SLURM 上的多处理不使用多个 CPU

Question

I am on a SLURM cluster and want to run the following multiprocess. The tasks are totally parallelizable but it seems they're still occurring serially.

Code is:

#load data (this is a df of files that need to be processed)
left = loadData()

processes = []

#split the list of files in 22 groups based on column chrom
for i in range(1,23):
            left_chrom = left[left['chrom'] == i]
            #Pass each DF of files to multiprocessing (note this function calls a subprocess to process the file)
            p_ins = multiprocessing.Process(target=ViewVCFConvert, args = (left_chrom,))
            processes.append(p_ins)
            p_ins.start()
            for process in processes:
                process.join()

My slurm settings are:

#!/bin/bash
#SBATCH --job-name=VCF
#SBATCH --partition=abc
#SBATCH --nodes=1
#SBATCH --cpus-per-task=22
#SBATCH --mem=1G
#SBATCH --time=10:00:00
   

However when I run this, the files are processed serially. I have checked this by adding a print function to show when a file is processed. I would expect the output of those print statements to be like:

file1, chrom=2
file4, chrom=5
file3, chrom=8

Instead the output I get is:

file1, chrom=4
file2, chrom=4
file3, chrom=4

This implies the files are being processed in order (although multiprocessing is doing something as it does not always start with chrom=1 as in a normal for loop).

Answer 1

So the solution came from another answer ( Python multiprocessing pool inside a loop ). Code is below. Basically I needed to use Pool and not Process as I wanted to run ViewVCFConvert in parallel for all list chrom. If I had several functions and I wanted to run them all in parallel one chrom at a time then I would use Processing. This is why it was still running serially, it was doing ViewVCFConvert once at a time.

from multiprocessing import Pool
    def main():
        chrom = [i for i in range(1,23)]
        pool = Pool(22)
        pool.map(ViewVCFConvert, chrom)
        pool.close()
        pool.join()

view the documentation on the site ( https://docs.python.org/3/library/multiprocessing.html ) to see the difference between Pool and Process.