Speed Up Your Data Processing: Parallel and Asynchronous Programming in Python

Speed Up Your Data Processing: Parallel and Asynchronous Programming in Python Presented by: Ong Chin Hwee (@ongchinhwee) 20 March 2020 FOSSASIA Summit 2020, Singapore

About me Ong Chin Hwee 王敬惠 ● Data Engineer @ ST Engineering ● Background in aerospace engineering + computational modelling ● Contributor to pandas 1.0 release ● Mentor team at BigDataX @ongchinhwee

A typical data science workflow 1. 2. 3. 4. Extract raw data Process data Train model Deploy model @ongchinhwee

Bottlenecks in a data science project ● Lack of data / Poor quality data ● Data processing ○ The 80/20 data science dilemma ■ In reality, it’s closer to 90/10 @ongchinhwee

Data Processing in Python ● For loops in Python ○ Run on the interpreter, not compiled ○ Slow compared with C a_list = [] for i in range(100): a_list.append(i*i) @ongchinhwee

Data Processing in Python ● List comprehensions ○ Slightly faster than for loops ○ No need to call append function at each iteration a_list = [i*i for i in range(100)] @ongchinhwee

Challenges with Data Processing ● Pandas ○ Optimized for in-memory analytics using DataFrames ○ Performance + out-of-memory issues when dealing with large datasets (> 1 GB) import pandas as pd import numpy as np df = pd.DataFrame(list(range(100))) df.apply(np.square) @ongchinhwee

Challenges with Data Processing ● “Why not just use a Spark cluster?” Communication overhead: Distributed computing involves communicating between (independent) machines across a network! “Small Big Data”(): Data too big to fit in memory, but not large enough to justify using a Spark cluster. () Credits to Itamar Turner-Trauring (@itamarst) for this term @ongchinhwee

What is parallel processing? @ongchinhwee

Let’s imagine I work at a cafe which sells toast. @ongchinhwee

Task 1: Toast 100 slices of bread Assumptions: 1. I’m using single-slice toasters. (Yes, they actually exist.) 2. Each slice of toast takes 2 minutes to make. 3. No overhead time. Image taken from: https://www.mitsubishielectric.co.jp/home/breadoven/product/to-st1-t/feature/index.html @ongchinhwee

Sequential Processing = 25 bread slices @ongchinhwee

Sequential Processing = 25 bread slices Processor/Worker: Toaster @ongchinhwee

Sequential Processing = 25 bread slices Processor/Worker: Toaster = 25 toasts @ongchinhwee

Sequential Processing Execution Time = 100 toasts × 2 minutes/toast = 200 minutes @ongchinhwee

Parallel Processing = 25 bread slices @ongchinhwee

Parallel Processing @ongchinhwee

Parallel Processing Processor (Core): Toaster @ongchinhwee

Parallel Processing Processor (Core): Toaster Task is executed using a pool of 4 toaster subprocesses. Each toasting subprocess runs in parallel and independently from each other. @ongchinhwee

Parallel Processing Processor (Core): Toaster Output of each toasting process is consolidated and returned as an overall output (which may or may not be ordered). @ongchinhwee

Parallel Processing Execution Time = 100 toasts × 2 minutes/toast ÷ 4 toasters = 50 minutes Speedup = 4 times @ongchinhwee

Synchronous vs Asynchronous Execution @ongchinhwee

What do you mean by “Asynchronous”? @ongchinhwee

Task 2: Brew gourmet coffee Assumptions: 1. I can do other stuff while making coffee. 2. One coffee maker to make one cup of coffee. 3. Each cup of coffee takes 5 minutes to make. Image taken from: https://www.crateandbarrel.com/breville-barista-espresso-machine/s267619 @ongchinhwee

Synchronous Execution Task 2: Brew a cup of coffee on coffee machine Duration: 5 minutes @ongchinhwee

Synchronous Execution Task 1: Toast a slice of bread on single-slice toaster after Task 2 is completed Duration: 2 minutes Task 2: Brew a cup of coffee on coffee machine Duration: 5 minutes @ongchinhwee

Synchronous Execution Task 1: Toast a slice of bread on single-slice toaster after Task 2 is completed Duration: 2 minutes Task 2: Brew a cup of coffee on coffee machine Duration: 5 minutes Output: 1 toast + 1 coffee Total Execution Time = 5 minutes + 2 minutes = 7 minutes @ongchinhwee

Asynchronous Execution While brewing coffee: Make some toasts: @ongchinhwee

Asynchronous Execution Output: 2 toasts + 1 coffee (1 more toast!) Total Execution Time = 5 minutes @ongchinhwee

When is it a good idea to go for parallelism? (or, “Is it a good idea to simply buy a 256-core processor and parallelize all your codes?”) @ongchinhwee

Practical Considerations ● Is your code already optimized? ○ Sometimes, you might need to rethink your approach. ○ Example: Use list comprehensions or map functions instead of for-loops for array iterations. @ongchinhwee

