Python 高性能并行计算之 mpi4py

Posted 2020-12-30 Hello_BeautifulWorld

MPI  和    MPI4PY   的搭建上一篇文章已经介绍，这里面介绍一些基本用法。

 

mpi4py  的  helloworld

from mpi4py import MPI
print("hello world")

 

mpiexec      -n     5    python3    x.py

 

 

 

2.   点对点通信

因为  mpi4py 中点对点的 通信  send 语句  在数据量较小的时候是把发送数据拷贝到缓存区，是非堵塞的操作，   然而在数据量较大时候是堵塞操作，由此如下：

在 发送较小数据时：

import mpi4py.MPI as MPI
 
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
 
# point to point communication
data_send = [comm_rank]*5

comm.send(data_send,dest=(comm_rank+1)%comm_size)

data_recv =comm.recv(source=(comm_rank-1)%comm_size)

print("my rank is %d, and Ireceived:" % comm_rank)
print(data_recv)

 

 

 

在数据量较大时，  比如发送  ：

# point to point communication
data_send = [comm_rank]*1000000

这时候就会造成各个进程之间的死锁。（因为这时候各个进程是堵塞执行，每个进程都在等待另一个进程的发送数据）

 

 

 

修改后的代码，所有进程顺序执行， 0进程发送给1,1接收然后发送给2，以此类推：

import mpi4py.MPI as MPI
     
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
     
data_send = [comm_rank]*1000000

if comm_rank == 0:
   comm.send(data_send, dest=(comm_rank+1)%comm_size)

if comm_rank > 0:
   data_recv = comm.recv(source=(comm_rank-1)%comm_size)
   comm.send(data_send, dest=(comm_rank+1)%comm_size)

if comm_rank == 0:
   data_recv = comm.recv(source=(comm_rank-1)%comm_size)

print("my rank is %d, and Ireceived:" % comm_rank)
print(data_recv)

 

 

3   群体通信

3.1  广播bcast

一个进程把数据发送给所有进程

import mpi4py.MPI as MPI
 
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
 
if comm_rank == 0:
   data = range(comm_size)

dat = comm.bcast(data if comm_rank == 0 else None, root=0)

print(\'rank %d, got:\' % (comm_rank))
print(dat)

 

发送方 也会收到  这部分数据，当然发送方这份数据并不是网络传输接受的，而是本身内存空间中就是存在的。

 

 

3.2   散播scatter

 

import mpi4py.MPI as MPI
 
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
 
if comm_rank == 0:
   data = range(comm_size)
else:
   data = None

local_data = comm.scatter(data, root=0)

print(\'rank %d, got:\' % comm_rank)
print(local_data)

 

 

 

 

3.3  收集gather

将所有数据搜集回来

 

import mpi4py.MPI as MPI
 
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()
 
if comm_rank == 0:
   data = range(comm_size)
else:
   data = None

local_data = comm.scatter(data, root=0)
local_data = local_data * 2

print(\'rank %d, got and do:\' % comm_rank)
print(local_data)

combine_data = comm.gather(local_data,root=0)

if comm_rank == 0:
    print("root recv {0}".format(combine_data))

 

 

 

 

3.4  规约reduce

import mpi4py.MPI as MPI
 
comm = MPI.COMM_WORLD
comm_rank = comm.Get_rank()
comm_size = comm.Get_size()

if comm_rank == 0:
   data = range(comm_size)
else:
   data = None

local_data = comm.scatter(data, root=0)
local_data = local_data * 2

print(\'rank %d, got and do:\' % comm_rank)
print(local_data)

all_sum = comm.reduce(local_data, root=0,op=MPI.SUM)

if comm_rank == 0:
    print(\'sum is:%d\' % all_sum)

SUM   MAX   MIN  等操作在数据搜集是在各个进程中进行一次操作后汇总到  root 进程中再进行一次总的操作。

op=MPI.SUM

op=MPI.MAX

op=MPI.MIN

 

 

 

 

 3.5   对一个文件的多个行并行处理

#!usr/bin/env python
#-*- coding: utf-8 -*-
import sys
import os
import mpi4py.MPI as MPI
import numpy as np

