ducc_ling only switches the default group
Hi everyone, I discovered today that ducc_ling is taking only the default group of the submitter user to switch the group of the process to be launched. I discovered this by chance because a new user, whose group definition is not in the same order as the others, tried to launch some tasks on Ducc. Besides being a restriction which is difficult to discover, this would also limit the the number of groups that we can use to protect our resources to only one. I am not an expert in systems programming, but I found on the web that it is also possible to get and assign a list of groups (getgrouplist/setgroups) to a process. I was wondering if there is any particular reason for not assigning the whole list of groups of the submitter user to the process in ducc_ling? If not, can we expect this feature to be implemented soon? Thanks in advance for your feedback! Erdem Ozcan
Re: uima jcas get annotation type from string
There are a couple of different ways to get a pointer to specific Type object.
jcas.getRequiredType(“mypackage.AnnotationType”);
(cas|jcas).getTypeSystem.getType(“mypackage.AnnotationType”);
The question is what do you want to do with the Type object once you have it.
Thanks,
Thomas Ginter
801-448-7676
thomas.gin...@utah.edu
On Feb 13, 2014, at 6:03 AM, hannes schantl wrote:
> Hi,
>
> Is there a way to get an annotation Type from the cas(or Jcas) from a
> string.
> For example, i am looking for something like that:
> jcas.getCasType("AnnotationName")
>
> greetings Hannes
Re: Error deploying pear on AS 2.4.2
Gotcha. Thanks. :)
On Thu, Feb 13, 2014 at 2:40 PM, Eddie Epstein wrote:
> Using the OpenNLP pear described in the DUCC sample app, this would
> be a UIMA-AS deployment descriptor, Deploy_OpenNLP.xml:
>
>
>xmlns="http://uima.apache.org/resourceSpecifier";>
>
> OpenNLP Text Analyzer
> Deploys OpenNLP text analyzer.
>
>
>
>brokerURL="${defaultBrokerURL}"/>
>
>
>
>
>
>
>
>
> This descriptor assumes it is in the same directory as the pear descriptor
> in the import statement.
> Then, assuming the service is to be deployed from the same directory, that
> UIMA_HOME and PATH have been updated for the UIMA-AS SDK, and a JMS broker
> started with startBroker.sh, the command would be:
>
> UIMA_CLASSPATH=`pwd`/lib deployAsyncService.sh Deploy_OpenNLP.xml
>
>
>
>
> On Wed, Feb 12, 2014 at 3:53 PM, Bai Shen wrote:
>
> > That would explain why it's not working. :) What command should I use to
> > deploy my pear?
> >
> > The documentation talks about merging, packaging, and installing the
> pear,
> > but I can't find any mention about deploying it.
> >
> > Is there a specific section that I should be looking at?
> >
> > Thanks.
> >
> >
> > On Wed, Feb 12, 2014 at 3:09 PM, Eddie Epstein
> > wrote:
> >
> > > A pear is a packed UIMA analysis engine, or AE. UIMA-AS deploys
> services
> > > that contain AEs. The command deployAsyncService requires a UIMA-AS
> > > Deployment Descriptor.
> > >
> > >
> > > On Wed, Feb 12, 2014 at 10:52 AM, Bai Shen
> > > wrote:
> > >
> > > > I'm running the following command to deploy my pear to UIMA-AS 2.4.2.
> > > >
> > > > deployAsyncService.sh test_pear.xml -brokerURL
> tcp://uima-broker:61616
> > > >
> > > > I'm getting the following error.
> > > >
> > > > SEPM0004: When 'standalone' or 'doctype-system' is specified, the
> > > document
> > > > must be
> > > > well-formed; but this document contains a top-level text node
> > > >
> > > > It's a saxon error, but I can't tell what causing it. Any
> suggestions
> > > for
> > > > where to look?
> > > >
> > > > Thanks.
