Python UDF Guide

Step-by-step guide to creating UDFs with the Python API

The following guide provides step-by-step instructions to get started writing and running UDFs in Python. This example is a simple distributed UDF that copies data from one table to another using a CSV configuration file to determine on which processing node(s) data will be copied.

Standard (non-replicated) tables have their data distributed across all processing nodes, while replicated tables have all of their data on every processing node. In this example, we'll use a standard table and copy only the portions of its data that reside on the nodes named in the CSV file.

Note that only copying data from some processing nodes typically would not have "real" applications and this exercise is purely to demonstrate the many facets of the UDF API.

References

Prerequisites

The general prerequisites for using UDFs in Kinetica can be found on the User-Defined Function Implementation page.

Program Files

There are three files associated with the Python UDF tutorial. All the files can be found in the Python Tutorial Git Repo, which is cloned in the API Download and Installation section.

  • A UDF management program, udf_tc_py_manager.py , written using the Python API, which creates the input & output tables, and creates the UDF and executes it.
  • A UDF, udf_tc_py_proc.py , written using the Python UDF API, which contains a table copying example.
  • A CSV input file, rank_tom.csv , used to identify which processing nodes should copy data.

API Download and Installation

The Python UDF tutorial requires local access to the Python UDF API & tutorial repositories and the Python API. The native Python API is also used to run the UDF simulator (details found in Development).

  1. In the desired directory, run the following to download the Kinetica Python UDF tutorial repository:

    git clone -b release/v7.1 --single-branch https://github.com/kineticadb/kinetica-tutorial-python-udf-api.git
    
  2. In the same directory, run the following to download the Kinetica Python UDF API repository:

    git clone -b release/v7.1 --single-branch https://github.com/kineticadb/kinetica-udf-api-python.git
    
  3. In the same directory, run the following to download the Kinetica Python API repository:

    git clone -b release/v7.1 --single-branch https://github.com/kineticadb/kinetica-api-python.git
    
  4. Install the pandas Python library:

    pip3 install pandas
    
  5. Change directory into the newly downloaded native Python API repository:

    cd kinetica-api-python
    
  6. In the root directory of the repository, install the Kinetica API:

    sudo python3 setup.py install
    
  7. Change directory into the UDF tutorial root:

    cd ..
    
  8. Add the Python UDF API directory to the PYTHONPATH:

    export PYTHONPATH=$PYTHONPATH:$(cd kinetica-udf-api-python;pwd)
    

Development

The steps below outline using the UDF Simulator, included with the Python API. The UDF Simulator simulates the mechanics of execute_proc() without actually calling it in the database; this is useful for developing UDFs piece-by-piece and test incrementally, avoiding memory ramifications for the database.

  1. Ensure that the Python UDF API directory is in the PYTHONPATH.

  2. Change directory into the newly downloaded Python UDF tutorial repository:

    cd kinetica-tutorial-python-udf-api/table-copy
    
  3. Run the UDF manager script with the init option, specifying the database URL and a username & password:

    python3 udf_tc_py_manager.py init <url> <username> <password>
    
  4. In the native Python API directory, run the UDF Simulator in execute mode with the following options to simulate running the UDF:

    python3 ../../kinetica-api-python/examples/udfsim.py execute -d \
       -i [<schema>.]<input-table> -o [<schema>.]<output-table> \
       -K <url> -U <username> -P <password>
    

    Where:

    • -i - schema-qualified UDF input table
    • -o - schema-qualified UDF output table
    • -K - Kinetica URL
    • -U - Kinetica username
    • -P - Kinetica password

    For instance:

    python3 ../../kinetica-api-python/examples/udfsim.py execute -d \
       -i udf_tc_py_in_table -o udf_tc_py_out_table \
       -K https://<azure.fqdn>/<azure.cluster.name>/gpudb-0 -U kadmin -P kadmin123
    
  5. Copy & execute the export command output by the previous command; this will prepare the execution environment for simulating the UDF:

    export KINETICA_PCF=/tmp/udf-sim-control-files/kinetica-udf-sim-icf-xMGW32
    

    Important

    The export command shown above is an example of what the udfsim.py script will output--it should not be copied to the terminal in which this example is being run. Make sure to copy & execute the actual command output by udfsim.py in the previous step.

