Update N5 configuration#115
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May 1, 2020 12:01
the changes were made in saalfeldlab/n5-google-cloud#11
spark uses 2.6.7.1, and aws-java-sdk-s3 uses 2.6.7.3. There are no conflicts between the two, so we can explicitly use the latter. When running spark with the newer version of jackson-databind (2.10.2), it produces the following runtime error: Exception in thread "main" java.lang.ExceptionInInitializerError at org.apache.spark.SparkContext.withScope(SparkContext.scala:693) at org.apache.spark.SparkContext.parallelize(SparkContext.scala:710) at org.apache.spark.api.java.JavaSparkContext.parallelize(JavaSparkContext.scala:134) at org.janelia.stitching.PipelineFusionStepExecutor.fuse(PipelineFusionStepExecutor.java:276) at org.janelia.stitching.PipelineFusionStepExecutor.runImpl(PipelineFusionStepExecutor.java:179) at org.janelia.stitching.PipelineFusionStepExecutor.run(PipelineFusionStepExecutor.java:69) at org.janelia.stitching.StitchingSpark.run(StitchingSpark.java:87) at org.janelia.stitching.StitchingSpark.main(StitchingSpark.java:34) Caused by: com.fasterxml.jackson.databind.JsonMappingException: Incompatible Jackson version: 2.10.2 at com.fasterxml.jackson.module.scala.JacksonModule$class.setupModule(JacksonModule.scala:64) at com.fasterxml.jackson.module.scala.DefaultScalaModule.setupModule(DefaultScalaModule.scala:19) at com.fasterxml.jackson.databind.ObjectMapper.registerModule(ObjectMapper.java:808) at org.apache.spark.rdd.RDDOperationScope$.<init>(RDDOperationScope.scala:82) at org.apache.spark.rdd.RDDOperationScope$.<clinit>(RDDOperationScope.scala) ... 8 more
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n5-google-cloudjackson-databindbecause Spark and AWS SDK still use an older version and were producing runtime errors if running with the newer version