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java application being abrutply terminated on shutdown without having signal sent

To be clear, this is a upstart/linux debugging problem not a java problem per-se.
I have a java application installing a shutdownhook. It shows some funny behaviour in ubuntu-GNOME, namely that the shutdown hook never run if a restart or power off were scheduled. At first i thought it was a problem with my shutdown hook, so i simplified it until it was only writing a line to file (yes i know about the log4j2 logger problem with shutdownhooks so i disabled theirs too). Then when that didn't work i started hacking /etc/init/sendsigs
I added this to the beginning of the do_stop function:
app="$(jps | grep appname.jar | cut -d' ' -f1)"
echo "$app" >> "/home/i30817/output.txt"
sure enough, that showed that it was no longer running, so the shutdown hooks were never activated by sendsigs
Then i used lastcomm from here replacing my edit of sendsigs by:
echo `/home/i30817/lastcomm` > "/home/i30817/output.txt"
And it told me that the java process exited with 1 and was not signaled:
java X i30817 ?? 10.26 secs Sun Mar 2 12:44 E 1
but this still didn't help me find what actually killed it and why. This problem is not reproducible with a smaller example, so it's probably something in the larger application (but not the shutdown hook, since it was minimized) that doesn't like the shutdown process and manages to kill the process, but i can't figure it out... redirecting the process output to a file doesn't say anything either eg:
java -jar /home/i30817/Documents/projects/app/dist/app.jar > allout.text 2>&1
is empty of everything but normal app output
Can you help me figure out this? There are a lot of duplicate questions about the same thing too (but they think it's the shutdownhooks malfunctioning).
edit: more detail, now that i understand the problem a bit better. I think now that processes not being there on sendsigs is normal. Java applications, and maybe others use a protocol from the window manager where SIGHUP, SIGHUP and SIGCONT is sent on shutdown/logout. The JVM hooks SIGHUP to launch the shutdown hooks. I tested this with a very small example that only adds a shutdownhook and has a infinite cycle on main, and ran it with a system tap script in the background:
java -jar app.jar
and in another shell
sudo stap -o process.txt sigkill.stp
However when i tried that with my application i think i found the culprit:
PROCESS: SIGSEGV java.signal_generate sent to java 2280
but don't really know what to do about it considering there is no thread dump or anything and this is strange to reproduce (only my app, only during shutdown).
edit2: now i suspect the reason for the 'abrupt' termination without core dump is the ulimit during shutdown. So i'm trying to solve that in preparation for a bug report. I edited /etc/security/limits.conf to add this and rebooted
* soft core unlimited
root hard core unlimited
* hard rss 10000
(fs.suid_dumpable=2 was set by ubuntu, no apparmor i think)
but during shutdown i edited /etc/init.d/sendsigs again to print ulimit -a and sleep for 30 seconds before killing the processes, and it seems that during reboot the ulimit gets reset again? And moreover, it had a different output like it was using another executable version, for instance instead of saying 'core file size' it had 'core(dump)' or something like that).
edit3: ah, i need to have fs.suid_dumpable=1 instead - gonna try now.
Maybe the init ulimit doesn't matter for shutdown core dump triggering. After all the jvm was executed from the user env so it should be using the user ulimit.
edit4: eh. After much commenting of code i reached the following conclusion that i could have reached from RTFM:
the sigsegvs are harmless.
the non-zero exit code is not.
If the AWT is still up, the signal is always non zero and the shutdown hooks never run. Even a small example still prevents execution of shutdown hooks in linux reboot if a JFrame is up (unlike windows, where they will start). Looking at the source, the application shutdownhooks are run on a slot by themselves, slot 1. I bet slot '0' is the AWT and that is halting the system somehow.
I guess it's time to check the package private signal handling libs to see if i can get SIGHUP before the JVM decides to terminate everything without even giving the opportunity for cleanup code to run.

According to docs
http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html#addShutdownHook(java.lang.Thread)
In rare circumstances the virtual machine may abort, that is, stop running without shutting down cleanly....
If the virtual machine aborts then no guarantee can be made about whether or not any shutdown hooks will be run.

Tomcat stopped without any log or any stack

We have trouble with Tomcat 5.5 which stops at night on our production servers (Linux CentOS 4.8) and we have no idea why it stops...
There is no Tomcat's log in catalina.out or any application's log.
We tried different things to find why the server stops:
configure Tomcat to be able to generate a core dump
instrument System.exit() method with javassist to find if the method was called
add a shutdown hook to the JVM (with Runtime.getRuntime().addShutdownHook())
None of them worked, we have no core dump, the Exit method and the shutdown hook are not called.
My conclusions are:
The VM is not terminated properly but crash without any log.
Any idea or log to read to find why Tomcat stops?