> > > >
> > >
> >
>
Re: Error deploying pear on AS 2.4.2
Using the OpenNLP pear described in the DUCC sample app, this would be a UIMA-AS deployment descriptor, Deploy_OpenNLP.xml: http://uima.apache.org/resourceSpecifier";> OpenNLP Text Analyzer Deploys OpenNLP text analyzer. This descriptor assumes it is in the same directory as the pear descriptor in the import statement. Then, assuming the service is to be deployed from the same directory, that UIMA_HOME and PATH have been updated for the UIMA-AS SDK, and a JMS broker started with startBroker.sh, the command would be: UIMA_CLASSPATH=`pwd`/lib deployAsyncService.sh Deploy_OpenNLP.xml On Wed, Feb 12, 2014 at 3:53 PM, Bai Shen wrote: > That would explain why it's not working. :) What command should I use to > deploy my pear? > > The documentation talks about merging, packaging, and installing the pear, > but I can't find any mention about deploying it. > > Is there a specific section that I should be looking at? > > Thanks. > > > On Wed, Feb 12, 2014 at 3:09 PM, Eddie Epstein > wrote: > > > A pear is a packed UIMA analysis engine, or AE. UIMA-AS deploys services > > that contain AEs. The command deployAsyncService requires a UIMA-AS > > Deployment Descriptor. > > > > > > On Wed, Feb 12, 2014 at 10:52 AM, Bai Shen > > wrote: > > > > > I'm running the following command to deploy my pear to UIMA-AS 2.4.2. > > > > > > deployAsyncService.sh test_pear.xml -brokerURL tcp://uima-broker:61616 > > > > > > I'm getting the following error. > > > > > > SEPM0004: When 'standalone' or 'doctype-system' is specified, the > > document > > > must be > > > well-formed; but this document contains a top-level text node > > > > > > It's a saxon error, but I can't tell what causing it. Any suggestions > > for > > > where to look? > > > > > > Thanks. > > > > > >
Re: uima jcas get annotation type from string
On 2/13/2014 8:13 AM, Peter Klügl wrote:
> maybe something like
>
> cas.getTypeSystem().getType("my.package.AnnotationName")
+1. See the Javadocs for TypeSystem:
http://uima.apache.org/d/uimaj-2.5.0/apidocs/org/apache/uima/cas/TypeSystem.html
-Marshall
>
> Best,
>
> Peter
>
> Am 13.02.2014 14:03, schrieb hannes schantl:
>> Hi,
>>
>> Is there a way to get an annotation Type from the cas(or Jcas) from a
>> string.
>> For example, i am looking for something like that:
>> jcas.getCasType("AnnotationName")
>>
>> greetings Hannes
>>
>
Re: uima jcas get annotation type from string
maybe something like
cas.getTypeSystem().getType("my.package.AnnotationName")
Best,
Peter
Am 13.02.2014 14:03, schrieb hannes schantl:
> Hi,
>
> Is there a way to get an annotation Type from the cas(or Jcas) from a
> string.
> For example, i am looking for something like that:
> jcas.getCasType("AnnotationName")
>
> greetings Hannes
>
uima jcas get annotation type from string
Hi,
Is there a way to get an annotation Type from the cas(or Jcas) from a
string.
