boolean[]isPrime = new boolean [N/2+1];

boolean[]isPrime = new boolean [N+1];

for (int i = 3; i <= N; i=i+2) {
    isPrime[i] = true;
    }

for (int i = 3; i <= N; i=i+2) {
        if (isPrime[i]) primes++;
  ...
   }

Full code:

public class PrimeSieve {
    public static void main(String[] args) {

        if (args.length < 1) {
            System.out.println("Usage: java PrimeSieve N [-s(ilent)]");
            System.exit(0);
        }

        int N = Integer.parseInt(args[0]);

        // initially assume all odd integers are prime

        boolean[]isPrime = new boolean [N/2+1];

        isPrime[2] = true;

        for (int i = 3; i <= N; i=i+2) {
            isPrime[i] = true;
        }

        int tripCount = 0;

        // mark non-primes <= N using Sieve of Eratosthenes
        for (int i = 3; i * i <= N; i=i+2) {

            // if i is prime, then mark multiples of i as nonprime
        if (isPrime[i]) {
          int j = i * i;
          while (j <= N){
            tripCount++;
            isPrime[j] = false;
            j = j + 2*i;
            }
                        }
                                            }

        System.out.println("Number of times in the inner loop: " + tripCount);

        // count and display primes
        int primes = 0;
        if(N >= 2 ){
            primes = 1;
        }
        for (int i = 3; i <= N; i=i+2) {
            if (isPrime[i]) primes++;
            if (args.length == 2 && args[1].equals("-s"))
                ; // do nothing
            else
                System.out.print(i + " ");
        }
        System.out.println("The number of primes <= " + N + " is " + primes);
    }
}

for (int i = 3; i <= N; i=i+2)

for (int i = 3; i <= N/2; i=i+2)