Segmentation Fault with Eigen Library (3.3.4) - c++

Question

I am using Eigen for some simulations. I get segmentation fault error (more precisely Segmentation fault (core dumped) with no other details) whenever I include even the smallest overload Eigen operation (even if I have x=y where x,y are Eigen::VectorXd of the same size). What make this very strange is that it only happens if I have the matrix operations in certain functions.
Let me show you:
//main.cu
#include <Eigen/Dense>
#include "def.h"
using namespace std;
int main(int argc, char *argv[])
{
params p;
int ns;
//some code here
MatrixXR A(ns,ns);
VectorXR u(ns);
VectorXR v(ns);
VectorXR unew(ns);
VectorXR aux(ns);
VectorXR vnew(ns);
VectorXR vcouple(ns);
VectorXR q(ns);
Real* output;
output=new Real[output_size];
//output_size is a number depending on the system I am simulating, usually about 1000000.
CPUsim(output,p,u,v,A,unew,vnew,q,aux,vcouple);
delete [] &(output[0]);
return 0;
}
//def.h
#ifndef DEF_H_
#include <Eigen/Dense>
#define DEF_H_
#ifdef DOUBLE
typedef double Real;
typedef Eigen::MatrixXd MatrixXR;
typedef Eigen::VectorXd VectorXR;
#else
typedef float Real;
typedef Eigen::MatrixXf MatrixXR;
typedef Eigen::VectorXf VectorXR;
#endif
struct params
{
//some parameters
};
#endif
//sim.h
#ifndef SIM_H_
#define SIM_H_
#include "def.h"
#include <Eigen/Dense>
void CPUsim(Real* output,params &p, VectorXR& u,VectorXR& v,MatrixXR& A,VectorXR& unew,VectorXR& vnew,VectorXR& q,VectorXR& aux,VectorXR& vcouple);
//other functions
#endif
//sim.cu
#include "sim.h"
#include "coupling.h"
//some functions
void CPUsim(Real* output,params &p, VectorXR& u,VectorXR& v,MatrixXR& A,VectorXR& unew,VectorXR& vnew,VectorXR& q,VectorXR& aux,VectorXR& vcouple)
{
//some code
coupling(u,unew,v,vnew,p,A,vcouple,aux,no);
}
//coupling.h
#ifndef COUPLING_H_
#define COUPLING_H_
#include <Eigen/Dense>
#include "def.h"
//some declarations
void coupling(VectorXR& u,VectorXR& unew,VectorXR& v,VectorXR& vnew,params& p,MatrixXR& A,VectorXR& vcouple,VectorXR& aux,noise& no);
//coupling.cpp
void coupling(VectorXR& u,VectorXR& unew,VectorXR& v,VectorXR& vnew,params& p,MatrixXR& A,VectorXR& vcouple,VectorXR& aux,noise& no)
{
vcouple=A*v;
//some other stuff
}
Now, some explanations:
If I have vcouple=vcouple in coupling, I get no error, if I have vcouple=v, I do get the error. I get no errors if I have vcouple=A*v in main or in CPUsim. Somebody recommended defining 'EIGEN_DONT_ALIGN', but that works only in some cases (i.e. for the same ns, but different values for the elements of the matrices and vectors, it might show the error or it might not). Do you happen to know what might be causing this error?
BTW, I use the nvcc compiler because I am using CUDA for some parts of the simulation. However, Eigen is used only for portions of the code that run entirely on the CPU. For the host compiler, I use GCC 5.4.1 and I have ubuntu 16.04.
Edit:
The error disappears if I don't store the result (i.e. just A*v; instead of vcouple=A*v;)

Answer 1

I finally found the answer. Apparently nvcc and gcc align Eigen arrays differently. This explains why there was no problem when calculating (and assigning) the matrix product in the .cu files while getting an error in the .cpp ones. Simply changing the extension of the coupling.cpp file to .cu solved the problem.
More details can be found here:
https://listengine.tuxfamily.org/lists.tuxfamily.org/eigen/2016/06/msg00003.html