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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> > >> 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 <[email protected]> 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 <[email protected] > > > >> > > 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 <[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 > >> > > >> > >> > > > >> > > >> > > > > >
