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Profiling memory leak in a non-redundant uptime-critical application

We have a major challenge which have been stumping us for months now.
A couple of months ago, we took over the maintenance of a legacy application, where the last developer to touch the code, left the company several years ago.
This application needs to be more or less always online. It's developed many years ago without staging and test environments, and without a redundant infrastructure setup.
We're dealing with a legacy Java EJB application running on Payara application server (Glassfish derivative) on an Ubuntu server.
Within the last year or two, it has been necessary to restart Payara approximately once a week, and the Ubuntu server once a month.
This is due to a memory leak which slows down the application over a period of around a week. The GUI becomes almost entirely non-responsive, but a restart of Payara fixes this, at least for a while.
However after each Payara restart, there is still some kind of residual memory use. The baseline memory usage increases, thereby reducing the time between Payara restarts. Around every month, we thus do a full Ubuntu reboot, which fixes the issue.
Naturally we want to find the memory leak, but we are unable to run a profiler on the server because it's resource intensive, and would need to run for several days in order to capture the memory leak.
We have also tried several times to dump the heap using "gcore" command, but it always result in a segfault and then we need to reboot the Ubuntu server.
What other options / approaches do we have to figure out which objects in the heap are not being garbage collected?

I would try to clone the server in some way to another system where you can perform tests without clients being affected. Could even be a system with less resources, if you want to trigger a resource based problem.
To be able to observe the memory leak without having to wait for days, I would create a load test, maybe with Apache JMeter, to simulate accesses of a week within a day or even hours or minutes (don't know if the base load is at a level where that is feasible from the server and network infrastructure).
First you could set up the load test to act as a "regular" mix of requests like seen in the wild. After you can trigger the loss of response, you can try to find out, if there are specific requests that are more likely to be the cause for the leak than others. (It also could be that some basic component that is reused in nearly any call contains the leak, and so you cannot find out "the" call with the leak.)
Then you can instrument this test server with a profiler.
To get another approach (you could do it in parallel) you also can use a static code inspection tool like SonarQube to analyze the source code for typical patterns of memory leaks.
And one other idea comes to my mind, but it is coming with many preconditions: if you have recorded typical scenarios for the backend calls, and if you have enough development resources, and if it is a stateless web application where each call could be inspoected more or less individually, then you could try to set up partial integration tests where you simulate the incoming web calls, with database and file access, but if possible without the application server, and record the increase of the heap usage after each of the calls. Statistically you might be able to find out the "bad" call this way. (So this would be something I would try as very last option.)

Apart from heap dump have to tried any realtime app perf monitoring (APM) like appdynamics or the opensource alternative like https://github.com/scouter-project/scouter.
Alternate approach would be to analyse existing application issue Eg: Payara issues like these https://github.com/payara/Payara/issues/4098 or maybe the ubuntu patch you are currently running app on.

You can use jmap, an exe bundled with the JDK, to check the memory. From the documentation:-
jmap prints shared object memory maps or heap memory details of a given process or core file or a remote debug server.
For more information you can see the documentation or see the stackoverflow question How to analyse the heap dump using jmap in java
There is also a tool called jhat which can be used tp analise java heap.
From the documentation:-
The jhat command parses a java heap dump file and launches a webserver. jhat enables you to browse heap dumps using your favorite webbrowser. jhat supports pre-designed queries (such as 'show all instances of a known class "Foo"') as well as OQL (Object Query Language) - a SQL-like query language to query heap dumps. Help on OQL is available from the OQL help page shown by jhat. With the default port, OQL help is available at http://localhost:7000/oqlhelp/
See JHat Dcoumentation, or How to analyze the heap dump using jhat

Is there a Java local queue library I can use that keeps memory usage low by dumping to the hard drive?