For example, i am looking for something like that:
jcas.getCasType("AnnotationName")
greetings Hannes
Re: Ruta - Text Ruler - NullPointerException with the example project
Hello Peter I confirm that your procedure makes it works ! Thank you On Thu, Feb 13, 2014 at 11:10 AM, Peter Klügl wrote: > Hi, > > the nasty thing I did was not to include the descriptors for the scripts > in svn. > > I will add a comment in the documentation and will improve the TextRuler > view to report the problem to the user. > > Best, > > Peter > > Am 13.02.2014 10:49, schrieb Peter Klügl: > > Hi, > > > > Am 12.02.2014 23:57, schrieb Nicolas Hernandez: > >> Hi everyone, > >> > >> I'm testing the TextRuler framework to induce annotation rules. In > >> particular I follow the example in the documentation [1] which should > works > >> on the example project present in the svn repository [2]. > >> > >> Unfortunately, when I press the start button, the view freezes on > >> "MethodPreprocessing..." and that's all. In the console, when I launch > >> Eclipse in command line I can read the following trace exception [3]. > >> > >> The same for all the learning algorithms. > >> I use Eclipse Kepler. There is no eclipse update available for the > plugins. > >> The java version is "1.7.0_51" OpenJDK. > >> > >> If anyone (Peter ;-) has a clue ? > > I just tested it. It works, but I had to regenerate the descriptors. > > > > Can you please update the TextRulerExample project (right click on > > project, popup menu->UIMA Ruta-> Update Project) and then clean the > > project in order to create the descriptors again (Menu->Project-> Clean: > > Select TextRulerExample). Best, clean it twice ;-) > > > > Peter > > > > > >> /Nicolas > >> > >> [1] > >> > https://uima.apache.org/d/ruta-current/tools.ruta.book.html#section.tools.ruta.workbench.textruler.example > >> > >> [2] > >> > https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/TextRulerExample/ > >> > >> [3] Trace > >> $ eclipse > >> uima.ruta.example.Author > >> uima.ruta.example.Date > >> uima.ruta.example.Pages > >> uima.ruta.example.Publisher > >> uima.ruta.example.Institution > >> uima.ruta.example.Volume > >> uima.ruta.example.Editor > >> uima.ruta.example.Title > >> uima.ruta.example.Booktitle > >> uima.ruta.example.Note > >> uima.ruta.example.Journal > >> uima.ruta.example.Location > >> uima.ruta.example.Tech > >> Exception in thread "Thread-7" java.lang.NullPointerException > >> at > >> > org.apache.uima.ruta.textruler.core.TextRulerToolkit.addBoundaryTypes(TextRulerToolkit.java:154) > >> at > >> > org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:58) > >> at > >> > org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:44) > >> at > >> > org.apache.uima.ruta.textruler.extension.TextRulerController$1.run(TextRulerController.java:174) > >> at java.lang.Thread.run(Thread.java:744) > >> > > -- Dr. Nicolas Hernandez Associate Professor (Maître de Conférences) Université de Nantes - LINA CNRS UMR 6241 http://enicolashernandez.blogspot.com http://www.univ-nantes.fr/hernandez-n +33 (0)2 51 12 53 94 +33 (0)2 40 30 60 67
Re: uima-as 2.3.1 - java.io.IOException: Frame size of 147 MB larger than max allowed 100 MB
I don't know why it doesn't work because I have explicitly set the brokerUrl to
the deployment descriptors, ran the UIMA_Service with argument
-defaultBrokerURL and set also the system property -DdefaultBrokerURL. All were
set with value:
tcp://127.0.0.1:61616?wireFormat.maxInactivityDuration=0&wireFormat.maxFrameSize=209715200&jms.useCompression=true.
The pipeline has the following components: one main aggregate with a remote RDF
Consumer and one remote aggregate. The remote aggregate has one remote
primitive annotator and one local primitive annotator.
I don't know exactly how many connections are created for the services to
communicate with each other but in the log file of each of the components I
noticed that there is ONLY ONE connection which is built with default frame
size of 100 MB instead of 200 MB as the others.
In the aggregators I see a line like the following:
02/13/2014 05:36:37.081 [DEBUG] [main]
org.apache.activemq.transport.WireFormatNegotiator - Sending: WireFormatInfo {
version=9, properties={MaxFrameSize=104857600, CacheSize=1024,
