Develop Reference

Not receiving output from ProcessBuilder in YARN job

I have a Hadoop YARN cluster set up on some machines at my university (all machines running Linux Fedora 25). When running a mapreduce job in YARN, I am unable to receive the output from a call I make to a separate program. Interestingly, if I run my job locally (configured in mapred-site.xml), my method for calling the program and receiving its output works just fine. Below is my executeShellCommand class, which is instantiated and used in my first map task.
public class ExecuteShellCommand {
public String executeCommand(String command) {
StringBuffer output = new StringBuffer();
Process p;
try {
String [] args = command.split(" ");
String cmd = args[0];
ProcessBuilder pb = new ProcessBuilder().command(cmd, args[1], args[2], args[3], args[4], args[5], args[6], args[7]).directory(new File("path to executable"));
p = pb.start();
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
p.waitFor();
String line = "";
while ((line = reader.readLine())!= null) {
output.append(line + "\n");
}
} catch (Exception e) {
e.printStackTrace();
return e.toString();
}
return output.toString();
}
}
Things I have made sure to check:
1) Permissions are appropriately set for all files/directories needed
2) Map tasks are run as current user (me), so no issues with illegal access
3) I am not receiving a file not found exception, so the path to the program I'm calling is correct
4) Checked the input/output stream for Process p (input stream set as java.lang.UNIXProcess$ProcessPipeInputStream#1000e80, output stream is null)
5) Instead of calling the program I need to use, I have tried a simple "echo" command, and could not receive that output either.
6) I have also tried using
p = Runtime.getRuntime().exec("myCommand")
but the results are the same (no output received)
As I already mentioned, when I run a job locally, my executeCommand method functions perfectly, and returns the output from the program I call. Only in YARN do the issues occur. I have a feeling that the problem caused by either not reading from the correct buffer, or the command issued to ProcessBuilder is never actually executed. I am quite stumped as to how to debug what is going on here, and any tips would be greatly appreciated!

After hours of trying all sorts of solutions, I figured out how to get the error stream from the process spawned with ProcessBuilder. Turns out when I set the working directory for the process, I forgot to update the path to one of the arguments I was passing it. D'oh!!!

How to make Runtime.getRuntime().exec execute command one by one and get output rather than executing all commands

I am trying to run a *.bat file (which is capable of running several commands and retrieve the output one by one) from my java application. My intention is to send one command, read output use this output for second command and again retrieve the output.
To achieve this, through Runtime.getRuntime().exec I am passing more than one command as an input to PrintWriter. Issue is that after completing all the steps only I can read the output from *.bat through buffer ,but my intention is to run one command get the output and manipulate this output to send second command.
Unfortunately is not working. Any resolution for this?..
I got the idea to send more than one command to Runtime.getRuntime().exec from this link (How to execute cmd commands via Java)
The following is the same code which I got from above link
String[] command =
{
"cmd",
};
Process p = Runtime.getRuntime().exec(command);
new Thread(new SyncPipe(p.getErrorStream(), System.err)).start();
new Thread(new SyncPipe(p.getInputStream(), System.out)).start();
PrintWriter stdin = new PrintWriter(p.getOutputStream());
stdin.println("dir c:\\ /A /Q");
// write any other commands you want here
stdin.close();
int returnCode = p.waitFor();
System.out.println("Return code = " + returnCode);
class SyncPipe implements Runnable
{
public SyncPipe(InputStream istrm, OutputStream ostrm) {
istrm_ = istrm;
ostrm_ = ostrm;
}
public void run() {
try
{
final byte[] buffer = new byte[1024];
for (int length = 0; (length = istrm_.read(buffer)) != -1; )
{
ostrm_.write(buffer, 0, length);
}
}
catch (Exception e)
{
e.printStackTrace();
}
}
private final OutputStream ostrm_;
private final InputStream istrm_;
}

In your case I would not use Threads, you want a sequential execution path.

Actually, instead of trying to reinvent the wheel, I strongly suggest you to use an expect-like java library to do that kind of thing.
Just because there are several things that you'll have to deal with, such as timeout between requests, waiting for the output to return, etc.
Take a look at these libraries
http://expectj.sourceforge.net/
https://code.google.com/p/expect4j/
https://github.com/ronniedong/Expect-for-Java
http://code.google.com/p/enchanter/
In particular, I use expectj in my project and it works pretty well (although I think expect4j is more popular)
With expectj, your code will look like this (from http://expectj.sourceforge.net/)
// Create a new ExpectJ object with a timeout of 5s
ExpectJ expectinator = new ExpectJ(5);
// Fork the process
Spawn shell = expectinator.spawn("/bin/sh");
// Talk to it
shell.send("echo Chunder\n");
shell.expect("Chunder");
shell.send("exit\n");
shell.expectClose();

You can do the redirection of output of one command to other in the bat file itself using pipe.
I am sorry, i hadn't noticed that you want to manipulate the output first.
So instead of using bat file, you can run the commands that are in bat file from java using exec , get the out put, and use the out put to execute the next command.

