Does anyone knows if there is any tool out there to calculate the heap fragmentation using heap dumps?
I have a tool to visualize the heap (http://bobah.net/d4d/tools/cpp-heapmap) but it consumes the list of {op;address;size} triplets, not a raw heap dump. You can use it to visually estimate how bad the heap is. In some cases it's just enough. It's malloc interceptor would obviously not fit for Java app, but the UI does not care where numbers come from and would display ones from any source.
But let's assume we are able build a heap map from the dump (I'm sure someone will answer here how exactly). The main part of the problem is to calculate fragmentation curve F(s), s - target allocation size. F(s) - the ratio of (total_free_space/s), to number of blocks of size s which can actually be allocated considering particular heap layout.
Once the F(s) is built, one can integrate it in the interval from 1 to S (total heap size) to have a single number representing the heap fragmentation or usage efficiency.
The IBM Garbage Collection and Memory Analyzer is excellent for that sort of thing and is free.
Related
This is a screen shot of a JVM (win64, 6u17) running ActiveMQ, after every garbage collection the heap size is reducing. As the heap size reduces garbage collection gets more frequent and the heap reduces more quickly. Eventually the VM locks up as it's spending all it's time in GC.
-Xms is the default and -Xmx is 2048mb.
What is happening!!? How can I avoid this?
http://imagebin.org/92614
Shrinking heap http://imagebin.org/index.php?mode=image&id=92614
n.b originally posted on serverfault.com, moved to stackoverflow.com as requested
Google found me the following, from the IBM JVM FAQ (how's that for an NLA):
When does the Java heap shrink?
Heap shrinkage occurs when GC determines that there is a lot of free heap storage, and releasing some heap memory is beneficial for system performance. Heap shrinkage occurs after GC, but when all the threads are still suspended.
The Sun JVM does something similar. Below is an excerpt from an Oracle Technology Network article entitled Ergonomics in the 5.0 Java Virtual Machine.
The heap will grow or shrink to a size that will support the chosen throughput goal. Some oscillations in the size of the heap during initialization and during a change in the application's behavior can be expected.
...
It is typical that the size of the heap will oscillate as the garbage collector tries to satisfy competing goals. This is true even if the application has reached a steady state. The pressure to achieve a throughput goal (which may require a larger heap) competes with the goals for a maximum pause time and a minimum footprint (which both may require a small heap).
I suggest you have a look at the rest of that document; it may have more information relevant to your problem.
There is a JVM argument that controls when the heap is resized.
-XX:MaxHeapFreeRatio
The default value for this is 70. The free ratio is the amount of space not allocated on the heap over the total heap size. It the percentage of free space rises above the default of 70% the jvm will rreduce the size of the heap to allow the OS to use the memory.
If the heap is shrinking too often you can increase the value of -XX:MaxHeapFreeRatio. If it is set to 100 presumably it will never skrink.
Just a guess:
It looks like the system is pretty much idle. There might be some caching going on, and stuff drops out of the cache and gets gc'd. Or since it is a queuing system, maybe it has some messages, in the queue, which slowly get delivered and gc'd afterwards.
The increased frequence of gc-runs might be due to ever decreasing load on the system.
As to how to avoid it. Why do you want to avoid it? It seems like your CPU load is zero. So you are free to let the gc do whatever it wants
A. If I execute a huge simulation program with -Xmx100000m (~100GB) I see some spikes in the used heap (~30 GB). That spikes increase the heap size and decreases the memory that can be used by other programs. I would like to limit the heap size to the size that is actually required to run the program without memory exceptions.
B. If I execute my simulation program with -Xmx10000 (~10GB) I am able to limit the used heap size (~ 7 GB). The total heap size is less, too (of course). I do not get out of memory exceptions in the first phase of the program that is shown in the VisualVM figures (about 16 minutes).
I naively expected that if I increase xmx from 10GB (B) to 100GB (A) that the used heap would stay about the same and that Java only would use more memory in order to avoid out of memory exceptions. However, the behavior seems to be different. I guess that Java works this way in order to improve performance.
An explanation for the large used heap in A might be that the growth behavior of hash maps is different if xmx is larger? Does xmx have an effect on the load factor?
In the phase of the program where a lot of mini spikes exist (see for example B at 12:06) instead of a few large ones (A) some java streams are processed. Does the memory allocation for stream processing automatically adapt with the xmx value? (There is still some memory left that could be used to have less mini spikes at 12:06 in B.)
If not, what might be the reasons for the larger used heap in A?
How can I tell Java to keep the used heap low if possible (like in the curves for B) but to take more memory if an out of memory exception could occur (allow to temporarily switch to A). Could this be done by tuning some garbage collection properties?
Edit
As stated by the answer below, the profile can be altered by garbage collection parameters. Applying -Xmx100000m -XX:MaxGCPauseMillis=1000 adapts the profile from A to consume less memory (~ 20 GB used) and more time (~ 22 min).
I would like to limit the heap size to the size that is actually required to run the program without memory exceptions.