#  Global variables for MPI
# instance for invoking MPI relatedfunctions
comm = MPI.COMM_WORLD
# the node rank in the whole community
comm_rank = comm.Get_rank()
# the size of the whole community, i.e.,the total number of working nodes in the MPI cluster
comm_size = comm.Get_size()

 
if __name__ == \'__main__\':
    if comm_rank == 0:
        sys.stderr.write("processor root starts reading data...\\n")
        all_lines = sys.stdin.readlines()

    all_lines = comm.bcast(all_lines if comm_rank == 0 else None, root = 0)

    num_lines = len(all_lines)
    local_lines_offset = np.linspace(0, num_lines, comm_size +1).astype(\'int\')

    local_lines = all_lines[local_lines_offset[comm_rank] :local_lines_offset[comm_rank + 1]]

    sys.stderr.write("%d/%d processor gets %d/%d data \\n" %(comm_rank, comm_size, len(local_lines), num_lines))

    for line in local_lines:
        output = line.strip() + \' : process every line here\'
        print(output)

 

 

 

 

 3.6   对多个文件并行处理

#!usr/bin/env python
#-*- coding: utf-8 -*-
import sys
import os
import mpi4py.MPI as MPI
import numpy as np
 
#  Global variables for MPI
# instance for invoking MPI relatedfunctions
comm = MPI.COMM_WORLD
# the node rank in the whole community
comm_rank = comm.Get_rank()
# the size of the whole community, i.e.,the total number of working nodes in the MPI cluster
comm_size = comm.Get_size()
 
 
if __name__ == \'__main__\':
   if len(sys.argv) != 2:
       sys.stderr.write("Usage: python *.py directoty_with_files\\n")
       sys.exit(1)

   path = sys.argv[1]

   if comm_rank == 0:
       file_list = os.listdir(path)
       sys.stderr.write("......%d files......\\n" % len(file_list))

   file_list = comm.bcast(file_list if comm_rank == 0 else None, root = 0)
   num_files = len(file_list)
   local_files_offset = np.linspace(0, num_files, comm_size +1).astype(\'int\')
   local_files = file_list[local_files_offset[comm_rank] :local_files_offset[comm_rank + 1]]

   sys.stderr.write("%d/%d processor gets %d/%d data \\n" %(comm_rank, comm_size, len(local_files), num_files))

   sys.stderr.write("processor %d has %s files \\n"%(comm_rank, local_files))

 

 

 

3.7    联合numpy对矩阵的多个行或者多列并行处理

import os, sys, time
import numpy as np
import mpi4py.MPI as MPI
 
# instance for invoking MPI relatedfunctions
comm = MPI.COMM_WORLD
# the node rank in the whole community
comm_rank = comm.Get_rank()
# the size of the whole community, i.e.,the total number of working nodes in the MPI cluster
comm_size = comm.Get_size()
 
# test MPI
if __name__ == "__main__":
    #create a matrix
    if comm_rank == 0:
        all_data = np.arange(20).reshape(4, 5)
        print("************ data start******************")
        print(all_data)
        print("************ data end******************")
   
    #broadcast the data to all processors
    all_data = comm.bcast(all_data if comm_rank == 0 else None, root = 0)
   
    #divide the data to each processor
    num_samples = all_data.shape[0]
    local_data_offset = np.linspace(0, num_samples, comm_size + 1).astype(\'int\')
   
    #get the local data which will be processed in this processor
    local_data = all_data[local_data_offset[comm_rank] :local_data_offset[comm_rank + 1]]
    print("****** %d/%d processor gets local data ****" %(comm_rank, comm_size))
    print(local_data)
   
    #reduce to get sum of elements
    local_sum = local_data.sum()
    all_sum = comm.reduce(local_sum, root = 0, op = MPI.SUM)
   
    #process in local
    local_result = local_data ** 2
   
    #gather the result from all processors and broadcast it
    result = comm.allgather(local_result)
    result = np.vstack(result)
   
    if comm_rank == 0:
        print("*** sum: ", all_sum)
        print("************ result ******************")
        print(result)

 

 

 

 

 

 

 

 

参考文章：

《Python多核编程mpi4py实践》

https://blog.csdn.net/zouxy09/article/details/49031845