Home Forums Kamanja Forums Use Cases & Samples running kamanja for medical sample

This topic contains 4 replies, has 4 voices, and was last updated by  Archived_User64 1 year, 8 months ago.

  • Author
    Posts
  • #13447 Reply

    Archived_User57
    Participant

    Hi,
    When I run “kamanja start -v” for the medical sample, I get the following output. I’m concerned about the:

    ERROR [pool-8-thread-2] – Failed to get data from container:com.ligadata.kamanja.samples.messages.beneficiary.

    error. Should I just ignore?
    thanks,
    alison

    WARN [main] – DATABASE_SCHEMA remains unset
    WARN [main] – DO_AUTH remains unset
    WARN [main] – MODEL_EXEC_LOG remains unset
    WARN [main] – JAR_TARGET_DIR remains unset
    WARN [main] – ADAPTER_SPECIFIC_CONFIG remains unset
    WARN [main] – AUDIT_PARMS remains unset
    WARN [main] – ZOOKEEPER_CONNECT_STRING remains unset
    WARN [main] – SECURITY_IMPL_CLASS remains unset
    WARN [main] – DATABASE remains unset
    WARN [main] – AUDIT_IMPL_JAR remains unset
    WARN [main] – SECURITY_IMPL_JAR remains unset
    WARN [main] – FUNCTION_FILES_DIR remains unset
    WARN [main] – MESSAGE_FILES_DIR remains unset
    WARN [main] – COMPILER_WORK_DIR remains unset
    WARN [main] – CONTAINER_FILES_DIR remains unset
    WARN [main] – ZNODE_PATH remains unset
    WARN [main] – NOTIFY_ENGINE remains unset
    WARN [main] – DATABASE_HOST remains unset
    WARN [main] – SCALA_HOME remains unset
    WARN [main] – SERVICE_PORT remains unset
    WARN [main] – CLASSPATH remains unset
    WARN [main] – AUDIT_IMPL_CLASS remains unset
    WARN [main] – SSL_PASSWD remains unset
    WARN [main] – SSL_CERTIFICATE remains unset
    WARN [main] – SERVICE_HOST remains unset
    WARN [main] – CONCEPT_FILES_DIR remains unset
    WARN [main] – DATABASE_LOCATION remains unset
    WARN [main] – JAVA_HOME remains unset
    WARN [main] – MANIFEST_PATH remains unset
    WARN [main] – TYPE_FILES_DIR remains unset
    WARN [main] – MODEL_FILES_DIR remains unset
    WARN [main] – DO_AUDIT remains unset
    WARN [main] – JAR_PATHS remains unset
    WARN [main] – GIT_ROOT remains unset
    WARN [main] – CONFIG_FILES_DIR remains unset
    WARN [main] – ROOT_DIR remains unset
    log4j:WARN No appenders could be found for logger (kafka.utils.VerifiableProperties).
    log4j:WARN Please initialize the log4j system properly.
    log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
    WARN [main] – KamanjaManager is running now. Waiting for user to terminate with SIGTERM, SIGINT or SIGABRT signals
    WARN [main-EventThread] – NodeId:1, IsLeader:false, Leader:1, AllParticipents:{1}
    WARN [main-EventThread] – NodeId:1, IsLeader:true, Leader:1, AllParticipents:{1}
    WARN [pool-2-thread-1] – Got Redistribution request. Participents are {1}. Looks like all nodes are not yet up. Waiting for 30000 milli seconds to see whether there are any more changes in participents
    WARN [pool-2-thread-1] – Distribution NodeId:1, IsLeader:true, Leader:1, AllParticipents:{1}
    ERROR [pool-8-thread-2] – Failed to get data from container:com.ligadata.kamanja.samples.messages.beneficiary.
    StackTrace:java.io.IOError: java.io.IOException: Wrong index checksum, store was not closed properly and could be corrupted.
    at org.mapdb.StoreDirect.checkHeaders(StoreDirect.java:258)
    at org.mapdb.StoreDirect.<init>(StoreDirect.java:207)
    at org.mapdb.DBMaker.extendStoreDirect(DBMaker.java:918)
    at org.mapdb.DBMaker.makeEngine(DBMaker.java:722)
    at org.mapdb.DBMaker.make(DBMaker.java:665)
    at com.ligadata.keyvaluestore.HashMapAdapter.createTable(HashMapAdapter.scala:140)
    at com.ligadata.keyvaluestore.HashMapAdapter.liftedTree1$1(HashMapAdapter.scala:196)
    at com.ligadata.keyvaluestore.HashMapAdapter.com$ligadata$keyvaluestore$HashMapAdapter$$CreateContainer(HashMapAdapter.scala:195)
    at com.ligadata.keyvaluestore.HashMapAdapter.com$ligadata$keyvaluestore$HashMapAdapter$$CheckTableExists(HashMapAdapter.scala:174)
    at com.ligadata.keyvaluestore.HashMapAdapter.get(HashMapAdapter.scala:631)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$.com$ligadata$SimpleEnvContextImpl$SimpleEnvContextImpl$$callGetData(SimpleEnvContextImpl.scala:2295)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$$anonfun$com$ligadata$SimpleEnvContextImpl$SimpleEnvContextImpl$$LoadDataIfNeeded$1.apply(SimpleEnvContextImpl.scala:1011)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$$anonfun$com$ligadata$SimpleEnvContextImpl$SimpleEnvContextImpl$$LoadDataIfNeeded$1.apply(SimpleEnvContextImpl.scala:968)
    at scala.collection.immutable.Range.foreach(Range.scala:141)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$.com$ligadata$SimpleEnvContextImpl$SimpleEnvContextImpl$$LoadDataIfNeeded(SimpleEnvContextImpl.scala:968)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$.localGetObject(SimpleEnvContextImpl.scala:684)
    at com.ligadata.SimpleEnvContextImpl.SimpleEnvContextImpl$.getObject(SimpleEnvContextImpl.scala:1366)
    at com.ligadata.KamanjaManager.LearningEngine.execute(LearningEngine.scala:224)
    at com.ligadata.KamanjaManager.ExecContextImpl$$anonfun$execute$1.apply(ExecContext.scala:84)
    at com.ligadata.KamanjaManager.ExecContextImpl$$anonfun$execute$1.apply(ExecContext.scala:82)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
    at com.ligadata.KamanjaManager.ExecContextImpl.execute(ExecContext.scala:82)
    at com.ligadata.InputAdapters.KafkaSimpleConsumer$$anonfun$StartProcessing$3$$anon$1$$anonfun$run$1$$anonfun$apply$1.apply$mcV$sp(KafkaSimpleConsumer.scala:288)
    at scala.util.control.Breaks.breakable(Breaks.scala:37)
    at com.ligadata.InputAdapters.KafkaSimpleConsumer$$anonfun$StartProcessing$3$$anon$1$$anonfun$run$1.apply(KafkaSimpleConsumer.scala:264)
    at com.ligadata.InputAdapters.KafkaSimpleConsumer$$anonfun$StartProcessing$3$$anon$1$$anonfun$run$1.apply(KafkaSimpleConsumer.scala:260)
    at scala.collection.Iterator$class.foreach(Iterator.scala:727)
    at kafka.utils.IteratorTemplate.foreach(IteratorTemplate.scala:32)
    at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
    at kafka.message.MessageSet.foreach(MessageSet.scala:67)
    at com.ligadata.InputAdapters.KafkaSimpleConsumer$$anonfun$StartProcessing$3$$anon$1.run(KafkaSimpleConsumer.scala:260)
    at scala.actors.threadpool.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1060)
    at scala.actors.threadpool.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:574)
    at java.lang.Thread.run(Thread.java:745)
    Caused by: java.io.IOException: Wrong index checksum, store was not closed properly and could be corrupted.
    … 35 more

