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How to run a Jar in Amazon EC2?

I am fairly new to Amazon. I have a Java file which reads GBs of crawled data and I am running this using AWS ToolKit for Eclipse. The disadvantage here is, I have to keep my machine running for weeks if I need to read the entire crawled data and that is not possible. Apart from that, I can't download GBs of data in to my local PC (Because it is reading data).
Is there any way that I can upload the Jar to Amazon, and Amazon run it without engaging with my computer? I have heard about web crawlers running in Amazon for weeks without downloading data into the developers machine, and without letting the developer to turn on his machine without shutting down for months.
The feature I am asking is just like "job flows" in Amazon Elastic Map-Reduce. You upload the code, it runs it inside. It doesn't matter whether you keep "your" machine turned on or not.

You can run with the nohup command for *nix
nohup java -jar myjar.jar 2>&1 >> logfile.log &
This will run your jar file, directing the output [stderr and stdout] to logfile.log. The & is needed so that it runs in the background, freeing up the command line / shell/
!! EDIT !!
It's worth noting that the easiest way I've found for stopping the job once it's started is:
ps -ef | grep java
Returns ec2-user 19082 19056 98 18:12 pts/0 00:00:11 java -jar myjar.jar
Then kill 19082.
Note, you can tail -f logfile.log or other such derivatives [less, cat, head] to view the output from the jar.
Answer to question/comment
Hi. You can use System.out.println(), yes, and that'll end up in logfile.log. The command that indicates that is the 2&>1 which means "redirect stream 2 into stream 1". In unix speak that means redirect/pipe stderr into stdout. We then specify >> logfile.log which means "append output to logfile.log". As System.out.println() writes to stdout it'll end up in logfile.log.
However, if you're app is set up to use Log4j/commons-logging then using LOG.info("statement"); will end up in the configured 'log4j.properties' log file. With this configuration the only statements that will end up in logfile.log will be those that are either System generated (errors, linux internal system messages) or anything that's written explicitly to the stdout (ie System.out.println()) statements;

Find name of .jar in java(w).exe process list

In my company environment, there's this script that runs on plenty computers and that I occasionally ask the users to kill because it's known to lock up from time to time.
I was thinking of a way to kill it myself. I've noticed I can remotely list using pslist and then killing it using pskill.
Now the problem is, when somebody's running multiple java applications (ex. Eclipse, this application, another java.exe app,...) it becomes tricky to kill the correct application in the pslist, that would look something like this:
javaw 4214 .. ...
javaw 5000 .. ...
And so on. These are different applications, but they all run from javaw.exe. Is there a way of finding out the name of the .jar they are running, so I can kill the process based on that?

You can list java processes with
jps
or
jps -v
Jps is a tool provided with JDK and JRE, you'll find it in JDK_HOME/bin.
Option -v shows additional info (JVM start parameters)

You can use jps. It alone doesn't provide much helpful information to identify the java application. You need little bit extra details.
You can use the following options with jps to print the complete command line arguments passed to the java appliation (JVM arguments and main method arguments),
jps -lvm
Reference: https://docs.oracle.com/javase/8/docs/technotes/tools/unix/jps.html

Wrapping a jar file in a Windows service

Have you had experience with running a jar file using a command line, wrapped in a Windows service?
I'm trying to find a way to run a jar file without being logged into the machine, and since it allows command shell, I was wondering if it's a good idea.
Thanks!
Original Post:
I'm trying to run Associated Press's Web Feeds Manager, which is basically a jar file that can be run when logged in by double clicking it.
I'd like to run the same file but without being logged in to the machine. In their manual (http://wfm.ap.org/admin/content/help/Running_Agent_on_a_Remote_Server.htm) they write how to do that, using a commandline parameter.
Basically I'd like the jar to run as a Windows service, regardless of who's logged in, but Googling it showed it was problematic.
Have you had experience with remotely running jar files? What are the pitfalls?
Thanks!

On a google search, I came across this article -
Running Jar Applications as a Windows Service
It mentions about open source Java Service Wrapper project from Tanukisoftware.org for accomplishing this task.
Note: I've not used this personally.

If you are not interested in having the service started/stopped at boot/shutdown, but you just want the program to be started manually and keep running after logout, here is what you do:
$ nohup java -jar foobar.jar > foobar.log 2>&1 &
which means: start my foobar.jar (java -jar) and keep it running after I logout (nohup) redirect stdout to foobar.log (>) and also the stderr (2>&1), and make it running in background (& at the end).
Instead, if you are interested in installing a "service" in your linux box, there are many options, depending on what distribution you are using.
The most common are upstart (for ubuntu) and System V init scripts (Redhat or others). Also cron can be used to start/stop services at startup/shutdown.
You can find an example of installing a java app (hudson) on an init system here, or doing the same thing with upstart. Or, as I said, cron could be an option.
On Windows, there is Java Service Wrapper. And not much more.

For windows Java Service Wrapper is a better choice

My favourite is the upstart on linux, but it is Ubuntu only.
On Windows I see many alternatives according to this forum.