1) Make sure you know where stderr is redirected and check if anything got printed there.
2) Check the memory limits on Tomcat and how much free memory does the system have. Review the Linux system logs under /var/log to see if anything suspicious happened during the time. For example, kernel can randomly kill a process (almost) without a trace if the system is running low on memory.
We've ran 5.5 in production for years and never had any unexplained shutdowns, FWIW.

This worked for me.
As suggested here in other answers checked system logs in /var/log/messages but permission denied for me. So, I used dmesg command instead and got this in the logs
"Out of memory: Kill process 14606 (java) score 106 or sacrifice child".
In the output I also noticed Swap Memory free 0 K. Ran top command to confirm the same. So, somehow there was a high memory usage which caused the OS to kill my tomcat process.
After spending hours finally got the reason.
ps -ef | grep tomcat showed that there were several tomcat processes running for the same application. It seems that, earlier tomcat shutdowns might not have been completed successfully and due to some reason the processes were not killed even after the shutdown, which was causing the high memory usage.
So, killed all running tomcat processes using kill. SWAP memory got freed.
Started tomcat again, worked fine. :)

Tomcat 7 has an option inside catalina to prevent the System.exit class call or something similar: http://ci.apache.org/projects/tomcat/tomcat7/docs/security-manager-howto.html .
Maybe there's a similar option for the 5.5 version. Try the documentation.
There are options to redirect the output to the same console that you use to start Tomcat. This information is redirected to logs when you execute on Unix based systems, on Windows, it remains with the console if not redirected.

Most probably there is a stack-overflow exception. This is typical behavior of Tomcat when it happens. For example, you're trying to serialize to JSON or XML beans with cyclic dependencies (but without handling of the cycles).
Everytime I had this issue (several times) it always has been this one. All other stops are usually logged properly (like OutOfMemory etc).
This type of stops leaves no trace anywhere.

No threaddump generated on kill -3

Is there a possibility that kill -3 / quit PID prints nothing i.e. an empty thread dump? We heard a story from a support engineer and was wondering if some experts could validate.
This is on Java 6_26 on RHEL 5

I have only seen this when the server redirects to stdout, like JBoss, and stdout has been redirected to /dev/null because whoever set up the server thought that everything going to stdout was already going to a named log file.

The console output of JVM thread dump on some servers is redirected to a log file. In case of Tomcat Server it is usually Catalina.out.

I have seen the behavior you describe in a standalone Java application (Oracle JDK 1.6.20+, Linux), but I can't tell how to reproduce this behavior consistently. It may have been after an OutOfMemoryError in one of the threads but I'm not sure any more.
I also think that what I got was not just an empty dump, but that the command actually froze and didn't return me to the shell until I pressed ctrl+C after waiting for a while. Either way, I'm sure that the behavior of jstack was exactly the same as of kill -3. When it happened, the app was in such bad shape that it didn't react to normal kill and only kill -9 worked on it. There were no redirections and under normal circumstances the app reacted to kill -3 as it should.

Problems with jetty crashing intermittently

I'm having problems with jetty crashing intermittently, I'm using Jetty 6.1.24.
I'm running a neo4j Spring MVC webapp, Jetty will stay running for approx 1 hour and then I have to restart Jetty. It is running on small amazon ec2 instance, debian with 1.7gb of RAM.
I start Jetty using java -Xmx900m -server -jar start.jar
I am connecting to the server using putty, when Jetty crashes the putty session disconnects, I cannot see what error caused it to crash.
I would like to be able to see if it is an error generated by Spring, I'm not sure how to log the output from the spring app with Jetty. Or if it is Jetty or a memory issue, what would be the best way to monitor Jetty? I cannot recreate this on my local machine running windows. What do you think would be the best way to approach this? Thanks

This isn't really a programmer question; perhaps it'll be moved over to ServerFault.
You didn't specifically state which operating system you're using, but I'm hazarding a guess at some Linux distribution. You have two options of figuring out what's wrong:
Start your session in screen. Screen will live for as long as the actual machine is powered on, until you reboot the operating system (or you exit screen).
you start screen like this
screen
and you get a new prompt where you can start your program (cd foo, jetty, etc). When you're happy and you just need to go somewhere, you can disconnect the screen by hitting CTRL+A and then CTRL+D. you'll drop back to the place you were before you invoked screen.
To get back to seeing the screen you type screen -R which means to resume an existing screen. you should see jetty again.
The nice thing is that if you lose connection (or you close putty by accident or whatever) then you can use screen -list to get a list of running screens, and then forcibly detach them -D and reattach them to the current putty -R, no harm done!
Use nohup. Nohup more or less detaches the process you're running from the console, so none of its output comes to the terminal. You start your program in the normal fashion, but you add the word nohup to your command.
For example:
nohup ls -l &
After ls -l is complete, your output is stored in nohup.out.

