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geotrellis / vagrant.geotrellis

A vagrant environment for doing GeoTrellis development.
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Ingest test failure - "no gdaljni in java.library.path" #4

Open jwalgran opened 9 years ago

jwalgran commented 9 years ago

I tried provisioning with the addition of azavea.libgdal-java but that was not enough:

[info] Ingest
[info] - should ingest GeoTiff
Native library load failed.
java.lang.UnsatisfiedLinkError: no gdaljni in java.library.path
00:54:28 Executor: Exception in task 0.0 in stage 432.0 (TID 1630)
java.lang.UnsatisfiedLinkError: org.gdal.gdal.gdalJNI.AllRegister()V
    at org.gdal.gdal.gdalJNI.AllRegister(Native Method)
    at org.gdal.gdal.gdal.AllRegister(gdal.java:499)
    at geotrellis.gdal.Gdal$.<init>(Gdal.scala:17)
    at geotrellis.gdal.Gdal$.<clinit>(Gdal.scala)
    at geotrellis.spark.io.hadoop.formats.GdalRecordReader.initialize(GdalInputFormat.scala:102)
    at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:135)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:107)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:69)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
    at org.apache.spark.scheduler.Task.run(Task.scala:56)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
00:54:28 SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker-4,5,main]
java.lang.UnsatisfiedLinkError: org.gdal.gdal.gdalJNI.AllRegister()V
    at org.gdal.gdal.gdalJNI.AllRegister(Native Method)
    at org.gdal.gdal.gdal.AllRegister(gdal.java:499)
    at geotrellis.gdal.Gdal$.<init>(Gdal.scala:17)
    at geotrellis.gdal.Gdal$.<clinit>(Gdal.scala)
    at geotrellis.spark.io.hadoop.formats.GdalRecordReader.initialize(GdalInputFormat.scala:102)
    at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:135)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:107)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:69)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
    at org.apache.spark.scheduler.Task.run(Task.scala:56)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
00:54:28 TaskSetManager: Lost task 0.0 in stage 432.0 (TID 1630, localhost): java.lang.UnsatisfiedLinkError: org.gdal.gdal.gdalJNI.AllRegister()V
    at org.gdal.gdal.gdalJNI.AllRegister(Native Method)
    at org.gdal.gdal.gdal.AllRegister(gdal.java:499)
    at geotrellis.gdal.Gdal$.<init>(Gdal.scala:17)
    at geotrellis.gdal.Gdal$.<clinit>(Gdal.scala)
    at geotrellis.spark.io.hadoop.formats.GdalRecordReader.initialize(GdalInputFormat.scala:102)
    at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:135)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:107)
    at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:69)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
    at org.apache.spark.scheduler.Task.run(Task.scala:56)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

