Anyone able to load tfrecords into TFRS generated with the spark-to-tf-records connector?

[dgoldenberg-audiomack]

Anyone see this kind of error when trying to load TF records generated from Spark by the spark to tf records connector or linkedin's spark tf record library?

Error: Error when deserializing tfrecord's in TF 2.x: Only integers, slices (:), ellipsis (...), tf.newaxis (None) and scalar tf.int32/tf.int64 tensors are valid indices

Filed tickets there with details

• https://github.com/linkedin/spark-tfrecord/issues/19
• https://github.com/tensorflow/ecosystem/issues/178

Really just doing a simple thing, using the small movielens dataset:

    # Code for the connector
    movies_df.write.format("tfrecords").mode("overwrite").save(tf_movies_dir)
    ratings_df.write.format("tfrecords").mode("overwrite").save(tf_ratings_dir)

    # Alternatively, code for the spark to tfrecord
    movies_df.write.format("tfrecord").mode("overwrite").option("recordType", "Example").save(tf_movies_dir)
    ratings_df.write.format("tfrecord").mode("overwrite").option("recordType", "Example").save(tf_ratings_dir)

    s3 = boto3.resource("s3", verify=False)
    bucket = s3.Bucket("mybucket")

    filenames = []
    for object_summary in bucket.objects.filter(
            Prefix=f"emr/spark_apps/myapp/movielens-100k-conversion/movies-0001/part"
    ):
        filenames.append(os.path.join("s3://audiomack-master-airflow/", object_summary.key))
    movies_dataset = tf.data.TFRecordDataset(filenames)

    filenames = []
    for object_summary in bucket.objects.filter(
            Prefix=f"emr/spark_apps/myapp/movielens-100k-conversion/ratings-0001/part"
    ):
        filenames.append(os.path.join("s3://audiomack-master-airflow/", object_summary.key))
    ratings_dataset = tf.data.TFRecordDataset(filenames)

[dgoldenberg-audiomack]

That said, there's the CSV consuming api's... https://www.tensorflow.org/guide/data#consuming_csv_data, wonder if that's just a better, more direct approach anyway. I have Parquet data to consume; in theory should be able to load it as described here https://github.com/tensorflow/io/issues/1121

[maciejkula]

It might help folks answer this if you post the entire stack trace of your error. It's hard to say what's going on based on your summary of the error message.

[dgoldenberg-audiomack]

Hi @maciejkula, there are two slightly different stack traces in the linked tickets I've included.

However here's one of them:

Traceback (most recent call last): File "/mnt/tmp/spark-9eb04118-c94f-4ed6-bb6b-75927f4d389f/recsys_tfrs_proto.py", line 304, in main(sys.argv) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/autograph/impl/api.py", line 302, in wrapper return func(*args, kwargs) File "/mnt/tmp/spark-9eb04118-c94f-4ed6-bb6b-75927f4d389f/recsys_tfrs_proto.py", line 50, in main movies, test, train, unique_movie_titles, unique_user_ids = prepare_data(movies, ratings) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/autograph/impl/api.py", line 302, in wrapper return func(*args, *kwargs) File "/mnt/tmp/spark-9eb04118-c94f-4ed6-bb6b-75927f4d389f/recsys_tfrs_proto.py", line 155, in prepare_data ratings = ratings.map(lambda x: {"movie_title": x["movie_title"], "user_id": x["user_id"]}) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/data/ops/dataset_ops.py", line 1695, in map return MapDataset(self, map_func, preserve_cardinality=True) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/data/ops/dataset_ops.py", line 4045, in init use_legacy_function=use_legacy_function) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/data/ops/dataset_ops.py", line 3371, in init self._function = wrapper_fn.get_concrete_function() File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/eager/function.py", line 2939, in get_concrete_function args, kwargs) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/eager/function.py", line 2906, in _get_concrete_function_garbage_collected graph_function, args, kwargs = self._maybe_define_function(args, kwargs) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/eager/function.py", line 3213, in _maybe_define_function graph_function = self._create_graph_function(args, kwargs) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/eager/function.py", line 3075, in _create_graph_function capture_by_value=self._capture_by_value), File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/framework/func_graph.py", line 986, in func_graph_from_py_func func_outputs = python_func(*func_args, func_kwargs) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/data/ops/dataset_ops.py", line 3364, in wrapper_fn ret = _wrapper_helper(args) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/data/ops/dataset_ops.py", line 3299, in _wrapper_helper ret = autograph.tf_convert(func, ag_ctx)(nested_args) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/autograph/impl/api.py", line 302, in wrapper return func(*args, *kwargs) File "/mnt/tmp/spark-9eb04118-c94f-4ed6-bb6b-75927f4d389f/recsys_tfrs_proto.py", line 155, in ratings = ratings.map(lambda x: {"movie_title": x["movie_title"], "user_id": x["user_id"]}) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/util/dispatch.py", line 201, in wrapper return target(args, kwargs) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 986, in _slice_helper _check_index(s) File "/usr/local/lib64/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 865, in _check_index raise TypeError(_SLICE_TYPE_ERROR + ", got {!r}".format(idx)) TypeError: Only integers, slices (:), ellipsis (...), tf.newaxis (None) and scalar tf.int32/tf.int64 tensors are valid indices, got 'movie_title'