This maybe not possible but I thought I might just give it a try. I have some work that process some data, it makes 3 decisions with each data it proceses: keep, discard or modify/reprocess(because its unsure to keep/discard). This generates a very large amount of data because the reprocess may break the data into many different parts.
My initial method was to send it to my executionservice that was processing the data but because the number of items to process was large I would run out of memory very quickly. Then I decided to maybe offload the queue off to a messaging server(rabbitmq) which works fine but now I'm bound by network IO. What I like about rabbitmq is it keeps messages in memory up to a certain level and then dumps old messages to the local drive so if I have 8 gigs of memory on my server I can still have a 100 gig message queue.
So my question is, is there any library that has a similar feature in Java? Something that I can use as a nonblocking queue that keeps only X items in queue(either by number of items or size) and writes the rest to the local drive.
note: Right now I'm only asking for this to be used on one server. In the future I might add more servers but because each server is self-generating data I would try to take messages from one queue and push them to another if one server's queue is empty. The library would not need to have network access but I would need to access the queue from another Java process. I know this is a long shot but thought if anyone knew it would be SO.

Not sure if it id the approach you are looking for, but why not using a lightweight database like hsqldb and a persistence layer like hibernate? You can have your messages in memory, then commit to db to save on disk, and later query them, with a convenient SQL query.

Actually, as Cuevas wrote, HSQLDB could be a solution. If you use the "cached table" provided, you can specify the maximum amount of memory used, exceeding data will be sent to the hard drive.

Use the filesystem. It's old-school, yet so many engineers get bitten with libraries because they are lazy. True that HSQLDB provides lots of value-add features, but in the context of being light weight....

Java Web App has a high rate of CPU consumption

I'm new here and I'm not that very good in CPU consumption and Multi Threading. But I was wondering why my web app is consuming too much of the CPU process? What my program does is update values in the background so that users don't have to wait for the processing of the data and will only need to fetch it upon request. The updating processes are scheduled tasks using executor library that fires off 8 threads every 5 seconds to update my data.
Now I'm wondering why my application is consuming too much of the CPU. Is it because of bad code or is it because of a low spec server? (2 cores with 2 database and 1 major application running with my web app)
Thank you very much for your help.

You need to profile your application to find out where the CPU is actually being consumed. Java has some basic profiling methods built in, or if your environment permits it, you could run the built in "hprof" compiler:
java -Xrunhprof ...
(In reality, you probably want to set some extra options: Google "hprof" for more details.)
The latter is easier in principle, but I mention the possibility of adding your own profiling routine because it's more flexible and you can do it e.g. in a Servlet environment where running another profiler is more cumbersome.

Paulo,
It is not possible for someone here to say whether the problem is that your code is inefficient or the server is under spec. It could be either or both of those, or something else.
You are going to need to do some research of your own:
Profile the code. This will allow you to identify where your webapp is spending most of its time.
Look at the OS-level stats that are available to you. This might tell you that the real problem is memory usage or disk I/O.
Look at the performance of the back-end database. Is it using a lot of CPU?
Once you have identified the area(s) where the CPU is being used, you need to figure out the real cause of the problem is and work out how to fix it. And once you've got a potential fix implemented, you can rerun your profiling, etc to see it has helped.