You do not actually want to do that because it would make your program extremely slow because only providing the amount equivalent to the application peak footprint means that every single allocation would trigger a garbage collection while the application is near the maximum.
I guess that Java works this way in order to improve performance.
Indeed.
The JVM has several goals, in descending order:
pause times (latency)
allocation throughput
footprint
If you want to prioritize footprint over other goals you have to relax the other ones.
set -XX:MaxGCPauseMillis=18446744073709551615, this is the default for the parallel collector but G1 has a 200ms default.
configure it to keep less breathing room
I am new to Java, I just gone through heap dump analysis using eclispe's MAT. So i just wanted to below points
a) understand what is Shallow and retained heap size and how it is being calculated? It would be great if you provide example.
b) For performance issue,most of people adviced me to keep minimum and maximum heap size same, so is is ok or it is subjective to application to application?
Shallow heap is the memory consumed by one object. An object needs 32 or 64 bits (depending on the OS architecture) per reference, 4 bytes per Integer, 8 bytes per Long, etc. Depending on the heap dump format the size may be adjusted
Retained heap of X is the sum of shallow sizes of all objects in the retained set of X, i.e. memory kept alive by X.
Refer this link.
JVM sizing and tuning is not an exact science, so taking a blanket decision to set min and max size the same is not necessarily the best config to choose.
I find this to be an excellent explanation of the sorts of decisions that you need to make. In addressing your question, it says :
Setting -Xms and -Xmx to the same value increases predictability by removing the most important sizing decision from the virtual machine. However, the virtual machine is then unable to compensate if you make a poor choice.
If you set the min and max the same, but have an inappropriately sized Eden space, you may still end up with poor garbage collection performance.
The only way to make decisions about sizing is to run your application under a variety of workloads and see how the GC performs.
This is a screen shot of a JVM (win64, 6u17) running ActiveMQ, after every garbage collection the heap size is reducing. As the heap size reduces garbage collection gets more frequent and the heap reduces more quickly. Eventually the VM locks up as it's spending all it's time in GC.
-Xms is the default and -Xmx is 2048mb.
What is happening!!? How can I avoid this?
http://imagebin.org/92614
Shrinking heap http://imagebin.org/index.php?mode=image&id=92614
n.b originally posted on serverfault.com, moved to stackoverflow.com as requested
Google found me the following, from the IBM JVM FAQ (how's that for an NLA):
When does the Java heap shrink?
Heap shrinkage occurs when GC determines that there is a lot of free heap storage, and releasing some heap memory is beneficial for system performance. Heap shrinkage occurs after GC, but when all the threads are still suspended.
The Sun JVM does something similar. Below is an excerpt from an Oracle Technology Network article entitled Ergonomics in the 5.0 Java Virtual Machine.
The heap will grow or shrink to a size that will support the chosen throughput goal. Some oscillations in the size of the heap during initialization and during a change in the application's behavior can be expected.
...
It is typical that the size of the heap will oscillate as the garbage collector tries to satisfy competing goals. This is true even if the application has reached a steady state. The pressure to achieve a throughput goal (which may require a larger heap) competes with the goals for a maximum pause time and a minimum footprint (which both may require a small heap).
I suggest you have a look at the rest of that document; it may have more information relevant to your problem.
There is a JVM argument that controls when the heap is resized.
-XX:MaxHeapFreeRatio
The default value for this is 70. The free ratio is the amount of space not allocated on the heap over the total heap size. It the percentage of free space rises above the default of 70% the jvm will rreduce the size of the heap to allow the OS to use the memory.
If the heap is shrinking too often you can increase the value of -XX:MaxHeapFreeRatio. If it is set to 100 presumably it will never skrink.
Just a guess:
It looks like the system is pretty much idle. There might be some caching going on, and stuff drops out of the cache and gets gc'd. Or since it is a queuing system, maybe it has some messages, in the queue, which slowly get delivered and gc'd afterwards.
The increased frequence of gc-runs might be due to ever decreasing load on the system.
As to how to avoid it. Why do you want to avoid it? It seems like your CPU load is zero. So you are free to let the gc do whatever it wants
It is not possible to increase the maximum size of Java's heap after the VM has started. What are the technical reasons for this? Do the garbage collection algorithms depend on having a fixed amount of memory to work with? Or is it for security reasons, to prevent a Java application from DOS'ing other applications on the system by consuming all available memory?
In Sun's JVM, last I knew, the entire heap must be allocated in a contiguous address space. I imagine that for large heap values, it's pretty hard to add to your address space after startup while ensuring it stays contiguous. You probably need to get it at startup, or not at all. Thus, it is fixed.
Even if it isn't all used immediately, the address space for the entire heap is reserved at startup. If it cannot reserve a large enough contiguous block of address space for the value of -Xmx that you pass it, it will fail to start. This is why it's tough to allocate >1.4GB heaps on 32-bit Windows - because it's hard to find contiguous address space in that size or larger, since some DLLs like to load in certain places, fragmenting the address space. This isn't really an issue when you go 64-bit, since there is so much more address space.
