Python内嵌了对mpirun的调用
Python内嵌了对mpirun的调用
提问于 2015-05-22 05:26:40
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，我还想使用mpi运行一个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)我使用以下命令运行该代码：
mpirun -np 20 python Script.py但是，我得到了以下错误：
[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脚本的调用和脚本内的调用)彼此冲突。关于如何解决这个问题有什么线索吗？
谢谢你！！
Stack Overflow用户
发布于 2015-05-24 21:19:04
参见Calling mpi binary in serial as subprocess of mpi application：最安全的方法是使用MPI_Comm_spawn()。以this manager-worker example为例。
一个快速的解决办法是使用@EdSmith表示的subprocess.Popen。但是，请注意，subprocess.Popen的默认行为使用父对象的环境。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，这取决于MPI实现，例如OMPI_COMM_WORLD_RANK或OMPI_MCA_orte_ess_num_procs。要查看这些环境变量，可以在mpi4py代码和基本的python shell中输入import os ; print os.environ。这些环境变量可能导致子进程失败。所以我不得不添加一行代码来去掉them...which是相当脏的…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])Basic worker，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;
}页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/30384649
复制相关文章
相似问题
腾讯云开发者
