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If a Java app is running as a service how can the Spring context be closed?

I wrote a java application meant to run as a service which is using Spring for DI.
Since this app is running "forever" it will never get to the point it closes the Spring context.
May this cause issues in long term? For these cases is it maybe better to create objects in standard way rather than injecting them using Spring?
I can also see the heap usage slowly increasing, I am not sure this could be the cause.
Thank you.

It shouldn't be a problem if you don't have memory leaks in your application.
If you see your heap increasing continuously then there might be something which has nothing to do with Spring.
If you don't have any ideas what's causing the memory consumption then I'd suggest to take a look on some JVM tools, for example JVisualVM is one option which is available in the JDK. With this you can easily check what your threads are doing, which objects you have in the memory which are growing.

Why do some webservers complain about memory leaks they create?

The title might be a bit strong, but let me explain how I understand what happens. I guess this happened with Tomcat (and the message cited comes from Tomcat), but I'm not sure anymore.
TL;DR At the bottom there's a summary why I'm claiming that it is the web servers' fault.
I might be wrong (but without the possibility of being wrong there would be no reason to ask):
An application uses a library
the library uses a ThreadLocal
the ThreadLocal refers to an object from the library
each object refers to its ClassLoader
The webserver
pools its worker threads for efficiency
lends an arbitrary thread to an application
does nothing special (w.r.t. the thread pool) when an application stops or redeploys
If I understand it correctly, after a redeploy the old "dirty" threads continue to be reused. Their ThreadLocals refer to the old classes which refer to their ClassLoader which refer to the whole old class hierarchy. So a lot of stuff stays in the PermGen space which over time leads to an OutOfMemoryError. Is this right so far?
I'm assuming two things:
the redeploy frequency is a few time per hour
the thread creation overhead is a fraction of a millisecond
So a complete thread pool renewal upon each redeploy costs a fraction of a millisecond a few times per hour, i.e., there's a time overhead of 0.0001 * 12/3600 * 100% i.e. 0.000033%.
But instead of accepting this tiny overhead, there are countless problems. Is my calculation wrong or what am I overlooking?
As a warning we get the message
The web application ... created a ThreadLocal with key of type ... and a value of type ... but failed to remove it when the web application was stopped.
which should be better stated as
The web server ... uses a thread pool but failed to renew it after stopping (or redeploying) an application.
Or am I wrong? The time overhead is negligible even when all threads get recreated from time to time. But clearing their ThreadLocals before they are provided to the applications would suffice and be even faster.
Summary
There are some real problems (recently this one) and the user can do nothing about it. The library writers sometimes can and sometimes can not. IMHO the web servers could solve it pretty easily. The thing happens and has a cause. So I'm blaming the only one party which could do anything about it.
Proposal for what the web server should exactly do
The title of this question is more provocative than correct, but it has its point. And so does the answer by raphw. This linked question has another open bounty.
I think the web servers could solve it as follows:
ensure that each thread gets reused (or killed) sometime
store a LastCleanupTimestamp in a ThreadLocal (for new threads it's the creation time)
when re-using a thread, check if the cleanup timestamp is below some threshold (e.g., now minus some delta, e.g., 1 hour)
if so, clean all ThreadLocals and set a new LastCleanupTimestamp
This would assure that no such leak exists longer than delta plus the duration of the longest request plus the thread turnaround time. The cost would compose as follows:
checking a single ThreadLocal (i.e., some nanoseconds) per request
cleaning all ThreadLocals reflectively (i.e., some more nanoseconds once each delta per thread)
the cost from removing the data possibly useful for the application which stored them. This can't break an application as no application can assume to see a thread containing the thread locals it has set (since it can't even assume to see the thread itself anymore), but it may cost time needed to recreate the data (e.g., a cached DateFormat instance if someone still uses such a terrible thing).
It could be switched off by simply setting the thresold, if no app has been undeployed or redeployed recently.