[maciejkula]

It looks like the error is in the map function:

ratings.map(lambda x: {"movie_title": x["movie_title"], "user_id": x["user_id"]})

Whatever the elements of ratings are, they are not dictionaries. What are they?

[dgoldenberg-audiomack]

That's true, unlike with tfds.load, when using the connector and then feeding the files into a tf.data.TFRecordDataset, the elements are not dictionaries, rather they're of type class bytes.

The question is, how does one decode these bytes?

b'\ns\n\x11\n\x08movie_id\x12\x05\x1a\x03\n\x01\x01\n#\n\x0bmovie_title'\x12\x14\n\x12\n\x10Toy Story (1995)\n9\n\x06genres\x12/\n-\n+Adventure|Animation|Children|Comedy|Fantasy'

Clearly this has movie_id, movie_title, and genres. .decode("utf-8") doesn't work and this doesn't cleanly un-hexify, either.

Similarly, for ratings b'\n|\n\x10\n\x07user_id\x12\x05\x1a\x03\n\x01\x01\n\x11\n\x08movie_id\x12\x05\x1a\x03\n\x01\x1f\n)\n\x0bmovie_title\x12\x1a\n\x18\n\x16Dangerous Minds (1995)\n\x12\n\x06rating\x12\x08\x12\x06\n\x04\x00\x00 @\n\x16\n\ttimestamp\x12\t\x1a\x07\n\x05\xe8\xd0\x96\xd9\x04'

Wonder if there's a utility method in tf somewhere..

[maciejkula]

I'm pretty sure the problem is on the writing side. What things do you expect Spark to be writing to these files? Is it writing what you think it's writing?

[dgoldenberg-audiomack]

It's writing the right keys (column names) and the right values, but I don't know enough about the internal tf record format. So this binary blob arrangement I can't pass a judgement on as far as correctness and the encoding it's using. It seems that there's some kind of a disconnect between what's being written and how it's being read into the dataset.

Maybe it's a TF 1.x vs. TF 2.x issue. Or maybe when reading into a TF dataset, tfrecords need to pass through another conversion layer.

All in all, not a critical issue for me because now I want to load Parquet into TF datasets directly; experimenting with that now. I had thought I'd have to write Spark dataframes into intermediary tfrecord files first then load them into tf datasets. But there seems to be a more direct way to just go Parquet -> DS.

That said, I think the load of tfrecord files into a TF DS "should work".

[maciejkula]

Have you looked at the docs for reading TFRecord files containing tf.train.Examples?

