Splash Flows Globus

This repo contains configuration and code for Prefect workflows to move data and run computing tasks. Many of the workflows use Globus for data movement between local servers and back and forth to NERSC.

These flows can be run from the command line or built into a self-contained docker container.

Getting started

Clone this repo and set up the python enviornment:

$   git clone git@github.com:als-computing/splash_flows_globus.git
$   cd splash_flows_globus
$   pip3 install -e .

Provide Prefect and Globus authentication in .env:

Use .env.example as a template.

GLOBUS_CLIENT_ID=<globus_client_id>
GLOBUS_CLIENT_SECRET=<globus_client_secret>
PREFECT_API_URL=<url_of_prefect_server>
PREFECT_API_KEY=<prefect_client_secret>

Current workflow overview and status:

Name	Description	Status	Notes
move.py	Move data from spot832 to data832, schedule pruning, and ingest into scicat	Deployed	Details
prune.py	Run data pruning flows as scheduled	Deployed
alcf.py	Run tomography reconstruction Globus Compute Flows at ALCF	Deployed
nersc.py	Run tomography reconstruction using SFAPI at NERSC	WIP
dispatcher.py	Dispatch flow to control beamline subflows	WIP
create_deployments_<bl>.sh	Deploy functions as prefect flows. Run once, or after updating underlying flow code
globus/flows.py and globus/transfer.py	Connect Python with globus API – could use better error handling
scripts/check_globus_compute.py	Check if CC has access to compute endpoint and if it is available
scripts/check_globus_transfer.py	Check if CC has r/w/d access to an endpoint. Also ability to delete data
source scripts/login_to_globus_and_prefect.py	Login to globus/prefect in current terminal from .env file
init_<data_task>_globus_flow.py	Register and update globus flow UUIDs in Prefect
init_<data_task>_globus_flow.py	Register and update globus flow UUIDs in Prefect
orchestration/tests/<pytest_scripts>.py	Test scripts using pytest

Further development

Globus collection endpoints are defined in config.yml:

globus:
  globus_endpoints:
    spot832:
      root_path: /
      uri: spot832.lbl.gov
      uuid: 44ae904c-ab64-4145-a8f0-7287de38324d

Prefect workflows are deployed using the create_deployments_[name].sh scripts.

These are meant to be run on flow-prd, in bl832_agent with properly set .env variables (i.e. prefect id/secret, globus id/secret, ..)

General anatomy of a file:

prefect deployment build <path_of_file>:<prefect_function> -n 'name_of_the_workflow' -q <tag>
prefect deployment apply <prefect_function>-deployment.yaml

Example: The following creates a Prefect workflow for the function of process_new_file in file of ./orchestration/flows/bl7012/move.py

prefect deployment build ./orchestration/flows/bl7012/move.py:process_new_file -n 'process_newdata7012' -q bl7012
prefect deployment apply process_new_file-deployment.yaml

Starting a Prefect workflow manually

Below is the command to start the Prefect workflow:

python -m orchestration.flows.bl7012.move <Relative path of file respect to the root_path defined in Globus endpoint>

Submitting workflow via Prefect API

An example is shown example.ipynb to submit a PREFECT workflow to PREFECT server.

Once the job is submitted, a workflow agent is needed to work on jobs in queue. A workflow agent can be launched by:

prefect agent start -q <name-of-work-queue>

It requires to have the PREFECT_API_URL and PREFECT_API_KEY stored as an environment variables, such that the agent knows where to get the work queue. Once the agent is launched, the following message indicates where the agent is currently listening to.

Starting v2.7.9 agent connected to https://.../api...

  ___ ___ ___ ___ ___ ___ _____     _   ___ ___ _  _ _____
 | _ \ _ \ __| __| __/ __|_   _|   /_\ / __| __| \| |_   _|
 |  _/   / _|| _|| _| (__  | |    / _ \ (_ | _|| .` | | |
 |_| |_|_\___|_| |___\___| |_|   /_/ \_\___|___|_|\_| |_|


Agent started! Looking for work from queue(s): <name-of-work-queue>...

More specific documentation can be found in the docs folder:

• "Globus configuration"
• "8.3.2 ALCF Globus Flow And Reconstruction Setup"
• "Data movement for BL7012"