TL;DR It's not web servers that create memory leaks. It's you.
Let me first state the problem more explicitly: ThreadLocal variables often refer to an instance of a Class that was loaded by a ClassLoader that was meant to be exclusively used by a container's application. When this application gets undeployed, the ThreadLocal reference gets orphaned. Since each instance keeps a reference to its Class and since each Class keeps a reference to its ClassLoader and since each ClassLoader keeps a reference to all classes it ever loaded, the entire class tree of the undeployed application cannot get garbage collected and the JVM instance suffers a memory leak.
Looking at this problem, you can optimize for either:
Allow as many requests per second as possible even throughout a redeploy (thus keep response time short and reuse threads from a thread pool)
Make sure that threads stay clean by discarding threads once they were used when a redeploy occurred (thus patch forgotten manual cleaning)
Most developers of web applications would argue that the first is more important since the second can be achieved by writing good code. And what would happen when a redeploy would happen concurrently to long lasting requests? You cannot shut down the old thread pool since this would interrupt running requests. (There is no globally defined maximum for how long a request cycle can take.) In the end, you would need a quite complex protocol for that and that would bring its own problems.
The ThreadLocal induced leak can however be avoided by always writing:
myThreadLocal.set( ... );
try {
// Do something here.
} finally {
myThreadLocal.remove();
}
That way, your thread will always turn out clean. (On a side note, this is almost like creating global variables: It is almost always a terrible idea. There are some web frameworks like for example Wicket that make a lot of use of this. Web frameworks like this are terrible to use when you need to do things concurrently and get very unintuitive for others to use. There is a trend away from the typical Java one thread per request model such as demonstrated with Play and Netty. Do not get stuck with this anti-pattern. Do use ThreadLocal sparingly! It is almost always a sign of bad design.)
You should further be aware that memory leaks that are induced by ThreadLocal are not always detected. Memory leaks are detected by scanning the web server's worker thread pool for ThreadLocal variables. If a ThreadLocal variable was found the variable's Class reveals its ClassLoader. If this ClassLoader or one of its parents is that of the web application that just got undeployed, the web server can safely assume a memory leak.
However, imagine that you stored some large array of Strings in a ThreadLocal variable. How can the web server assume that this array belongs to your application? The String.class was of course loaded with the JVM's bootstrap ClassLoader instance and cannot be associated with a particular web application. By removing the array, the web server might break some other application that is running in the same container. By not removing it, the web server might leak a large amount of memory. (This time, it is not a ClassLoader and its Classes that are leaked. Depending on the size of the array, this leak might however even be worse.)
And it gets worse. This time, imagine that you stored an ArrayList in your ThreadLocal variable. The ArrayList is part of the Java standard library and therefore loaded with the system ClassLoader. Again, there is no way of telling that the instance belongs to a particular web application. However, this time your ClassLoader and all its Classes will leak as well as all instances of such classes that are stored in the thread local ArrayList. This time, the web server even cannot certainly determine that a memory leak occurred when it finds that the ClassLoader was not garbage collected since garbage collection can only be recommended to a JVM (via System#gc()) but not enforced.
Renewing the thread pool is not as cheap as you might assume.
A web application cannot just go and throw away all threads in a thread pool whenever an application is undeployed. What if you stored some values in those threads? When a web application recycles a thread, it should (I am not sure if all web servers do this) find all non-leaking thread local variables and reregister them in the replaced Thread. The numbers you stated about efficiency would therefore not longer hold.
At the same time, the web server need to implement some logic that manages the replacement of all thread pool's Threads what does neither work in favor of your proposed time calculation. (You might have to deal with long lasting requests - think of running an FTP server in a servlet container -- such that this thread pool transition logic might be active for quite a long time.)
Furthermore, ThreadLocal is not the only possibility of creating a memory leak in a servlet container.
Setting a shut down hook is another example. (And it is unfortunately a common one. Here, you should manually remove the shut down hook when your application is undeployed. This problem would not be solved by discarding threads.) Shut down hooks are furthermore instances of custom subclasses of Thread that were always loaded by an application's class loader.
In general, any application that keeps a reference to an object that was loaded by a child class loader might create a memory leak. (This is generally possible via Thread#getContextClassLoader().) In the end, it is the developer's resposibility to not cause memory leaks, even in Java applications where many developer's misinterpret the automatic garbage collection as there are no memory leaks. (Think of Jochua Bloch's famous stack implementation example.)
After this general statement, I want to comment on Tomcat's memory leak protection:
Tomcat does not promise you to detect all memory leaks but covers specific types of such leaks as they are listed in their wiki. What Tomcat actually does:
Each Thread in the JVM is examined, and the internal structures of the
Thread and ThreadLocal classes are introspected to see if either the
ThreadLocal instance or the value bound to it were loaded by the
WebAppClassLoader of the application being stopped.
Some versions of Tomcat even try to compensate for the leak:
Tomcat 6.0.24 to 6.0.26 modify internal structures of the JDK
(ThreadLocalMap) to remove the reference to the ThreadLocal instance,
but this is unsafe (see #48895) so that it became optional and
disabled by default from 6.0.27. Starting with Tomcat 7.0.6, the
threads of the pool are renewed so that the leak is safely fixed.
However, you have to properly configure Tomcat to do so. The wiki entry on its memory leak protection even warns you how you can break other applications when TimerThreads are involved or how you might leak memory leaks when starting your own Threads or ThreadPoolExecutors or when using common dependencies for several web applications.
All the clean up work offered by Tomcat is a last resort! Its nothing you want to have in your production code.
Summarized: It is not Tomcat that creates a memory leak, it is your code. Some versions of Tomcat try to compensate for such leaks which are detectable if it is configured to do so. However, it is your responsibility to take care of memory leaks and you should see Tomcat's warnings as an invitation to fix your code rather than to reconfigure Tomcat to clean up your mess. If Tomcat detects memory leaks in your application, there might even be more. So take a heap and thread dump out of your application and find out where your code is leaking.