How can I run multiple commands in just one cmd windows in Java?

what I would like to do is run a batch file multiple times from a java application. Therefore I set up a for-loop that runs this code n times:
for (int i = 0; i < n; i++) {
Runtime.getRuntime().exec("cmd /c start somefile.bat");
}
The problem is that now each time the command is run a new cmd window pops up. However, what I want is just one window that pops up at the beginning and that is used to display all data from the following command calls.
How can I do that?

With && you can execute more than one commands, one after another:
Runtime.getRuntime().exec("cmd /c \"start somefile.bat && start other.bat && cd C:\\test && test.exe\"");
Using multiple commands and conditional processing symbols
You can run multiple commands from a single command line or script using conditional processing symbols. When you run multiple commands with conditional processing symbols, the commands to the right of the conditional processing symbol act based upon the results of the command to the left of the conditional processing symbol.
For example, you might want to run a command only if the previous command fails. Or, you might want to run a command only if the previous command is successful.
You can use the special characters listed in the following table to pass multiple commands.
& [...] command1 & command2
Use to separate multiple commands on one command line. Cmd.exe runs the first command, and then the second command.
&& [...] command1 && command2
Use to run the command following && only if the command preceding the symbol is successful. Cmd.exe runs the first command, and then runs the second command only if the first command completed successfully.
|| [...] command1 || command2
Use to run the command following || only if the command preceding || fails. Cmd.exe runs the first command, and then runs the second command only if the first command did not complete successfully (receives an error code greater than zero).
( ) [...] (command1 & command2)
Use to group or nest multiple commands.
; or , command1 parameter1;parameter2
Use to separate command parameters.

I would use Java's ProcessBuilder or another class which simulates/uses a shell. The following snippet demonstrates the idea (for Linux with bash).
import java.util.Scanner;
import java.io.*;
public class MyExec {
public static void main(String[] args)
{
//init shell
ProcessBuilder builder = new ProcessBuilder( "/bin/bash" );
Process p=null;
try {
p = builder.start();
}
catch (IOException e) {
System.out.println(e);
}
//get stdin of shell
BufferedWriter p_stdin =
new BufferedWriter(new OutputStreamWriter(p.getOutputStream()));
// execute the desired command (here: ls) n times
int n=10;
for (int i=0; i<n; i++) {
try {
//single execution
p_stdin.write("ls");
p_stdin.newLine();
p_stdin.flush();
}
catch (IOException e) {
System.out.println(e);
}
}
// finally close the shell by execution exit command
try {
p_stdin.write("exit");
p_stdin.newLine();
p_stdin.flush();
}
catch (IOException e) {
System.out.println(e);
}
// write stdout of shell (=output of all commands)
Scanner s = new Scanner( p.getInputStream() );
while (s.hasNext())
{
System.out.println( s.next() );
}
s.close();
}
}
Please note that it is only a snippet, which needs to be adapted for Windows, but in general it should work with cmd.exe.

public void TestCommandRun(){
Process process = null;
String[] command_arr = new String[]{"cmd.exe","/K","start"};
ProcessBuilder pBuilder = new ProcessBuilder("C:/Windows/System32/cmd.exe");
try{
process = pBuilder.start();
}
catch(IOException e){
e.printStackTrace();
System.out.println("Process failed");
}
if(null != process){
OutputStream out = process.getOutputStream();
OutputStreamWriter outWriter = new OutputStreamWriter(out);
BufferedWriter bWriter = new BufferedWriter(outWriter);
try{
bWriter.write("dir");
bWriter.newLine();
bWriter.write("ipconfig");
bWriter.flush();
bWriter.close();
}
catch(IOException e){
e.printStackTrace();
System.out.println("bWriter Failed");
}
}
}

Runtime.exec().waitFor() not actually waiting for

I've got some code that uses Runtime.exec() to run an external .jar (built as an IzPack installer).
If I run this external.jar from the command line like so:
java -jar external.jar
Then the command prompt does not return control until the application is finished. However, if I run external.jar from within some java class, using:
Process p = Runtime.getRuntime().exec("java -jar external.jar");
int exitCode = p.waitFor();
System.out.println("Process p returned: " + exitCode);
Then p returns almost instantly with a success code of 0, despite external.jar having not yet completed execution (i've also tried this via the ProcessBuilder route of external file execution).
Why does it wait to return from the command line, but not when executed from within another java program?
I've also set up 3 jars, A, B and C where A calls B which calls C (using Runtime.exec()), where C Thread.sleeps for 10 seconds, as a simple test, and as expected, A doesn't return until 10 seconds after it runs.
I figure this is probably some kind of a threading issue with external.jar where execution is being handed over from one thing to another, but given that it works directly from the command line i kind of expected to see the same behaviour (perhaps naively) when called from within another java program.
I've tested this on Windows and Ubuntu with Java 6.
Thanks!

another possible way to achieve this might be to capture the output of the process and wait for it to finish.
For example:
Process tr = Runtime.getRuntime().exec( new String[]{"wkhtmltopdf",mainPage,mainPagePDF});
BufferedReader stdOut=new BufferedReader(new InputStreamReader(tr.getInputStream()));
String s;
while((s=stdOut.readLine())!=null){
//nothing or print
}
Normally the output stream is tr.getInputStream() but depending on the program you are executing the process output stream migh be:
tr.getInputStream()
tr.getErrorStream()
tr.getOutputStream()
By doing this while loop you force your program to wait the process to finish.

