Vertica Documentation – TensorFlow models

Data-Analysis: TensorFlow integration and directory structure

Mon, 01 Jan 0001 00:00:00 +0000

This page covers importing Tensorflow models into Vertica, making predictions on data in the Vertica database, and exporting the model for use on another Vertica cluster or a third-party platform.

For a start-to-finish example through each operation, see TensorFlow example.

Vertica supports models created with either TensorFlow 1.x and 2.x, but 2.x is strongly recommended.

To use TensorFlow with Vertica, install the TFIntegration UDX package on any node. You only need to do this once:

$ /opt/vertica/bin/admintools -t install_package -d database_name -p 'password' --package TFIntegration

Directory and file structure for TensorFlow models

Before importing your models, you should have a separate directory for each model that contains one of each of the following. Note that Vertica uses the directory name as the model name when you import it:

model_name.pb: a trained model in frozen graph format
tf_model_desc.json: a description of the model

You can generate both files for a given TensorFlow 2 model with the script freeze_tf2_model.py included in Machine-Learning-Examples/TensorFlow repository (or in opt/vertica/packages/TFIntegration/examples), though you may need to make modifications to the description based on your use-case and how you want your Vertica database to interact with your model:

$ python3 Tensorflow/freeze_tf2_model.py your/model/directory

For example, the tf_models directory contains two models, tf_mnist_estimator and tf_mnist_keras:

tf_models/
├── tf_mnist_estimator
│   ├── mnist_estimator.pb
│   └── tf_model_desc.json
└── tf_mnist_keras
    ├── mnist_keras.pb
    └── tf_model_desc.json

tf_model_desc.json

The tf_model_desc.json file forms the bridge between TensorFlow and Vertica. It describes the structure of the model so that Vertica can correctly match up its inputs and outputs to input/output tables.

Notice that the freeze_tf2_model.py script automatically generates this file for your model, and this generated file can often be used as-is. For more complex models or use cases, you might have to edit this file. For a detailed breakdown of each field, see tf_model_desc.json overview.

Importing TensorFlow models into Vertica

To import TensorFlow models, use IMPORT_MODELS with the category 'TENSORFLOW'.

Import a single model. Keep in mind that the Vertica database uses the directory name as the model name:

select IMPORT_MODELS ( '/path/tf_models/tf_mnist_keras' USING PARAMETERS category='TENSORFLOW');
 import_models
---------------
 Success
(1 row)

Import all models in the directory (where each model has its own directory) with a wildcard (*):

select IMPORT_MODELS ('/path/tf_models/*' USING PARAMETERS category='TENSORFLOW');
 import_models
---------------
 Success
(1 row)

Predicting with an imported TensorFlow model

After importing your TensorFlow model, you can use the model to predict on data in a Vertica table.

The PREDICT_TENSORFLOW function is different from the other predict functions in that it does not accept any parameters that affect the input columns such as "exclude_columns" or "id_column"; rather, the function always predicts on all the input columns provided. However, it does accept a num_passthru_cols parameter which allows the user to "skip" some number of input columns, as shown below.

The OVER(PARTITION BEST) clause tells Vertica to parallelize the operation across multiple nodes. See Window Partition Clause for details:

=> select PREDICT_TENSORFLOW (*
                   USING PARAMETERS model_name='tf_mnist_keras', num_passthru_cols=1)
                   OVER(PARTITION BEST) FROM tf_mnist_test_images;

--example output, the skipped columns are displayed as the first columns of the output
 ID | col0 | col1 | col2 | col3 | col4 | col5 | col6 | col7 | col8 | col9
----+------+------+------+------+------+------+------+------+------+------
  1 |    0 |    0 |    1 |    0 |    0 |    0 |    0 |    0 |    0 |    0
  3 |    1 |    0 |    0 |    0 |    0 |    0 |    0 |    0 |    0 |    0
  6 |    0 |    0 |    0 |    0 |    1 |    0 |    0 |    0 |    0 |    0
...

Exporting TensorFlow models

Vertica exports the model as a frozen graph, which can then be re-imported at any time. Keep in mind that models that are saved as a frozen graph cannot be trained further.

Use EXPORT_MODELS to export TensorFlow models. For example, to export the tf_mnist_keras model to the /path/to/export/to directory:

=> SELECT EXPORT_MODELS ('/path/to/export/to', 'tf_mnist_keras');
 export_models
---------------
 Success
(1 row)

When you export a TensorFlow model, the Vertica database creates and uses the specified directory to store files that describe the model:

$ ls tf_mnist_keras/
crc.json  metadata.json  mnist_keras.pb  model.json  tf_model_desc.json

The .pb and tf_model_desc.json files describe the model, and the rest are organizational files created by the Vertica database.