00:54:28 TaskSetManager: Task 0 in stage 432.0 failed 1 times; aborting job
Exception in thread "Thread-1" Exception in thread "Thread-5" java.io.EOFException
    at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2598)
    at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1318)
    at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
    at sbt.React.react(ForkTests.scala:117)
    at sbt.ForkTests$$anonfun$mainTestTask$1$Acceptor$2$.run(ForkTests.scala:76)
    at java.lang.Thread.run(Thread.java:745)
java.io.EOFException
    at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2598)
    at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1318)
    at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
    at org.scalatest.tools.Framework$ScalaTestRunner$Skeleton$1$React.react(Framework.scala:945)
    at org.scalatest.tools.Framework$ScalaTestRunner$Skeleton$1.run(Framework.scala:934)
    at java.lang.Thread.run(Thread.java:745)
[info] Run completed in 2 minutes, 14 seconds.
[info] Total number of tests run: 87
[info] Suites: completed 25, aborted 0
[info] Tests: succeeded 87, failed 0, canceled 0, ignored 0, pending 0
[info] All tests passed.
[error] Error during tests:
[error]     Running java with options -classpath /home/vagrant/geotrellis/spark/target/scala-2.11/test-classes:/home/vagrant/geotrellis/spark/target/scala-2.11/classes:/home/vagrant/geotrellis/raster/target/scala-2.11/classes:/home/vagrant/geotrellis/macros/target/scala-2.11/classes:/home/vagrant/geotrellis/vector/target/scala-2.11/classes:/home/vagrant/geotrellis/proj4/target/scala-2.11/classes:/home/vagrant/geotrellis/gdal/target/scala-2.11/classes:/home/vagrant/.ivy2/cache/org.scala-lang/scala-library/jars/scala-library-2.11.5.jar:/home/vagrant/.ivy2/cache/org.scala-lang/scala-reflect/jars/scala-reflect-2.11.5.jar:/home/vagrant/.ivy2/cache/net.sf.opencsv/opencsv/jars/opencsv-2.3.jar:/home/vagrant/.ivy2/cache/com.vividsolutions/jts/jars/jts-1.13.jar:/home/vagrant/.ivy2/cache/io.spray/spray-json_2.11/bundles/spray-json_2.11-1.3.1.jar:/home/vagrant/.ivy2/cache/org.apache.commons/commons-math3/jars/commons-math3-3.2.jar:/home/vagrant/.ivy2/cache/org.spire-math/spire_2.11/jars/spire_2.11-0.7.5.jar:/home/vagrant/.ivy2/cache/org.spire-math/spire-macros_2.11/jars/spire-macros_2.11-0.7.5.jar:/home/vagrant/.ivy2/cache/com.typesafe/config/bundles/config-1.2.1.jar:/home/vagrant/.ivy2/cache/com.github.julien-truffaut/monocle-core_2.11/jars/monocle-core_2.11-1.0.1.jar:/home/vagrant/.ivy2/cache/org.scalaz/scalaz-core_2.11/bundles/scalaz-core_2.11-7.1.0.jar:/home/vagrant/.ivy2/cache/org.scala-lang.modules/scala-parser-combinators_2.11/bundles/scala-parser-combinators_2.11-1.0.2.jar:/home/vagrant/.ivy2/cache/org.scala-lang.modules/scala-xml_2.11/bundles/scala-xml_2.11-1.0.2.jar:/home/vagrant/.ivy2/cache/com.github.julien-truffaut/monocle-macro_2.11/jars/monocle-macro_2.11-1.0.1.jar:/home/vagrant/.ivy2/cache/org.gdal/gdal/jars/gdal-1.10.1.jar:/home/vagrant/.ivy2/cache/com.github.scopt/scopt_2.10/jars/scopt_2.10-3.2.0.jar:/home/vagrant/.ivy2/cache/com.quantifind/sumac_2.11/jars/sumac_2.11-0.3.0.jar:/home/vagrant/.ivy2/cache/org.apache.accumulo/accumulo-core/jars/accumulo-core-1.5.2.jar:/home/vagrant/.ivy2/cache/com.beust/jcommander/jars/jcommander-1.30.jar:/home/vagrant/.ivy2/cache/com.google