Python嵌入了对mpirun的调用

Python with embedded call to mpirun

本文关键字：mpirun 调用 Python      更新时间：2023-10-16

我正在尝试使用PyOpt运行一些并行优化。棘手的部分是，在我的目标函数中，我也想使用mpi运行c++代码。

我的python脚本如下: 
#!/usr/bin/env python    
# Standard Python modules
import os, sys, time, math
import subprocess

# External Python modules
try:
    from mpi4py import MPI
    comm = MPI.COMM_WORLD
    myrank = comm.Get_rank()
except:
    raise ImportError('mpi4py is required for parallelization')
# Extension modules
from pyOpt import Optimization
from pyOpt import ALPSO
# Predefine the BashCommand
RunCprogram = "mpirun -np 2 CProgram" # Parallel C++ program

######################### 
def objfunc(x):
    f = -(((math.sin(2*math.pi*x[0])**3)*math.sin(2*math.pi*x[1]))/((x[0]**3)*(x[0]+x[1])))
    # Run CProgram 
    os.system(RunCprogram) #where the mpirun call occurs
    g = [0.0]*2
    g[0] = x[0]**2 - x[1] + 1
    g[1] = 1 - x[0] + (x[1]-4)**2
    time.sleep(0.01)
    fail = 0
    return f,g, fail
# Instantiate Optimization Problem 
opt_prob = Optimization('Thermal Conductivity Optimization',objfunc)
opt_prob.addVar('x1','c',lower=5.0,upper=1e-6,value=10.0)
opt_prob.addVar('x2','c',lower=5.0,upper=1e-6,value=10.0)
opt_prob.addObj('f')
opt_prob.addCon('g1','i')
opt_prob.addCon('g2','i')
# Solve Problem (DPM-Parallelization)
alpso_dpm = ALPSO(pll_type='DPM')
alpso_dpm.setOption('fileout',0)
alpso_dpm(opt_prob)
print opt_prob.solution(0)

我使用:

mpirun -np 20 python Script.py

但是，我得到以下错误:

[user:28323] *** Process received signal ***
[user:28323] Signal: Segmentation fault (11)
[user:28323] Signal code: Address not mapped (1)
[user:28323] Failing at address: (nil)
[user:28323] [ 0] /lib64/libpthread.so.0() [0x3ccfc0f500]
[user:28323] *** End of error message ***

我认为两个不同的mpirun调用(调用python脚本的一个和脚本内的一个)相互冲突。有解决这个问题的线索吗?

谢谢! !

参见在mpi应用程序的子进程中串行调用mpi二进制:最安全的方法是使用MPI_Comm_spawn()。以这个经理-员工的例子为例。

一个快速的解决方案是使用subprocess.Popen作为@EdSmith的信号。但是，请注意subprocess.Popen的默认行为使用父环境。我的猜测是os.system()也是如此。不幸的是，一些环境变量是由mpirun添加的，具体取决于MPI实现，如OMPI_COMM_WORLD_RANK或OMPI_MCA_orte_ess_num_procs。要查看这些环境变量，请在mpi4py代码和基本python shell中键入import os ; print os.environ。这些环境变量可能导致子流程失败。所以我不得不添加一行来摆脱它们……这很脏……它可以归结为: 
    args = shlex.split(RunCprogram)
    env=os.environ
    # to remove all environment variables with "MPI" in it...rather dirty...
    new_env = {k: v for k, v in env.iteritems() if "MPI" not in k}
    #print new_env
    # shell=True : watch for security issues...
    p = subprocess.Popen(RunCprogram,shell=True, env=new_env,stdout=subprocess.PIPE, stdin=subprocess.PIPE)
    p.wait()
    result="process myrank "+str(myrank)+" got "+p.stdout.read()
    print result
完整的测试代码，由mpirun -np 2 python opti.py运行: 
#!/usr/bin/env python    
# Standard Python modules
import os, sys, time, math
import subprocess
import shlex

# External Python modules
try:
    from mpi4py import MPI
    comm = MPI.COMM_WORLD
    myrank = comm.Get_rank()
except:
    raise ImportError('mpi4py is required for parallelization')
# Predefine the BashCommand
RunCprogram = "mpirun -np 2 main" # Parallel C++ program

######################### 
def objfunc(x):
    f = -(((math.sin(2*math.pi*x[0])**3)*math.sin(2*math.pi*x[1]))/((x[0]**3)*(x[0]+x[1])))
    # Run CProgram 
    #os.system(RunCprogram) #where the mpirun call occurs
    args = shlex.split(RunCprogram)
    env=os.environ
    new_env = {k: v for k, v in env.iteritems() if "MPI" not in k}
    #print new_env
    p = subprocess.Popen(RunCprogram,shell=True, env=new_env,stdout=subprocess.PIPE, stdin=subprocess.PIPE)
    p.wait()
    result="process myrank "+str(myrank)+" got "+p.stdout.read()
    print result

    g = [0.0]*2
    g[0] = x[0]**2 - x[1] + 1
    g[1] = 1 - x[0] + (x[1]-4)**2
    time.sleep(0.01)
    fail = 0
    return f,g, fail
print objfunc([1.0,0.0])

基本工作者，由mpiCC main.cpp -o main编译:

#include "mpi.h"
int main(int argc, char* argv[]) { 
    int rank, size;
    MPI_Init (&argc, &argv);    
    MPI_Comm_rank (MPI_COMM_WORLD, &rank);  
    MPI_Comm_size (MPI_COMM_WORLD, &size);  
    if(rank==0){
        std::cout<<" size "<<size<<std::endl;
    }
    MPI_Finalize();
    return 0;
}
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