Java Webapp Performance Issues

I have a Web Application, Made entirely with Java. The Webapp doesn't use any Graphical / Model Framework, instead, the webapp uses The Model-View Controller. It's made only with Servlet specification (Servlet ver. 2.4).
The webapp it's developed since 2001, and it's very complex. Initially, was built for work with Tomcat 4.x/5.x. Actually, runs on Tomcat 6.x. But, we still having memory Leaks.
In Depth, the specifications of The Webapp can resumed as:
Uses Servlet v. 2.4 Specification.
It doesn't use Any Framework
It doesn't use JavaEE (Not EJB)
It's based on JavaSE (With Servlets)
Works Only on IE 6+ (Because of it's age)
Infrastructure Specification
Actually, the webapp works in three environments:
First
IBM Server (I don't remember exactly the model)
Intel Xeon 2.4 Ghz
32GB RAM
1TB HDD
Tomcat (Version 6) is configured to use 8GB of RAM
Second
Dell Server
Intel Xeon 2.0Ghz
4GB RAM
500GB HDD
Tomcat (Version 5.5) is configured to use 1.5GB of RAM
Third
Dell Server
Amd Opteron 1214 2.20Ghz
4GB RAM
320GB HDD
Tomcat (Version 6) is Configured to use 1.5GB of RAM
Database specification
The webapp uses SQL Server 2008 R2 Express Edition as a DBMS, except for the user of the first server-specification, that uses SQL Server 2008 R2 Standard Edition. For the connection pools, the app uses Apache DBCP.
Problem
Well, it has very serious performance issues. The webapp slow down continually, and, many times Denies the Service. The only way to recover the app is restarting The Apache Tomcat Service.
During a performance Audit, i've found several programming issues (Like database connections that never closes, excesive use of Vector collection [instead of ArrayList]).
I want to know how can improve the performance for the app, which applications can help me to monitoring the Tomcat performance and the Webapp Memory usage.
All suggestions are gladly accepted.

You could also try stagemonitor. It is an open source performance monitoring library. It records request response times, JVM metrics, request details including a call stack (profile) of the called methods during the request and more. Because of the low overhead, you can also use it in production.
The tuning procedure would be the following.
Identify slow requests with the Request Dashboard
Analyze the stack trace of the request with the Request Detail Dashboard to find out about slow methods
Dive into your code and try to optimize those slow methods
You can also correlate some metrics like the throughput or number of sessions with the response time or cpu usage
Analyze the heap with the JVM Memory Dashboard
Note: I am the developer of stagemonitor.

I would start with some tools that can help you profiling the application. Since you are developing webapp start with Lambda Probe and Java melody.
The first step is to determine the conditions under which the app starts to behave oddly. Ask yourself few questions:
Do performance issues arise right after applications starts, or overtime?
Do performance issues are correlated to quantity of client requests?
What is the real performance problem - high load on the server or lack of memory (note that they are related, so check which one starts first)
Are there any background processes which are performing some massive operations? Are they scheduled to run at some particular time period?
Try to find some clues before going deep into code. It will help you to narrow down possible causes.
As Joshua Bloch has stated in his book entitled "Effective Java" - performance issues are rarely the effect of some minor mistakes in source code (although, of course, misuse of Java constructs can lead to disaster). Usually the cause is bad system (API) architecture.
The last suggestion based on my experience - try not to think that high memory consumption is something bad. Tomcat will use as much memory as operating system and JVM will let him (not more than max settings) and just when it needs more - Tomcat will perform garbage collection. So a typical (proper!) graph of memory consumption looks like a saw. If you are dealing with memory leak, then the graph will be increasing constantly, but indefinitely. This is the most often misunderstood of memory leaks, so keep it in mind.
To be honest - we cannot help you much further. Those are just pointers, now you will have to make extensive research to figure out the cause :)

The general solution is to use a profiler e.g. YourKit, with a realistic workload which reproduces the problem.
What I do first is a CPU only profile, a memory only profile and finally a CPU & Memory profile on at once (I then look at the CPU profile results)
YourKit can also monitor your high level operations such a Java EE resources and JDBC connections. I haven't tried these as I don't use them. ;)
It can be a good idea to improve the efficiency even if its not the cause of the problem as it will reduce the amount of "noise" in these profiles and make your issues more obvious.
You could try increasing the amount of memory available but a suspect it will just delay the problem.

Ok. So I have seen huge Java applications run lesser configurations. You should try to do the following -
First connect a Profiler to your application and see which part of your application takes the most time. You can use JProfiler or Eclipse MAT ( I personally prefer JProfiler). Also try to take a look at the objects taking the most memory. This will help you narrow down to the parts which you need to rewrite to improve the performance.
Once you have taken a look at the memory leaks update your application to use 64bit JDK(assuming it already does not do so)
Take a look at your JVM arguments and optimize them.

