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Run FireWorks workflows in Google Cloud

Project description

Borealis

Runs FireWorks workflows on Google Cloud Platform computing services (GCP).

See the repo Borealis and the PyPI page borealis-fireworks.

What is it?

FireWorks is an open-source workflow management system, that is, it drives interdependent computing tasks. Among the many workflow systems available, FireWorks is exceptionally straightforward, lightweight, and adaptable. It's well tested and supported. The only shared services it needs are a MongoDB server (acting as the workflow "LaunchPad") and a file store.

Borealis lets you spin up as many temporary worker machines as you want in the Google Cloud Platform to run your workflow. That means pay-per-use and no contention between workflows.

How does Borealis support workflows on Google Cloud Platform?

TL;DR: Spin up worker machines when you need them, deploy your task code to the workers in Docker Images, and store the data in Google Cloud Storage instead of NFS.

Diagram of Borealis Fireworks on Google Cloud Platform

Figure 1. Blue hexagons represent Google Cloud Platform services. The LaunchPad is shown in a blue hexagon because it's implemented as a MongoDB server that you can run on Compute Engine.

Worker VMs: As a cloud computing platform, Google Compute Engine (GCE) has a vast number of machines available. You can spin up lots of GCE "instances" (also called Virtual Machines or VMs) to run your workflow, change your code, re-run some tasks, then let the workers time out and shut down. Google will charge you based on usage and there's no resource contention with your teammates.

Borealis provides the ComputeEngine class and its command line wrapper gce to create, tweak, and delete groups of worker VMs.

Borealis provides the fireworker Python script to run as the top level program of each worker. It calls FireWorks' rlaunch feature.

You can run these Fireworkers on and off GCE as long as they can connect to your MongoDB server and to the data store for their input and output files.

Docker: You need to deploy your payload task code to those GCE VMs. It might be Python source code and its runtime environment, e.g. Python 3.8, Python pip packages, Linux apt packages, compiled Cython code, data files, and environment variable settings. A GCE VM starts up from a GCE Disk Image which could have all that preinstalled (with or without the Python source code) but it'd be hard to keep it up to date and hard to keep track of how to reproduce it.

This is what Docker Images are designed for. You maintain a Dockerfile containing instructions to build the Docker Image, then use the Google Cloud Build service to build the Image and store it in the Google Container Registry.

Borealis provides the DockerTask Firetask to run a task in Docker. It pulls a named Docker Image, starts up a Docker Container, runs a given shell command in that Container, and shuts down the Container. Running in a Container also isolates the task's runtime environment and side effects from the Fireworker and other tasks.

Google Cloud Storage: Although you can set up an NFS shared file service for the workers' files, Google Cloud Storage (GCS) is the native storage service. GCS costs literally 1/10th as much as NFS service and it scales up better. GCS lets you archive your files in yet lower cost tiers intended for infrequent access. Pretty much all of Google's cloud services revolve around GCS, e.g., Pub/Sub can trigger an action on a particular upload to GCS.

But Cloud Storage is not a file system. It's an object store with a light weight protocol to fetch/store/list whole files, called "blobs." It does not support simultaneous writers. Instead, the last "store" of a blob wins. Blob pathnames can contain / characters but GCS doesn't have actual directory objects, so e.g. there's no way to atomically rename a directory.

DockerTask supports Cloud Storage by fetching the task's input files from GCS and storing its output files to GCS.

Logging: DockerTask logs the Container's stdout and stderr, and fireworker sets up Python logging to write to Google's StackDriver cloud logging service so you can watch your workers running in real time.

Projects: With Google Cloud Platform, you set up a project for your team to use. All services, VMs, data, and access controls are scoped by the project.

How to run a workflow

After doing one-time setup, the steps to run a workflow are:

  1. Build a Docker container Image containing your payload tasks to run in the workflow. The gcloud builds submit command will upload your code and a Dockerfile, then trigger a Google Cloud Build server server to build the Docker Image and store it in the Google Container Registry.

