awflow 0.0.1

Reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your laptop!

Reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!

Under development, but it works.

Motivation

Tired of writing and managing Slurm submission scripts? Do you have comment out large parts of your pipeline whenever its results have been generated? No more! awflow allows you to directly prototype in Python, on your personal computer. The module will take care of Slurm for you!

import awflow as aw
import glob
import numpy as np

n = 100000
tasks = 10

@aw.cpus(4)  # Request 4 CPU cores
@aw.memory("4GB")  # Request 4 GB of RAM
@aw.postcondition(aw.num_files('pi-*.npy', 10))
@aw.tasks(tasks)  # Requests '10' parallel tasks
def estimate(task_index):
    print("Executing task {} / {}.".format(task_index + 1, tasks))
    x = np.random.random(n)
    y = np.random.random(n)
    pi_estimate = (x**2 + y**2 <= 1)
    np.save('pi-' + str(task_index) + '.npy', pi_estimate)

@aw.dependency(estimate)
def merge():
    files = glob.glob('pi-*.npy')
    stack = np.vstack([np.load(f) for f in files])
    np.save('pi.npy', stack.sum() / (n * tasks) * 4)

@aw.dependency(merge)
@aw.postcondition(aw.exists('pi.npy'))  # Prevent execution if postcondition is satisfied.
def show_result():
    print("Pi:", np.load('pi.npy'))

aw.execute()

Executing this Python program (python examples/pi.py) on a Slurm HPC cluster will launch the following jobs.

           1803299       all    merge username PD       0:00      1 (Dependency)
           1803300       all show_res username PD       0:00      1 (Dependency)
     1803298_[6-9]       all estimate username PD       0:00      1 (Resources)
         1803298_3       all estimate username  R       0:01      1 compute-xx
         1803298_4       all estimate username  R       0:01      1 compute-xx
         1803298_5       all estimate username  R       0:01      1 compute-xx

Installation

TODO

you@local:~ $ pip install awflow

Roadmap

• Documentation
• Enforce acyclicity of compute graph
• README
• Utility scripts to manage workflows running on Slurm.