You can use Process Builder....
ProcessBuilder pb = new ProcessBuilder("java", "-jar", "/fielname.jar");
Process p = pb.start();
p.waitFor();

Are you spawning a new thread to handle the spawning of the process? If so the origional program will continue to operate independently of the spawned process and therefore waitFor() will only work on the new process and not the parent.

Process.waitFor() is useless for some native system command.
You need to get the process's output to determine if it is returned.
I wrote a sample code for you
/**
*
* #param cmdarray command and parameter of System call
* #param dir the directory execute system call
* #param returnImmediately true indicate return after system call immediately;
* false otherwise.
* if set true, the returned call result does not have reference value
* #return the return code of system call , default is -1
*/
public static int systemCall(String[] cmdarray,File dir,boolean returnImmediately)
{
int result = -1;
try {
Process p = Runtime.getRuntime().exec(cmdarray,null,dir);
if(!returnImmediately)
{
java.io.InputStream stdin = p.getInputStream();
java.io.InputStreamReader isr = new java.io.InputStreamReader(stdin);
java.io.BufferedReader br = new java.io.BufferedReader(isr);
String line = null;
while ( (line = br.readLine()) != null)
System.out.println(line);
}
try{result = p.exitValue();}
catch(Exception ie){;}
} catch (IOException e) {
e.printStackTrace();}
return result;
}
public static void main(String[] argc){
String[] cmdarray = {"jar","cvf","s2.jar","*"};
File dir = new File("D:\\src\\struts-2.3.1");
int k = systemCall(cmdarray,dir,true);
System.out.println("k="+k);
}

I had the same problem using processs to execute some software using the console, and i just solved it using process.waitFor()
For me it worked perfectly.
try{
Process tr = Runtime.getRuntime().exec( new String[]{ "wkhtmltopdf",frontPage,frontPagePDF});
tr.waitFor();
} catch (Exception ex) {
EverLogger.logEntry("Error al pasar a PDF la portada", "error", "activity");
return;
}
some more code here.

How to execute a interactive shell script using java Runtime?

I am wondering is there any way to execute following shell script, which waits for user input using java's Runtime class?
#!/bin/bash
echo "Please enter your name:"
read name
echo "Welcome $name"
I am using following java code to do this task but it just shows blank console.
public class TestShellScript {
public static void main(String[] args) {
File wd = new File("/mnt/client/");
System.out.println("Working Directory: " +wd);
Process proc = null;
try {
proc = Runtime.getRuntime().exec("sudo ./test.sh", null, wd);
} catch (Exception e) {
e.printStackTrace();
}
}
}
Thing is when I execute above program, I believed it will execute a shell script and that shell script will wait for user input, but it just prints current directory and then exits. Is there any way to do this or it is not possible at all in java?
Thanks in advance

The reason it prints the current dir and exits is because your java app exits. You need to add a (threaded) listener to the input and error streams of your created process, and you'll probably want to add a printStream to the process's output stream
example:
proc = Runtime.getRuntime().exec(cmds);
PrintStream pw = new PrintStream(proc.getOutputStream());
FetcherListener fl = new FetcherListener() {
#Override
public void fetchedMore(byte[] buf, int start, int end) {
textOut.println(new String(buf, start, end - start));
}
#Override
public void fetchedAll(byte[] buf) {
}
};
IOUtils.loadDataASync(proc.getInputStream(), fl);
IOUtils.loadDataASync(proc.getErrorStream(), fl);
String home = System.getProperty("user.home");
//System.out.println("home: " + home);
String profile = IOUtils.loadTextFile(new File(home + "/.profile"));
pw.println(profile);
pw.flush();
To run this, you will need to download my sourceforge project: http://tus.sourceforge.net/ but hopefully the code snippet is instructive enough that you can just adapt to J2SE and whatever else you are using.

If you use a Java ProcessBuilder you should be able to get the Input, Error and Output streams of the Process you create.
These streams can be used to get information coming out of the process (like prompts for input) but they can also be written to to put information into the process directly too. For instance:
InputStream stdout = process.getInputStream ();
BufferedReader reader = new BufferedReader (new InputStreamReader(stdout));
String line;
while(true){
line = reader.readLine();
//...
That'll get you the output from the process directly. I've not done it myself, but I'm pretty sure that process.getOutputStream() gives you something that can be written to directly to send input to the process.

The problem with running interactive programs, such as sudo, from Runtime.exec is that it attaches their stdin and stdout to pipes rather than the console device they need. You can make it work by redirecting the input and output to /dev/tty.
You can achieve the same behaviour using the new ProcessBuilder class, setting up the redirection using ProcessBuilder.Redirect.INHERIT.

Note sure at all you can send input to your script from Java. However I very strongly recommend to have a look at Commons Exec if you are to execute external scripts from Java:
Commons Exec homepage
Commons Exec API