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java heap and thread analysis for memory leak

My WebLogic server was configured with 16gb of heap space, but it was 90% used within 1 hour of production usage when most of the users started work. I observed there were several stuck threads whenever this happens.
I have captured the heap dump when the heap was approx 10% free. How do I inspect the heap dump to find out the memory leak, or process, codes which is causing this issue.
I have tried to understand the memory leak, running tools like JMap and Eclipse MAT, but it maybe due to lack of experience, I couldn't understand what these tools are trying to show. Or how/what should I look out for?
I have both the before/after GC heap dump to analyze.
I have reviewed the thread dumps, there were no "waiting to lock" objects threads, the threads were similar as shown below, with threads stuck with no obvious reasons.

According to your heap dump, your biggest memory issue is the int arrays, indeed it takes nearly 70 % of your heap (Yes sort the Size Column instead).
Select it in your heap dump, right click and select on Show in Instances View
Then browse the biggest objects and for each of them right click and select Show Nearest GC Root to see which Object has still an hard reference to the int array which prevents to be eligible for the GC.
It could help you to find your memory leak assuming that it is a memory leak.
See below an example of Nearest GC Root allowing to identify a leak that I added intentionally to my program just to show the idea. As you can see in the screenshot, I have an array of int which cannot be eligible for the GC because it is stored in an HashMap called leak in my class Application, so I know that my memory issue could be due to this particular HashMap especially if I have many other objects which lead to this HashMap.
NB: Be patient when you try to identify a leak as it is not always obvious, the ideal situation is where you have a huge object that takes the whole heap but obviously it is not your case there is nothing really obvious that is the reason why I propose to investigate the int arrays first. Don't forget that it could also be little int arrays but thousands of them with the same Nearest GC Root.
Another trick, If you have JProfiler you can simply follow this wonderful tutorial to find your leak.
Response Update:
One simple way to better identify the root cause of the memory leak is to take at least 2 heap dumps then compare them using a tool like jhat with the syntax
jhat -J-Xmx2G -baseline ${path-to-the-first-heap-dump} ${path-to-the-second-heap-dump}
It will launch a small HTTP sever on port 7000 so:
Launch http://localhost:7000/
Then click on Show instance counts for all classes (including platform)
You will then see the list of Classes ordered by total amount of new instances created. You can then use VisualVM to do what I described in the first part of my answer to find the root cause of your memory leak.
You can also use jhat
By selecting of the Top Classes then for each of them
click on one "Reference to this Object"
then click on Exclude weak refs
You will then see the GC root of each instances like the next screenshot:
Another way is to use Eclipse Memory Analyzer also called MAT.
Open the second snapshot with it
Select the view histogram
Then for each of the Top Classes right click
Choose Merge Shortest Paths To GC Roots/ Exclude All references
you will then see something like the next screenshot:

The JDK's "jmap -histo" command will dump object counts/bytes for all classes to a text file. If you capture/compare a few of these dumps over time, you will see which ones grow continually -- your memory leak. The overhead of -histo is much lower than that of capturing a full heap dump.
Comparing just a few dumps (like the python script detailed here) seems like too small of a sample, so I wrote an open-source tool (here) that runs this jmap -histo command in the background (at an interval). It has a live display and tracks the % of time that the byte count for each class is on the rise.

It seems you, probably, have a memory leak situation. Your best approach is to use Java Mission Control with Flight Recorder to get the class and method leaking.
You should setup your weblogic managed server with the following parameters:
-Dcom.sun.management.jmxremote
-Dcom.sun.management.jmxremote.port=8999
-Dcom.sun.management.jmxremote.ssl=false
-Dcom.sun.management.jmxremote.authenticate=false
-XX:+UnlockCommercialFeatures
-XX:+FlightRecorder
When you set this up, follow the instructions here to detect the leak.
Hope it helps !!

I am one of the developers of the tool called Plumbr. Among other things we make an automatic analysis of heap contents in case of excessive memory usage. You may find it useful.

Per your comments: you have Java 7 with 16GB heap, no GC algorithm explicitly specified, so default for Java 7 is Throughput GC, which is not suitable for most web apps, for it leads to long GC pauses for big heaps.
Switch to ConcurrentMarkSweep GC, this way GC will not wait till your memory fills up and will try its best to collect garbage incrementally, so that you will have fewer Stop The World pauses.

Did you try yourkit profiler? It's not free, but you can evaluate it for 30 days. In this case if you dump contains all object (not only live), you will be able to check roots for them as well. Because it could be that you don't have memory leak, but too big memory footprint. Also it would be great to enable GC logs and parse how much FullGC pauses do you have:
grep "Full GC" jvm_gc.log | wc -l
In ideal world it should be 0 :)
Btw, whole this article could be helpful for you.

java: General approach to out-of-memory error

I have been working on this project on Java with multiple modules. Since quite some time, I have been occasionally getting "java: Out Of Memory" error! I am pretty new to this 'popular' error and wanted to know the general approach to solve such errors.
Also, are there standard tools accepted by the industry to help figure out the cause of such errors?
The modules in my project include every minute polling from a third party (using web service), multi-threading among other things. However, this is just a pointer and I seek a general approach and not something very specific to my project.
Thanks.