This is almost certainly for performance reasons. I could not find a terrific link detailing this further, but here is a pretty good quote from Peter Kessler (full link - be sure to read the comments) that I found when searching. I believe he works on the JVM at Sun.
The reason we need a contiguous memory
region for the heap is that we have a
bunch of side data structures that are
indexed by (scaled) offsets from the
start of the heap. For example, we
track object reference updates with a
"card mark array" that has one byte
for each 512 bytes of heap. When we
store a reference in the heap we have
to mark the corresponding byte in the
card mark array. We right shift the
destination address of the store and
use that to index the card mark array.
Fun addressing arithmetic games you
can't do in Java that you get to (have
to :-) play in C++.
This was in 2004 - I'm not sure what's changed since then, but I am pretty sure it still holds. If you use a tool like Process Explorer, you can see that the virtual size (add the virtual size and private size memory columns) of the Java application includes the total heap size (plus other required space, no doubt) from the point of startup, even though the memory 'used' by the process will be no where near that until the heap starts to fill up...
Historically there has been a reason for this limitiation, which was not to allow Applets in the browser to eat up all of the users memory. The Microsoft VM which never had such a limitiation actually allowed to do this which could lead to some sort of Denial of Service attack against the users computer. It was only a year ago that Sun introduced in the 1.6.0 Update 10 VM a way to let applets specify how much memory they want (limited to a certain fixed share of the physical memory) instead of always limiting them to 64MB even on computers that have 8GB or more available.
Now since the JVM has evolved it should have been possible to get rid of this limitation when the VM is not running inside a browser, but Sun obviously never considered it such a high priority issue even though there have been numerous bug reports been filed to finally allow the heap to grow.
I think the short, snarky, answer is because Sun hasn't found it worth the time and cost to develop.
The most compelling use case for such a feature is on the desktop, IMO, and Java has always been a disaster on the desktop when it comes to the mechanics of launching the JVM. I suspect that those who think the most about those issues tend to focus on the server side and view any other details best left to native wrappers. It is an unfortunate decision, but it should just be one of the decision points when deciding on the right platform for an application.
My gut feel is that it has to do with memory management with respect to the other applications running on the operating system.
If you set the maximum heap size to, for example, the amount of RAM on the box you effectively let the VM decide how much memory it requires (up to this limit). The problem with this is that the VM could effectively cripple the machine it is running on because it will take over all the memory on the box before it decides that it needs to garbage collect.
When you specify max heap size, what you're saying to the VM is, you are allowed to use this amount of memory before you need to start garbage collecting. You cannot have more because if you take more then the other applications running on the box will slow down and you will start swapping to the disk if you use more than this.
Also be aware that they are two values with respect to memory, that is "current heap size" and "max heap size". The current heap size is how much memory the heap size is currently using and, if it requires more it can resize the heap but it cannot resize the heap above the value of maximum heap size.
From IBM's performance tuning tips (so may not be directly applicable to Sun's VMs)
The Java heap parameters influence the behavior of garbage collection. Increasing the heap size supports more object creation. Because a large heap takes longer to fill, the application runs longer before a garbage collection occurs. However, a larger heap also takes longer to compact and causes garbage collection to take longer.
The JVM has thresholds it uses to manage the JVM's storage. When the thresholds are reached, the garbage collector gets invoked to free up unused storage. Therefore, garbage collection can cause significant degradation of Java performance. Before changing the initial and maximum heap sizes, you should consider the following information:
In the majority of cases you should set the maximum JVM heap size to value higher than the initial JVM heap size. This allows for the JVM to operate efficiently during normal, steady state periods within the confines of the initial heap but also to operate effectively during periods of high transaction volume by expanding the heap up to the maximum JVM heap size. In some rare cases where absolute optimal performance is required you might want to specify the same value for both the initial and maximum heap size. This will eliminate some overhead that occurs when the JVM needs to expand or contract the size of the JVM heap. Make sure the region is large enough to hold the specified JVM heap.
Beware of making the Initial Heap Size too large. While a large heap size initially improves performance by delaying garbage collection, a large heap size ultimately affects response time when garbage collection eventually kicks in because the collection process takes more time.
So, I guess the reason that you can't change the value at runtime is because it may not help: either you have enough space in your heap or you don't. Once you run out, a GC cycle will be triggered. If that doesn't free up the space, you're stuffed anyway. You'd need to catch the OutOfMemoryException, increase the heap size, and then retry you calculation, hoping that this time you have enough memory.
In general the VM won't use the maximum heap size unless you need it, so if you think you might need to expand the memory at runtime, you could just specify a large maximum heap size.
I admit that's all a bit unsatisfying, and seems a bit lazy, since I can imagine a reasonable garbage collection strategy which would increase the heap size when GC fails to free enough space. Whether my imagination translates to a high performance GC implementation is another matter though ;)