    See Building Your Docker Image for how to build the Docker Image, starting with writing the Dockerfile.

  2. Build your workflow and upload it to MongoDB. You can do this manually by writing a .yaml file and running the lpad command line tool to upload it, or automate it by implementing a workflow builder program which calls FireWorks APIs to construct and upload a Workflow object.

    The workflow will run instances of the DockerTask Firetask. Of course it can run other Firetasks as well; they just won't get deployment, storage, logging, and timeout features from DockerTask.

    If you need to open a secure ssh tunnel to the MongoDB server running in a Google Compute Engine VM, use the borealis/setup/example_mongo_ssh.sh shell script.

  3. Start one or more fireworker processes to run the workflow tasks.

    There are three ways to do this:

    • Run the fireworker process locally (this is handy for debugging) by running the fireworker Python script.
    • Launch a group of fireworkers on Compute Engine VMs (this is handy for getting a lot of work done in parallel) by running the Python script gce.
    • Automate the launching of a group of fireworkers on GCE by making your workflow builder code call on the Borealis ComputeEngine class after it builds and uploads the workflow.
  4. While it runs and afterwards, you can:

    • watch the main GCP dashboard

      Tip: Add VM load charts to this page.

    • watch the Compute Engine VM Instances console to see your list of workers

    • watch the Google Cloud Logs Viewer of your running workers
      (The INFO level will include the big picture for running workers. The DEBUG level will also include the console output and other details for the firetasks. Filter to just your worker nodes with an advanced filter like resource.labels.instance_id:"fireworker-USER-", inserting your $USER name.)

    • open the Fireworks Web GUI

      lpad webgui
      

      Workaround: If this command prints an error
      TypeError: cannot pickle '_thread.lock' object
      there's a compatibility problem with FireWorks on Python 3. As a workaround, run

      lpad webgui -s
      

      which starts the webgui server without the web browser. It prints the server URL such as http://127.0.0.1:5000. Then open a browser to that URL. (Just CMD-click the URL in iTerm.)

    • query your Fireworks tasks and Workflows

      lpad get_fws
      lpad get_wflows
      lpad report
      
    • rerun Fireworks tasks or Workflows

      lpad rerun_fws -i <FW_IDS>
      lpad rerun_fws -s FIZZLED
      
    • pause/restart Fireworks tasks or Workflows

      lpad pause_fws -i <FW_IDS>
      lpad resume_fws -i <FW_IDS>
      lpad defuse_fws -i <FW_IDS>
      lpad reignite_fws -i <FW_IDS>
      
      lpad pause_wflows -i <FW_IDS>
      lpad defuse_wflows -i <FW_IDS>
      lpad rerun_fws -i <FW_IDS>
      lpad reignite_wflows -i <FW_IDS>
      
    • build a new Docker Image containing bug-fixes, then re-run Fireworks tasks.

      If all the fireworkers have exited, run the gce command to launch new fireworkers.

    • launch additional fireworkers:

      gce --base <BASE> --count <COUNT> <NAME-PREFIX>
      

      Set the BASE number argument or NAME-PREFIX argument so the new VM names won't conflict with your already-running VMs.

    • Archive or delete a workflow or reset the entire Launchpad database:

      lpad archive_wflows -i <FW_IDS>
      
      lpad delete_wflows -i <FW_IDS>
      
      lpad reset
      
  5. Access the output files in GCS via the gsutil command line tool, the gcsfuse file mounting tool, and the Storage Browser in the Google Cloud Platform web console.

    Tip: Use gsutil -m to transfer multiple files in parallel. (If it prints TypeError: cannot pickle..., configure gcloud and gsutil to use Python 3.7 per the note in Install the development tools.)

More detail on the Borealis components

The Borealis components can be used separately. Together they enable running FireWorks workflows in Google Cloud.

gce: The ComputeEngine class and its command line wrapper gce create, tweak, and delete a group of worker VMs.

