Run a Prefect Cloud Data Pipeline on a Dask Cluster

Create a prefect flow and distribute all tasks across Dask clusters. Register this flow with Prefect Cloud
Run a Prefect Cloud Data Pipeline on a Dask Cluster
Try this example in seconds on Saturn Cloud

Overview

Prefect Cloud is a hosted, high-availability, fault-tolerant service that handles all the orchestration responsibilities for running data pipelines. It gives you complete oversight of your workflows and makes it easy to manage them.

This example shows how to create a set of tasks for a project and execute these tasks on dask. We will then register this flow with Prefect Cloud so that service can be used for orchestrating when the flow runs.

By using a Dask cluster, tasks can be executed parallel to each other across multiple machines which can dramatically speed up overall run time. If you only want to use a single machine for the entire run, see the single machine example.

The code within each task will only be running on a single machine in the cluster. There might be situations where you want the tasks be able to execute on a Dask cluster themselves, such as when each task is parallelizable within itself. For an example of that, see Run a Prefect Cloud Data Pipeline with access to a Dask Cluster.

Prefect Execution

Model Details

The data used for this example is the “Incident management process enriched event log” dataset from the UCI Machine Learning Repository.This dataset contains tickets from an IT support system, including characteristics like the priority of the ticket, the time it was opened, and the time it was closed.

We will use this dataset in our example to solve following regression task:

Given the characteristics of a ticket, how long will it be until it is closed?

We wil then evaluate the performance of above model, that predicts time-to-close for tickets in an IT support system.

Modelling Process

Prerequisites

  • created a Prefect Cloud account
  • set up the appropriate credentials in Saturn
  • set up a Prefect Cloud agent in Saturn Cloud

Details on these prerequisites can be found in Using Prefect Cloud with Saturn Cloud.

Environment Setup

The code in this example uses prefect for orchestration (figuring out what to do, and in what order) and Dask Cluster for execution (doing the things).

It relies on the following additional non-builtin libraries:

  • numpy: data manipulation
  • pandas: data manipulation
  • requests: read in data from the internet
  • scikit-learn: evaluation metric functions
  • dask-saturn: create and interact with Saturn Cloud Dask clusters.
  • prefect-saturn: register Prefect flows with both Prefect Cloud and have them run on Saturn Cloud Dask clusters.
import json
import os
import uuid
from datetime import datetime, timedelta
from io import BytesIO
from zipfile import ZipFile

import numpy as np
import pandas as pd
import requests
from prefect.schedules import IntervalSchedule
from prefect_saturn import PrefectCloudIntegration
from sklearn.metrics import (
    mean_absolute_error,
    mean_squared_error,
    median_absolute_error,
    r2_score,
)

import prefect
from prefect import Flow, Parameter, task

PREFECT_CLOUD_PROJECT_NAME = os.environ["PREFECT_CLOUD_PROJECT_NAME"]
SATURN_USERNAME = os.environ["SATURN_USERNAME"]

Authenticate with Prefect Cloud.

!prefect auth login --key ${PREFECT_USER_TOKEN}

Create a Prefect Cloud Project

Prefect Cloud organizes flows within workspaces called “projects”. Before you can register a flow with Prefect Cloud, it’s necessary to create a project, if you don’t have one yet.

The code below will create a new project in whatever Prefect Cloud tenant you’re authenticated with. If that project already exists, this code does not have any side effects.

client = prefect.Client()
client.create_project(project_name=PREFECT_CLOUD_PROJECT_NAME)

Define Tasks

Prefect refers to a workload as a “flow”, which comprises multiple individual things to do called “tasks”. From the Prefect docs:

A task is like a function: it optionally takes inputs, performs an action, and produces an optional result.

The goal of this notebook’s flow is to evaluate, on an ongoing basis, the performance of a model that predicts time-to-close for tickets in an IT support system.

That can be broken down into the following tasks

  • get_trial_id(): assign a unique ID to each run
  • get_ticket_data_batch(): get a random set of newly-closed tickets
  • get_target(): given a batch of tickets, compute how long it took to close them
  • predict(): predict the time-to-close, using the heuristic “higher-priority tickets close faster”
  • evaluate_model(): compute evaluation metrics comparing predicted and actual time-to-close
  • get_trial_summary(): collect all evaluation metrics in one object
  • write_trial_summary(): write trial results somewhere
@task
def get_trial_id() -> str:
    """
    Generate a unique identifier for this trial.
    """
    return str(uuid.uuid4())


@task
def get_ticket_data_batch(batch_size: int) -> pd.DataFrame:
    """
    Simulate the experience of getting a random sample of new tickets
    from an IT system, to test the performance of a model.
    """
    url = "https://archive.ics.uci.edu/ml/machine-learning-databases/00498/incident_event_log.zip"
    resp = requests.get(url)
    zipfile = ZipFile(BytesIO(resp.content))
    data_file = "incident_event_log.csv"
    # _date_parser has to be a lambda or pandas won't convert dates correctly
    _date_parser = lambda x: pd.NaT if x == "?" else datetime.strptime(x, "%d/%m/%Y %H:%M")
    df = pd.read_csv(
        zipfile.open(data_file),
        parse_dates=[
            "opened_at",
            "resolved_at",
            "closed_at",
            "sys_created_at",
            "sys_updated_at",
        ],
        infer_datetime_format=False,
        converters={
            "opened_at": _date_parser,
            "resolved_at": _date_parser,
            "closed_at": _date_parser,
            "sys_created_at": _date_parser,
            "sys_updated_at": _date_parser,
        },
        na_values=["?"],
    )
    df["sys_updated_at"] = pd.to_datetime(df["sys_updated_at"])
    rows_to_score = np.random.randint(0, df.shape[0], 100)
    return df.iloc[rows_to_score]


@task
def get_target(df):
    """
    Compute time-til-close on a data frame of tickets
    """
    time_til_close = (df["closed_at"] - df["sys_updated_at"]) / np.timedelta64(1, "s")
    return time_til_close


@task
def predict(df):
    """
    Given an input data frame, predict how long it will be until the ticket is closed.
    For simplicity, using a super simple model that just says
    "high-priority tickets get closed faster".
    """
    seconds_in_an_hour = 60.0 * 60.0
    preds = df["priority"].map(
        {
            "1 - Critical": 6.0 * seconds_in_an_hour,
            "2 - High": 24.0 * seconds_in_an_hour,
            "3 - Moderate": 120.0 * seconds_in_an_hour,
            "4 - Lower": 240.0 * seconds_in_an_hour,
        }
    )
    default_guess_for_no_priority = 180.0 * seconds_in_an_hour
    preds = preds.fillna(default_guess_for_no_priority)
    return preds


@task
def evaluate_model(y_true, y_pred, metric_name: str) -> float:
    metric_func_lookup = {
        "mae": mean_absolute_error,
        "medae": median_absolute_error,
        "mse": mean_squared_error,
        "r2": r2_score,
    }
    metric_func = metric_func_lookup[metric_name]
    return metric_func(y_true, y_pred)


@task
def get_trial_summary(trial_id: str, actuals, input_df: pd.DataFrame, metrics: dict) -> dict:
    out = {"id": trial_id}
    out["data"] = {
        "num_obs": input_df.shape[0],
        "metrics": metrics,
        "target": {
            "mean": actuals.mean(),
            "median": actuals.median(),
            "min": actuals.min(),
            "max": actuals.max(),
        },
    }
    return out


@task(log_stdout=True)
def write_trial_summary(trial_summary: str):
    """
    Write out a summary of the file. Currently just logs back to the
    Prefect logger
    """
    logger = prefect.context.get("logger")
    logger.info(json.dumps(trial_summary))

Construct a Flow

Now that all of the task logic has been defined, the next step is to compose those tasks into a “flow”. From the Prefect docs:

A Flow is a container for Tasks. It represents an entire workflow or application by describing the dependencies between tasks.

Flows are DAGs, or “directed acyclic graphs.” This is a mathematical way of describing certain organizational principles:

  • A graph is a data structure that uses “edges” to connect “nodes.” Prefect models each Flow as a graph in which Task dependencies are modeled by Edges.
  • A directed graph means that edges have a start and an end: when two tasks are connected, one of them unambiguously runs first and the other one runs second.
  • An acyclic directed graph has no circular dependencies: if you walk through the graph, you will never revisit a task you’ve seen before.

If you want to run this job to run on a schedule, include “schedule” object as one additional argument to Flow(). In this case, the code below says “run this flow once every 24 hours”.

schedule = IntervalSchedule(interval=timedelta(hours=24))

*NOTE: prefect flows do not have to be run on a schedule. If you want to run prefect flows on a schedule add schedule=schedule as an additional argument to Flow() in code below.

with Flow(f"{SATURN_USERNAME}-ticket-model-evaluation-dask") as flow:
    batch_size = Parameter("batch-size", default=1000)
    trial_id = get_trial_id()
    # pull sample data
    sample_ticket_df = get_ticket_data_batch(batch_size)
    # compute target
    actuals = get_target(sample_ticket_df)
    # get prediction
    preds = predict(sample_ticket_df)
    # compute evaluation metrics
    mae = evaluate_model(actuals, preds, "mae")
    medae = evaluate_model(actuals, preds, "medae")
    mse = evaluate_model(actuals, preds, "mse")
    r2 = evaluate_model(actuals, preds, "r2")
    # get trial summary in a string
    trial_summary = get_trial_summary(
        trial_id=trial_id,
        input_df=sample_ticket_df,
        actuals=actuals,
        metrics={"MAE": mae, "MedAE": medae, "MSE": mse, "R2": r2},
    )
    # store trial summary
    trial_complete = write_trial_summary(trial_summary)

At this point, we have all of the work defined in tasks and arranged within a flow, but none of the tasks have run yet. In the next section, we’ll do that using Dask.