Execute shell command in Tomcat

So I have the following problem: I have a web service running inside a Tomcat7 server on Linux. The web service however has to execute some commands (mostly file operations such as copy and mount). Copy I've replaced with java.nio, but I don't think that there is a replacement for mount.
So I'm trying to execute shell commands out of my Tomcat Java process. Unfortunately it doesn't execute my commands. I've implemented the execution of shell commands in Java before. So my code should be correct:
Process pr = Runtime.getRuntime().exec("mount -o loop -t iso9660 <myimage> <mymountpoint>");
pr.waitFor();
<myimage> and <mymountpoint> are absolute paths, so no issues there either.
I've debugged my commands and they are working when executed on the console.
I've tried sending other commands. Simple commands such as id and pwd are working!
I've tried using /bin/bash -c "<command>", which didn't work.
I've tried executing a shell script, which executes the command, which didn't work.
I've tried escaping the spaces in my command, which didn't work.
So I've digged even deeper and now I'm suspecting some Tomcat security policy (Sandbox?), which prevents me from executing the command. Since security is no issue for me (it's an internal system, completely isolated from the outside world), I've tried a hack, which became quite popular just recently:
System.setSecurityManager(null);
This didn't work either. I'm using Java7 and Tomcat7 on RHEL6. Tomcat7 is just extracted! I don't have any files in /etc/.. or any other folder than /opt/tomcat/, where I've extracted the zip from the Tomcat home page. I've searched the /opt/tomcat/conf folder for security settings, but all I could find was the file catalina.policy, where it didn't seem like I could set some security level for shell commands.
Any ideas?

A few things:
System.setSecurityManager(null);
you have just killed the security of your application.
Yes, Tomcat is running as root. If I execute id I'm root as well.
Fix this immediately!
Now on to the question. You shouldnt have Tomcat executing anything, you need to defer this to a separate process whether that be a shell script or another Java program. This should also remove what (I hope) was a dependency on root running Tomcat. It should be possible to perform this command as a non-privileged user that cannot log into the system normally. You would do this by configuring /etc/fstab and supplying that same user the permissions to do this. From a pure security POV the process that mounts should not be owned by the tomcat user. Nor should the tomcat user ever be root. So to recap:
1) Stop running Tomcat as root
2) Create a separate process outside of the context of Tomcat to run this mount
3) Create a tomcat user, this user should not be able to log into the system nor should it be a privileged user (admin,super user, etc)
4) Create a process user, this user should be configured exactly as the tomcat user
5) Edit /etc/fstab giving the process user the necessary permissions to mount correctly.

It's generally a bad idea to use the single-string form of Runtime.exec. A better option is to use ProcessBuilder, and split up the arguments yourself rather than relying on Java to split them for you (which it does very naïvely).
ProcessBuilder pb = new ProcessBuilder("/bin/mount", "-o", "loop", /*...*/);
pb.redirectErrorStream(true); // equivalent of 2>&1
Process p = pb.start();
You say you're on RHEL so do you have selinux active? Check your logs and see if this is what's blocking you (I think it's audit.log you're looking for, it's been a few years since I've used selinux). If this does turn out to be the problem then you should probably ask on superuser or serverfault rather than SO...

I'm not sure if that's the problem you are having, but I've seen issues when Runtime.exec() is used without reading the associated output buffers. You can find a detailed explanation and potential solutions here. Reading the output and error streams can also help you figure out what's going on at the OS level when you run the command.

I've recently had to do something like this from a Swing app.
You'll probably be able to pull it off with ProcessBuilder, as in Ian's answer, but I found that once things start to get complex, it's easier to write a shell script that does what you want, enabling you to pass as few parameters as possible. Then use ProcessBuilder to invoke the shell script.
If you're invoking anything that has more than really minimal output, you'll also have to read the output and error streams to keep the process from blocking when the output buffers fill, as it seems you are already doing.

I use sudo -S before command and for the tomcat7 user: tomcat7 ALL=(ALL) NOPASSWD:ALL

Linux Daemon written in Java location

I'm currently writing a Java daemon. I'm writing a script that will have the standard daemon commands (start, stop, restart, status) and I'm trying to decide on where things should go when installing the daemon.
My current idea is:
PID File: /var/run/myapp.pid
Daemon Script: /etc/init.d/myapp
Java App (.jar): /usr/bin/myapp
Logs: /var/log/myapp.err, /var/log/myapp.log, /var/log/myapp.info (you get the idea)
Configs: /etc/myapp.conf (or /etc/myapp/configs-go-here if I have more than one in the future)
I'm still new to the Linux directory structure so if I'm doing something wrong let me know. Whats confusing me the most is that my Java app is a .jar file (archive) and not a binary. So does that mean that /usr/bin/ isn't the "right" place for it?

You could put the .jar file in /usr/lib/myapp/myapp.jar and make the startup script do java -j /usr/lib/myapp/myapp.jar
Looking it from that side, the jar is effectively a library that the /usr/bin/java binary uses, so those locations look good to me.

The /usr/lib/myapp/myapp.jar suggestion is on the right track, but /usr/lib is for architecture-specific files - since Java jar archives are platform-independent, /usr/share/myapp/myapp.jar is a better location.