    ERROR [pool-8-thread-2] – Failed to get data from datastore. Waiting for another 15000 milli seconds and going to start them again.
    Executing COPD Risk Assessment against Beneficiary message:
    Message Name: Beneficiary
    Message Version: 000000.000001.000000
    Message Desynpuf ID: 00001C24EE7B06AC
    Desynpuf ID: 00001C24EE7B06AC
    COPD Risk Level:
    Is Over 40 Years Old: true
    Has Smoking History: false
    Has Environmental Exposure: false
    Has Dyspnea: false
    Has Chronic Cough: false
    Has Chronic Sputum: false
    Has AAT Deficiency: false
    Inpatient Claim Costs: 0.0
    Outpatient Claim Costs: 0.0
    ******************************************************************************

  • #13448 Reply

    Archived_User1
    Participant

    This error is seen when using hash map. This means that your data store is corrupted and you need to clear your data. This occurs usually when two processing open a connection to the hash map at the same time. Shut down your processes, remove all files from $KAMANJA_HOME/storage and start again.

  • #13449 Reply

    Archived_User42
    Participant

    Did this fix you problem?

  • #13450 Reply

    Archived_User57
    Participant

    I understand they are still working on a fix. Stay tuned..

  • #13451 Reply

    Archived_User64
    Participant

    Hi Donald,

    The exceptions that you are seeing below are due to the “corrupted” hash map. This is an issue that is solved by running William’s new clean up script, or by cleaning up your logs and storage directories manually. The utility for cleanup has been checked in.

    dan

Reply To: running kamanja for medical sample
Your information: