Issues of writes to unknown address in odeint #257
Description
I am trying to use boost library's odeint with std::vector or std::array. I have no issues with compilation in either case, however, I have runtime issues regarding write to unknown address in the case of std::array. Given below is a MWE.
I have defined two classes: ODE1, and ODE2 with std::vector, and std::array respectively in the header file ode.hpp.
#ifndef ODE_HPP_
#define ODE_HPP_
// c++ standard library headers
#include <array>
#include <iostream>
#include <vector>
namespace ode {
constexpr size_t n_sections = 1800;
constexpr size_t n_nodes_per_section = 6;
constexpr size_t n_variables = n_sections * n_nodes_per_section;
} // namespace ode
class ODE1 {
public:
ODE1(const double o) : V_(ode::n_variables, o) {} // explicit constructor
std::vector<double>& GetVoltage() { return V_; }
void operator()(const std::vector<double>& Y, std::vector<double>& dYdt,
const double /* time */) {
using namespace ode;
for (size_t n = 0; n < n_sections; n++) {
dYdt[n * n_nodes_per_section + 0] = Y[n * n_nodes_per_section + 0];
dYdt[n * n_nodes_per_section + 1] = Y[n * n_nodes_per_section + 1];
dYdt[n * n_nodes_per_section + 2] = Y[n * n_nodes_per_section + 2];
dYdt[n * n_nodes_per_section + 3] = Y[n * n_nodes_per_section + 3];
dYdt[n * n_nodes_per_section + 4] = Y[n * n_nodes_per_section + 4];
dYdt[n * n_nodes_per_section + 5] = Y[n * n_nodes_per_section + 5];
}
}
private:
std::vector<double> V_{};
};
class ODE2 {
using Array = std::array<double, ode::n_variables>;
public:
// constructors
ODE2(const double o) { V_.fill(o); } // explicit constructor
Array& GetVoltage() { return V_; }
void operator()(const Array& Y, Array& dYdt, const double /* time */) {
using namespace ode;
for (size_t n = 0; n < n_sections; n++) {
dYdt[n * n_nodes_per_section + 0] = Y[n * n_nodes_per_section + 0];
dYdt[n * n_nodes_per_section + 1] = Y[n * n_nodes_per_section + 1];
dYdt[n * n_nodes_per_section + 2] = Y[n * n_nodes_per_section + 2];
dYdt[n * n_nodes_per_section + 3] = Y[n * n_nodes_per_section + 3];
dYdt[n * n_nodes_per_section + 4] = Y[n * n_nodes_per_section + 4];
dYdt[n * n_nodes_per_section + 5] = Y[n * n_nodes_per_section + 5];
}
}
private:
Array V_{};
};
#endif // ODE_HPP_
And the main function is defined in the file `ode.cpp'
// related header
#include "ode.hpp"
// other library headers
#include <boost/numeric/odeint.hpp>
int main() {
constexpr double abs_err = 1.0e-10;
constexpr double rel_err = 1.0e-8;
constexpr double sim_duration = 20.0; // ms
constexpr double t_start = 0; // ms
constexpr double t_stop = t_start + sim_duration; // ms
constexpr double dt = 5e-3; // ms
{
std::cout << "ODE 1: ";
using namespace boost::numeric::odeint;
using error_stepper_type = runge_kutta_dopri5<std::vector<double>>;
ODE1 o(-60.0);
integrate_adaptive(make_controlled<error_stepper_type>(abs_err, rel_err), o,
o.GetVoltage(), t_start, t_stop, dt);
}
{
std::cout << "ODE 1: ";
using namespace boost::numeric::odeint;
using error_stepper_type =
runge_kutta_dopri5<std::array<double, ode::n_variables>>;
ODE2 o(-60.0);
integrate_adaptive(make_controlled<error_stepper_type>(abs_err, rel_err), o,
o.GetVoltage(), t_start, t_stop, dt);
}
return 0;
}
I am compiling using the clang compiler as follows
c++ -O0 -g -fsanitize=address -fno-omit-frame-pointer -Wall -Wextra -Wpedantic -std=c++17 ode.cpp -o ode
Compilation output (warnings)
In file included from ode.cpp:5:
In file included from /usr/local/include/boost/numeric/odeint.hpp:79:
In file included from /usr/local/include/boost/numeric/odeint/stepper/generation.hpp:32:
/usr/local/include/boost/numeric/odeint/stepper/generation/generation_controlled_adams_bashforth_moulton.hpp:43:99: warning: unused parameter 'stepper' [-Wunused-parameter]
controller_type operator()( value_type abs_error , value_type rel_error , const stepper_type &stepper )
^
/usr/local/include/boost/numeric/odeint/stepper/generation/generation_controlled_adams_bashforth_moulton.hpp:49:71: warning: unused parameter 'stepper' [-Wunused-parameter]
time_type max_dt, const stepper_type &stepper )
^
2 warnings generated.
