Mar 06 2008

Chasing the cause for performance degradation

Tags: , , , , Rajiv @ 5:14 am UTC

Spoiler: The last three pictures speak more than the thousand odd words that precede them

Day before:
Too many issues resizing photos in Java. Takes too much memory, takes too long, runs out of mem on Mac. A quick comparison with ImageResizer PowerToy shows that the Java code is taking too much memory and time. The difference is an order of magnitude higher on V’s machine which is slightly older and has lesser memory.
Yesterday (and day before):
Implement a photo resize server using GDI+. Go to bed happy that mem consumption is low, speed is very good and all kinks in passing around UTF-8 filenames between Java and VC++ have been ironed out.
Noon:
J integrates the new resizer into the code base.
2pm:
J verifies perf is 4 times better
6pm:
Code is checked in … waiting for integration build
8pm:
Leave for home
10pm:
Receive an e-mail, integration build ready .. start downloading with the hope of gloating in the perf gains
10.30pm:
Installation started … baby crying … unplug the laptop move closer to baby … play with the baby and complete the installation … start the test case in background
10.35pm:
No sign of test completing … should have finished 2mins ago
10.40pm:
Suspect some “first time” bug, run the test case again …
10.46pm:
No luck … still pathetic perf … does not match what I saw in the morning
10.50pm:
Pissed … shoot of a mail to J … “dood, did you checkin the integration … i see no diff in perf …
10.55pm:
No reply … shall I wait till morn …
11:00pm:
Let me try to recreate morning’s perf numbers … run the main method on java wrapper for the resizer … the same run which took 2mins in the morning is taking 6mins … as bad as the java resizer …damn ..
11:10pm:
WTF?!!
11:11pm:
Maybe I messed up the java wrapper … run the main method on exe resizer …
11:18pm:
Just as bad … three times slower than what it was in the morn …
11:20pm to 12:05am:
Make many runs trying to change some code in the exe … nothing seems to improve perf
12:05am:
Low battery alert … curse the laptop … can’t run even a few hrs without power
12:07am:
Make some more changes to c++ code … build … run …
12:09am:
By Joe! Done in 2mins instead of 6!… damn thing … why is this small change causing the whole thing to be 3 times slower … do some googling …
12:10am:
Undo the changes … recompile and run … see if it becomes slow again …
12:09am:
Thighs are burning … prop up the laptop
12:12am:
Hain?! Done in 2mins … WTF … it was taking 6mins just a few mins ago …
12:15am:
Rollback all the changes … recompile … run …
12:17am:
Done in two mins … WTF … How can this be … Check the logs for the timining … it was taking 6mins till a few mins ago … and the whole thing is back to 2mins now … no changes done … desperate to blame it on something … maybe anti virus was running earlier (should I check the anti virus logs?)… maybe the windows kernel has cached the files now (should I restart the laptop and see?) … maybe it became slow when i was running on battery …
12:18am:
Is that really possible … will my CPU run slow if it is running out of power …
12:18am:
Or will it be slow if it is running on battery … to save power
12:19am:
Hain … what a joke … laptop can’t be so smart … it was just a coincidence … I plugged in the power and it became faster …
12:19am:
There are no coincidences in this business … unplug the power … run the test …
12:22am:
No sign of ending it really is slow
12:25am:
Back to 6mins for the test
12:25am:
… can’t be … really i mean … can the laptop be so smart … what was that thing that showed clock speed … cpu-z … google: cpu-z … download … run … wow! It is true … clock speed has been reduced to 598MHz instead of 1.6GHz

12:25am:
OK … now connect the power and see … there goes my theory … still 598MHz

12:25am:
Hmmm … maybe it realized though it is powered, I am not running any CPU intensive task …. could it really really that smart … nyaaah …
12:26am:
Start the test with power still connected … run cpu-z … whoa! 1.6GHz …

More googling reveals, this is Intel SpeedStepTM technology at work. It can be enabled/disabled from BIOS. A quick intro at Bay Wolf. Implementation details at Intel.

Now I have to locate some java API to detect if the CPU is running at a lower clock speed so I can warn the users to power up!

Update June 05, 2008: I was wrong in suspecting my dying battery. Replacing it with a brand new one didn’t help.

