Java program to execute a command taking a long time

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?

What is "forever"? Have you tried other commands, both simple and difficult? There probably is an extra delay depending on what is in the command. — Juru, Oct 01 '14 at 20:44
More details, please. What is the exact command you're running? What are the timings for running the command directly, and what are the timings for a `public static void main` that just executes this command and then terminates? — chiastic-security, Oct 01 '14 at 20:44
The command has been running for 14 minutes and is still running. — Tad, Oct 01 '14 at 20:45
the command is basically time tabix file pos1 pos2 pos3 ... pos190 > /dev/null — Tad, Oct 01 '14 at 20:46
I've had a similar problem with an execution with parameters, take a look at this answer: http://stackoverflow.com/a/25082093/869783 — MarcioB, Oct 01 '14 at 20:56
You need to attach the reader to the process **before** calling it's `waitFor`. Without that it will fill it's allocated output buffer and then block - but only for big output, small output will seem to be fine. — OldCurmudgeon, Oct 01 '14 at 21:15
@OldCurmudgeon thank you! that had fixed it! One more question - why is the redirection to dev/null still displayed? — Tad, Oct 01 '14 at 21:18

OldCurmudgeon · Accepted Answer · 2014-10-02T10:26:21.140

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");
}

Java program to execute a command taking a long time

1 Answers1