Runtime.getRuntime.exec() works on Windows but not Linux - java

I am building a Java application that calls a system command and executes that command before returning control to the Java thread. The debugging step that I have is that I have made a perl script called test.pl and I call that script from the Java method and in Windows I get the expected output and a return value of 0. In Linux I get no output or error output and I get a return value of 136. I have spent extensive time online trying to figure out where I have gone wrong but as I have said, on Windows it runs. I think it must be a simple error that I am just not catching.
Here is the code derived from the excellent Runtime.exec() tutorial at http://www.javaworld.com/jw-12-2000/jw-1229-traps.html
try {
FileOutputStream fos = new FileOutputStream("output/" + this.startPosition + ".txt");
Runtime rt = Runtime.getRuntime();
Process proc = rt.exec(new String[]{"perl", "/data/stat-positive-selection/thaddeus/treesim/chr2YRI/test.pl"});
//System.out.println(commandLine);
// any error message?
StreamGobbler errorGobbler = new
StreamGobbler(proc.getErrorStream(), "ERROR");
// any output?
StreamGobbler outputGobbler = new
StreamGobbler(proc.getInputStream(), "OUTPUT", fos);
// kick them off
errorGobbler.start();
outputGobbler.start();
// any error???
int exitVal = proc.waitFor();
System.out.println("ExitValue: " + exitVal);
fos.flush();
fos.close();
} catch (Throwable e){
e.printStackTrace();
}
}
I have figured it out and fixed the code
new exec call, the use of the shell and the path to perl are required
Process proc = rt.exec(new String[]{"/bin/bash", "-c", "/usr/bin/perl /data/stat-positive-selection/thaddeus/treesim/chr2YRI/test.pl"});

The differences between the old and new versions are:
you are running the command from a shell, and
you are specifying the full pathname of the "perl" command.
In fact, in this context there doesn't seem to be a great deal of point in running the command from a shell. (Hypothetically, your Perl application might depend on environment variables that are set during shell initialization. However, the same environment variables would normally be inherited by and then from the Java command's environment. So unless the Java command is being launched in a strange way, this scenario is ... unlikely.)
So I think the substantative difference1 is that you are using the full pathname for "perl" ... and you don't a subshell to do that.
So, in the interests of science ( :-) ) I suggest you try this:
Process proc = rt.exec(new String[]{
"/usr/bin/perl",
"/data/stat-positive-selection/thaddeus/treesim/chr2YRI/test.pl"});
1 - ... the difference that makes a difference

I replaced the whole Runtime.exec() structure with the Apache Commons Exec library. It fixed the problem I was having.
http://commons.apache.org/proper/commons-exec/tutorial.html

Related

Trying to show the execution of bat file in eclipse console [duplicate]

