2022-09-24

cppyy OPENMP error: nullptr result where temporary expected

I've been trying to run some parallelised code in C++ from Python through cppyy but am facing an error.

The executable (compilted through GCC with -fopenmp -O2) runs without errors and shows the expected drop in runtime from parallelisation.

When the #pragma omp parallel for is commented out of the C++ code, cppyy doesn't raise any errors. However, when the pragma is part of the code I get the error below:

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

Here is the short Python script:

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')

The C++ toy code is below. It generates a random matrix with Eigen, calculates its pseudo-inverse, and then sleeps for 1 ms.

#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;
}

System + OS specs:

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

Non-default precompiled cppyy header used:

As per this link I ran the following commands on terminal export EXTRA_CLING_ARGS='-fopenmp' and then ran the code with cppyy_backend.loader, and then finally added the CLING_STANDARD_PCH environment variable with another export.

C++ Executable compiled with g++-11 easy_example.cpp -fopenmp -O2 -I <path_to_Eigen_library here>

Code on Windows: No errors, success

Oddly enough, when I run the same code on my Win 11 laptop (with only the EXTRA_CLING_ARGS=-fopenmp=libiomp5 in the environmental variables) - the code runs without any problems.



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