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From Yi-Wen Liu <yiwen...@usc.edu>
Subject Re: run fails but has output
Date Tue, 17 Nov 2015 23:07:48 GMT
Hi,

I run both, remotely and locally, and no errors from logs.
2015.11.17 14:47:17 Tue Received
2015.11.17 14:47:17 Tue WaitingForResources
2015.11.17 14:47:22 Tue Initializing
2015.11.17 14:47:22 Tue Running
2015.11.17 14:48:18 Tue Completing
2015.11.17 14:48:18 Tue Completed
2015.11.17 14:48:18 Tue completion type: ProgramExit
2015.11.17 14:48:18 Tue rationale: code=1

However I didn't get any output.
If run without all in one there's output, it is quite confusing..

Thanks,
Yi-Wen

On Tue, Nov 17, 2015 at 3:04 PM, Lou DeGenaro <lou.degenaro@gmail.com>
wrote:

> Yi-Wen,
>
> Oh, I see now you ran all-in-one local.  But that had errors or ran to
> completion successfully?
>
> Lou.
>
> On Tue, Nov 17, 2015 at 5:29 PM, Lou DeGenaro <lou.degenaro@gmail.com>
> wrote:
>
> > Yi-Wen,
> >
> > With respect to the ducc.log, I still saw that the DUCC Job was Running
> > as far as the JD was concerned (as evidenced by the JD's log file).
> > There may be some latency in reflecting this fact back to the
> Orchestrator
> > daemon from the JD.  Note that the Orchestrator writes the ducc.log
> > file.  The ducc.log not showing Running could be the subject of a Jira,
> > but is not of concern with respect to getting your Job to actually run.
> >
> > I'm not sure I understand your statements regarding All-In-One testing.
> > You ran your Job successfully without any error using All-In-One, or that
> > had some issue too?  Did you run All-In-One locally or remotely?
> >
> > Lou.
> >
> > On Tue, Nov 17, 2015 at 5:18 PM, Yi-Wen Liu <yiwenliu@usc.edu> wrote:
> >
> >> Hi,
> >>
> >> The ducc.log didn't show running:
> >> 2015.11.16 23:29:26 Mon Received
> >> 2015.11.16 23:29:26 Mon WaitingForDriver
> >> 2015.11.16 23:29:54 Mon WaitingForResources
> >> 2015.11.16 23:30:04 Mon Assigned
> >> 2015.11.16 23:30:14 Mon Initializing
> >> 2015.11.16 23:34:48 Mon Completing
> >> 2015.11.16 23:35:18 Mon Completed
> >> 2015.11.16 23:35:18 Mon completion type: CanceledByDriver
> >> 2015.11.16 23:35:18 Mon rationale: unspecified
> >>
> >> And I didn't find error in all_in_one local:
> >>
> >> [1] Loading model:
> >>
> >> [1] ...
> >>
> >> [1] Loading model:
> >>
> >> [1] .
> >>
> >> [1] Loading configuration.
> >>
> >> [1] Loading feature templates.
> >>
> >> [1] Loading lexica.
> >>
> >> [1] Loading model:
> >>
> >> [1] ................................
> >>
> >> [1] Loading model:
> >>
> >> [1] .............................