Sometimes you just have an class that uses a lot of memory and you need to increase the heap size or make a more space-efficient algorithm. Other times it is a leak and you need to deference objects.
Run jvisualvm (it's included in the JDK).
Connect to your process and try if you can to recreate the
out-of-memory error while keeping an eye on the heap size.
Perform a heap dump when the memory grows large. Search for the
largest objects by size - often that will give you the culprit
class.
Look at the dependencies to see what is holding a references. If it is a memory leak make sure to dereference unneeded objects.

Also, are there standard tools accepted by the industry to help figure out the cause of such errors?
Yes, there are memory profilers such as VisualVM and YourKit. I use the latter extensively, for both CPU and memory profiling, and find it extremely useful. To get some idea of what it's capable of, take a look at this page: link.

If you can't increase the available memory you have to consume less.
Don't keep references to Objects that you don't need at the time of execution (like data you can reload dynamically) and if necessary redesign your flow (e.g. don't process all objects in parallel and do it sequentially) to require less memory at that time. The garbage collection should do the rest for you.
Especially if you load big data objects into memory consider to use a streaming approach if possible. E.g. you don't need to load a whole file into memory if you want to search through it. You can just step through it.
Besides architectural problems you can also have leaks: keeping unintentional references to objects you don't need anymore. Since they are referenced, the garbage collector can't free the memory and you run out of memory at some point. That is probably the #1 reason for OutOfMemoryExceptions and it usually has to do with static references since classes and therefore the statics are usually not unloaded after the first time you touch a class. The internet has many articles on finding / fixing those, e.g. How to Fix Memory Leaks in Java
one tool I know of is MAT

You likely have a memory leak. Finding it is a challenge. Netbeans has some tools to help you profile the VM . You can profile your project and view men usage while it runs. Apache JMeter is also available as a plug-in or you can run it on its own.
JMeter.apache.org

If you get OOM too often, then start java with correct options, get a heap dump and analyze it with jhat or with memory analyzer from eclipse (http://www.eclipse.org/mat/)
-XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=<path to dump file>

Memory Leak in a Java based application

There is a memory leak happens in an application when a short lived object holds a long lived object,
My question is how can we identify
1) which object lives longer and shorter, any tool which measures life of an object?
2nd Question
I am constantly getting the Out of Memory Space Error and I tried increasing the Heap memory to 2 GB, but still i am getting, please suggest me any open source tool with which i can identify the memory leak issue and fix.
At present I am restarting the server every time as a temporary solution, but Suggest me any thing which i can fix permanently.

You can use the VisualVM tool included in the JDK:
http://download.oracle.com/javase/6/docs/technotes/tools/share/jvisualvm.html
Documentation available here:
https://visualvm.dev.java.net/docindex.html

There are 2 options:
It just may be your application doesn't have enough heap allocated. Measure size of your input and give application corresponding heap;
There's memory-leak: take profiler, examine your heap, find objects which shouldn't be there or there too much of them ('short-living objects', in your terms), identify which 'long-living' object holds them, fix this. You should know your code to understand which objects must be 'short-living' and which must be 'long-living'.

I've found the Heap Walker in Netbeans very usefull

As said, jvisualvm have good tools to analyze the heap live.
But you can also use jvisualvm or -XX:+HeapDumpOnOutOfMemoryError to take a heap dump in a file. And then take the file to your destkop, to open it in Eclipse Memory Analyzer. Eclipse MAT is even better to analyze the memory.

Out of Memory occurs on a server because it literally uses up all memory it's allowed to have. Not sure about what application you're using for hosting the server, but for Apache, you need to add the line -Xmx512m where 512 is the maximum amount of megabytes it's allowed to have.
If you leave the application to run long enough, it's going to happen. This isn't because of memory leaks in Java but the server itself which has a tendency to do so. You can't change this behavior, but you can at least increase the default memory of 256 mb. With the heavy loading site that I work on everyday, 256 mb lasts about 30 minutes for me unfortunately. I've found that 1024 mb is reasonable and rarely crashes due to out of memory exceptions.
I'd strike me as very unusual for Java to be incapable of garbage collecting correctly unless the programmer took a hand at overriding typical functionality.

I think you can track memory leaks with jsconsole (which comes shipped with JDK6 if i'm not mistaken).

A short-lived object holding a reference to a long-lived object will not cause problems. (a good overview , including generational garbage collection).
2GB is an awful lot of objects/references. If you're running out of heap space at 2Gb you're likely holding onto massive amounts of data and/or keeping open resources when you're done with them. You should post at the very least a description of what your application does and how long it takes to die.
You can get some sense of what's happening quickly by watching the garbage collector (e.g. run with "-verbose:gc" which will tell you when the garbage collector is running and how much it collects).

General strategy to resolve Java memory leak?

I have a standalone program that I run locally, it is meant to be a server type program running 24/7. Recently I found that it has a memory leak, right now our only solution is to restart it every 4 hours. What is the best way to go about finding this memory leak? Which tool and method should we use?