Long long ago I was bugged by the fact that the screen would go blank when I was reading some content heavy websites. I opened up the power management dialog, noticed that the default power scheme used to switch off the monitor too soon when running on battery. So I decided to change the power scheme to Presentation. There is NO indication that this setting does anything other than affect: Monitor, Hard Disc and System Standby.

However, following Alexander’s suggestion when I changed the power scheme from “Presentation” to “Home/Office desktop”. I notice that the clock speed behaves the same when on battery or power: When there is no CPU intensive task, it runs on low clock speed and when there is a CPU intensive task it runs at the rated clock speed.

I wish XP warned me or atleast hinted in some fashion that the power scheme would affect the clock speed. *sigh*


Jun 17 2004

Of Thread dumps and stack traces …

Tags: , , , Rajiv @ 10:45 am UTC

Thread dumps and stack traces are probably some of the least understood features of java. Why else would I come across developers who have no clue what do do after looking at an Exception stack trace? 

Street Side Programmer?!

An ex-colleague of mine, Manoj “The Anger” Acharya, had coined the phrase Street Side Programmer [a la Server Side Programmer] and he would dole out this title to all those who would come to him with annoying questions. Nothing annoyed him more than having some one come and ask him I am getting some exception when I do *blah* *blah*. His typical answer *bleep*’ing Street Side Programmers … what is some exception supposed to mean?! Doesn’t it have a name? Doesn’t it have a stack trace??

I was reminded of him the other day, when a trainee learning java came to me saying My program is not running … there seems to be some problem … can you come and take a look?. The kid is quite sweet, so instead of telling him about Anger, I just went to his seat. The command prompt had something like this:

C:\learn\classes>java Test
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
        at Test.run(Test.java:11)
        at Test.<init>(Test.java:4)
        at Test.main(Test.java:19)

I wonder if the book he was reading had any section on reading stack traces. [Monsieur Bruce Eckel ... are you listening?!] I really think any introduction to java book should have this as one of the earliest chapters … right after defining a class and method! Some one makes an error while trying out samples, or is tinkering around with the code, which typically results in an exception … what is one supposed to do next?!

Anatomy of a Stack Trace

Well I explained that an exception stack trace is java’s way of telling you exactly what went wrong and where it went wrong. The first line of the stack trace gives you the exception name and the exception message and what follows is the “stack trace”. The stack trace is to be read from top to bottom, line by line. Each line has the name of the class and the name of the method being executed followed by the file name and line number in parentheses. 

In this case a java.lang.ArrayIndexOutOfBoundsException with the message “5” was raised. To know where it was raised, we look at the next line. It tells us that the exception was raised while executing the run method of the Test class at line number 11 in Test.java file. The next line tells us that the run method was called by the constructor [the stack trace shows Constructors as <init> and static blocks in a class as <clinit>] of the Test class at line number 4 in Test.java file. The next line tells us that the constructor was called by the main method of Test class at line number 19 of Test.java file.

So the java stack trace would read in English would be like:

You accessed an array with an index of 5, however the array does not have 6 elements [thanks to zero based index]. This happened when I was executing the run method of Test class which happens to be in line number 11 of Test.java file. The run method was called by the constructor of Test class at line number 4 of Test.java file. The constructor was called by the main method of the Test class at line number 19 of Test.java file. 

Well… there is a wealth of information here. It tells you exactly what the VM was doing when the exception was raised. Let us see how to debug the issue given all this information. The Test.java file looks like this: 

1    public class Test
2    {
3        public Test(int[] nums){
4            run(nums);
5        }
6
7        private void run(int[] nums)
8        {
9            int n = nums.length;
10           for (int i = 0; i < nums.length; i++) {
11               int num = nums[n];
12               System.out.println(num);
13           }
14       }
15
16       public static void main(String argv[])
17               throws Exception
18       {
19           new Test(new int[]{1,3,5,7,9});
20       }
21   } 

Stepping through the code [as per the stack trace], we called the main method, which invoked the constructor at line number 19, which in turn called the run method at line number 4. Hey the stack trace was correct after all! Now we look at line number 11 where the exception was raised. The exception says that we accessed an array with incorrect index. The only array we are accessing at line number 11 is the num array. The index being used to access the array was n. So what the VM is trying to tell you is that the n is larger that the size of the array nums. Which is in fact true. n happens to be the length of the array. So it IS greater than the last index of the array. What the user really wanted to do was use i as the loop index and not n.

