Memory Leak when calling ConcreteFunction

[lucaro]

System information

• OS Platform and Distribution (e.g., Linux Ubuntu 16.04 x86_64): Windows 10
• TensorFlow version (use command below): 0.4.2

I have an application where I need to write a large amount of data as TFRecords to be used externally. To encode these records properly, I need to invoke tf.io.serializeTensor inside a ConcreteFunction. When running this repeatedly, memory usage increases until the program eventually runs out of memory and crashes. When inspecting the process with VisualVM, I can see that the memory does not build up in the JVM, so it must be some sort of memory leak when calling native code. I added a minimal example below. Did I improperly close something or is this indeed a bug?

Code to reproduce the issue

import java.util.Random;
import org.tensorflow.ConcreteFunction;
import org.tensorflow.Signature;
import org.tensorflow.ndarray.Shape;
import org.tensorflow.ndarray.buffer.DataBuffer;
import org.tensorflow.ndarray.buffer.DataBuffers;
import org.tensorflow.ndarray.buffer.FloatDataBuffer;
import org.tensorflow.op.Ops;
import org.tensorflow.op.core.Placeholder;
import org.tensorflow.op.io.SerializeTensor;
import org.tensorflow.types.TFloat32;
import org.tensorflow.types.TString;

public class MemoryLeakTest {

  public static Signature serializeTensor(Ops tf) {
    Placeholder<TFloat32> input = tf.placeholder(TFloat32.class);
    SerializeTensor output = tf.io.serializeTensor(input);
    return Signature.builder().input("tensor", input).output("out", output).build();
  }

  public static void main(String[] args) {

    ConcreteFunction function = ConcreteFunction.create(MemoryLeakTest::serializeTensor);

    Random random = new Random(0);

    //run same operation for many tensors
    for (int loop = 0; loop < 10000; loop++) {

      //generate some tensor
      float[] arr = new float[512 * 512 * 512];
      for (int i = 0; i < arr.length; i++) {
        arr[i] = random.nextFloat();
      }
      FloatDataBuffer buf = DataBuffers.of(arr);
      TFloat32 inputTensor = TFloat32.tensorOf(Shape.of(512, 512, 512), buf);

      //serialize tensor
      TString outputTensor = (TString) function.call(inputTensor);
      DataBuffer<byte[]> outputBuffer = DataBuffers.ofObjects(byte[].class, 1);
      outputTensor.asBytes().read(outputBuffer);
      byte[] serialized = outputBuffer.getObject(0);

      System.out.println("Generated serialized tensor with " + serialized.length + " bytes");

      //close tensors
      inputTensor.close();
      outputTensor.close();
    }

    //close function in the end
    function.close();
  }

}

[Craigacp]

I think the example looks ok. Can you take a heap dump with VisualVM and see what Java objects it's allocating?

[lucaro]

VisualVM shows no exceptionally high memory usage, remaining stable over time:

The largest memory use within the JVM is generated by the expected arrays:

At the time I took this snapshot, Windows reported over 60GB in use by that process:

On my machine, this example leaks roughly 10GB of memory per minute.

[karllessard]

Just out of curiosity @lucaro , what happens if you don't copy the tensor values to a byte array but simple access the string in the tensor like this?

            TString outputTensor = (TString) function.call(inputTensor);
            String serialized = outputTensor.getObject();

            System.out.println("Generated serialized tensor with " + serialized.length() + " bytes");

Just want to narrow down the possible source of leakage

[karllessard]

Also, if that may unblock you until we find the problem, you can build a TensorProto directly instead of invoking tf.io.serializeTensor

[lucaro]

Getting the String rather than the byte[] doesn't change anything with respect to the leakage.

Thanks for pointing me to the TensorProto, that was what I was looking for initially. However, I did some tests and what I get from serializing the TensorProto and what I get by calling tf.io.serializeTensor is not exactly the same. The tensor serialized via TensorProto produces an array that is 2 bytes shorter, specifically the leading two. I extended the example below. I haven't yet been able to check if the byte array generated via the TensorProto can also be read in e.g., a Python-based environment or if these two bytes are actually important.

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Random;
import org.tensorflow.ConcreteFunction;
import org.tensorflow.Signature;
import org.tensorflow.ndarray.Shape;
import org.tensorflow.ndarray.buffer.DataBuffer;
import org.tensorflow.ndarray.buffer.DataBuffers;
import org.tensorflow.ndarray.buffer.FloatDataBuffer;
import org.tensorflow.op.Ops;
import org.tensorflow.op.core.Placeholder;
import org.tensorflow.op.io.SerializeTensor;
import org.tensorflow.proto.framework.TensorProto;
import org.tensorflow.proto.framework.TensorShapeProto;
import org.tensorflow.proto.framework.TensorShapeProto.Dim;
import org.tensorflow.types.TFloat32;
import org.tensorflow.types.TString;

public class MemoryLeakTest {

  public static Signature serializeTensor(Ops tf) {
    Placeholder<TFloat32> input = tf.placeholder(TFloat32.class);
    SerializeTensor output = tf.io.serializeTensor(input);
    return Signature.builder().input("tensor", input).output("out", output).build();
  }

  public static void main(String[] args) {

    ConcreteFunction function = ConcreteFunction.create(MemoryLeakTest::serializeTensor);

    Random random = new Random(0);

    //run same operation for many tensors
    for (int loop = 0; loop < 10000; loop++) {

      //generate some tensor
      float[] arr = new float[512 * 512 * 512];
      ArrayList<Float> farr = new ArrayList<>(512 * 512 * 512);
      for (int i = 0; i < arr.length; i++) {
        arr[i] = random.nextFloat();
        farr.add(arr[i]);
      }
      FloatDataBuffer buf = DataBuffers.of(arr);
      TFloat32 inputTensor = TFloat32.tensorOf(Shape.of(512, 512, 512), buf);

      //serialize tensor via native tensorflow
      TString outputTensor = (TString) function.call(inputTensor);
      DataBuffer<byte[]> outputBuffer = DataBuffers.ofObjects(byte[].class, 1);
      outputTensor.asBytes().read(outputBuffer);
      byte[] serialized = outputBuffer.getObject(0);

      //serialize tensor via TensorProto
      TensorProto proto = TensorProto.newBuilder()
          .setTensorShape(TensorShapeProto.newBuilder()
              .addDim(Dim.newBuilder().setSize(512).build())
              .addDim(Dim.newBuilder().setSize(512).build())
              .addDim(Dim.newBuilder().setSize(512).build())
              .build())
          .addAllFloatVal(farr)
          .build();

      System.out.println("Generated serialized tensor 1 with " + serialized.length + " bytes");

      byte[] serialized2 = proto.toByteArray();

      System.out.println("Generated serialized tensor 2 with " + serialized2.length + " bytes");

      if (Arrays.equals(serialized, serialized2)) {
        System.out.println("Arrays are the same");
      } else {
        System.out.println("Arrays are not the same");
      }

      //close tensors
      inputTensor.close();
      outputTensor.close();

    }

    //close function in the end
    function.close();

  }

}

Generated serialized tensor 1 with 536870937 bytes
Generated serialized tensor 2 with 536870935 bytes
Arrays are not the same

[lucaro]

So the two missing bytes came from me forgetting to set the data type, after adding .setDtype(DataType.DT_FLOAT) the two arrays have the same length. They are still not identical, but the TensorProto-serialized bytes can be read again, so my use-case is satisfied.