I haven't been able to reproduce this with other datasets. Taking a smaller sample from the large dataset I'm using (link to data <http://www.csie.ntu.edu.tw/~cjlin/libsvmtools/datasets/binary.html#epsilon>) causes the same problem however.
I'm wondering if the implementation of readLibSVM is what's wrong here. I've tried the new version commited recently by Chiwan, but I still get the same error. I'll see if I can spot a bug in readLibSVM. On Wed, Jan 20, 2016 at 1:43 PM, Theodore Vasiloudis < theodoros.vasilou...@gmail.com> wrote: > It's on 0.10. > > I've tried explicitly registering SparseVector (which is done anyway by > registerFlinkMLTypes > <https://github.com/apache/flink/blob/e9bf13d8626099a1d6ddb6ebe98c50be848fe79e/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/common/FlinkMLTools.scala#L49> > which is called when the SVM predict or evaluate functions are called > <https://github.com/apache/flink/blob/e9bf13d8626099a1d6ddb6ebe98c50be848fe79e/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/pipeline/Predictor.scala#L58>) > in my job but I still get the same. I will try a couple different datasets > and try to see if it's the number of features that is causing this or > something else. > > So far it works fine for a dataset with 8 features, but the large one has > 2000 and I get the above error there. I will try large datasets with a few > features and small datasets with many features as well. > > On Wed, Jan 20, 2016 at 11:39 AM, Stephan Ewen <se...@apache.org> wrote: > >> Hi! >> >> Does this error occur in 0.10 or im 1.0-SNAPSHOT? >> >> It is probably an incorrectly configured Kryo instance (not a problem of >> the sorter). >> What is strange is that it occurs in the "MapReferenceResolver" - there >> should be no reference resolution during serialization / deserialization. >> >> Can you try what happens when you explicitly register the type >> SparseVector at the ExecutionEnvironment? >> >> Stephan >> >> >> On Wed, Jan 20, 2016 at 11:24 AM, Theodore Vasiloudis < >> theodoros.vasilou...@gmail.com> wrote: >> >>> Hello all, >>> >>> I'm trying to run a job using FlinkML and I'm confused about the source >>> of an error. >>> >>> The job reads a libSVM formatted file and trains an SVM classifier on it. >>> >>> I've tried this with small datasets and everything works out fine. >>> >>> When trying to run the same job on a large dataset (~11GB uncompressed) >>> however, I get the following error: >>> >>> >>>> java.lang.RuntimeException: Error obtaining the sorted input: Thread >>>> 'SortMerger spilling thread' terminated due to an exception: >>>> java.lang.IndexOutOfBoundsException: Index: 14, Size: 2 >>>> Serialization trace: >>>> indices (org.apache.flink.ml.math.SparseVector) >>>> at >>>> org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619) >>>> at >>>> org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1089) >>>> at >>>> org.apache.flink.runtime.operators.NoOpDriver.run(NoOpDriver.java:78) >>>> at >>>> org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:489) >>>> at >>>> org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:354) >>>> at org.apache.flink.runtime.taskmanager.Task.run(Task.java:584) >>>> at java.lang.Thread.run(Thread.java:745) >>>> Caused by: java.io.IOException: Thread 'SortMerger spilling thread' >>>> terminated due to an exception: java.lang.IndexOutOfBoundsException: Index: >>>> 14, Size: 2 >>>> Serialization trace: >>>> indices (org.apache.flink.ml.math.SparseVector) >>>> at >>>> org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:800) >>>> Caused by: com.esotericsoftware.kryo.KryoException: >>>> java.lang.IndexOutOfBoundsException: Index: 14, Size: 2 >>>> Serialization trace: >>>> indices (org.apache.flink.ml.math.SparseVector) >>>> at >>>> com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:125) >>>> at >>>> com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:528) >>>> at >>>> com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761) >>>> at >>>> org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:222) >>>> at >>>> org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:236) >>>> at >>>> org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.copy(KryoSerializer.java:246) >>>> at >>>> org.apache.flink.api.java.typeutils.runtime.TupleSerializerBase.copy(TupleSerializerBase.java:73) >>>> at >>>> org.apache.flink.api.java.typeutils.runtime.TupleSerializerBase.copy(TupleSerializerBase.java:73) >>>> at >>>> org.apache.flink.runtime.operators.sort.NormalizedKeySorter.writeToOutput(NormalizedKeySorter.java:499) >>>> at >>>> org.apache.flink.runtime.operators.sort.UnilateralSortMerger$SpillingThread.go(UnilateralSortMerger.java:1344) >>>> at >>>> org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:796) >>>> Caused by: java.lang.IndexOutOfBoundsException: Index: 14, Size: 2 >>>> at java.util.ArrayList.rangeCheck(ArrayList.java:653) >>>> at java.util.ArrayList.set(ArrayList.java:444) >>>> at >>>> com.esotericsoftware.kryo.util.MapReferenceResolver.setReadObject(MapReferenceResolver.java:38) >>>> at com.esotericsoftware.kryo.Kryo.reference(Kryo.java:823) >>>> at >>>> com.esotericsoftware.kryo.Kryo.readObjectOrNull(Kryo.java:731) >>>> at >>>> com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:113) >>>> ... 10 more >>> >>> >>> >>> Any idea what might be causing this? I'm running the job in local mode, >>> 1 TM with 8 slots and ~32GB heap size. >>> >>> All the vectors created by the libSVM loader have the correct size. >>> >> >> >
