> -d descriptors/Deploy_MeetingAnnotator.xml
>>> >> >>
>>> >> >>
>>> >> >> I get a NullPointerException and a transport warning about
a
>>> >> >> java.io.EOFException
>>> >> >>
>>> >> >>
>>> >> >> runRemoteAsyncAE.sh tcp://localhost:61616 MeetingAnnotator
-d
>>> >> >> descriptors/Deploy_MeetingAnnotator.xml -o `pwd`/out
>>> >> >>
>>> >> >> Attempting to deploy descriptors/Deploy_MeetingAnnotator.xml
...
>>> >> >>
>>> >> >> Waiting for Uima C++ service to connect...
>>> >> >>
>>> >> >> Waiting for Uima C++ service to connect...
>>> >> >>
>>> >> >> Waiting for Uima C++ service to report init status...
>>> >> >>
>>> >> >> deployCppService.cpp91 Start receiving messages
>>> >> >>
>>> >> >>
>>> >> >> Startinging GetMetaData instance
>>> >> >>
>>> >> >>
>>> >> >> Starting Annotator instance 0
>>> >> >>
>>> >> >>
>>> >> >> deployCppService.cpp UIMA C++ Service MeetingAnnotator at
>>> >> >> tcp://localhost:61616 Ready to process...
>>> >> >>
>>> >> >>
>>> >> >> Uima C++ service at MeetingAnnotator Ready to process...
>>> >> >>
>>> >> >> UIMA AS Service Initialization Complete
>>> >> >>
>>> >> >> .Completed 1 documents
>>> >> >>
>>> >> >> Time Elapsed : 2184 ms
>>> >> >>
>>> >> >> java.lang.NullPointerException
>>> >> >>
>>> >> >>         at
>>> >> >>org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_
>>> >> >> impl.undeploy(BaseUIMAAsynchronousEngine_impl.java:964)
>>> >> >>
>>> >> >>         at
>>> >> >>org.apache.uima.adapter.jms.client.BaseUIMAAsynchronousEngine_
>>> >> >> impl.undeploy(BaseUIMAAsynchronousEngine_impl.java:906)
>>> >> >>
>>> >> >>         at org.apache.uima.examples.as.RunRemoteAsyncAE.run(
>>> >> >> RunRemoteAsyncAE.java:260)
>>> >> >>
>>> >> >>         at org.apache.uima.examples.as.RunRemoteAsyncAE.main(
>>> >> >> RunRemoteAsyncAE.java:314)
>>> >> >>
>>> >> >>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>> >>Method)
>>> >> >>
>>> >> >>         at sun.reflect.NativeMethodAccessorImpl.invoke(
>>> >> >> NativeMethodAccessorImpl.java:62)
>>> >> >>
>>> >> >>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(
>>> >> >> DelegatingMethodAccessorImpl.java:43)
>>> >> >>
>>> >> >>         at java.lang.reflect.Method.invoke(Method.java:497)
>>> >> >>
>>> >> >>         at org.apache.uima.bootstrap.UimaBootstrap.main(
>>> >> >> UimaBootstrap.java:87)
>>> >> >>
>>> >> >> WARN  Transport                      - Transport Connection
to:
>>> >>tcp://
>>> >> >> 127.0.0.1:56221 failed: java.io.EOFException
>>> >> >>
>>> >> >> I'm
>>> >> >> I can also run with a collection reader:
>>> >> >>
>>> >> >>
>>> >> >> runRemoteAsyncAE.sh tcp://localhost:61616 MeetingAnnotator
-d
>>> >> >> descriptors/Deploy_MeetingAnnotator.xml -o `pwd`/out -c
>>> >> >> /misc/NLP/dfox/scratch/uima/apache-uima-as-2.8.1/examples/
>>> >> >> descriptors/collection_reader/FileSystemCollectionReader.mine.xml
>>> >> >>
>>> >> >> (where the modified collection reader points to
>>> >> >>$UIMA_HOME/examples/data)
>>> >> >> in which case I get ³Completed 8 documents², and xmi output
for
>>>each
>>> >>in
>>> >> >>the
>>> >> >> out/ directory, but still get the same exception and warning.
>>>Based
>>> >>on
>>> >> >> that (plus looking at the RunRemoteAsyncAE java source), it
looks
>>> >>like
>>> >> >>my
>>> >> >> analysis engine is running fine, but then hitting some problem
>>>when
>>> >> >> RunRemoteAsyncAE tries to undeploy the C++ annotator.
>>> >> >>
>>> >> >> I¹m trying to figure out if this is something I should worry
>>>about
>>> >> >> (especially if it reflects a problem with running UIMA C++
2.4
>>>and
>>> >>UIMA
>>> >> >>AS
>>> >> >> 2.8.1), or if it is normal or harmless.
>>> >> >>
>>> >> >> When I run the similar test with one of the Java-only UIMA
AS
>>> >>samples:
>>> >> >>
>>> >> >>
>>> >> >> runRemoteAsyncAE.sh tcp://localhost:61616
>>>MeetingDetectorTaeQueue -d
>>> >> >> deploy/as/Deploy_MeetingDetectorTAE.xml -c
>>> >> >>descriptors/collection_reader/
>>> >> >> FileSystemCollectionReader.mine.xml
>>> >> >>
>>> >> >> I still get the transport warning
>>> >> >>
>>> >> >>
>>> >> >> WARN  Transport                      - Transport Connection
to:
>>> >>tcp://
>>> >> >> 127.0.0.1:56261 failed: java.io.EOFException
>>> >> >>
>>> >> >> but not the NullPointerException
>>> >> >>
>>> >> >> Thanks,
>>> >> >> David
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >>
>>> >>
>>>
>>>
>>

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