> >>
> >> [1] 17 Nov 2015 13:49:33  INFO Chunker - Chunker model file:
> >> org/apache/ctakes/chunker/models/chunker-model.zip
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
> >> established to:
> >> jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
> >> established to:
> >> jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO JdbcConnectionResourceImpl - Connection
> >> established to:
> >>
> >>
> jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO UmlsDictionaryLookupAnnotator - Parsing
> >> descriptor:
> >>
> >>
> /Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO FirstTokenPermLookupInitializerImpl -
> >> Exclusion tagset loaded: [dt, to, rp, ls, pos, md, vbd, vbg, vb, ex,
> vbp,
> >> vbn, pdt, vbz, wp, wrb, in, wps, pp$, prp$, wdt, prp, pp, cc, cd]
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO FirstTokenPermLookupInitializerImpl -
> >> Exclusion tagset loaded: [to, dt, rp, ex, vbp, ls, vbn, pdt, wp, vbz,
> wrb,
> >> in, pos, wps, md, wdt, pp$, vbd, vb, vbg, pp, cc, cd]
> >>
> >> [1] 17 Nov 2015 13:49:35  INFO UmlsDictionaryLookupAnnotator - Using
> >> ctakes.umlsaddr: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
> >> yiwenliu
> >>
> >> [1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - Loading NLM Norm
> >> and
> >> Lvg with config file =
> >>
> >>
> /Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> [1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl -   config file
> >> absolute path =
> >>
> >>
> /Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> [1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - cwd =
> >> /Users/ducc/src
> >>
> >> [1] 17 Nov 2015 13:49:39  INFO LvgCmdApiResourceImpl - cd
> >> /Users/ducc/src/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/
> >>
> >> [1] 17 Nov 2015 13:49:40  INFO LvgCmdApiResourceImpl - cd
> /Users/ducc/src
> >>
> >> It looks like it suddenly canceled by driver and no more output on
> screen.
> >> Another log file shows connection refused so I checked driver logs, and
> >> found the three errors in first email.
> >>
> >> Is that error org.xml.sax.SAXParseException; Trying to serialize non-XML
> >> 1.0 character caused by invalid space and characters in Xml, or it's
> more
> >> like syntax error of CR Xml?
> >>
> >> Thanks,
> >> Yi-Wen
> >>
> >> On Tue, Nov 17, 2015 at 1:36 PM, Lou DeGenaro <lou.degenaro@gmail.com>
> >> wrote:
> >>
> >> > Hi Yi-Wen,
> >> >
> >> > Does your CR function correctly outside of DUCC?  Have you tired
> >> debugging
> >> > using DUCC's All-In-One feature as suggested previously by Eddie?
> >> >
> >> > Lou.
> >> >
> >> > On Tue, Nov 17, 2015 at 3:54 PM, Yi-Wen Liu <yiwenliu@usc.edu> wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > I tried to remove redundant white spaces but it doesn't work, and
I
> >> > didn't
> >> > > add any other special characters in CR.
> >> > >
> >> > > Is that error caused by invalid space and characters in Xml, or it's
> >> more
> >> > > like syntax error of CR Xml?
> >> > >
> >> > >
> >> > >
> >> > > Thanks,
> >> > > Yi-Wen
> >> > >
> >> > > > On Nov 17, 2015, at 5:37 AM, Lou DeGenaro <lou.degenaro@gmail.com
> >
> >> > > wrote:
> >> > > >
> >> > > > Yi-Wen,
> >> > > >
> >> > > > The DUCC Job first visits the Initialization state.  This is
when
> >> the
> >> > Job
> >> > > > Driver (JD) initializes your UIMA CollecitonReader (CR). The
CR
> that
> >> > you
> >> > > > specified in your DUCC Job submission is constructed and its
> >> getTotal()
> >> > > > method is invoked to determine the number of work items.  But
I
> >> think
> >> > > your
> >> > > > Job made it past the Initialization state and into the Running
> >> state.
> >> > > > Looking at the log snippits that you posted, I see:
> >> > > >
> >> > > > 16 Nov 2015 23:34:38,353  INFO JobDriver - T[18] advanceJdState
> >> > > > current=Initializing request=Active result=Active
> >> > > >
> >> > > > This means the JD has exited its Initializing state and is now
> >> Active
> >> > and
> >> > > > is fetching work items.  Further evidence is the entry:
> >> > > >
> >> > > > 16 Nov 2015 23:34:39,066 ERROR CasManager - T[17] getMetaCas
> >> > > >
> >> > > > What do the contents of the file ducc.log in your Job's log
> >> directory
> >> > > > show?  You should see "Initializing" followed by "Running".