In my Java application, I want to run a batch file that calls "scons -Q implicit-deps-changed build\file_load_type export\file_load_type"
It seems that I can't even get my batch file to execute. I'm out of ideas.
This is what I have in Java:
Runtime.
getRuntime().
exec("build.bat", null, new File("."));
Previously, I had a Python Sconscript file that I wanted to run but since that didn't work I decided I would call the script via a batch file but that method has not been successful as of yet.
Batch files are not an executable. They need an application to run them (i.e. cmd).
On UNIX, the script file has shebang (#!) at the start of a file to specify the program that executes it. Double-clicking in Windows is performed by Windows Explorer. CreateProcess does not know anything about that.
Runtime.
getRuntime().
exec("cmd /c start \"\" build.bat");
Note: With the start \"\" command, a separate command window will be opened with a blank title and any output from the batch file will be displayed there. It should also work with just `cmd /c build.bat", in which case the output can be read from the sub-process in Java if desired.
Sometimes the thread execution process time is higher than JVM thread waiting process time, it use to happen when the process you're invoking takes some time to be processed, use the waitFor() command as follows:
try{
Process p = Runtime.getRuntime().exec("file location here, don't forget using / instead of \\ to make it interoperable");
p.waitFor();
}catch( IOException ex ){
//Validate the case the file can't be accesed (not enought permissions)
}catch( InterruptedException ex ){
//Validate the case the process is being stopped by some external situation
}
This way the JVM will stop until the process you're invoking is done before it continue with the thread execution stack.
Runtime runtime = Runtime.getRuntime();
try {
Process p1 = runtime.exec("cmd /c start D:\\temp\\a.bat");
InputStream is = p1.getInputStream();
int i = 0;
while( (i = is.read() ) != -1) {
System.out.print((char)i);
}
} catch(IOException ioException) {
System.out.println(ioException.getMessage() );
}
ProcessBuilder is the Java 5/6 way to run external processes.
To run batch files using java if that's you're talking about...
String path="cmd /c start d:\\sample\\sample.bat";
Runtime rn=Runtime.getRuntime();
Process pr=rn.exec(path);`
This should do it.
The executable used to run batch scripts is cmd.exe which uses the /c flag to specify the name of the batch file to run:
Runtime.getRuntime().exec(new String[]{"cmd.exe", "/c", "build.bat"});
Theoretically you should also be able to run Scons in this manner, though I haven't tested this:
Runtime.getRuntime().exec(new String[]{"scons", "-Q", "implicit-deps-changed", "build\file_load_type", "export\file_load_type"});
EDIT: Amara, you say that this isn't working. The error you listed is the error you'd get when running Java from a Cygwin terminal on a Windows box; is this what you're doing? The problem with that is that Windows and Cygwin have different paths, so the Windows version of Java won't find the scons executable on your Cygwin path. I can explain further if this turns out to be your problem.
Process p = Runtime.getRuntime().exec(
new String[]{"cmd", "/C", "orgreg.bat"},
null,
new File("D://TEST//home//libs//"));
tested with jdk1.5 and jdk1.6
This was working fine for me, hope it helps others too.
to get this i have struggled more days. :(
I had the same issue. However sometimes CMD failed to run my files.
That's why i create a temp.bat on my desktop, next this temp.bat is going to run my file, and next the temp file is going to be deleted.
I know this is a bigger code, however worked for me in 100% when even Runtime.getRuntime().exec() failed.
// creating a string for the Userprofile (either C:\Admin or whatever)
String userprofile = System.getenv("USERPROFILE");
BufferedWriter writer = null;
try {
//create a temporary file
File logFile = new File(userprofile+"\\Desktop\\temp.bat");
writer = new BufferedWriter(new FileWriter(logFile));
// Here comes the lines for the batch file!
// First line is #echo off
// Next line is the directory of our file
// Then we open our file in that directory and exit the cmd
// To seperate each line, please use \r\n
writer.write("cd %ProgramFiles(x86)%\\SOME_FOLDER \r\nstart xyz.bat \r\nexit");
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
// Close the writer regardless of what happens...
writer.close();
} catch (Exception e) {
}
}
// running our temp.bat file
Runtime rt = Runtime.getRuntime();
try {
Process pr = rt.exec("cmd /c start \"\" \""+userprofile+"\\Desktop\\temp.bat" );
pr.getOutputStream().close();
} catch (IOException ex) {
Logger.getLogger(MainFrame.class.getName()).log(Level.SEVERE, null, ex);
}
// deleting our temp file
File databl = new File(userprofile+"\\Desktop\\temp.bat");
databl.delete();
The following is working fine:
String path="cmd /c start d:\\sample\\sample.bat";
Runtime rn=Runtime.getRuntime();
Process pr=rn.exec(path);
This code will execute two commands.bat that exist in the path C:/folders/folder.
Runtime.getRuntime().exec("cd C:/folders/folder & call commands.bat");
import java.io.IOException;
public class TestBatch {
public static void main(String[] args) {
{
try {
String[] command = {"cmd.exe", "/C", "Start", "C:\\temp\\runtest.bat"};
Process p = Runtime.getRuntime().exec(command);
} catch (IOException ex) {
}
}
}
}
To expand on #Isha's anwser you could just do the following to get the returned output (post-facto not in rea-ltime) of the script that was run:
try {
Process process = Runtime.getRuntime().exec("cmd /c start D:\\temp\\a.bat");
System.out.println(process.getText());
} catch(IOException e) {
e.printStackTrace();
}

How to get MemoryUsage statistics for a java Process object

Is it possible to get the current RAM usage of a java Process that is created with Runtime.getRuntime().exec(...);. I am creating a minecraft server instance and I need to monitor the resource usage of the server.
Here is exactly how I am creating the process.
private void runStartCommand(){
try {
lines = new ArrayList<>();
String cmd = "cmd.exe /c cd " + service.getLocation() + "& java -jar -Xmx2G -Xms2G "+service.getLocation()+"spigot-1.9.2.jar";
process = Runtime.getRuntime().exec(cmd);
input = new BufferedReader(new InputStreamReader(process.getInputStream()),8*1024);
writer = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
running = true;
} catch (IOException e) {
e.printStackTrace();
}
}
Bukkit already provides a custom plugin for monitoring and managing Minecraft server performance that should suit you perfectly.
Usually you would use something like Java Melody or a JMX console to monitor the application server process. You can also instrument and monitor it with the built-in VisualVM.
http://linux.die.net/man/1/dstat
if you are under linux, you can try dstat. We use it to take control over cpu, disk e ram usage
You could try to run systeminfo but you should really consider not doing it from Java but running some other tool (your could use nagios) on the OS - that way your monitoring isn't dependent on the app you're running.