If you are using Java from Sun and you use at least Java 6 update 10 (i.e. the newest), then try running jvisualvm from the JDK on the same machine as your program is running, and attach to it and enable profiling.
This is most likely the simplest way to get started.

When it comes to hunting memory problems, I use SAP Memory Analyzer Eclipse Memory Analyser (MAT), a Heap Dump analysis tool.
The Memory Analyzer provides a general purpose toolkit to analyze Java heap dumps. Besides heap walking and fast calculation of retained sizes, the Eclipse tool reports leak suspects and memory consumption anti-patterns. The main area of application are Out Of Memory Errors and high memory consumption.
Initiated by SAP, the project has since been open sourced and is now know as Eclipse Memory Analyser. Check out the Getting Started page and especially the Finding Memory Leaks section (I'm pasting it below because I fixed some links):
Start by running the leak report to automatically check for memory leaks.
This blog details How to Find a Leaking Workbench Window.
The Memory Analyzer grew up at SAP. Back then, Krum blogged about Finding Memory Leaks with SAP Memory Analyzer. The content is still relevant!
This is probably the best tool you can get (even for money) for heap dump analysis (and memory leaks).
PS: I do not work for SAP/IBM/Eclipse, I'm just a very happy MAT user with positive feedback.

You need a memory profiler. I recommend trying the Netbeans profiler.

One approach would be to take heap dumps on a regular basis, then trend the instance counts of your classes to try to work out which objects are being consistently created but not collected.
Another would be to switch off parts of your app to try to narrow down where the problem is.
Look at tools like jmap and jhat.

You might look up JMX and the jconsole app that ships with Java. You can get some interesting statistics out-of-the-box, and adding some simple instrumentation to your classes can provide a whole lot more.

As already stated jvisualvm is a great way to get started, but once you know what is leaking you may need to find what is holding references to the objects in question for which I'd recommend jmap and jhat, e.g
jmap -dump:live,file=heap.dump.out,format=b <pid>
and
jhat heap.dump.out
where <pid> is easily found from jvisualvm. Then in a browser navigate to localhost:7000 and begin exploring.

You need to try and capture Java heap dump which is a memory print of the Java process.
It's a critical process for memory consumption optimisation and finding memory leaks.
Java heap dump is an essential object for diagnosing memory-linked issues including java.lang.OutOfMemoryError, Garbage Collection issues, and memory leaks which are all part of Java web development process
For clarity, a Heap dump contains information such as Java classes and objects in a heap during instant of taking the snapshot.
To do it, you need to run jmap -dump:file=myheap.bin <program pid>.
To learn more about how to capture Java heat dumps, check out: https://javatutorial.net/capture-java-heap-dump

Strategies for the diagnosis of Java memory issues

I've been tasked with debugging a Java (J2SE) application which after some period of activity begins to throw OutOfMemory exceptions. I am new to Java, but have programming experience. I'm interested in getting your opinions on what a good approach to diagnosing a problem like this might be?
This far I've employed JConsole to get a picture of what's going on. I have a hunch that there are object which are not being released properly and therefor not being cleaned up during garbage collection.
Are there any tools I might use to get a picture of the object ecosystem? Where would you start?

I'd start with a proper Java profiler. JConsole is free, but it's nowhere near as full featured as the ones that cost money. I used JProfiler, and it was well worth the money. See https://stackoverflow.com/questions/14762/please-recommend-a-java-profiler for more options and opinions.

Try the Eclipse Memory Analyzer, or any other tool that can process a java heap dump, and then run your app with the flap that generates a heap dump when you run out of memory.
Then analyze the heap dump and look for suspiciously high object counts.
See this article for more information on the heap dump.
EDIT: Also, please note that your app may just legitimately require more memory than you initially thought. You might try increasing the java minimum and maximum memory allocation to something significantly larger first and see if your application runs indefinitely or simply gets slightly further.

The latest version of the Sun JDK includes VisualVM which is essentially the Netbeans profiler by itself. It works really well.

http://www.yourkit.com/download/index.jsp is the only tool you'll need.
You can take snapshots at (1) app start time, and (2) after running app for N amount of time, then comparing the snapshots to see where memory gets allocated. It will also take a snapshot on OutOfMemoryError so you can compare this snapshot with (1).
For instance, the latest project I had to troubleshoot threw OutOfMemoryError exceptions, and after firing up YourKit I realised that most memory were in fact being allocated to some ehcache "LFU " class, the point being that we specified loads of a certain POJO to be cached in memory, but us not specifying enough -Xms and -Xmx (starting- and max- JVM memory allocation).
I've also used Linux's vmstat e.g. some Linux platforms just don't have enough swap enabled, or don't allocate contiguous blocks of memory, and then there's jstat (bundled with JDK).
UPDATE see https://stackoverflow.com/questions/14762/please-recommend-a-java-profiler

You can also add an "UnhandledExceptionHandler" to your Application's Thread. This will catch 'uncaught' exception, like an out of memory error, and you will at least have an idea where the exception was thrown. Usually this not were the problem is but the 'new' that couldn't be satisfied. As a rule I always add the UnhandledExceptionHandler to a Thread if nothing else to add logging.