How to parallel the following code using Multiprocessing in Python

Question

I have a function generate(file_path) which returns an integer index and a numpy array. The simplified of generate function is as follows:

def generate(file_path):
  temp = np.load(file_path)
  #get index from the string file_path
  idx = int(file_path.split["_"][0])
  #do some mathematical operation on temp
  result = operate(temp)
  return idx, result

I need to glob through a directory and collect the results of generate(file_path) into a hdf5 file. My serialization code is as follows:

for path in glob.glob(directory):
    idx, result = generate(path)

    hdf5_file["results"][idx,:] = result
    
hdf5_file.close()

I hope to write a multi-thread or multi-process code to speed up the above code. How could I modify it? Pretty thanks!

My try is to modify my generate function and to modify my "main" as follows:

def generate(file_path):
    temp = np.load(file_path)
    #get index from the string file_path
    idx = int(file_path.split["_"][0])
    #do some mathematical operation on temp
    result = operate(temp)
      
    hdf5_path = "./result.hdf5"
    hdf5_file = h5py.File(hdf5_path, 'w')
    hdf5_file["results"][idx,:] = result

    hdf5_file.close()

if __name__ == '__main__':
    ##construct hdf5 file
    hdf5_path = "./output.hdf5"
    hdf5_file = h5py.File(hdf5_path, 'w')
    hdf5_file.create_dataset("results", [2000,15000], np.uint8)

    hdf5_file.close()

    path_ = "./compute/*"
    p = Pool(mp.cpu_count())
    p.map(generate, glob.glob(path_))
    hdf5_file.close()
   
    print("finished")

However, it does not work. It will throw error

KeyError: "Unable to open object (object 'results' doesn't exist)"

Asked By: Bill

||

Source

Answer 1

I detected some errors in initialising the dataset after examining your code;

You produced the hdf5 file with the path ""./result.hdf5" inside the generate function.

However, I think you neglected to create a "results" dataset beneath that file, as that is what is causing the Object Does Not Exist issue.

Kindly reply if you still face the same issue with error message

Answered By: sudharsan

Answer 2

You can use a thread or process pool to execute multiple function calls concurrently. Here is an example which uses a process pool:

from concurrent.futures import ProcessPoolExecutor
from time import sleep


def generate(file_path: str) -> int:
    sleep(1.0)
    return file_path.split("_")[1]


def main():
    file_paths = ["path_1", "path_2", "path_3"]
    
    with ProcessPoolExecutor() as pool:
        results = pool.map(generate, file_paths)
        
        for result in results:
            # Write to the HDF5 file
            print(result)
    

if __name__ == "__main__":
    main()

Note that you should not write to the same HDF5 file concurrently, i.e. the file writing should not append in the generate function.

Answered By: Louis Lac

How to parallel the following code using Multiprocessing in Python

Question:

Answers: