Allocate a struct which includes a 3d linked list

Question

I want to implement a simple N-body simulation and to manage all the pairwise interactions I wanted to use a linked list to compute only interactions between neighbours. This is the code:

#include <stdio.h>
#include <stdlib.h>

#define V 20
#define N_P 100

typedef struct _node{
  int id;
  struct _node *next;
} node;

typedef struct _particle{
  double r[3];
  node* n;
  int coor[3];
} particle;

typedef struct _simulation_struct{
  int N;
  particle *system;
  double L[3];
  double s[3];

  int nc[3];
  node*** cell;
} simulation_struct;

  simulation_struct *new_simulation(int N, double Lx, double Ly,double Lz,double R);

int main()
{
  simulation_struct *simulation=new_simulation(N_P,V,V,V,2);

  return 0;
}

simulation_struct *new_simulation(int N, double Lx, double Ly, double Lz,double R)
{
  simulation_struct *simulation;
  int i, j,k;

  simulation =(simulation_struct*) malloc(1*sizeof(simulation));

  simulation->N = N;

  simulation->L[0] = Lx;
  simulation->L[1] = Ly;
  simulation->L[2] = Lz;

  simulation->nc[0] = (int) (Lx/R)+1;
  simulation->nc[1] = (int) (Lx/R)+1;
  simulation->nc[2] = (int) (Lx/R)+1;

  simulation->s[0] = Lx/simulation->nc[0];
  simulation->s[1] = Ly/simulation->nc[1];
  simulation->s[2] = Lz/simulation->nc[2];

  simulation->system = (particle*)malloc(N*sizeof(particle));

  simulation->cell =(node***) malloc ((simulation->nc[0])*sizeof(node **));
  for (i=0; i < simulation->nc[0]; i++)
  {
    simulation->cell[i] = (node**)malloc((simulation >nc[1])*sizeof(node*));
    for (j=0; j < simulation->nc[1];j++)
    {
        simulation->cell[i][j] = (node*)malloc((simulation->nc[2])*sizeof(node));

        for (k=0; k < simulation->nc[2];k++)
        {
           simulation->cell[i][j][k].id = -1;
           simulation->cell[i][j][k].next = NULL;
        }
    }
  }

   for (i=0; i < simulation->nc[0]; i++)
   {
      simulation->system[i].n = (node*)malloc(1*sizeof(node));
      simulation->system[i].n->id = i;
   }

   return simulation;
}

I can compile it, and if the parameters V and N_P are small (e.g. V=10 N_P=20) the programs works fine, but if the parameters are a little bit bigger when I execute the program I find a segmentation fault error.Could someone tell me what I'm doing wrong?

Thanks in advance!!!!

Just for your information, being called a [three star programmers](http://c2.com/cgi/wiki?ThreeStarProgrammer) is usually *not* a compliment. — Some programmer dude, Oct 01 '16 at 21:15
Do *NOT* cast the return of `malloc`, it is unnecessary. See: [**Do I cast the result of malloc?**](http://stackoverflow.com/q/605845/995714) for thorough explanation. — David C. Rankin, Oct 01 '16 at 21:23

Jean-François Fabre · Accepted Answer · 2016-10-01T21:23:56.697

Running through a debugger crashes on

simulation->system = (particle*)malloc(N*sizeof(particle));

There's nothing wrong with that malloc, so the problem must come from the previous instructions, which seem fine, well, that is if the previous malloc is OK. But it's not:

simulation =(simulation_struct*) malloc(1*sizeof(simulation));

Bingo: sizeof(simulation) should be sizeof(simulation_struct) or there isn't enough mem for the structure (simulation is a pointer, of size 4 or 8, ...) : corrupt memory.

Fixed:

simulation = malloc(sizeof(simulation_struct));

I tested the fixed version and it does not crash anymore.

Note: as simulation_struct is small, it should be even better to avoid allocating it, and use & return a simulation_struct: slightly more overhead, but one less malloc.

And C++ & vector or good matrix templates could also fix your node *** complex structure which normally leads to memory corruption/memory leaks when trying to copy one in another.

Allocate a struct which includes a 3d linked list

1 Answers1