After you generate a workflow, call FireWorks' LaunchPad.add_wf() (or run FireWorks' lpad add command line tool) to upload it to the LaunchPad. Then call ComputeEngine.create() (or the gce command line) to spin up a group of worker VMs to run that workflow and pass in the parameters such as the LaunchPad db name and username (via GCE metadata fields).

ComputeEngine and gce can also immediately delete a group of worker VMs or ask them to quit cleanly between Firetasks, although we usually let fireworkers shut down on their own after an idle timeout.

ComputeEngine and gce can also set GCE metadata fields on a group of workers. This is used to implement the --quit-soon feature.

After installing the borealis-fireworks pip:

$ gce -h
usage: gce [-h] [--delete | --set-metadata | --quit-soon] [-d] [-b BASE]
           [-c COUNT] [-f FAMILY] [-l LAUNCHPAD_FILENAME]
           [-m METADATA_KEY=VALUE,...] [-o OPTION_KEY=VALUE,...]
           NAME-PREFIX

Create, delete, or set metadata on a group of Google Compute Engine VMs, e.g.
workflow workers that start up from a disk image-family. (This code also has
an API for direct use.)

...

Or to run it within the borealis-fireworks source code repository:

$ python -m borealis.gce -h

fireworker: The fireworker Python script runs as as the top level program of each worker node. fireworker reads the worker launch parameters and calls the FireWorks library to "rapidfire" launch your FireWorks "rockets." It also handles server shutdown.

fireworker connects Python logging to Google Cloud's StackDriver logging so you can watch all your worker machines in real time.

To run fireworker on GCE VMs, you'll need to create a GCE Disk Image that contains Python, the borealis-fireworks pip, and such. See the instructions in how-to-install-gce-server.txt.

The fireworker command can also run on your local computer for easier debugging. For that, you'll need to install the borealis-fireworks pip and set up your computer to access the right Google Cloud Project.

$ fireworker -h
usage: fireworker.py [-h] [-l LAUNCHPAD_FILENAME] [-s] [--development]

Run as a FireWorks worker node, launching rockets rapidfire. Gets configuration
settings from Google Compute Engine (GCE) metadata attributes when running on
GCE, else from the Launchpad file (see the `-l` option), with fallbacks. The
setup source files are "/Users/jerry/dev/borealis/borealis/setup/*"
...

DockerTask: The DockerTask Firetask pulls a named Docker Image, starts up a Docker Container, runs a given shell command in that Container, and stops the container.

Required params:

  • task name for logging
  • Docker image to load up into a Container
  • shell command to run in the Container
  • internal_prefix input/output base pathname in the Container
  • storage_prefix input/output base pathname in GCS

Optional params:

  • inputs input files and directory trees
  • outputs output files and directory trees
  • timeout for stopping the shell command, in seconds

Docker always runs a shell command in the Container. If you want to run a Firetask in the Container, include a little Python script to bridge the gap: Take a Firetask name and a JSON dictionary as command line arguments, instantiate the Firetask with those arguments, and call the Firetask's run_task() method.

DockerTask supports Google Cloud Storage (GCS) by fetching the task's input files from GCS, mapping them into the Docker Container, running the task, and storing its output files to GCS. This means you'll need to specify the input and output paths as DockerTask arguments. (Your workflow builder code could use this path information to compute the task-to-task interdependencies for FireWorks.)

Each path you specify in DockerTask's inputs and outputs denotes a directory tree of files iff it ends with a /.

When storing task output files, DockerTask creates entries with names ending in / to act as directory placeholders that speed up tree-oriented traversal. This means you can run gcsfuse without using the --implicit-dirs flag, resulting in mounted directories that run 10x faster.

DockerTask imposes a given timeout on the task running in the Docker container.

DockerTask logs the Container's stdout and stderr to a file and to Python logging (which fireworker connects to StackDriver).

What's next?

See the Team Setup steps and the Developer Setup steps.

See Building Your Docker Image.

Also see Handy Links.

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