CacheEnabled=true, SizePrefixDisabled=false,
MaxInactivityDurationInitalDelay=1, TcpNoDelayEnabled=true,
MaxInactivityDuration=0, TightEncodingEnabled=true, StackTraceEnabled=true},
magic=[A,c,t,i,v,e,M,Q]}
02/13/2014 05:36:37.082 [TRACE] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616] org.apache.activemq.transport.tcp.TcpTransport
- TCP consumer thread for tcp://localhost/127.0.0.1:61616 starting
02/13/2014 05:36:37.083 [DEBUG] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616]
org.apache.activemq.transport.InactivityMonitor - Using min of local:
WireFormatInfo { version=9, properties={MaxFrameSize=104857600, CacheSize=1024,
CacheEnabled=true, SizePrefixDisabled=false,
MaxInactivityDurationInitalDelay=1, TcpNoDelayEnabled=true,
MaxInactivityDuration=0, TightEncodingEnabled=true, StackTraceEnabled=true},
magic=[A,c,t,i,v,e,M,Q]} and remote: WireFormatInfo { version=9,
properties={CacheSize=1024, MaxFrameSize=209715200, CacheEnabled=true,
SizePrefixDisabled=false, TcpNoDelayEnabled=true,
MaxInactivityDurationInitalDelay=1, MaxInactivityDuration=0,
TightEncodingEnabled=true, StackTraceEnabled=true}, magic=[A,c,t,i,v,e,M,Q]}
02/13/2014 05:36:37.083 [DEBUG] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616]
org.apache.activemq.transport.WireFormatNegotiator - Received WireFormat:
WireFormatInfo { version=9, properties={CacheSize=1024, MaxFrameSize=209715200,
CacheEnabled=true, SizePrefixDisabled=false, TcpNoDelayEnabled=true,
MaxInactivityDurationInitalDelay=1, MaxInactivityDuration=0,
TightEncodingEnabled=true, StackTraceEnabled=true}, magic=[A,c,t,i,v,e,M,Q]}
02/13/2014 05:36:37.083 [DEBUG] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616]
org.apache.activemq.transport.WireFormatNegotiator -
tcp://localhost/127.0.0.1:61616 before negotiation: OpenWireFormat{version=9,
cacheEnabled=false, stackTraceEnabled=false, tightEncodingEnabled=false,
sizePrefixDisabled=false, maxFrameSize=104857600}
02/13/2014 05:36:37.083 [DEBUG] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616]
org.apache.activemq.transport.WireFormatNegotiator -
tcp://localhost/127.0.0.1:61616 after negotiation: OpenWireFormat{version=9,
cacheEnabled=true, stackTraceEnabled=true, tightEncodingEnabled=true,
sizePrefixDisabled=false, maxFrameSize=104857600}
and in the primitive annotator I see the following:
02/13/2014 05:36:37.122 [DEBUG]
[primitive_input_msgLsnrCntnr_TokenizerQueue_1_getMeta - Thread - 18]
org.apache.uima.adapter.jms.activemq.UimaDefaultMessageListenerContainer -
Received message of type [class
org.apache.activemq.command.ActiveMQTextMessage] from consumer
[ActiveMQMessageConsumer { value=ID:PCCS000630WS-56652-1392287793445-1:2:1:1,
started=true }] of session [ActiveMQSession
{id=ID:PCCS000630WS-56652-1392287793445-1:2:1,started=true}]
02/13/2014 05:36:37.143
[DEBUG][primitive_input_msgLsnrCntnr_TokenizerQueue_1_getMeta - Thread - 18]
org.apache.activemq.transport.WireFormatNegotiator - Sending: WireFormatInfo {
version=9, properties={MaxFrameSize=104857600, CacheSize=1024,
CacheEnabled=true, SizePrefixDisabled=false,
MaxInactivityDurationInitalDelay=1, TcpNoDelayEnabled=true,
MaxInactivityDuration=0, TightEncodingEnabled=true, StackTraceEnabled=true},
magic=[A,c,t,i,v,e,M,Q]}
02/13/2014 05:36:37.146 [TRACE] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616] org.apache.activemq.transport.tcp.TcpTransport
- TCP consumer thread for tcp://localhost/127.0.0.1:61616 starting
02/13/2014 05:36:37.146 [DEBUG] [ActiveMQ Transport:
tcp://localhost/127.0.0.1:61616]
org.apache.activemq.transport.InactivityMonitor - Using min of local:
WireFormatInfo { version=9, properties={MaxFrameSize=104857600, CacheSize=1024,
CacheEnabled=true, SizePrefixDisabled=false,
MaxInactivityDurationInitalDelay=1, TcpNoDelayEnabled=true,
MaxInactivityDuration=0, TightEncodingEnabled=true, StackTraceEn
Re: Ruta - Text Ruler - NullPointerException with the example project