Practical Considerations ● Is your code already optimized? ● Problem architecture ○ Nature of problem limits how successful parallelization can be. ○ If your problem consists of processes which depend on each others’ outputs, maybe not. (Task + Data independence) @ongchinhwee

Practical Considerations ● Is your code already optimized? ● Problem architecture ● Overhead in parallelism ○ There will always be parts of the work that cannot be parallelized. → Amdahl’s Law ○ Extra time required for coding and debugging (parallelism vs sequential code) → Increased complexity ○ System overhead including communication overhead @ongchinhwee

Amdahl’s Law and Parallelism Amdahl’s Law states that the theoretical speedup is defined by the fraction of code p that can be parallelized: S: Theoretical speedup (theoretical latency) p: Fraction of the code that can be parallelized N: Number of processors (cores) @ongchinhwee

Amdahl’s Law and Parallelism If there are no parallel parts (p = 0): Speedup = 0 @ongchinhwee

Amdahl’s Law and Parallelism If there are no parallel parts (p = 0): Speedup = 0 If all parts are parallel (p = 1): Speedup = N → ∞ @ongchinhwee

Amdahl’s Law and Parallelism If there are no parallel parts (p = 0): Speedup = 0 If all parts are parallel (p = 1): Speedup = N → ∞ Speedup is limited by fraction of the work that is not parallelizable - will not improve even with infinite number of processors @ongchinhwee

Multiprocessing vs Multithreading Multiprocessing: System allows executing multiple processes at the same time using multiple processors @ongchinhwee

Multiprocessing vs Multithreading Multiprocessing: Multithreading: System allows executing multiple processes at the same time using multiple processors System executes multiple threads of sub-processes at the same time within a single processor @ongchinhwee

Multiprocessing vs Multithreading Multiprocessing: Multithreading: System allows executing multiple processes at the same time using multiple processors System executes multiple threads of sub-processes at the same time within a single processor Better for processing large volumes of data Best suited for I/O or blocking operations @ongchinhwee

Some Considerations Data processing tends to be more compute-intensive → Switching between threads become increasingly inefficient → Global Interpreter Lock (GIL) in Python does not allow parallel thread execution @ongchinhwee

How to do Parallel + Asynchronous in Python? @ongchinhwee

Parallel + Asynchronous Programming in Python concurrent.futures module ● High-level API for launching asynchronous (async) parallel tasks ● Introduced in Python 3.2 as an abstraction layer over multiprocessing module ● Two modes of execution: ○ ThreadPoolExecutor() for async multithreading ○ ProcessPoolExecutor() for async multiprocessing @ongchinhwee

ProcessPoolExecutor vs ThreadPoolExecutor From the Python Standard Library documentation: For ProcessPoolExecutor, this method chops iterables into a number of chunks which it submits to the pool as separate tasks. The (approximate) size of these chunks can be specified by setting chunksize to a positive integer. For very long iterables, using a large value for chunksize can significantly improve performance compared to the default size of 1. With ThreadPoolExecutor, chunksize has no effect. @ongchinhwee

ProcessPoolExecutor vs ThreadPoolExecutor ProcessPoolExecutor: ThreadPoolExecutor: System allows executing multiple processes asynchronously using multiple processors System executes multiple threads of sub-processes asynchronously within a single processor Uses multiprocessing module - side-steps GIL Subject to GIL - not truly “concurrent” @ongchinhwee

submit() in concurrent.futures Executor.submit() takes as input: 1. The function (callable) that you would like to run, and 2. Input arguments (*args, **kwargs) for that function; and returns a futures object that represents the execution of the function. @ongchinhwee

map() in concurrent.futures Similar to map(), Executor.map() takes as input: 1. The function (callable) that you would like to run, and 2. A list (iterable) where each element of the list is a single input to that function; and returns an iterator that yields the results of the function being applied to every element of the list. @ongchinhwee

Case: Network I/O Operations Dataset: Data.gov.sg Realtime Weather Readings (https://data.gov.sg/dataset/realtime-weather-readings) API Endpoint URL: https://api.data.gov.sg/v1/environment/ Response: JSON format @ongchinhwee

Initialize Python modules import numpy as np import requests import json import sys import time import datetime from tqdm import trange, tqdm from time import sleep from retrying import retry import threading @ongchinhwee

Initialize API request task @retry(wait_exponential_multiplier=1000, wait_exponential_max=10000) def get_airtemp_data_from_date(date): print(‘{}: running {}’.format(threading.current_thread().name, date)) # for daily API request url = “https://api.data.gov.sg/v1/environment/air-temperature?date=”\ + str(date) JSONContent = requests.get(url).json() content = json.dumps(JSONContent, sort_keys=True) sleep(1) threading module to print(‘{}: done with {}’.format( threading.current_thread().name, date)) monitor thread execution return content @ongchinhwee

Initialize Submission List date_range = np.array(sorted( [datetime.datetime.strftime( datetime.datetime.now() - datetime.timedelta(i) ,’%Y-%m-%d’) for i in trange(100)])) @ongchinhwee

