It looks like I had a stuck process or resource that prevented the
pipeline from finishing.
Killing all java processes and re-running solved it.
Thanks!
On Thu, Aug 23, 2018 at 1:49 PM, Gandhi Rajan Natarajan
<gandhi.natara...@arisglobal.com> wrote:
> Hi Ory,
>
> As per the trace you sent, I don’t see any error in that. The processing is
> done actually. Did you checked your output directory after processing?
>
> You can pass the output directory path using the option : " --xmiOut
> {directory_path}"
>
> -----Original Message-----
> From: Ory Henn <o...@trialjectory.com>
> Sent: Thursday, August 23, 2018 3:18 PM
> To: user@ctakes.apache.org
> Subject: runClinicalPipeline gets stuck?
>
> I am trying to run the default Clinical Pipeline, scanning one document of
> ~30 lines.
> When running the same doc through CVD/CPE according to the instructions in
> the cTakes user install guide, the doc is processed in a few seconds.
> When running the bin/runClinicalPipeLine.sh script on an input folder
> containing just this one doc, the process just gets stuck (for over an
> hour) on 100% CPU and does not appear to be doing anything.
> This happens even when I increased -Xmx flag in the script from 3g to 6g.
>
> Can anyone help please?
>
> Log output below. After the last line, nothing else is displayed for over an
> hour.
> I'm running on Ubuntu 18.04, with 16GB RAM.
>
> Log output:
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressAppender] additivity to [false].
> log4j: Level value for ProgressAppender is [INFO].
> log4j: ProgressAppender level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m].
> log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressDone] additivity to [false].
> log4j: Level value for ProgressDone is [INFO].
> log4j: ProgressDone level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m%n].
> log4j: Adding appender named [eolAppender] to category [ProgressDone].
> log4j: Level value for root is [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p
> %c{1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 23 Aug 2018 11:51:29 INFO SentenceDetector - Sentence detector model
> file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 23 Aug 2018 11:51:30 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 23 Aug 2018 11:51:30 INFO ContextDependentTokenizerAnnotator - Finite state
> machines loaded.
> 23 Aug 2018 11:51:30 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 23 Aug 2018 11:51:30 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
> 23 Aug 2018 11:51:31 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type:
> org.apache.ctakes.typesystem.type.textspan.Sentence
> 23 Aug 2018 11:51:31 INFO AbstractJCasTermAnnotator - Exclusion tagset
> loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP
> VBZ WDT WP WPS WRB
> 23 Aug 2018 11:51:31 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
> 23 Aug 2018 11:51:31 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor:
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
> 23 Aug 2018 11:51:31 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
> 23 Aug 2018 11:51:31 INFO UmlsUserApprover - Checking UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user
> trialjectory:
> .......23 Aug 2018 11:51:33 INFO UmlsUserApprover - UMLS Account at
> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user trialjectory has
> been validated
>
> 23 Aug 2018 11:51:33 INFO JdbcConnectionFactory - Connecting to
> jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab:
> 23 Aug 2018 11:51:33 INFO ENGINE - open start - state not modified
> ..............
> 23 Aug 2018 11:51:38 INFO JdbcConnectionFactory - Database connected
> 23 Aug 2018 11:51:38 INFO JdbcRareWordDictionary - Connected to cui and term
> table CUI_TERMS
> 23 Aug 2018 11:51:38 INFO JdbcConceptFactory - Connected to concept table
> TUI with class TUI
> 23 Aug 2018 11:51:38 INFO JdbcConceptFactory - Connected to concept table
> SNOMEDCT_US with class LONG
> 23 Aug 2018 11:51:38 INFO JdbcConceptFactory - Connected to concept table
> PREFTERM with class PREFTERM
> 23 Aug 2018 11:51:38 INFO JdbcConceptFactory - Connected to concept table
> RXNORM with class LONG
> 23 Aug 2018 11:51:38 INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true Loading configuration.
> Loading feature templates.
> Loading lexica.
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> 23 Aug 2018 11:51:45 INFO SentenceDetector - Starting processing.
> 23 Aug 2018 11:51:45 INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 23 Aug 2018 11:51:45 INFO ContextDependentTokenizerAnnotator - process(JCas)
> 23 Aug 2018 11:51:45 INFO POSTagger - process(JCas)
> 23 Aug 2018 11:51:46 INFO Chunker - process(JCas)
> 23 Aug 2018 11:51:46 INFO ChunkAdjuster - process(JCas)
> 23 Aug 2018 11:51:46 INFO ChunkAdjuster - process(JCas)
> 23 Aug 2018 11:51:46 INFO AbstractJCasTermAnnotator - Starting processing
> 23 Aug 2018 11:51:46 INFO AbstractJCasTermAnnotator - Finished processing
> 23 Aug 2018 11:51:46 INFO ClearNLPSemanticRoleLabelerAE - Starting processing
> 23 Aug 2018 11:51:46 INFO ClearNLPSemanticRoleLabelerAE - Finished processing
> 23 Aug 2018 11:51:48 INFO SentenceDetector - Starting processing.
> 23 Aug 2018 11:51:49 INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 23 Aug 2018 11:51:51 INFO ContextDependentTokenizerAnnotator - process(JCas)
> 23 Aug 2018 11:51:53 INFO POSTagger - process(JCas)
> 23 Aug 2018 11:52:01 INFO Chunker - process(JCas)
> 23 Aug 2018 11:52:29 INFO ChunkAdjuster - process(JCas)
> 23 Aug 2018 11:52:29 INFO ChunkAdjuster - process(JCas)
> 23 Aug 2018 11:52:30 INFO AbstractJCasTermAnnotator - Starting processing
> 23 Aug 2018 11:52:33 INFO AbstractJCasTermAnnotator - Finished processing
> 23 Aug 2018 11:52:54 INFO ClearNLPSemanticRoleLabelerAE - Starting processing
> 23 Aug 2018 11:52:57 INFO ClearNLPSemanticRoleLabelerAE - Finished processing
>
> --
>
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