When you say crash do you mean the JVM segfaults and disappears? If that's the case I'd check and make sure you aren't exhausting the machine's available memory. Java on linux will crash when the system memory gets so low the JVM cannot allocate up to its maximum memory. For example, you've set the max JVM memory to 500MB of which it's using 250MB at the moment. However, the Linux OS only has 128MB available. This produces unstable results and the JVM will segfault.
On windows the JVM is more well behaved in this scenario and throws OutOfMemoryError when the system is running low on memory.
Validate how much system memory is available around the time of your crashes.
Verify if other processes on your box are eating up a lot of memory. Turn off anything that could be competing with the JVM.
Run jconsole and connect it to your JVM. That will tell you how memory is being used in your JVM process and give you a history to look back through when it does crash.
Eliminate any native code you might be loading into the JVM when doing this type of testing.
I believe Jetty has some native code to do high volume request processing. Make sure that's not being used. You want to isolate the crashes to Java and NOT some strange native lib. If you take out the native stuff and find it works then you have your answer as to what's causing it. If it continues to crash then it very well could be what I'm describing.
You can force the JVM to allocate all the memory at startup with -Xms900m that can make sure the JVM doesn't fight with other processes for memory. Once it has the full Xmx amount allocated it won't crash. Not a solution, but you can easily test it this way.

When you start java, redirect both outputs (stdout and stderr) to a file:
Using Bash:
java -Xmx900m -server -jar start.jar > stdout.txt 2> stderr.txt
After the crash, inspect those files.
If the crash is due to a signal (like SEGV=segmentation fault), there should be a file dump by the JVM at the location you've started java. For Sun VM (hotspot), it's something like hs_err_pid12121.log (here 12121 is the process ID).

Putty disconnecting STRONGLY hints that the server is running out of memory and starts shutting down processes left and right. It is probably your jetty instance growing too big.
The easiest thing to do now, is adding 1-2 Gb more swap space and do it again. Also note that you can use the jvisualvm to attach to the jetty instance to get runtime information directly.

Restoring/Restarting a java daemon from crash

I am running a java app as daemon on a linux machine using a customized shell script.
Since I am new to java and linux, I want to know is it possible that the app itself resurrects itself(just like restart) and recovers from cases like app crashing, unhandled exceptions or out of memory etc.
thanks in advance
Ashish Sharma

The JVM is designed to die when there is an unrecoverable error. The ones you described fall in this category.
You could, however, easily write a shell script or a Python script that checks if the process is alive, and if it is dead, waits a few seconds and revive it. As a hint to doing this, the Unix command "pgrep" is your friend, as you can check for the exact command line used to fire a JVM (and thus including the starting class file). This way, you can determine if that specific JVM instance is running, and restart it.
All that being said, you may want to add some reporting or logging capability and check if often, because it is too easy to assume that things are ok when in fact the daemon is dying every few minutes. Make sure you've done what you could to prevent it from dying before resurrecting it.

There are Wrappers that can handle that, like Java Service Wrapper (Be aware, that the Community Edition ist under GPL) and some alternatives, mentioned here

To be honest, relaunching the daemon without any question after a crash is probably not a good idea; well it depends greatly on the type of processing achieved by your daemon, but if for example it processes files from a given directory, or requests coming from a queue manager, and the file / message contains some unexpected data causing the crash, relaunching the daemon would make it crash again immediately (excepting when the file / message is removed no matter it has been correctly processed or not, but as well it seems not to be a good idea).
In short, it's probably better to track down the possible crash reasons and fix them when possible (or at least log the the problem and go ahead, provided that the log message would ever be scanned to warn at last a human being, so some action can be engaged upon such "failures").
Anyway if you have very good reasons to do such, a solution even simpler than "checking that the process is alive" (as it would probably in some way involve some "ps -blahblah" stuff), you could just put the java program launching in a shell "while true" loop as follows :
while true
do
# launch the java program here, no background
# when crashing, the shell will be given hand back
java -classpath blahblah...
echo "program crashed, relaunching it..."
done

On unix based systems, you may use "inittab" to specify the program. If process dies, it is re-started by OS.(respawn)

I am not sure if the app itself can handle such crashes. You could write a shell script in linux which could be running as a cron job itself to manage the app, checking if the java app is running on scheduled intervals and if not, it will restart it automatically.