What happens to a Java Web Container's memory when there are too many concurrent sessions?

A question came up at work today:
Imagine that I have a lot of concurrent users accessing my website, each with their own data stored in user sessions. Considering that I have a limited amount of memory available in my JVM, what happens, or what is supposed to happen, when the concurrent active sessions reach a point where the container JVM runs out of memory?
I tried to find something in the servlet spec about what should happen but there is nothing definitive in there, it just says that the developer will have access to the session objects, etc. This makes me think that it must be provider specific.
Taking Tomcat as an example, does the webserver just start throwing OutOfMemoryExceptions? Or is it more clever about the way it deals with this, for example paging the sessions off to another cache? Or another way all together?

The servlet specification does not say anything about memory considerations, so you'll get no help there.
Unless configured specifically to do otherwise, Tomcat will allow you to use-up all available memory with your HttpSession objects (realy, their contents) and ultimately the JVM will start throwing OutOfMemoryErrors, potentially taking your server down (though the JVM will continue to run, many things will behave ... unpredictably and unfortunately).
If a single request starts using a lot of memory in local variables, etc., the request-processing thread will suffer an OutOfMemoryError and stop processing the current request. (I believe in this case, the request-processing thread will actually be recycled by the Tomcat request-processing thread pool). The garbage collector will likely run shortly thereafter and re-claim the memory used by that request and your server will stabilize.
On the other hand, if you use-up a lot of memory and store those objects into the user's HttpSession, then the GC cannot free any memory and your server will continuously suffer from OutOfMemoryErrors. Though Tomcat will expire sessions on a specified schedule (the default is after 30 minutes of inactivity), the session-cleansing thread may encounter an OutOfMemoryError during operation and therefore fail to perform its duty, compounding the whole situation (because, effectively, HttpSessions will never expire).
There are several ways to mitigate the above unfortunate scenario. Which one makes sense to you is up to your requirements and environment.
Increase your heap size. This will obviously only get you so far. If you are filling-up a 16GiB heap with HttpSession and related objects, then you are reaching the limits of commodity hardware and you can't simply buy-a-bigger-box.
Reduce the session expiration time (default is 30 minutes). If a session isn't explicitly terminated (say, through a logout function), then the HttpSession object and all its contents stick around until the expiration interval has passed. If you have lots of data in lots of abandoned sessions, reducing the session expiration time may give you some breathing room.
Stop putting so much data into the user's HttpSession. While this may seem like an obnoxious suggestion ("stop doing that"), it is honestly a valid one: do you really need to store so much stuff in the session itself? How about using a data store of some kind (relational database, non-relational database like Cassandra, webcache, etc.)? Maybe store the data in a file on the disk? While these suggestions will certainly limit your ability to access your data quickly, they are certainly better options than having your server come crashing down under the weight of so much stuff in your session.
Use Tomcat's PersistentManager, which is a session manager capable of swapping active (but idle) sessions to some external storage (file-based and JDBC-based storage mechanisms are available by default). This can get you a long way while you figure out some other place to put all that data you are shoving into the user's session.
All but #4 are applicable to any servlet container. #4 should be available to JBoss users, as JBoss uses Tomcat internally. For other containers, you may find that a similar capability exists.

Generally this is vendor dependent. It is, however, frequent that containers can serialize sessions to disk at its discretion (if the session data can be serialized).
If the container can do this, it can push out inactive sessions when needed and restore them again when needed, using memory better and thereby postponing any OutOfMemoryExceptions.

