cppyy调用含OPENMP的C++代码出现nullptr错误求助

问题描述 #

用cppyy在Python中调用包含OpenMP并行化的C++代码时遭遇错误：

• 用GCC编译（参数-fopenmp -O2）的可执行文件运行正常，并行化带来的性能提升符合预期；
• 但C++代码保留#pragma omp parallel for指令时，cppyy抛出未解析符号错误（如__kmpc_for_static_fini等），最终触发ValueError: nullptr result where temporary expected；
• 注释掉该OpenMP指令后，无异常出现。

报错信息 #

IncrementalExecutor::executeFunction: symbol '__kmpc_for_static_fini' unresolved while linking symbol '__cf_4'!
IncrementalExecutor::executeFunction: symbol '__kmpc_for_static_init_4' unresolved while linking symbol '__cf_4'!
IncrementalExecutor::executeFunction: symbol '__kmpc_fork_call' unresolved while linking symbol '__cf_4'!
IncrementalExecutor::executeFunction: symbol '__kmpc_global_thread_num' unresolved while linking symbol '__cf_4'!
Traceback (most recent call last):
  File "...../SO_troubleshooting/example_pll_cppyy_code.py", line 8, in <module>
    output = cppyy.gbl.pll_somelinalgeb()
ValueError: std::vector<std::vector<Eigen::Matrix<double,-1,-1,0,-1,-1> > > ::pll_somelinalgeb() =>
    ValueError: nullptr result where temporary expected

Python调用脚本 #

import cppyy
cppyy.add_include_path('../np_vs_eigen/eigen/')
cppyy.include('easy_example.cpp')
vector = cppyy.gbl.std.vector
import datetime as dt
print('Starting the function call now ')

start = dt.datetime.now()
output = cppyy.gbl.pll_somelinalgeb()
stop = dt.datetime.now()
print((stop-start), 'seconds')

C++测试代码 #

#include <omp.h>
#include <iostream>
#include <Eigen/Dense>
#include <chrono>
#include <vector>
#include <thread>

using Eigen::VectorXd;
using Eigen::MatrixXd;

std::vector<MatrixXd> some_linearalgebra(){
    std::vector<MatrixXd> solutions;
    std::srand((unsigned int) time(0));//ensures a new random matrix each time
    MatrixXd arraygeom(5,3);
    arraygeom = MatrixXd::Random(5,3);
    VectorXd row1 = arraygeom.block(0,0,1,3).transpose();
    arraygeom.rowwise() -= row1.transpose();
    MatrixXd pinv_arraygeom(3,5);


    // calculate the pseudoinverse of arraygeom
    pinv_arraygeom = arraygeom.completeOrthogonalDecomposition().pseudoInverse();
    //std::cout << pinv_arraygeom << std::endl;
    solutions.push_back(pinv_arraygeom);
    solutions.push_back(pinv_arraygeom);
    std::this_thread::sleep_for(std::chrono::milliseconds(1));
    return solutions;
}

std::vector<std::vector<MatrixXd>> pll_somelinalgeb(){
int num_runs = 5000;
std::vector<std::vector<MatrixXd>> all_solns(num_runs);
#pragma omp parallel for
for (int i=0; i<num_runs; i++){
    all_solns[i] = some_linearalgebra();
}
return all_solns;
}


int main(){
std::vector<MatrixXd> main_out;
main_out = some_linearalgebra();

auto start = std::chrono::system_clock::now();

std::vector<std::vector<MatrixXd>> main2_out;
main2_out = pll_somelinalgeb();
auto end = std::chrono::system_clock::now();
std::cout << std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count() << " ms" << std::endl;

return 0;
}

系统环境 #

• Ubuntu 18.04.2 LTS，Intel® Core™ i7-10700 CPU @ 2.90GHz × 16，64位
• Python 3.9.0
• cppyy 2.4.0（pip安装）
• Eigen 3.4.0

已尝试操作 #

• 按照cppyy官方文档设置环境变量EXTRA_CLING_ARGS='-fopenmp'及CLING_STANDARD_PCH
• C++可执行文件编译命令：g++-11 easy_example.cpp -fopenmp -O2 -I <path_to_Eigen_library here>

内容的提问来源于stack exchange，提问作者Thejasvi