Kratos: Errors Load function for StreamSerializer object

[riccardotosi]

Hi to everyone,

If in https://github.com/KratosMultiphysics/Kratos/blob/master/kratos/tests/test_model.py in the function "test_file_serialization" I modify/add the lines

    # ######## here we pickle the serializer
    # try:
    #     import cpickle as pickle  # Use cPickle on Python 2.7
    # except ImportError:
    #     import pickle

    # #pickle dataserialized_data
    # pickled_data = pickle.dumps(serializer, 2) #second argument is the protocol and is NECESSARY (according to pybind11 docs)

    # #overwrite the old serializer with the unpickled one
    # serializer = pickle.loads(pickled_data)

    loaded_model = KratosMultiphysics.Model()
    serializer.Load("ModelSerialization",loaded_model)
    self.assertTrue(loaded_model["Main"].HasNodalSolutionStepVariable(KratosMultiphysics.TEMPERATURE))
    self.assertTrue(loaded_model["Other"].HasNodalSolutionStepVariable(KratosMultiphysics.PRESSURE))

    self.assertTrue(loaded_model.HasModelPart("Main.Inlets"))
    self.assertTrue(loaded_model.HasModelPart("Main.Temp"))
    self.assertTrue(1 in loaded_model["Main"].Nodes)
    self.assertTrue(1 in loaded_model["Other"].Nodes)

    del(loaded_model)

    loaded_model_again = KratosMultiphysics.Model()
    serializer.Load("ModelSerialization",loaded_model_again)

I am not able to deserialize a second time the StreaSerializer object. I get the following error:
serializer.Load("ModelSerialization",loaded_model_again)
MemoryError: std::bad_alloc

For the parameters I get a similar problem when I deserealize a second time. In https://github.com/KratosMultiphysics/Kratos/blob/master/kratos/tests/test_kratos_parameters.py in the function "test_stream_serialization" I modify/add the following lines

    # ######## here we pickle the serializer
    # try:
    #     import cickle as pickle  # Use cPickle on Python 2.7
    # except ImportError:
    #     import pickle

    # #pickle dataserialized_data
    # pickled_data = pickle.dumps(serializer, 2) #second argument is the protocol and is NECESSARY (according to pybind11 docs)
    # del(serializer)

    #unpickle data - note that here i override "serialized_data"
    # serializer = pickle.loads(pickled_data)

    loaded_parameters = Parameters()
    serializer.Load("ParametersSerialization",loaded_parameters)

    loaded_parameters_again = Parameters()
    serializer.Load("ParametersSerialization",loaded_parameters_again)

to deserialize a second time the StreamSerializer Kratos object, and I get the following error:
The document is empty. offset of the error from the beginning of the string = 0

I attach the two files I modifed.

Serializer_errors.zip

[pooyan-dadvand]

Seems to be a not symmetric load and save. Can you try to construct the serializer with debug flag and see what it is saying?

[riccardotosi]

What do you mean with debug flag?

[roigcarlo]

Look for the call of FileSerializer(Filename) and add trace flag: SERIALIZER_TRACE_ALL in the constructor

Ex:

serializer = Kratos.FileSerializer("serialized_model.txt", Kratos.SERIALIZER_TRACE_ALL)

We did something similar 2 weeks ago when we were debugging the problem with the parameters.

[philbucher]

is this still active?

[roigcarlo]

Yep, still working on this

[roigcarlo]

Btw this will be fixed when we #5071

[RiccardoRossi]

@riccardotosi independently of tbis been solved i would avoid using neighbours in your algorithm. we ll discuss thjs in person