> >> > > >
> >> > > > It looks like the root cause of your problem is that your CR's
> >> > getNext()
> >> > > is
> >> > > > trying to produce work items for the JD but is failing:
> >> > > >
> >> > > > org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
> >> > > > character: , 0x0
> >> > > >        at
> >> > > org.apache.uima.util.XMLSerializer$CharacterValidatingContentHand
> >> > > > ler.checkForInvalidXmlChars(XMLSerializer.java:254)
> >> > > >
> >> > > > I recommend determining why your CR is broken, fixing, and
> >> > re-submitting
> >> > > > your Job to DUCC.
> >> > > >
> >> > > > Lou.
> >> > > >
> >> > > >> On Tue, Nov 17, 2015 at 2:46 AM, Yi-Wen Liu <yiwenliu@usc.edu>
> >> wrote:
> >> > > >>
> >> > > >> Hello,
> >> > > >>
> >> > > >> I am still stuck in the following error of DUCC and job always
> got
> >> > > canceled
> >> > > >> by driver:
> >> > > >>
> >> > > >> 16 Nov 2015 23:34:38,353  INFO JobDriver - T[18] advanceJdState
> >> > > >> current=Initializing request=Active result=Active
> >> > > >> 16 Nov 2015 23:34:39,066 ERROR ProxyLogger - T[17] loggify
> >> > > >> org.xml.sax.SAXParseException; Trying to serialize non-XML
1.0
> >> > > >> character: , 0x0
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.util.XMLSerializer$CharacterValidatingContentHandler.checkForInvalidXmlChars(XMLSerializer.java:254)
> >> > > >>
> >> > > >> 16 Nov 2015 23:34:39,066 ERROR CasManager - T[17] getMetaCas
> >> > > >> org.apache.uima.ducc.container.common.classloader.ProxyException
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.ducc.container.jd.classload.ProxyJobDriverCollectionReader.getMetaCas(ProxyJobDriverCollectionReader.java:127)
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.ducc.container.jd.cas.CasManager.getMetaCas(CasManager.java:65)
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.ducc.container.jd.fsm.wi.ActionGet.engage(ActionGet.java:118)
> >> > > >>        at
> >> > > >>
> >> org.apache.uima.ducc.container.common.fsm.Fsm.transition(Fsm.java:172)
> >> > > >>
> >> > > >> 16 Nov 2015 23:34:39,068 ERROR ActionGet - T[17] engage
> >> > > >> org.apache.uima.ducc.container.jd.JobDriverException
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.ducc.container.jd.cas.CasManager.getMetaCas(CasManager.java:74)
> >> > > >>        at
> >> > > >>
> >> > >
> >> >
> >>
> org.apache.uima.ducc.container.jd.fsm.wi.ActionGet.engage(ActionGet.java:118)
> >> > > >>
> >> > > >>
> >> > > >> However, when I looked into output directory, there were
output
> >> (much
> >> > > >> omitted from below):
> >> > > >>
> >> > > >> <?xml version="1.0" encoding="UTF-8"?><CAS version="2">
> >> > > >>    <uima.cas.Sofa _indexed="0" _id="1" sofaNum="1"
> >> > sofaID="_InitialView"
> >> > > >> mimeType="text" sofaString="&#13;&#10;Dr.
> >> > > >> Nutritious&#13;&#10;&#13;&#10;Medical Nutrition
Therapy for
> >> > > >> Hyperlipidemia&#13;&#10;&#13;&#10;Referral
from: Julie Tester,
> RD,
> >> LD,
> >> > > >> CNSD&#13;&#10;Phone contact: (555) 555-1212&#13;&#10;Height:
144
> cm
> >> > > >> Current Weight: 45 kg   Date of current weight: 02-29-2001
>  Admit
> >> > > Weight:
> >> > > >> 53 kg   BMI: 18 kg/m2&#13;&#10;Diet: General&#13;&#10;Daily
> Calorie
> >> > > needs
> >> > > >> (kcals): 1500 calories, assessed as HB + 20% for
> >> > > activity.&#13;&#10;Daily
> >> > > >> Protein needs: 40 grams,  assessed as 1.0 g/kg.&#13;&#10;Pt
has
> >> been
> >> > on
> >> > > a
> >> > > >> 3-day calorie count and has had an average intake of 1100
> calories.