Register with Prefect Cloud

Now that the business logic of the flow is complete, we can add information that Saturn Cloud will need to know to run it.

integration = PrefectCloudIntegration(prefect_cloud_project_name=PREFECT_CLOUD_PROJECT_NAME)

Next, run `register_flow_with_saturn().

register_flow_with_saturn() does a few important things:

  • specifies how and where the flow’s code is stored so it can be retrieved by a Prefect Cloud agent (see flow.storage)
  • specifies the infrastructure needed to run the flow. In this case, it uses a KubernetesJobEnvironment with a Saturn Dask cluster (see flow.environment)

The code below also customizes the Dask cluster used when executing the flow.

  • n_workers = 3: use 3 workers
  • worker_size ="xlarge": each worker has 2 CPU cores and 16 GB RAM
    • NOTE: you can find the full list of sizes with prefect_saturn.describe_sizes()
  • worker_is_spot = False: don’t use spot instances for workers

NOTE: dask clusters associated with prefect cloud flows will be autoclosed when the flow run completes.

flow = integration.register_flow_with_saturn(
    flow=flow,
    dask_cluster_kwargs={
        "n_workers": 3,
        "worker_size": "xlarge",
        "scheduler_size": "medium",
        "worker_is_spot": False,
    },
)

The final step necessary is to “register” the flow with Prefect Cloud. If this is the first time you’ve registered this flow, it will create a new Prefect Cloud project PREFECT_CLOUD_PROJECT_NAME. If you already have a flow in this project with this name, it will create a new version of it in Prefect Cloud.

flow.register(project_name=PREFECT_CLOUD_PROJECT_NAME)

Run the flow

If you have scheduled your flow, it will be run once every 24 hours. You can confirm this by doing all of the following:

  • If you are an admin, go to Prefect Cloud Agent page of Saturn Cloud which is at the side bar and check logs for your agent.
  • Go to the “Dask” page in Saturn Cloud. You should see that a new Dask cluster has been created to run this flow.
  • Go to Prefect Cloud. If you navigate to this flow and click “Runs”, you should see task statuses and and logs for this flow.

If you have not scheduled your flow or want to run the flow immediately, navigate to the flow in the Prefect Cloud UI and click “Quick Run”.

Alternative way to run the flow immediately is to open a terminal and run the code below.

prefect auth login --key ${PREFECT_USER_TOKEN}
prefect run flow \
    --name ${SATURN_USERNAME}-test-flow1 \
    --project ${PREFECT_CLOUD_PROJECT_NAME}

Conclusion

Prefect makes your workflows more managable and fault tolerant. In this example, you learned how to create a prefect flow and distribute all tasks across Dask clusters. We then registered this flow with Prefect Cloud.

Try changing the code above and re-running the flow. Add logging, add new tasks, or customize the Dask cluster.If you have existing prefect flows, try running one of them on Saturn using this notebook as a template.

import json
import os
import uuid
from datetime import datetime, timedelta
from io import BytesIO
from zipfile import ZipFile

import numpy as np
import pandas as pd
import requests
from prefect.schedules import IntervalSchedule
from prefect_saturn import PrefectCloudIntegration
from sklearn.metrics import (
    mean_absolute_error,
    mean_squared_error,
    median_absolute_error,
    r2_score,
)

import prefect
from prefect import Flow, Parameter, task

PREFECT_CLOUD_PROJECT_NAME = os.environ["PREFECT_CLOUD_PROJECT_NAME"]
SATURN_USERNAME = os.environ["SATURN_USERNAME"]


!prefect auth login --key ${PREFECT_USER_TOKEN}


client = prefect.Client()
client.create_project(project_name=PREFECT_CLOUD_PROJECT_NAME)


@task
def get_trial_id() -> str:
    """
    Generate a unique identifier for this trial.
    """
    return str(uuid.uuid4())