.guava/guava/bundles/guava-14.0.1.jar:/home/vagrant/.ivy2/cache/jline/jline/jars/jline-1.0.jar:/home/vagrant/.ivy2/cache/org.apache.accumulo/accumulo-fate/jars/accumulo-fate-1.5.2.jar:/home/vagrant/.ivy2/cache/org.apache.accumulo/accumulo-start/jars/accumulo-start-1.5.2.jar:/home/vagrant/.ivy2/cache/org.apache.commons/commons-vfs2/jars/commons-vfs2-2.0.jar:/home/vagrant/.ivy2/cache/org.apache.maven.scm/maven-scm-api/jars/maven-scm-api-1.4.jar:/home/vagrant/.ivy2/cache/org.codehaus.plexus/plexus-utils/jars/plexus-utils-1.5.6.jar:/home/vagrant/.ivy2/cache/org.apache.maven.scm/maven-scm-provider-svnexe/jars/maven-scm-provider-svnexe-1.4.jar:/home/vagrant/.ivy2/cache/org.apache.maven.scm/maven-scm-provider-svn-commons/jars/maven-scm-provider-svn-commons-1.4.jar:/home/vagrant/.ivy2/cache/regexp/regexp/jars/regexp-1.3.jar:/home/vagrant/.ivy2/cache/org.apache.accumulo/accumulo-trace/jars/accumulo-trace-1.5.2.jar:/home/vagrant/.ivy2/cache/org.apache.thrift/libthrift/jars/libthrift-0.9.0.jar:/home/vagrant/.ivy2/cache/org.apache.commons/commons-math/jars/commons-math-2.1.jar:/home/vagrant/.ivy2/cache/de.javakaffee/kryo-serializers/bundles/kryo-serializers-0.27.jar:/home/vagrant/.ivy2/cache/com.esotericsoftware.kryo/kryo/bundles/kryo-2.24.0.jar:/home/vagrant/.ivy2/cache/com.esotericsoftware.minlog/minlog/jars/minlog-1.2.jar:/home/vagrant/.ivy2/cache/org.objenesis/objenesis/jars/objenesis-2.1.jar:/home/vagrant/.ivy2/cache/com.typesafe.scala-logging/scala-logging-slf4j_2.11/jars/scala-logging-slf4j_2.11-2.1.2.jar:/home/vagrant/.ivy2/cache/com.typesafe.scala-logging/scala-logging-api_2.11/jars/scala-logging-api_2.11-2.1.2.jar:/home/vagrant/.ivy2/cache/org.slf4j/slf4j-api/jars/slf4j-api-1.7.7.jar:/home/vagrant/.ivy2/cache/com.amazonaws/aws-java-sdk-s3/jars/aws-java-sdk-s3-1.9.16.jar:/home/vagrant/.ivy2/cache/com.amazonaws/aws-java-sdk-kms/jars/aws-java-sdk-kms-1.9.16.jar:/home/vagrant/.ivy2/cache/com.amazonaws/aws-java-sdk-core/jars/aws-java-sdk-core-1.9.16.jar:/home/vagrant/.ivy2/cache/commons-logging/commons-logging/jars/commons-logging-1.1.3.jar:/home/vagrant/.ivy2/cache/org.apache.httpcomponents/httpclient/jars/httpclient-4.3.4.jar:/home/vagrant/.ivy2/cache/org.apache.httpcomponents/httpcore/jars/httpcore-4.3.2.jar:/home/vagrant/.ivy2/cache/commons-codec/commons-codec/jars/commons-codec-1.6.jar:/home/vagrant/.ivy2/cache/com.fasterxml.jackson.core/jackson-databind/bundles/jackson-databind-2.3.2.jar:/home/vagrant/.ivy2/cache/com.fasterxml.jackson.core/jackson-annotations/bundles/jackson-annotations-2.3.0.jar:/home/vagrant/.ivy2/cache/com.fasterxml.jackson.core/jackson-core/bundles/jackson-core-2.3.2.jar:/home/vagrant/.ivy2/cache/joda-time/joda-time/jars/joda-time-2.7.jar:/home/vagrant/.ivy2/cache/com.github.nscala-time/nscala-time_2.11/jars/nscala-time_2.11-1.6.0.jar:/home/vagrant/.ivy2/cache/org.joda/joda-convert/jars/joda-convert-1.2.jar:/home/vagrant/.ivy2/cache/org.scalatest/scalatest_2.11/bu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sbt.ForkMain 32928 failed with exit code 50
[error] (spark/test:test) sbt.TestsFailedException: Tests unsuccessful
[error] Total time: 485 s, completed Mar 26, 2015 12:54:29 AM
notthatbreezy commented 9 years ago

Started to look into this - not sure what is up with it though yet. @lossyrob or @echeipesh might have a better idea