Threadlocal memory leak in Threadpool

I am getting threadlocal memory leak errors in Tomcat and I am using ThreadPool, but have no implementation of ThreadLocal in my webapp.
SEVERE: The web application [/myWebApp] created a ThreadLocal with key of type [org.a
pache.http.impl.cookie.DateUtils$DateFormatHolder$1] (value [org.apache.http.imp
l.cookie.DateUtils$DateFormatHolder$1#4c2849]) and a value of type [java.lang.re
f.SoftReference] (value [java.lang.ref.SoftReference#1e67280]) but failed to rem
ove it when the web application was stopped. Threads are going to be renewed ove
r time to try and avoid a probable memory leak.
What I dont understand is why i am getting threadlocal error although i have not implemented it? I want to get rid of these messages so I searched the web, and in here it is written that in order to clean the threadlocal i need to use:
ThreadLocal.remove()
but I have no implementation of ThreadLocal.. I'll be appreciated if someone show me a way.

Clearly, something is creating that / those ThreadLocal instances. If it is not your code, then it must be some library you are using, or (unlikely) Tomcat itself.
I would start by looking at what might be creating instances of
org.apache.http.impl.cookie.DateUtils$DateFormatHolder$1
(That's an anonymous class in a nested class in DataUtils, by the way ... so unless something weird is coing on, the creation will be occuring in the DateUtils.java file.)
If examining the source code doesn't help, try debugging the Tomcat instance and setting a breakpoint on the ThreadLocal constructor(s).

The problem lies within your third party library. You cannot use thread locals in a thread pooled environment unless you really clean them up after the end of each request.
This article explains the problem:
http://blog.maxant.co.uk/pebble/2008/09/23/1222200780000.html

The ThreadLocal was obviously created by some framework or library you use (look which one is using HttpClient), but as you can see in the log the value is a SoftReference which should minimize the memory leak.
In fact you can see in the code for DateUtils that it is creating the Threadlocal...

Here's the HttpClient JIRA: https://issues.apache.org/jira/browse/HTTPCLIENT-1216
From release 4.2.2 there's a clearThreadLocal() method, starting with 4.3 the cookie-DateUtils is deprecated and replaced with org.apache.http.client.utils.DateUtils.
Calling DateUtils.clearThreadLocal() once on shutdown is not enough, it only clears the ThreadLocal of the current thread, so you need to invoke it after performing an HTTP request which parses/formats dates, on that thread. This removes most of the performance benefit of using a ThreadLocal though.
Alternatively, if you perform HTTP requests from a thread under your control (not created by Tomcat), remember to shut down any thread pools/executors on application shutdown.
Big shame is that HttpClient could easily be modified to not override ThreadLocal, then the ThreadLocal wouldn't reference the webapp and its classloader, avoiding the bulk of the leak I believe :(

How to identify the cause of a JNI global reference memory leak?

I'm using Tomcat and after stopping my web application there's still a reference to the classloader instance of my web application.
With the consequence that a notable amount of memory (mostly related to static data) will not be freed. Sooner or later this results in an OutOfMemoryError.
I took a heap dump and I realized that its held by a JNI global reference which prevents that the classloader will be garbage collected.
My application does not use JNI. I am also not using the Apache Tomcat Native Library. I am using a Sun/Oracle JDK.
I'd like to track down the cause/origin of this global reference.
(My guess is that the JVM internally references the classloader - but why/where?).
Question:
Which approaches/toolsets exists to achieve this?
UPDATE
It seems that bestsss is right and the JNI global references has been introduced by the jvm debug mode. This helped me out but it does not answer the question so I am still curious to get an answer to the question which might be helpful in the future.

Besides the obvious case: Threads, there is one more:
Are you using your application in debug mode?
The JVM does not hold references to any classloader besides the system one, but it doesn't concern you. The rest of JNI references are either Threads or just debug held objects (provided you don't use JNI and lock the objects down yourself).
JNI references are just roots, edit your answer and post what exactly objects are held by those references.

The first thing i'd do is run with -Xcheck:jni on and see if it comes up with anything. I wouldn't expect it to; it doesn't sound there's anything weird happening with JNI, just incorrect use being made of it. However, it's good to make sure of that.
If you're on a Sun JVM, i think you can do -XX:TraceJNICalls to get an overwhelming listing of JNI calls as they happen. That should let you get an idea of what calls are being made, and from there work towards what is making them, and why this is causing a problem.

JRockit mission control: http://download.oracle.com/docs/cd/E13150_01/jrockit_jvm/jrockit/tools/index.html
A nice GUI tool that should help you find it pretty quick.

You could try jstack.
Maybe one of the listed stacktraces will show you the origin of the global reference.