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 <[email protected]>
Sent: Thursday, August 23, 2018 3:18 PM
To: [email protected]
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.
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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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