You can try the open source tool Webapp Watcher in order to identify where in the code is the performance issue.
You have first to add a filter in the webapp (as explained here) in order to record metrics, and then import the logs in the WAW Analyzer tool and follow the steps described in the doc to know where is the potential performance issue in the code.

How to detect Out Of Memory condition?

I have an application running on Websphere Application Server 6.0 and it crashes nearly every day because of Out-Of-Memory. From verbose GC is certain there are the memory leaks(many of them)
Unfortunately the application is provided by external vendor and getting things fixed is slow & painful process. As part of the process I need to gather the logs and heapdumps each time the OOM occurs.
Now I'm looking for some way how to automate it. Fundamental problem is how to detect OOM condition. One way would be to create shell script which will periodically search for new heapdumps. This approach seems me a kinda dirty. Another approach might be to leverage the JMX somehow. But I have little or no experience in this area and don't have much idea how to do it.
Or is in WAS some kind of trigger/hooks for this? Thank you very much for every advice!

You can pass the following arguments to the JVM on startup and a heap dump will be automatically generated on an OutOfMemoryError. The second argument lets you specify the path for the heap dump file. By using this at least you could check for the existence of a specific file to see if a heap dump has occurred.
-XX:+HeapDumpOnOutOfMemoryError
-XX:HeapDumpPath=<value>

I see two options if you want heap dumping automated but #Mark's solution with heap dump on OOM isn't satisfactory.
You can use the MemoryMXBean to detect high memory pressure, and then programmatically create a heap dump if the usage (or usage delta) seems high.
You can periodically get memory usage info and generate heap dumps with a cron'd shell script using jmap (works both locally and remote).
It would be nice if you could have a callback on OOM, but, uhm, that callback probably would just crash with an OOM error. :)

Have you looked at JConsole ? It uses JMX to give you visibility of a variety of JVM metrics, including memory info. It would probably be worth monitoring your application using this to begin with, to get a feel for how/when the memory is consumed. You may find the memory is consumed uniformly over the day, or when using certain features.
Take a look at the detecting low memory section of the above link.
If you need you can then write a JMX client to watch the application automatically and trigger whatever actions required. JConsole will indicate which JMX methods you need to poll.

And alternative to waiting until the application has crashed may be to script a controlled restart like every night if you're optimistic that it can survive for twelve hours..
Maybe even websphere can do that for you !?

You could add a listener (Session scoped or Application scope attribute listener) class that would be called each time a new object is added in session/app scope.
In this - you can attempt to check the total memory used by app (Log it) as as call run gc (note that invoking it will not imply gc will always run)
(The above is for the logging part and gc based on usage growth)
For scheduled gc:
In addition you can keep a timer task class that runs after every few hrs and does a request for gc.

Our experience with ITCAM has been less than stellar from the monitoring perspective. We dumped it in favor of CA Wily Introscope.

Have you had a look on the jvisualvm tool in the latest Java 6 JDK's?
It is great for inspecting running code.

I'd dispute that the you need the heap dumps when the OOM occurs. Periodic gathering of the information over time should give the picture of what's going on.
As has been observed various tools exist for analysing these problems. I have had success with ITCAM for WebSphere, as an IBMer I have ready access to that. We were very quickly able to indentify the exact lines of code in out problem situation.
If there's any way you can get a tool of that nature then that's the way to go.

It should be possible to write a simple program to get the process list from the kernel and scan it to see if your WAS process is still running. On a Unix box you could probably whip up something in Perl in a few minutes (if you know Perl), not sure how difficult it would be under Windows. Run it as a scheduled task every five minutes or so, and if the process doesn't show up you could have it fork off another process that would deal with the heap dump and re-start WAS.