Process is not completing even after putting the waitFor function

i am new to this Process Thing in java and i am having a problem with this shell command that i want to run in java.
I have this file with a large set of data in it and i want to convert it using XSL.
The command is working fine if run on cmd.exe but is not working in java code.
I have used the process wait too but still there is no output. Please help.
Thanks
Small fragment of code
String c="java -Xmx1g -jar c:\\temp\\FileConverter.jar xmlTransform title \"Data\" root \"c:\\temp\\\" src \"c:\\temp\\input.xml\" xsl \"converter.xsl\" xsl:MEMBER_CODE \"111\" xsl:MEMBER_NAME \"ABC\" xsl:MEMBER_PASSWORD \"abc\" dst \"c:\\temp\\dummy.xml\" src-error \"c:\\temp\\error\"";
Runtime rt = Runtime.getRuntime();
try {
Process proc = rt.exec(c);
synchronized (proc) {
proc.wait(10000);
}
System.out.println("Done");
}catch (IOException e) {
e.printStackTrace();
}

Why doesn't the Java console show when using ProcessBuilder?

I use the following to launch a Java application from another Java app.
ProcessBuilder pb = new ProcessBuilder(javaPath + javaCommand, maxMemStr,
minMemStr, stackSizeStr, jarCommand, jarfile, jarArg);
try {
Process p = pb.start();
} catch (IOException ex) {
Logger.getLogger(launch.class.getName()).log(Level.SEVERE, null, ex);
}
where javaCommand is either java or javaw (javaPath is empty most of the time unless a user points to an alternate path). The problem is, after the app launches, even when I verify the process list to contain java, it doesn't show the console.
Is it because PrcoessBuilder doesn't invoke the command shell? Is there a way to show the console programatically?
Thanks in advance.
This is because the "command console" itself is a process that attaches to the std-in/-out/-err streams of another process and displays them on the screen. When you launch Java all by itself, no other processes will be handling those streams, hence the lack of a command console. To get the results you want, you will need to launch a new instance of the command console and subsequently have it run your custom java command.
There may be a better way to do this... but I think the solution to this is going to be platform-dependent. In Windows, you could do something like:
ProcessBuilder pb = new ProcessBuilder("start", "\"JAwesomeSauce\"", "cmd.exe",
"/k", javaPath + javaCommand, maxMemStr, minMemStr, stackSizeStr, jarCommand,
jarfile, jarArg);
try {
Process p = pb.start();
} catch (IOException ex) {
Logger.getLogger(launch.class.getName()).log(Level.SEVERE, null, ex);
}
I assume you could do something similar in Linux/Mac if that's the O/S you're using.
You may want to run the command like this:
cmd /K java ...
or
cmd /C java ...
As far as I remember the Processbuilder opens a pipe to a specific process.
Your command window is a process itself with all you see. If you enter commands the cmd/bash usually creates new processes and attaches to them.

