The following code determines if a process with the specified pid is running. It was tested on Windows 7 and Ubuntu 13. On Windows it uses apache commons-exec to run tasklist and determines if they found the specified pid based on their exit code. It overcomes the fact that tasklist always returns 0 by piping the result to findstr. On linux it uses ps to do the same thing. It also suppresses stdout logging of the child process.

public static boolean isProcessRunning(int pid, int timeout, TimeUnit timeunit) throws java.io.IOException {
    String line;
    if (OS.isFamilyWindows()) {
        //tasklist exit code is always 0. Parse output
        //findstr exit code 0 if found pid, 1 if it doesn't
        line = "cmd /c \"tasklist /FI \"PID eq " + pid + "\" | findstr " + pid + "\"";
    }
    else {
        //ps exit code 0 if process exists, 1 if it doesn't
        line = "ps -p " + pid;
            //`-p` is POSIX/BSD-compliant, `--pid` isn't<ref>https://github.com/apache/storm/pull/296#discussion_r20535744</ref>
    }
    CommandLine cmdLine = CommandLine.parse(line);
    DefaultExecutor executor = new DefaultExecutor();
    // disable logging of stdout/strderr
    executor.setStreamHandler(new PumpStreamHandler(null, null, null));
    // disable exception for valid exit values
    executor.setExitValues(new int[]{0, 1});
    // set timer for zombie process
    ExecuteWatchdog timeoutWatchdog = new ExecuteWatchdog(timeunit.toMillis(timeout));
    executor.setWatchdog(timeoutWatchdog);
    int exitValue = executor.execute(cmdLine);
    // 0 is the default exit code which means the process exists
    return exitValue == 0;
}

Please see below ready to copy/paste example.

Boolean method isStillAllive(...) will get as a parameter the process id number(pid). Method call is quite generic and is meant to wrap device dependent logic to solve same problem on windows/linux/unix like operating systems.

public boolean isStillAllive(String pidStr) {
    String OS = System.getProperty("os.name").toLowerCase();
    String command = null;
    if (OS.indexOf("win") >= 0) {
        log.debug("Check alive Windows mode. Pid: [{}]", pidStr);
        command = "cmd /c tasklist /FI \"PID eq " + pidStr + "\"";            
    } else if (OS.indexOf("nix") >= 0 || OS.indexOf("nux") >= 0) {
        log.debug("Check alive Linux/Unix mode. Pid: [{}]", pidStr);
        command = "ps -p " + pidStr;            
    } else {
        log.warn("Unsuported OS: Check alive for Pid: [{}] return false", pidStr);
        return false;
    }
    return isProcessIdRunning(pidStr, command); // call generic implementation
}

Actual call to system is delegated to isProcessIdRunning(). This method will invoke preformed system dependent command in generic way and result obtained from system is consumed and parsed line by line. If at least one of response lines contains pid than we interpret this as success.

private boolean isProcessIdRunning(String pid, String command) {
    log.debug("Command [{}]",command );
    try {
        Runtime rt = Runtime.getRuntime();
        Process pr = rt.exec(command);

        InputStreamReader isReader = new InputStreamReader(pr.getInputStream());
        BufferedReader bReader = new BufferedReader(isReader);
        String strLine = null;
        while ((strLine= bReader.readLine()) != null) {
            if (strLine.contains(" " + pid + " ")) {
                return true;
            }
        }

        return false;
    } catch (Exception ex) {
        log.warn("Got exception using system command [{}].", command, ex);
        return true;
    }
}

On posix systems the typical way to query if a pid is running is to send it a null signal e.g. kill(pid, 0). If the call succeeds the process exists; if it returns ESRCH it does not. This is naturally subject to unavoidable race conditions which amount to much less in reality than they do in theory. Less uniform ways are to read the /proc file system (if the OS has one) which is more work, amounts to the same thing, and is still subject to the same race conditions.

Note that pid lockfile technique can be two-tiered. That is, the running process creates the file, locks it, and writes its pid. It holds the lock for the duration of its run and thus this pretty much does away with the above need to query whether the process is running because if the process crashes the file lock will be automatically released even though the file still exists. The logic goes like this:

if file exists
   if can get lock
       prev instance died unnaturally
       continue with this new process
   else
       instance already running
else
   good to go, continue with new process

This technique also has race conditions.

I don't remember enough Java to say whether it has wrappers for kill or file locking syscalls like flock, lockf and fcntl required to implement this scheme.