Communicate with external C program with Java using stdin and stdout

What I'm trying to do is launch the C program executable inside the Java application and allow them to communicate with each other using stdin and stdout. The C program will wait for a command from the java app and echo it back. I've tested the java code with "gnugo --mode gtp" (gnugo with in gtp mode communicates with stdin and stdout) and it works fine but my doesn't work with my C code. Any suggestion would greatly appreciated.

C code

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

int main(void) {

unsigned int byte_read;
char *string, *tok;
int cmd_id;

int len = 64;
string = (char *) malloc(len + 1);

while (1) {

    byte_read = getline(&string,&byte_read, stdin);

    if (byte_read == -1) {
        printf("Error reading input\n");

        free(string);
        exit(0);
        //
    } else {
        printf("Got command: %s\n", string);
    }
  }
return EXIT_SUCCESS;
}

Java code

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.BlockingQueue;

public class Test {

private BlockingQueue<String> m_queue;
private PrintWriter print_out;
private BufferedReader bufIn;
private InputThread inputThread;
private PrintWriter printOut;
private Process p;
public static void main(String[] args) {

    Test test = new Test();
    test.start();
}

public void start(){

    try
    {
        Runtime rt = Runtime.getRuntime() ;

        p = rt.exec("path/to/the/c/program") ;
        InputStream in = p.getInputStream() ;
        OutputStream out = p.getOutputStream ();
        InputStream err = p.getErrorStream();

        printOut = new PrintWriter(out);

        m_queue = new ArrayBlockingQueue<String>(10);
        inputThread = new InputThread(in, m_queue);
        inputThread.start();

        //send a command to 
        printOut.println("sample command");
        printOut.flush();

        //p.destroy() ;
    }catch(Exception exc){
        System.out.println("Err " + exc.getMessage());
    }
}

private void mainLoop(){
    String line;
    while (true){

        try
        {
            System.out.println("Before");
            line = bufIn.readLine();
            System.out.println("After");

            if (line != null)
                System.out.println(line);


        }
        catch (IOException e)
        {
            System.out.println("Error readline " + e.getMessage());
            return;
        }
    }
}
private class InputThread extends Thread
{
    InputThread(InputStream in, BlockingQueue<String> queue)
    {
        bufIn = new BufferedReader(new InputStreamReader(in));
        m_queue = queue;
    }
    public void run()
    {
        try
        {
            mainLoop();
        }
        catch (Throwable t)
        {

        }
    }
}

}