  6. Run the UDF:

    python3 udf_tc_py_proc.py
    
  7. Run the UDF Simulator in output mode to output the results to Kinetica (use the dry run flag -d to avoid writing to Kinetica). The results map will be returned (even if there's nothing in it) as well as the number of records that were (or will be in the case of a dry run) added to the given output table:

    python3 ../../kinetica-api-python/examples/udfsim.py output \
       -K <url> -U <username> -P <password>
    

    For instance:

    python3 ../../kinetica-api-python/examples/udfsim.py output \
       -K https://<azure.fqdn>/<azure.cluster.name>/gpudb-0 \
       -U kadmin -P kadmin123
    

    This should output the following:

    No results
    Output:
    
    udf_tc_py_out_table: 10000 records
    
  8. Clean the control files output by the UDF Simulator:

    python3 ../../kinetica-api-python/examples/udfsim.py clean
    

    Important

    The clean command is only necessary if data was output to Kinetica; otherwise, the UDF Simulator can be re-run as many times as desired without having to clean the output files and enter another export command.

Deployment

The UDF can be created and executed using the UDF functions: create_proc() and execute_proc() (respectively).

  1. Run the UDF manager script with the init option to reset the example tables:

    python3 udf_tc_py_manager.py init <url> <username> <password>
    
  2. Run the UDF manager script with the exec option to run the example:

    python3 udf_tc_py_manager.py exec <url> <username> <password>
    
  3. Verify the results, using a SQL client (KiSQL), Kinetica Workbench, or other:

    • The udf_tc_py_in_table table is created in the user's default schema (ki_home, unless a different one was assigned during account creation)

    • A matching udf_tc_py_out_table table is created in the same schema

    • The udf_tc_py_in_table contains 10,000 records of random data

    • The udf_tc_py_out_table contains the correct amount of copied data from udf_tc_py_in_table.

      On single-node installations, as is the case with Developer Edition, all data should be copied. This is because single-node instances have a default configuration of 2 worker ranks with one TOM each, and the rank_tom.csv configuration file contains a reference to rank 1/TOM 0 and rank 2/TOM 0, effectively naming both data TOMs to copy data from.

      In larger cluster configurations, only a fraction of the data in the input table will be stored on those two TOMs; so, the output table will contain that same fraction of the input table's data.

      The database logs should also show the portion of the data being copied:

      Copying <5071> records on rank/TOM <1/0> from <ki_home.udf_tc_py_in_table> to <ki_home.udf_tc_py_out_table>
      Copying <4929> records on rank/TOM <2/0> from <ki_home.udf_tc_py_in_table> to <ki_home.udf_tc_py_out_table>
      

UDF Detail

As mentioned previously, this section details a simple distributed UDF that copies data from one table to another. While the table copy UDF can run against multiple tables, the example run will use a single table, udf_tc_py_in_table, as input and a similar table, udf_tc_py_out_table, for output.

The input table will contain one int16 column (id) and two float columns (x and y). The id column will be an ordered integer field, with the first row containing 1, the second row containing 2, etc. Both float columns will contain 10,000 pairs of randomly-generated numbers:

+------+-----------+-----------+
| id   | x         | y         |
+======+===========+===========+
| 1    | 2.57434   | -3.357401 |
+------+-----------+-----------+
| 2    | 0.0996761 | 5.375546  |
+------+-----------+-----------+
| ...  | ...       | ...       |
+------+-----------+-----------+

The output table will also contain one int16 column (id) and two float columns (a and b). No data is inserted:

+------+-----------+-----------+
| id   | a         | b         |
+======+===========+===========+
|      |           |           |
+------+-----------+-----------+

The UDF will first read from a given CSV file to determine from which processing node container (rank) and processing node (TOM) to copy data:

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rank_num,tom_num
1,0
2,0

The tom_num column values refer to processing nodes that contain the many shards of data inside the database. The rank_num column values refer to processing node containers that hold the processing nodes for the database. For example, the given CSV file determines that the data from udf_tc_py_in_table on processing node container 1, processing node 0 and processing node container 2, processing node 0 will be copied to udf_tc_py_out_table on those same nodes.

Once the UDF is executed, a UDF instance (OS process) is spun up for each processing node to execute the UDF code against its assigned processing node's data. Each UDF process then determines if its corresponding processing node container/processing node pair matches one of the pairs of values in the CSV file. If there is a match, the UDF process will loop through the given input tables and copy the data contained in that processing node from the input tables to the output tables. If there isn't a match, no data will be copied by that process.