Hi, the nasty thing I did was not to include the descriptors for the scripts in svn. I will add a comment in the documentation and will improve the TextRuler view to report the problem to the user. Best, Peter Am 13.02.2014 10:49, schrieb Peter Klügl: > Hi, > > Am 12.02.2014 23:57, schrieb Nicolas Hernandez: >> Hi everyone, >> >> I'm testing the TextRuler framework to induce annotation rules. In >> particular I follow the example in the documentation [1] which should works >> on the example project present in the svn repository [2]. >> >> Unfortunately, when I press the start button, the view freezes on >> "MethodPreprocessing..." and that's all. In the console, when I launch >> Eclipse in command line I can read the following trace exception [3]. >> >> The same for all the learning algorithms. >> I use Eclipse Kepler. There is no eclipse update available for the plugins. >> The java version is "1.7.0_51" OpenJDK. >> >> If anyone (Peter ;-) has a clue ? > I just tested it. It works, but I had to regenerate the descriptors. > > Can you please update the TextRulerExample project (right click on > project, popup menu->UIMA Ruta-> Update Project) and then clean the > project in order to create the descriptors again (Menu->Project-> Clean: > Select TextRulerExample). Best, clean it twice ;-) > > Peter > > >> /Nicolas >> >> [1] >> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#section.tools.ruta.workbench.textruler.example >> >> [2] >> https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/TextRulerExample/ >> >> [3] Trace >> $ eclipse >> uima.ruta.example.Author >> uima.ruta.example.Date >> uima.ruta.example.Pages >> uima.ruta.example.Publisher >> uima.ruta.example.Institution >> uima.ruta.example.Volume >> uima.ruta.example.Editor >> uima.ruta.example.Title >> uima.ruta.example.Booktitle >> uima.ruta.example.Note >> uima.ruta.example.Journal >> uima.ruta.example.Location >> uima.ruta.example.Tech >> Exception in thread "Thread-7" java.lang.NullPointerException >> at >> org.apache.uima.ruta.textruler.core.TextRulerToolkit.addBoundaryTypes(TextRulerToolkit.java:154) >> at >> org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:58) >> at >> org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:44) >> at >> org.apache.uima.ruta.textruler.extension.TextRulerController$1.run(TextRulerController.java:174) >> at java.lang.Thread.run(Thread.java:744) >>
Re: Ruta - Text Ruler - NullPointerException with the example project
Hi, Am 12.02.2014 23:57, schrieb Nicolas Hernandez: > Hi everyone, > > I'm testing the TextRuler framework to induce annotation rules. In > particular I follow the example in the documentation [1] which should works > on the example project present in the svn repository [2]. > > Unfortunately, when I press the start button, the view freezes on > "MethodPreprocessing..." and that's all. In the console, when I launch > Eclipse in command line I can read the following trace exception [3]. > > The same for all the learning algorithms. > I use Eclipse Kepler. There is no eclipse update available for the plugins. > The java version is "1.7.0_51" OpenJDK. > > If anyone (Peter ;-) has a clue ? I just tested it. It works, but I had to regenerate the descriptors. Can you please update the TextRulerExample project (right click on project, popup menu->UIMA Ruta-> Update Project) and then clean the project in order to create the descriptors again (Menu->Project-> Clean: Select TextRulerExample). Best, clean it twice ;-) Peter > /Nicolas > > [1] > https://uima.apache.org/d/ruta-current/tools.ruta.book.html#section.tools.ruta.workbench.textruler.example > > [2] > https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/TextRulerExample/ > > [3] Trace > $ eclipse > uima.ruta.example.Author > uima.ruta.example.Date > uima.ruta.example.Pages > uima.ruta.example.Publisher > uima.ruta.example.Institution > uima.ruta.example.Volume > uima.ruta.example.Editor > uima.ruta.example.Title > uima.ruta.example.Booktitle > uima.ruta.example.Note > uima.ruta.example.Journal > uima.ruta.example.Location > uima.ruta.example.Tech > Exception in thread "Thread-7" java.lang.NullPointerException > at > org.apache.uima.ruta.textruler.core.TextRulerToolkit.addBoundaryTypes(TextRulerToolkit.java:154) > at > org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:58) > at > org.apache.uima.ruta.textruler.extension.TextRulerPreprocessor.run(TextRulerPreprocessor.java:44) > at > org.apache.uima.ruta.textruler.extension.TextRulerController$1.run(TextRulerController.java:174) > at java.lang.Thread.run(Thread.java:744) >