Java ProcessBuilder: Resultant Process Hangs

I've been trying to use Java's ProcessBuilder to launch an application in Linux that should run "long-term". The way this program runs is to launch a command (in this case, I am launching a media playback application), allow it to run, and check to ensure that it hasn't crashed. For instance, check to see if the PID is still active, and then relaunch the process, if it has died.
The problem I'm getting right now is that the PID remains alive in the system, but the GUI for the application hangs. I tried shifting the ProcessBuilder(cmd).start() into a separate thread, but that doesn't seem to be solving anything, as I hoped it would have.
Basically the result is that, to the user, the program APPEARS to have crashed, but killing the Java process that drives the ProcessBuilder.start() Process actually allows the created Process to resume its normal behavior. This means that something in the Java application is interfering with the spawned Process, but I have absolutely no idea what, at this point. (Hence why I tried separating it into another thread, which didn't seem to resolve anything)
If anyone has any input/thoughts, please let me know, as I can't for the life of me think of how to solve this problem.
Edit: I have no concern over the I/O stream created from the Process, and have thus taken no steps to deal with that--could this cause a hang in the Process itself?
If the process writes to stderr or stdout, and you're not reading it - it will just "hang" , blocking when writing to stdout/err. Either redirect stdout/err to /dev/null using a shell or merge stdout/err with redirectErrorStream(true) and spawn another thread that reads from stdout of the process
You want the trick?
Don't start your process from ProcessBuilder.start(). Don't try to mess with stream redirection/consumption from Java (especially if you give no s**t about it ; )
Use ProcessBuilder.start() to start a little shell script that gobbles all the input/output streams.
Something like that:
#!/bin/bash
nohup $1 >/dev/null 2>error.log &
That is: if you don't care about stdout and still want to log stderr (do you?) to a file (error.log here).
If you don't even care about stderr, just redirect it to stdout:
#!/bin/bash
nohup $1 >/dev/null 2>1 &
And you call that tiny script from Java, giving it as an argument the name of the process you want to run.
If a process running on Linux that is redirecting both stdout and stderr to /dev/null still produce anything then you've got a broken, non-compliant, Linux install ;)
In other word: the above Just Works [TM] and get rid of the problematic "you need to consume the streams in this and that order bla bla bla Java-specific non-sense".
The thread running the process may block if it does not handle the output. This can be done by spawning a new thread that reads the output of the process.
final ProcessBuilder builder = new ProcessBuilder("script")
.redirectErrorStream(true)
.directory(workDirectory);
final Process process = builder.start();
final StringWriter writer = new StringWriter();
new Thread(new Runnable() {
public void run() {
IOUtils.copy(process.getInputStream(), writer);
}
}).start();
final int exitValue = process.waitFor();
final String processOutput = writer.toString();
Just stumbled on this after I had a similar issue. Agreeing with nos, you need to handle the output. I had something like this:
ProcessBuilder myProc2 = new ProcessBuilder(command);
final Process process = myProc2.start();
and it was working great. The spawned process even did output some output but not much. When I started to output a lot more, it appeared my process wasn't even getting launched anymore. I updated to this:
ProcessBuilder myProc2 = new ProcessBuilder(command);
myProc2.redirectErrorStream(true);
final Process process = myProc2.start();
InputStream myIS = process.getInputStream();
String tempOut = convertStreamToStr(myIS);
and it started working again. (Refer to this link for convertStreamToStr() code)
Edit: I have no concern over the I/O stream created from the Process, and have thus taken no steps to deal with that--could this cause a hang in the Process itself?
If you don't read the output streams created by the process then it is possible that the application will block once the application's buffers are full. I've never seen this happen on Linux (although I'm not saying that it doesn't) but I have seen this exact problem on Windows. I think this is likely related.
JDK7 will have builtin support for subprocess I/O redirection:
http://download.oracle.com/javase/7/docs/api/java/lang/ProcessBuilder.html
In the meantime, if you really want to discard stdout/stderr, it seems best (on Linux) to invoke ProcessBuilder on a command that looks like:
["/bin/bash", "-c", "exec YOUR_COMMAND_HERE >/dev/null 2>&1"]
Another solution is to start the process with Redirect.PIPE and close the InputStream like this:
ProcessBuilder builder = new ProcessBuilder(cmd);
builder.redirectOutput(Redirect.PIPE);
builder.redirectErrorStream(true); // redirect the SysErr to SysOut
Process proc = builder.start();
proc.getInputStream().close(); // this will close the pipe and the output will "flow"
proc.waitFor(); //wait
I tested this in Windows and Linux, and works!
In case you need to capture stdout and stderr and monitor the process then using Apache Commons Exec helped me a lot.
I believe the problem is the buffering pipe from Linux itself.
Try to use stdbuf with your executable
new ProcessBuilder().command("/usr/bin/stdbuf","-o0","*executable*","*arguments*");**
The -o0 says not to buffer the output.
The same goes to -i0 and -e0 if you want to unbuffer the input and error pipe.
you need to read the output before waiting to finish the cycle. You will not be notified If the output doesn't fill the buffer. If it does, it will wait until you read the output.
Suppose you have some errors or responses regarding your command which you are not reading. This would cause the application to stop and waitFor to wait forever. A simple way around is to re-direct the errors to the regular output.
I was spent 2 days on this issue.
public static void exeCuteCommand(String command) {
try {
boolean isWindows = System.getProperty("os.name").toLowerCase().startsWith("windows");
ProcessBuilder builder = new ProcessBuilder();
if (isWindows) {
builder.command("cmd.exe", "/c", command);
} else {
builder.command("sh", "-c", command);
}
Process process = builder.start();
BufferedReader reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
String line;
while ((line = reader.readLine()) != null)
System.out.println("Cmd Response: " + line);
process.waitFor();
} catch (IOException e) {
e.printStackTrace();
} catch (InterruptedException e) {
e.printStackTrace();
}
}

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