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.degen...@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 <yiwen...@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.degen...@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 <yiwen...@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.degen...@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 <yiwen...@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=" 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 >> > > >> >> > > >> > >> > >