As I mentioned above, I do not run into issues with compilation. When I run the executable, I have the following issues
AddressSanitizer:DEADLYSIGNAL
=================================================================
==29478==ERROR: AddressSanitizer: stack-overflow on address 0x7ffee1db40e0 (pc 0x00010d66140c bp 0x7ffee1dde910 sp 0x7ffee1da5d80 T0)
#0 0x10d66140c in void boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>::do_step_impl<ODE2, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul> const&, std::__1::array<double, 7200ul> const&, double, std::__1::array<double, 7200ul>&, std::__1::array<double, 7200ul>&, double, std::__1::array<double, 7200ul>&) runge_kutta_dopri5.hpp:165
#1 0x10d660d9c in void boost::numeric::odeint::explicit_error_stepper_fsal_base<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, (unsigned short)5, (unsigned short)5, (unsigned short)4, std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>::do_step<ODE2, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul> const&, std::__1::array<double, 7200ul> const&, double, std::__1::array<double, 7200ul>&, std::__1::array<double, 7200ul>&, double, std::__1::array<double, 7200ul>&) explicit_error_stepper_fsal_base.hpp:272
#2 0x10d660451 in boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step<ODE2, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul> const&, std::__1::array<double, 7200ul> const&, double&, std::__1::array<double, 7200ul>&, std::__1::array<double, 7200ul>&, double&) controlled_runge_kutta.hpp:768
#3 0x10d65ea18 in boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step<ODE2, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul>&, std::__1::array<double, 7200ul>&, double&, double&) controlled_runge_kutta.hpp:718
#4 0x10d65d9b1 in boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1<ODE2, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul>&, double&, double&) controlled_runge_kutta.hpp:902
#5 0x10d65d112 in boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step<ODE2, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul>&, double&, double&) controlled_runge_kutta.hpp:619
#6 0x10d65cc3e in unsigned long boost::numeric::odeint::detail::integrate_adaptive<boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::null_observer>(boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>&, double&, double, double&, boost::numeric::odeint::null_observer, boost::numeric::odeint::controlled_stepper_tag) integrate_adaptive.hpp:103
#7 0x10d65c401 in unsigned long boost::numeric::odeint::integrate_adaptive<boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::null_observer>(boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>&, double, double, double, boost::numeric::odeint::null_observer) integrate_adaptive.hpp:42
#8 0x10d63acde in unsigned long boost::numeric::odeint::integrate_adaptive<boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>, double>(boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<double, double>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, ODE2, std::__1::array<double, 7200ul>&, double, double, double) integrate_adaptive.hpp:83
#9 0x10d639fac in main ode.cpp:30
#10 0x7fff203d0f3c in start+0x0 (libdyld.dylib:x86_64+0x15f3c)
SUMMARY: AddressSanitizer: stack-overflow runge_kutta_dopri5.hpp:165 in void boost::numeric::odeint::runge_kutta_dopri5<std::__1::array<double, 7200ul>, double, std::__1::array<double, 7200ul>, double, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>::do_step_impl<ODE2, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul>, std::__1::array<double, 7200ul> >(ODE2, std::__1::array<double, 7200ul> const&, std::__1::array<double, 7200ul> const&, double, std::__1::array<double, 7200ul>&, std::__1::array<double, 7200ul>&, double, std::__1::array<double, 7200ul>&)
==29478==ABORTING
ODE 1: ODE 1: zsh: abort ./ode
Strange enough, I do not have issues when I change the parameter, n_sections, in the header from 1800 to 1000. I could not figure out the issue, is this something to with the boost library containers? Any help would be greatly appreciated.