指摘を受け入出力を減らした

a.cl

; $ sbcl --load a.cl --eval '(sb-ext:save-lisp-and-die "a.out" :toplevel #'\''main :executable t)' && time ( echo 100000000 | ./a.out )
; ( echo 100000000 | ./a.out; )  4.30s user 0.15s system 99% cpu 4.468 total

; $ sbcl --version
; SBCL 1.2.6

(defun main ()
  (declare (optimize (speed 3) (debug 0) (safety 0) (compilation-speed 0)))
  (let* ((n (1+ (the fixnum (read))))
         (is-prime (make-array n :element-type 'boolean :initial-element t)))
    (declare (type fixnum n)
             (type (simple-array boolean (*)) is-prime))
    (setf (svref is-prime 0) nil)
    (setf (svref is-prime 1) nil)
    (dotimes (i n)
      (declare (type fixnum i))
      (if (svref is-prime i)
        (do ((j (* 2 i) (+ j i)))
          ((>= j n))
          (declare (type fixnum j))
          (setf (svref is-prime j) nil))))
    (let ((m 0))
      (dotimes (i n)
        (declare (type fixnum i))
        (if (svref is-prime i)
          (setq m (1+ m))))
      (write m)
      (write-char #\newline))))

a.cpp

// $ clang++ -std=c++11 -O2 a.cpp && time ( echo 100000000 | ./a.out )
// 2.10s user 0.00s system 99% cpu 2.116 total

// $ g++ -std=c++11 -O2 a.cpp && time ( echo 100000000 | ./a.out )
// 2.13s user 0.00s system 99% cpu 2.140 total

// $ g++ --version
// g++ (GCC) 4.9.2 20141224 (prerelease)

// $ clang++ --version
// clang version 3.5.1 (tags/RELEASE_351/final)

#include <iostream>
#include <vector>
#include <algorithm>
using namespace std;
int main() {
    ios_base::sync_with_stdio(false);
    size_t n; cin >> n;
    vector<bool> is_prime(n+1, true);
    is_prime[0] = is_prime[1] = false;
    for (size_t i = 0; i < n+1; ++i) {
        if (is_prime[i]) {
            for (size_t j = 2*i; j < n+1; j += i) {
                is_prime[j] = false;
            }
        }
    }
    cout << count(is_prime.begin(), is_prime.end(), true) << endl;
    return 0;
}