File Name	Purpose
`model_name.pb`	Frozen graph of the model.
`tf_model_desc.json`	Describes the model.
`crc.json`	Keeps track of files in this directory and their sizes. It is used for importing models.
`metadata.json`	Contains Vertica version, model type, and other information.
`model.json`	More verbose version of `tf_model_desc.json`.

Data-Analysis: TensorFlow example

Mon, 01 Jan 0001 00:00:00 +0000

Vertica uses the TFIntegration UDX package to integrate with TensorFlow. You can train your models outside of your Vertica database, then import them to Vertica and make predictions on your data.

TensorFlow scripts and datasets are included in the GitHub repository under Machine-Learning-Examples/TensorFlow.

The example below creates a Keras (a TensorFlow API) neural network model trained on the MNIST handwritten digit classification dataset, the layers of which are shown below.

The data is fed through each layer from top to bottom, and each layer modifies the input before returning a score. In this example, the data passed in is a set of images of handwritten Arabic numerals and the output would be the probability of the input image being a particular digit:

inputs = keras.Input(shape=(28, 28, 1), name="image")
x = layers.Conv2D(32, 5, activation="relu")(inputs)
x = layers.MaxPooling2D(2)(x)
x = layers.Conv2D(64, 5, activation="relu")(x)
x = layers.MaxPooling2D(2)(x)
x = layers.Flatten()(x)
x = layers.Dense(10, activation='softmax', name='OUTPUT')(x)
tfmodel = keras.Model(inputs, x)

For more information on how TensorFlow interacts with your Vertica database and how to import more complex models, see TensorFlow integration and directory structure.

Prepare a TensorFlow model for Vertica

The following procedures take place outside of Vertica.

Train and save a TensorFlow model

Install TensorFlow 2.
Train your model. For this particular example, you can run train_simple_model.py to train and save the model. Otherwise, and more generally, you can manually train your model in Python and then save it:
```
$ mymodel.save('my_saved_model_dir')
```
Run the freeze_tf2_model.py script included in the Machine-Learning-Examples repository or in opt/vertica/packages/TFIntegration/examples, specifying your model and an output directory (optional, defaults to frozen_tfmodel).

This script transforms your saved model into the Vertica-compatible frozen graph format and creates the tf_model_desc.json file, which describes how Vertica should translate its tables to TensorFlow tensors:
```
$ ./freeze_tf2_model.py path/to/tf/model frozen_model_dir
```

Import TensorFlow models and make predictions in Vertica

If you haven't already, as dbadmin, install the TFIntegration UDX package on any node. You only need to do this once.
```
$ /opt/vertica/bin/admintools -t install_package -d database_name -p 'password' --package TFIntegration
```

Copy the the directory to any node in your Vertica cluster and import the model:

=> SELECT IMPORT_MODELS('path/to/frozen_model_dir' USING PARAMETERS category='TENSORFLOW');

Import the dataset you want to make a prediction on. For this example:
1. Copy the Machine-Learning-Examples/TensorFlow/data directory to any node on your Vertica cluster.
2. From that data directory, run the SQL script load_tf_data.sql to load the MNIST dataset:
```
$ vsql -f load_tf_data.sql
```

Make a prediction with your model on your dataset with PREDICT_TENSORFLOW. In this example, the model is used to classify the images of handwritten numbers in the MNIST dataset:

=> SELECT PREDICT_TENSORFLOW (*
                   USING PARAMETERS model_name='tf_mnist_keras', num_passthru_cols=1)
                   OVER(PARTITION BEST) FROM tf_mnist_test_images;

--example output, the skipped columns are displayed as the first columns of the output
 ID | col0 | col1 | col2 | col3 | col4 | col5 | col6 | col7 | col8 | col9
----+------+------+------+------+------+------+------+------+------+------
  1 |    0 |    0 |    1 |    0 |    0 |    0 |    0 |    0 |    0 |    0
  3 |    1 |    0 |    0 |    0 |    0 |    0 |    0 |    0 |    0 |    0
  6 |    0 |    0 |    0 |    0 |    1 |    0 |    0 |    0 |    0 |    0
...

To export the model with EXPORT_MODELS:

=> SELECT EXPORT_MODELS('/path/to/export/to', 'tf_mnist_keras');
 EXPORT_MODELS
---------------
 Success
(1 row)

Note

While you cannot continue training a TensorFlow model after you export it from Vertica, you can use it to predict on data in another Vertica cluster, or outside Vertica on another platform.

TensorFlow 1 (deprecated)

Install TensorFlow 1.15 with Python 3.7 or below.
Run train_save_model.py in Machine-Learning-Examples/TensorFlow/tf1 to train and save the model in TensorFlow and frozen graph formats.