@task
def get_ticket_data_batch(batch_size: int) -> pd.DataFrame:
    """
    Simulate the experience of getting a random sample of new tickets
    from an IT system, to test the performance of a model.
    """
    url = "https://archive.ics.uci.edu/ml/machine-learning-databases/00498/incident_event_log.zip"
    resp = requests.get(url)
    zipfile = ZipFile(BytesIO(resp.content))
    data_file = "incident_event_log.csv"
    # _date_parser has to be a lambda or pandas won't convert dates correctly
    _date_parser = lambda x: pd.NaT if x == "?" else datetime.strptime(x, "%d/%m/%Y %H:%M")
    df = pd.read_csv(
        zipfile.open(data_file),
        parse_dates=[
            "opened_at",
            "resolved_at",
            "closed_at",
            "sys_created_at",
            "sys_updated_at",
        ],
        infer_datetime_format=False,
        converters={
            "opened_at": _date_parser,
            "resolved_at": _date_parser,
            "closed_at": _date_parser,
            "sys_created_at": _date_parser,
            "sys_updated_at": _date_parser,
        },
        na_values=["?"],
    )
    df["sys_updated_at"] = pd.to_datetime(df["sys_updated_at"])
    rows_to_score = np.random.randint(0, df.shape[0], 100)
    return df.iloc[rows_to_score]


@task
def get_target(df):
    """
    Compute time-til-close on a data frame of tickets
    """
    time_til_close = (df["closed_at"] - df["sys_updated_at"]) / np.timedelta64(1, "s")
    return time_til_close


@task
def predict(df):
    """
    Given an input data frame, predict how long it will be until the ticket is closed.
    For simplicity, using a super simple model that just says
    "high-priority tickets get closed faster".
    """
    seconds_in_an_hour = 60.0 * 60.0
    preds = df["priority"].map(
        {
            "1 - Critical": 6.0 * seconds_in_an_hour,
            "2 - High": 24.0 * seconds_in_an_hour,
            "3 - Moderate": 120.0 * seconds_in_an_hour,
            "4 - Lower": 240.0 * seconds_in_an_hour,
        }
    )
    default_guess_for_no_priority = 180.0 * seconds_in_an_hour
    preds = preds.fillna(default_guess_for_no_priority)
    return preds


@task
def evaluate_model(y_true, y_pred, metric_name: str) -> float:
    metric_func_lookup = {
        "mae": mean_absolute_error,
        "medae": median_absolute_error,
        "mse": mean_squared_error,
        "r2": r2_score,
    }
    metric_func = metric_func_lookup[metric_name]
    return metric_func(y_true, y_pred)


@task
def get_trial_summary(trial_id: str, actuals, input_df: pd.DataFrame, metrics: dict) -> dict:
    out = {"id": trial_id}
    out["data"] = {
        "num_obs": input_df.shape[0],
        "metrics": metrics,
        "target": {
            "mean": actuals.mean(),
            "median": actuals.median(),
            "min": actuals.min(),
            "max": actuals.max(),
        },
    }
    return out


@task(log_stdout=True)
def write_trial_summary(trial_summary: str):
    """
    Write out a summary of the file. Currently just logs back to the
    Prefect logger
    """
    logger = prefect.context.get("logger")
    logger.info(json.dumps(trial_summary))


schedule = IntervalSchedule(interval=timedelta(hours=24))


with Flow(f"{SATURN_USERNAME}-ticket-model-evaluation-dask") as flow:
    batch_size = Parameter("batch-size", default=1000)
    trial_id = get_trial_id()
    # pull sample data
    sample_ticket_df = get_ticket_data_batch(batch_size)
    # compute target
    actuals = get_target(sample_ticket_df)
    # get prediction
    preds = predict(sample_ticket_df)
    # compute evaluation metrics
    mae = evaluate_model(actuals, preds, "mae")
    medae = evaluate_model(actuals, preds, "medae")
    mse = evaluate_model(actuals, preds, "mse")
    r2 = evaluate_model(actuals, preds, "r2")
    # get trial summary in a string
    trial_summary = get_trial_summary(
        trial_id=trial_id,
        input_df=sample_ticket_df,
        actuals=actuals,
        metrics={"MAE": mae, "MedAE": medae, "MSE": mse, "R2": r2},
    )
    # store trial summary
    trial_complete = write_trial_summary(trial_summary)


integration = PrefectCloudIntegration(prefect_cloud_project_name=PREFECT_CLOUD_PROJECT_NAME)


flow = integration.register_flow_with_saturn(
    flow=flow,
    dask_cluster_kwargs={
        "n_workers": 3,
        "worker_size": "xlarge",
        "scheduler_size": "medium",
        "worker_is_spot": False,
    },
)


flow.register(project_name=PREFECT_CLOUD_PROJECT_NAME)


prefect auth login --key ${PREFECT_USER_TOKEN}
prefect run flow \
    --name ${SATURN_USERNAME}-test-flow1 \
    --project ${PREFECT_CLOUD_PROJECT_NAME}


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