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
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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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