Java program to execute a command taking a long ti

Question

I have read many examples and ended up using the following code to execute a command line command from inside of a Java program.

public static void executeCommand(final String command) throws IOException, 
    InterruptedException {
        System.out.println("Executing command " + command);
        final Runtime r = Runtime.getRuntime();
        final Process p = r.exec(command);
        System.out.println("waiting for the process");
        p.waitFor();
        System.out.println("waiting done");
        try (final BufferedReader b = new BufferedReader(new InputStreamReader(
            p.getInputStream()))) {
            String line;

            while ((line = b.readLine()) != null) {
                System.out.println(line);
            }
        }
    }

I have tested it with a simple ls command and it works fine. When I try to run another command, it is taking forever (kept running for 25 minutes and did not stop yet).

When I execute a tabix command on the command line, I get the following statistics

4.173u 0.012s 0:04.22 99.0% 0+0k 0+0io 0pf+0w

Hence it should finish fast.

The command is

time tabix file pos1 pos2 ... pos190 > /dev/null

Could the problem be that the tabix command includes > /dev/null at the end? If not, what could cause this issue?

Answer 1

You need to attach the reader to the process before calling it's waitFor. Without that it could fill it's allocated output buffer and then block - but only for big output, small (e.g. test) output will seem to be fine.

public static void executeCommand(final String command) throws IOException, InterruptedException {
    System.out.println("Executing command " + command);
    // Make me a Runtime.
    final Runtime r = Runtime.getRuntime();
    // Start the command process.
    final Process p = r.exec(command);
    // Pipe it's output to System.out.
    try (final BufferedReader b = new BufferedReader(new InputStreamReader(p.getInputStream()))) {
        String line;

        while ((line = b.readLine()) != null) {
            System.out.println(line);
        }
    }
    // Do this AFTER you've piped all the output from the process to System.out
    System.out.println("waiting for the process");
    p.waitFor();
    System.out.println("waiting done");
}