It looks like you're skipping the deserialization step (converting the serialized tf.train.Example protos to dictionaries of tensors).

[dgoldenberg-audiomack]

Oic, you mean this? -

parsed_dataset = raw_dataset.map(_parse_function)

It seems odd that one has to load the tfrecords into a dataset, then convert it while instructing it what's in the files :)

I would think that the dataset should be able to do the parsing itself, encapsulating the knowledge of how to parse these files...

I'll try this out a little later

[dgoldenberg-audiomack]

We can probably close the ticket; it may be worth mentioning in the docs that the 'parse' type of transformation is required; it's not obvious especially to a noob :)

[Data-Jack]

@dgoldenberg-audiomack Did you ever find a solution for this? I think I am experiencing a simlar issue when writing array of array column types.

I gtet the error "InvalidArgumentError: Feature: cold (data type: float) is required but could not be found. [Op:ParseSingleExample]" even though "cold" is clearly in the message byte string.

from pyspark.sql.types import *

data = [("A", 1, [1.1,2.0,3.0], [[0.0,1.0],[1.0,0.0]]),
         ("B", 2, [11.0,12.3,13.0], [[0.0,1.0],[1.0,0.0]]),
         ("C", 3, [21.0,22.0,23.5], [[1.0,0.0],[1.0,0.0]]),
  ]

schema = StructType([ \
    StructField("colA",StringType(),True), \
    StructField("colb",IntegerType(),True), \
    StructField("colc",ArrayType(FloatType()),True), \
    StructField("cold",ArrayType(ArrayType(FloatType())),True), \
  ])

df = spark.createDataFrame(data=data,schema=schema)
# df = 
#Write 
write_path = "/home/pathtowrite"

df.write.format("tfrecords").option("recordType", "SequenceExample").mode("overwrite").save(write_path)

### Readin with tensorflow

import tensorflow as tf
import os 

files = [f"{write_path}/{x}" for x in os.listdir(write_path) if x.startswith("part")]
dataset = tf.data.TFRecordDataset(files)
# Create a dictionary describing the features.
feature_description = {
    'colA': tf.io.FixedLenFeature([], tf.string),
    'colb': tf.io.FixedLenFeature([], tf.int64),
    'colc': tf.io.FixedLenFeature([3], tf.float32),
    'cold': tf.io.FixedLenFeature([2,2], tf.float32),
}

for i in dataset.take(1):
    print(repr(i))
    example = tf.io.parse_single_example(i, feature_description)
    print(example)

[dgoldenberg-audiomack]

@Data-Jack In my particular case, the solution was to make sure I use the map:

parsed_dataset = raw_dataset.map(_parse_function)

However generally I've moved away from using tf-records. At least, my current thinking is why bother :) TF has ways of loading CSV and Parquet data into its datasets. What I do is wrangle all the input data to CSV/Parquet using Spark, then load it into TF datasets.

I have filed this issue in TF for better interoperability with Spark.

However, there's also the Big DL project which presumably allows one to distribute TF training using Spark.

[Data-Jack]

@dgoldenberg-audiomack Unfortunately my data contains arrays of array fields and map still doesn't work. Chucking the below parsing function in my example still produces the same error for me.

def _parse_function(example_proto):
  # Parse the input tf.train.Example proto using the dictionary above.
  return tf.io.parse_single_example(example_proto, feature_description)

parsed_dataset = dataset.map(_parse_function)
for i in parsed_dataset.take(1):
    print(i)

Thanks for the tip, I will look into to a pipeline that reads from parquet. I was really hoping to just be able to write all my nested array fields to tf-record and read them in. I am going to settle for flattening all the arrays into 1 array for now whilst I research other options.

[dgoldenberg-audiomack]

@Data-Jack Have you considered filing an issue with tensorflow-io, or core TF? they might suggest something.

[Data-Jack]

@dgoldenberg-audiomack Yeah, I will do. My first guess was it was how it was being written.