First of all, you have initialized the array using the variable N, before assigning a value to it! Try using
int * simeio;
(a pointer to int, which will act as an array later) and use malloc() to allocate memory after you have read the value for N from the file. Take a look at www.cplusplus.com/malloc
] for information on malloc().
Second, according to your file "pulsars.in", it doesn't look like an NxN array. It looks like to me as an Nx2 array. So you can change the following code
Third, you need to correct the code
simeio[x][y] = i;
simeio[i] = x;
simeio[i] = y;
Additionally, insert some printf statements to check whether you read the values for N, x, and y from the file correctly. Then you should be OK.