Initialization (udf_tc_py_manager.py init)

The init option invokes the init() function in the udf_tc_py_manager.py script. This function will create the input table for the UDF to copy data from and the output table to copy data to. Sample data will also be generated and inserted into the input table.

To interact with Kinetica, you must first instantiate an object of the GPUdb class while providing the connection URL and username & password to use for logging in. This database object is later passed to the init() and exec() methods:

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kinetica = gpudb.GPUdb(host=[args.url], username=args.username, password=args.password)

The input table is created.

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columns = [
    ["id", "int", "int16", "primary_key"],
    ["x", "float"],
    ["y", "float"]
]

if kinetica.has_table(table_name=input_table)['table_exists']:
    kinetica.clear_table(table_name=input_table)

input_table_obj = gpudb.GPUdbTable(
    _type = columns,
    name = input_table,
    db = kinetica
)

Next, sample data is generated and inserted into the new input table.

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records = []
for val in range(1, MAX_RECORDS+1):
    records.append([val, random.gauss(1, 1), random.gauss(1, 2)])
input_table_obj.insert_records(records)

Lastly, an output table is created with a schema that is similar to the input table but is removed first if it already exists.

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columns = [
    ["id", "int", "int16", "primary_key"],
    ["a", "float"],
    ["b", "float"]
]

if kinetica.has_table(table_name=output_table)['table_exists']:
    kinetica.clear_table(table_name=output_table)

output_table_obj = gpudb.GPUdbTable(
    _type = columns,
    name = output_table,
    db = kinetica
)

UDF (udf_tc_py_proc.py)

The udf_tc_py_proc.py script is the UDF itself. It does the work of copying the input table data to the output table, based on the ranks & TOMs specified in the given CSV file.

First, instantiate a handle to the ProcData() class:

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proc_data = ProcData()

Retrieve the rank/TOM pair for this UDF process instance from the request info map:

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proc_rank_num = proc_data.request_info["rank_number"]
proc_tom_num = proc_data.request_info["tom_number"]

Then, the CSV file mentioned in Program Files is read (skipping the header):

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rank_tom_info = csv.reader(open("rank_tom.csv"))
next(rank_tom_info)

Compare the rank and TOM of the current UDF instance's processing node to each rank/TOM pair in the file to determine if the current UDF instance should copy the data on its corresponding processing node:

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for row in rank_tom_info:
    rank_num = row[0]
    tom_num = row[1]

    if (proc_rank_num == rank_num and proc_tom_num == tom_num):

For each input and output table found in the input_data and output_data objects (respectively), set the output tables' size to the input tables' size. This will allocate enough memory to copy all input records to the output table:

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for in_table, out_table in zip(
        proc_data.input_data, proc_data.output_data):
    out_table.size = in_table.size

For each input column in the input table(s), copy the input columns' values to the corresponding output table columns:

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for in_column, out_column in zip(in_table, out_table):
    out_column.extend(in_column)

Call complete() to tell Kinetica the UDF is finished.

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proc_data.complete()

Execution (udf_tc_py_manager.py exec)

The exec option invokes the exec() function in the udf_tc_py_manager.py script. This function will read files in as bytes, create a UDF, and upload the files to the database. The function will then execute the UDF.

To upload the udf_tc_py_proc.py and rank_tom.csv files to Kinetica, they will first need to be read in as bytes and added to a file data map:

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file_names = (CSV_FILE_NAME, PROC_FILE_NAME)
files = {}
for file_name in file_names:
    with open(file_name, 'rb') as file:
        files[file_name] = file.read()

After the files are placed in a data map, the distributed udf_tc_py_proc UDF can be created in Kinetica and the files can be associated with it:

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response = kinetica.create_proc(
    proc_name = PROC_NAME,
    execution_mode = "distributed",
    files = files,
    command = "python",
    args = [PROC_FILE_NAME],
    options = {}
)

Finally, after the UDF is created, it can be executed. The input & output tables created in the Initialization (udf_tc_py_manager.py init) section are passed in here:

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response = kinetica.execute_proc(
    proc_name = PROC_NAME,
    params = {},
    bin_params = {},
    input_table_names = [input_table],
    input_column_names = {},
    output_table_names = [output_table],
    options = {}
)