Using List Comprehensions start_cpu_time = time.clock() data_np = [get_airtemp_data_from_date(str(date)) for date in tqdm(date_range)] end_cpu_time = time.clock() print(end_cpu_time - start_cpu_time)

Using List Comprehensions List Comprehensions: start_cpu_time = time.clock() 977.88 seconds (~ 16.3mins) data_np = [get_airtemp_data_from_date(str(date)) for date in tqdm(date_range)] end_cpu_time = time.clock() print(end_cpu_time - start_cpu_time) @ongchinhwee

Using ThreadPoolExecutor from concurrent.futures import ThreadPoolExecutor, as_completed start_cpu_time = time.clock() with ThreadPoolExecutor() as executor: future = {executor.submit(get_airtemp_data_from_date, date):date for date in tqdm(date_range)} resultarray_np = [x.result() for x in as_completed(future)] end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘Using ThreadPoolExecutor: {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Using ThreadPoolExecutor from concurrent.futures import ThreadPoolExecutor, as_completed start_cpu_time = time.clock() ThreadPoolExecutor (40 threads): 46.83 seconds (~20.9 times faster) with ThreadPoolExecutor() as executor: future = {executor.submit(get_airtemp_data_from_date, date):date for date in tqdm(date_range)} resultarray_np = [x.result() for x in as_completed(future)] end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘Using ThreadPoolExecutor: {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Case: Image Processing Dataset: Chest X-Ray Images (Pneumonia) (https://www.kaggle.com/paultimothymooney/chest-xray-pneu monia) Size: 1.15GB of x-ray image files with normal and pneumonia (viral or bacterial) cases Data Quality: Images in the dataset are of different dimensions @ongchinhwee

Initialize Python modules import numpy as np from PIL import Image import os import sys import time @ongchinhwee

Initialize image resize process def image_resize(filepath): ”’Resize and reshape image”’ sys.stdout.write(‘{}: running {}\n’.format(os.getpid(),filepath)) im = Image.open(filepath) resized_im = np.array(im.resize((64,64))) sys.stdout.write(‘{}: done with os.getpid() to monitor process execution {}\n’.format(os.getpid(),filepath)) return resized_im @ongchinhwee

Initialize File List in Directory DIR = ‘./chest_xray/train/NORMAL/’ No. of images in ‘train/NORMAL’: 1431 train_normal = [DIR + name for name in os.listdir(DIR) if os.path.isfile(os.path.join(DIR, name))] @ongchinhwee

Using map() start_cpu_time = time.clock() result = map(image_resize, train_normal) output = np.array([x for x in result]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘Map completed in {} seconds.\n’.format(total_tpe_time))

Using map() start_cpu_time = time.clock() result = map(image_resize, train_normal) map(): 29.48 seconds output = np.array([x for x in result]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘Map completed in {} seconds.\n’.format(total_tpe_time))

Using List Comprehensions start_cpu_time = time.clock() listcomp_output = np.array([image_resize(x) for x in train_normal]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘List comprehension completed in {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Using List Comprehensions start_cpu_time = time.clock() List Comprehensions: 29.71 seconds listcomp_output = np.array([image_resize(x) for x in train_normal]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘List comprehension completed in {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Using ProcessPoolExecutor from concurrent.futures import ProcessPoolExecutor start_cpu_time = time.clock() with ProcessPoolExecutor() as executor: future = executor.map(image_resize, train_normal) array_np = np.array([x for x in future]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘ProcessPoolExecutor completed in {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Using ProcessPoolExecutor from concurrent.futures import ProcessPoolExecutor start_cpu_time = time.clock() ProcessPoolExecutor (8 cores): 6.98 seconds (~4.3 times faster) with ProcessPoolExecutor() as executor: future = executor.map(image_resize, train_normal) array_np = np.array([x for x in future]) end_cpu_time = time.clock() total_tpe_time = end_cpu_time - start_cpu_time sys.stdout.write(‘ProcessPoolExecutor completed in {} seconds.\n’.format( total_tpe_time)) @ongchinhwee

Key Takeaways @ongchinhwee

Not all processes should be parallelized ● Parallel processes come with overheads ○ Amdahl’s Law on parallelism ○ System overhead including communication overhead ○ If the cost of rewriting your code for parallelization outweighs the time savings from parallelizing your code, consider other ways of optimizing your code instead. @ongchinhwee

References Official Python documentation on concurrent.futures (https://docs.python.org/3/library/concurrent.futures.html) Source code for ThreadPoolExecutor (https://github.com/python/cpython/blob/3.8/Lib/concurrent/futures/thr ead.py) Source code for ProcessPoolExecutor (https://github.com/python/cpython/blob/3.8/Lib/concurrent/futures/thr ead.py) @ongchinhwee

Reach out to me! : ongchinhwee : @ongchinhwee : hweecat : https://ongchinhwee.me And check out my slides on: hweecat/talk_parallel-async-python @ongchinhwee