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$CharacterValidatingContentHand
ler.checkForInvalidXmlChars(XMLSerializer.java:254)
I recommend determining why your CR is broken, fixing, and re-submitting
your Job to DUCC.
Lou.
On Tue, Nov 17, 2015 at 2:46 AM, Yi-Wen Liu <[email protected]> wrote:
> Hello,
>
> I am still stuck in the following error of DUCC and job always got canceled
> by driver:
>
> 16 Nov 2015 23:34:38,353 INFO JobDriver - T[18] advanceJdState
> current=Initializing request=Active result=Active
> 16 Nov 2015 23:34:39,066 ERROR ProxyLogger - T[17] loggify
> org.xml.sax.SAXParseException; Trying to serialize non-XML 1.0
> character: , 0x0
> at
> org.apache.uima.util.XMLSerializer$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=" Dr.
> Nutritious Medical Nutrition Therapy for
> Hyperlipidemia Referral from: Julie Tester, RD, LD,
> CNSD Phone contact: (555) 555-1212 Height: 144 cm
> Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight:
> 53 kg BMI: 18 kg/m2 Diet: General Daily Calorie needs
> (kcals): 1500 calories, assessed as HB + 20% for activity. Daily
> Protein needs: 40 grams, assessed as 1.0 g/kg. 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. "/>
> <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
>
