GoogleCloudPlatform / healthcare-data-harmonization-dataflow

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A worker Docker container failed to start #16

Open NikolaiKovalenko opened 3 years ago

NikolaiKovalenko commented 3 years ago

When trying to run Google Cloud Dataflow Job and I keep getting errors:

  1. Error syncing pod, skipping: failed to "StartContainer" for "java-streaming" with CrashLoopBackOff: "back-off 2m40s restarting failed container=java-streaming pod=df-hl7v2tofhirstreamingrunne-10250437-hzcx-harness-43lz_default(9fe8124c78e1791250ba1ed88c87502b)" Could not start worker docker container .
  2. A fatal error has been detected by the Java Runtime Environment: The worker JRE crashed .

In the description of the problem in Google Guides, I found a little information about the problem here . According to the description, the docker container cannot be started because there was a problem using JNI:

This indicates that the pipeline is using Java Native Interface (JNI) to run non-Java code and that there is an error in that code or the JNI bindings.

I tried changing the env CFLAGS in https://github.com/GoogleCloudPlatform/healthcare-data-harmonization-dataflow/blob/master/deps/wrapping/main.go to use Java 11 only, but still get this error. Has anyone encountered such a problem? Thanks

rpydimarri-mw commented 2 years ago

We had the same issue where jre crashed . Our issue was resolved after changing the parser config of hl7store.

yogitaahire commented 2 years ago

@rpydimarri-mw we are facing the same JRE crashed error, what did you change in parser configuration of hl7store?

rpydimarri-mw commented 2 years ago

Ran this update -

curl -X PATCH \ -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \ -H "Content-Type: application/json; charset=utf-8" \ --data "{ 'parserConfig': { 'schema': { 'schematizedParsingType': 'HARD_FAIL', 'ignoreMinOccurs': true, 'unexpectedSegmentHandling': 'PARSE'} } }" "https://healthcare.googleapis.com/v1/projects/<_HL7STORE_>?updateMask=parser_config.schema"

yogitaahire commented 2 years ago

Thank you! This update along with renaming Java 11 to Java 8 has fixed JRE crashed error