> >> > She
> >> > > >> was instructed to drink 2-3 cans of liquid supplement to
help
> >> promote
> >> > > >> weight gain.  She agrees with the plan and has my number
for
> >> further
> >> > > >> assessment. May want a Resting Metabolic Rate as well. She
takes
> an
> >> > > aspirin
> >> > > >> a day for knee pain.&#13;&#10;"/>
> >> > > >>    <org.apache.ctakes.typesystem.type.structured.DocumentID
> >> > _indexed="1"
> >> > > >> _id="8" documentID="testpatient_plaintext_1.txt"/>
> >> > > >>    <uima.tcas.DocumentAnnotation _indexed="1" _id="10"
> >> _ref_sofa="1"
> >> > > >> begin="0" end="735" language="x-unspecified"/>
> >> > > >>    <org.apache.ctakes.typesystem.type.textspan.Segment
> _indexed="1"
> >> > > >> _id="15" _ref_sofa="1" begin="0" end="735" id="SIMPLE_SEGMENT"/>
> >> > > >>    <org.apache.ctakes.typesystem.type.textspan.Sentence
> >> _indexed="1"
> >> > > >> _id="21" _ref_sofa="1" begin="2" end="16" sentenceNumber="0"/>
> >> > > >> ..
> >> > > >> ..
> >> > > >> ..
> >> > > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept
> _id="2975"
> >> > > >> codingScheme="SNOMED" code="103733002" oid="103733002#SNOMED"
> >> > > score="0.0"
> >> > > >> disambiguated="false" cui="C0087111" tui="T061"/>
> >> > > >>    <uima.cas.FSArray _id="3005" size="4">
> >> > > >>        <i>2975</i>
> >> > > >>        <i>2985</i>
> >> > > >>        <i>2965</i>
> >> > > >>        <i>2995</i>
> >> > > >>    </uima.cas.FSArray>
> >> > > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept
> _id="2924"
> >> > > >> codingScheme="SNOMED" code="243121000" oid="243121000#SNOMED"
> >> > > score="0.0"
> >> > > >> disambiguated="false" cui="C0418981" tui="T061"/>
> >> > > >>    <uima.cas.FSArray _id="2934" size="1">
> >> > > >>        <i>2924</i>
> >> > > >>    </uima.cas.FSArray>
> >> > > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept
> _id="2870"
> >> > > >> codingScheme="RXNORM" code="1191" oid="1191#RXNORM" score="0.0"
> >> > > >> disambiguated="false" cui="C0004057" tui="T121"/>
> >> > > >>    <org.apache.ctakes.typesystem.type.refsem.UmlsConcept
> _id="2880"
> >> > > >> codingScheme="RXNORM" code="1191" oid="1191#RXNORM" score="0.0"
> >> > > >> disambiguated="false" cui="C0004057" tui="T109"/>
> >> > > >>    <uima.cas.FSArray _id="2890" size="2">
> >> > > >>        <i>2880</i>
> >> > > >>        <i>2870</i>
> >> > > >>    </uima.cas.FSArray>
> >> > > >> </CAS>
> >> > > >>
> >> > > >>
> >> > > >> I am not sure what's going on here, the job wasn't in running
> stage
> >> > but
> >> > > has
> >> > > >> output...
> >> > > >> It always got canceled by driver and showed run fails after
> >> > > initializing,
> >> > > >> so I didn't expect there would have any output file.
> >> > > >> And I also doubt whether the content in output file is
> >> correct....any
> >> > > >> suggestion is appreciated!
> >> > > >>
> >> > > >> Thanks,
> >> > > >> Yi-Wen
> >> > > >>
> >> > >
> >> >
> >>
> >
> >
>

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