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ERROR when running #6

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WRui opened this issue Mar 25, 2018 · 0 comments
Open

ERROR when running #6

WRui opened this issue Mar 25, 2018 · 0 comments

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@WRui
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WRui commented Mar 25, 2018

Hi, i meet the following error when runing the GRNBOOST with the
spark-submit
--class org.aertslab.grnboost.GRNBoost
--master local[*]
--deploy-mode client
--jars /home/XXX/.m2/repository/ml/dmlc/xgboost4j/0.8-SNAPSHOT/xgboost4j-0.8-SNAPSHOT.jar
/datb1/wangrui/software/GRNBoost/target/scala-2.11/GRNBoost.jar
infer -i /datb1/XXX/test.txt
-tf /datb1/XXX/mm_only_TF.xls
-o /datb1/XXX/net1_grnboost_depth3.tsv
-p eta=0.01
-p max_depth=3
-p colsample_bytree=0.1
--truncate 100000

the test.txt:
#####################
Tspan12 0 0.666 0 0 0.089
Gad1 1.800 0 0 0.061 0
Neurod1 0 0 1.301 0.232 0
#######################

18/03/26 00:27:02 ERROR Executor: Exception in task 10.0 in stage 8.0 (TID 37)
java.lang.NoClassDefFoundError: Could not initialize class ml.dmlc.xgboost4j.java.XGBoostJNI
at ml.dmlc.xgboost4j.java.DMatrix.(DMatrix.java:53)
at ml.dmlc.xgboost4j.scala.DMatrix.(DMatrix.scala:42)
at org.aertslab.grnboost.util.ExpressionCSCMatrixFunctions.iterateToLabeledDMatrix(Breez
at org.aertslab.grnboost.algo.EstimateNrBoostingRoundsIterated$$anonfun$apply$2.apply(Es
at org.aertslab.grnboost.algo.EstimateNrBoostingRoundsIterated$$anonfun$apply$2.apply(Es
at scala.Option.map(Option.scala:146)
at org.aertslab.grnboost.algo.EstimateNrBoostingRoundsIterated.apply(EstimateNrBoostingR
at org.aertslab.grnboost.GRNBoost$$anonf$$$$b53fb875fb4ddc549756c9a3b3bacf8$$$$st$$mapTa
at org.aertslab.grnboost.GRNBoost$$anonf$$$$b53fb875fb4ddc549756c9a3b3bacf8$$$$st$$mapTa
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggr
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNex
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:4
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(Whole
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuff
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
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)

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