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NPE when using mask arrays in a network with StackVertex #6490

timxyz opened this issue Sep 25, 2018 · 4 comments · Fixed by #6546


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commented Sep 25, 2018

Using deeplearning4j v1.0.0-beta2., I get the following crash immediately upon trying to fit a ComputationGraph with multiple inputs (each specified with a mask) and containing a StackVertex.

	at org.deeplearning4j.nn.graph.vertex.impl.StackVertex.feedForwardMaskArrays(
	at org.deeplearning4j.nn.graph.ComputationGraph.setLayerMaskArrays(
	at org.deeplearning4j.nn.graph.ComputationGraph.fitHelper(

In particular it is long size1_ex0 = maskArrays[0].size(1); failing, due to maskArrays[0] being null.

I've noticed in the implementation of feedForwardMaskArrays for other vertices (e.g. MergeVertex) that they are coded to explicitly expect some elements in INDArray[] maskArrays to be null, but I'm afraid I don't know enough about how mask arrays are implemented to say whether that is the cause of the issue in StackVertex..

The error seems to be independent of whether or not I have null entries in the mask array I specify in my MultiDataSets - it simply occurs whenever and however I use masks. The network works OK without masks, but I'd like it to take into account variable-length time series.

Thanks for any insights!


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commented Sep 25, 2018

Are you able to share your network architecture that's causing this?


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commented Oct 1, 2018

I have tried a number of different network configurations using StackVertex, and I was unable to reproduce this issue.
@timxyz can you share your network configuration? If I can't reproduce it, I can't fix it.


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commented Oct 3, 2018

@AlexDBlack Thanks for nudging me on this, I'd forgotten to get back. I investigated this a bit more and realised it is due to a second StackVertex appearing after UnstackVertex. In my case I realised the second Stack was unnecessary and was able to reformulate my network to get it working again.

Here is the simplest reproducing example I could make:

		val nnConfig = NeuralNetConfiguration.Builder()
			.addInputs("m1", "m2")
			.addVertex("m", StackVertex(), "m1", "m2")
			.addLayer("M", LastTimeStep(LSTM.Builder().nIn(d).nOut(1).activation(Activation.TANH).build()), "m")
			.addVertex("p1", UnstackVertex(0, 2), "M")
			.addVertex("p2", UnstackVertex(1, 2), "M")
			.addVertex("p", StackVertex(), "p1", "p2")
			.addVertex("q1", UnstackVertex(0, 2), "p")
			.addVertex("q2", UnstackVertex(1, 2), "p")
			.addVertex("q", MergeVertex(), "q1", "q2")
			.addLayer("probability", OutputLayer.Builder().nIn(d * 2).nOut(6).lossFunction(LossFunctions.LossFunction.MEAN_ABSOLUTE_ERROR).build(), "q")

@AlexDBlack AlexDBlack self-assigned this Oct 8, 2018

AlexDBlack added a commit that referenced this issue Oct 8, 2018
AlexDBlack added a commit that referenced this issue Oct 10, 2018
DL4J/ND4J Fixes (#6546)
* #6539 Handle 0 gradient case for gradient normalization

* #6521 Nd4j.gemm validation

* #6543 View/order checks for BaseNDArray.mmuli()

* #6542 mmuli shape validation

* #6545 Require scalars, vectors, or same shape for INDArray.assign()

* #6520 Fix setLearningRate(double) for the no updater state (SGD, etc) case

* #6490 Fix StackVertex NPE with some masking cases

* Cnn3DLossLayer. Typo in RecordReaderMultiDataSetIteratorTest.

* Small fix

* Cnn3DLossLayer gradient checks (not yet passing)

* Cnn3dLossLayer masking + test fixes

* Extra tests, CNN3D tweaks

* Fix Conv3d layer support for NDHWC data format

* Fix Cnn3DLossLayer

* Allow size 1 dimensions in assign shape check

* Minor test fixes

* Fix RollAxis; other tweaks

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commented Nov 9, 2018

This thread has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.

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