OK here's what I tried: * Build Flink (mvn clean install) from the branch you linked (kryo) * Build my uber-jar, I use SBT with 1.0-SNAPSHOT as the Flink version, added local maven repo to resolvers so that it picks up the previously installed version (I hope) * Launch local cluster from newly built Flink, try to run job
Still getting the same error. Is there a way to ensure that SBT is picking up the local version of Flink to build the uber-jar? Does it matter in this case, or is it enough that I'm sure the launched Flink instance comes from the branch you linked? On Wed, Jan 20, 2016 at 4:30 PM, Stephan Ewen <se...@apache.org> wrote: > The bug looks to be in the serialization via Kryo while spilling windows. > Note that Kryo is here used as a fallback serializer, since the > SparseVector is not transparent type to Flink. > > I think there are two possible reasons: > 1) Kryo, or our Kryo setup has an issue here > 2) Kryo is inconsistently configured. There are multiple Kryo instances > used across the serializers in the sorter. There may be a bug that they are > not initialized in sync. > > > To check this, can you build Flink with this pull request ( > https://github.com/apache/flink/pull/1528) or from this branch ( > https://github.com/StephanEwen/incubator-flink kryo) and see if that > fixes it? > > > Thanks, > Stephan > > > > > > On Wed, Jan 20, 2016 at 3:33 PM, Theodore Vasiloudis < > theodoros.vasilou...@gmail.com> wrote: > >> 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. >>>>> >>>> >>>> >>> >> >