Data-Analysis: tf_model_desc.json overview

Mon, 01 Jan 0001 00:00:00 +0000

Before importing your externally trained TensorFlow models, you must:

save the model in frozen graph (.pb) format
create tf_model_desc.json, which describes to your Vertica database how to map its inputs and outputs to input/output tables

Conveniently, the script freeze_tf2_model.py included in the TensorFlow directory of the Machine-Learning-Examples repository (and in opt/vertica/packages/TFIntegration/examples) will do both of these automatically. In most cases, the generated tf_model_desc.json can be used as-is, but for more complex datasets and use cases, you might need to edit it.

tf_model_desc.json for an example dataset

The following tf_model_desc.json is generated from the MNIST handwriting dataset used by the TensorFlow example.

{
    "frozen_graph": "mnist_keras.pb",
    "input_desc": [
        {
            "op_name": "image_input",
            "tensor_map": [
                {
                    "idx": 0,
                    "dim": [
                        1,
                        28,
                        28,
                        1
                    ],
                    "col_start": 0
                }
            ]
        }
    ],
    "output_desc": [
        {
            "op_name": "OUTPUT/Softmax",
            "tensor_map": [
                {
                    "idx": 0,
                    "dim": [
                        1,
                        10
                    ],
                    "col_start": 0
                }
            ]
        }
    ]
}

This file describes the structure of the model's inputs and outputs. It must contain a frozen_graph field that matches the filename of the .pb model, an input_desc field, and an output_desc field.

input_desc and output_desc: the descriptions of the input and output nodes in the TensorFlow graph. Each of these include the following fields:
- op_name: the name of the operation node which is set when creating and training the model. You can typically retrieve the names of these parameters from tfmodel.inputs and tfmodel.outputs. For example:
```
$ print({t.name:t for t in tfmodel.inputs})
{'image_input:0': <tf.Tensor 'image_input:0' shape=(?, 28, 28, 1) dtype=float32>}
```
```
$ print({t.name:t for t in tfmodel.outputs})
{'OUTPUT/Softmax:0': <tf.Tensor 'OUTPUT/Softmax:0' shape=(?, 10) dtype=float32>}
```
  In this case, the respective values for op_name would be the following.
  - input_desc: image_input
  - output_desc: OUTPUT/Softmax
  For a more detailed example of this process, review the code for freeze_tf2_model.py.
- tensor_map: how to map the tensor to Vertica columns, which can be specified with the following:
  - idx: the index of the tensor (should be 0 for the first input/output, 1 for the second input/output, etc.)
  - dim: the vector holding the dimensions of the tensor; it provides the number of columns
  - col_start (only used if col_idx is not specified): the starting column index. When used with dim, it specifies a range of indices of Vertica columns starting at col_start and ending at col_start+dim; Vertica starts at the column specified by the index col_start and gets the next dim columns
  - col_idx: the indices in the Vertica columns corresponding to the flattened tensors. This allows you explicitly specify the indices of the Vertica columns that couldn't otherwise be specified as a simple range with col_start and dim (e.g. 1, 3, 5, 7)
  - data_type (not shown): the data type of the input or output, one of the following:
    - TF_FLOAT (default)
    - TF_DOUBLE
    - TF_INT8
    - TF_INT16
    - TF_INT32
    - TF_INT64

Complex tf_model_desc.json example

Below is a more complex example that includes multiple inputs and outputs:

{
    "input_desc": [
        {
            "op_name": "input1",
            "tensor_map": [
                {
                    "idx": 0,
                    "dim": [
                        4
                    ],
                    "col_idx": [
                        0,
                        1,
                        2,
                        3
                    ]
                },
                {
                    "idx": 1,
                    "dim": [
                        2,
                        2
                    ],
                    "col_start": 4
                }
            ]
        },
        {
            "op_name": "input2",
            "tensor_map": [
                {
                    "idx": 0,
                    "dim": [],
                    "col_idx": [
                        8
                    ]
                },
                {
                    "idx": 1,
                    "dim": [
                        2
                    ],
                    "col_start": 9
                }
            ]
        }
    ],
    "output_desc": [
        {
            "op_name": "output",
            "tensor_map": [
                {
                    "idx": 0,
                    "dim": [
                        2
                    ],
                    "col_start": 0
                }
            ]
        }
    ]
}

Vertica Documentation – TensorFlow models

Data-Analysis: TensorFlow integration and directory structure

Directory and file structure for TensorFlow models

tf_model_desc.json

Importing TensorFlow models into Vertica

Predicting with an imported TensorFlow model

Exporting TensorFlow models

See also

Data-Analysis: TensorFlow example

Prepare a TensorFlow model for Vertica

Train and save a TensorFlow model

Import TensorFlow models and make predictions in Vertica

Note

TensorFlow 1 (deprecated)

See also

Data-Analysis: tf_model_desc.json overview

tf_model_desc.json for an example dataset

Complex tf_model_desc.json example

See also