Another common exception raised is the java.lang.NullPointerException. The NPE!  A NullPointerException is Java’s way of telling a user that a null object reference was being used. Take a look at the following lines from a stack trace [snipped for brevity]:

java.lang.NullPointerException:
        at foo.bar.MyServlet.doGet(MyServlet.java:36)

So now we know that a null object was being referened at line number 36 of MyServlet.java. The code for the servlet looks something like:

35    String userNameParam = request.getParameter("username");
36    if(userNameParam.equals("root"))
37    {

The only object reference being used in line number 36 happens to be userNameParam. So it was null when the VM was executing that line. Now we track down what values were assigned to the userNameParam. Line number 35 happens to be the only assignment in this case. It assigns the value of userNameParam to request.getParameter("username"). Since the VM told us that the userNameParam was null, it means that the method request.getParameter("username") returned a null value. Looking at the documentation of the method we know that the method may return null. So the users of the method need to code taking that into consideration. In this case we would change the condition like so:  

35    String userNameParam = request.getParameter("username");
36    if(userNameParam!=null && userNameParam.equals("root"))
37    {

Thanks to stack traces some one who is not even aware of the code can pin point the exact location of the error. In most of the cases a stack trace is definitely starting points for debugging erroneous behavior. Who wants messy
core dumps anyways when you have readable stack traces?!

Innovative uses of stack traces

Once you know what a stack trace provides, there are a lot of innovative ways to use it. Basically answer questions like how did I get here or to record the location of an event.

Recently a customer noticed that the VM was performing Full GC’s very frequently. This would happen even when the application is completely idle. Looking at java -verbose:gc -XX:+PrintGCTimeStamps ... , we realized that the Full GC would occur every one minute … on the dot. We then tried adding the -XX:+DisableExplicitGC option and voila no more full GCs! So looks like some one was doing a System.gc somewhere at every one minute.

So how do we find out who is calling it?! You would extract the System.java file from <jdk-home>/src.zip!/java/lang/System.java and edit it like so:

736    public static void gc() {
737	       new Exception("Some one triggered Full GC from here").printStackTrace();
738            Runtime.getRuntime().gc();
739       }
740

Compile the modified file and prepend it to your bootclasspath using the option -Xbootclasspath/p:outputDir. Next time we ran the application, we got the stack trace:

java.lang.Exception: Some one triggered Full GC from here
        at java.lang.System.gc(System.java:737)
	at sun.misc.GC$Daemon.run(GC.java:92)

Adding one more stack trace to GC.java [You will not find sources for the com.sun.* and sun.* packages in the src.zip that comes with your jdk. You will have to download it from Sun's Community Source site.] we get to know that sun.rmi.transport.ObjectTable is triggering the full GC based on an interval specified by the system property sun.rmi.dgc.server.gcInterval. The default value for the property happens to be one minute.

So using the printStackTrace method we could debug where Full GC was being triggered explicitly. You could
ofcourse do the same by setting a method break point for the System.gc method. Or you could be
a smart google’er and stumble upon the “Other considerations” section of the

GC options page!

Instead of doing a new Exception(…).printStackTrace(), you could alternatively do a Thread.dumpStack() which internally does the same. The only disadvantage is that Thread,dumpStack() does take a message as its
parameter.

Some times it makes sense to create an exception object and hold a reference to it until a later point in time. Suppose you have a class which looks like:

1    import java.io.IOException;
2
3    /** 
4     * A class that represents a heavy weight resource. 

5     */
6    public class Resource
7    {
8        private boolean closed;
9
10       public void close() throws IOException{
11           if(closed)
12               throw new IOException("Resource already closed.");
13           //resource cleanup 

14           closed=true;
15       }
16       //code snipped for brevity ...

The class throws an exception when a user invokes close on an already closed resource. The stack trace of the IOException is going to tell you where in the code you tried to close the already closed connection. For example the following output tells you that when you called close on the Resource at line 41 of ResourceTest.java it was already closed.

C:\learn\classes>java ResourceTest
java.io.IOException: Resource already closed.
        at Resource.close(Resource.java:12)
        at ResourceTest.closeResource(ResourceTest.java:37)
        at ResourceTest.run(ResourceTest.java:26)
        at ResourceTest.main(ResourceTest.java:50)

But now what if you want to know where did you close it the first time?! You would change the code like so:

1    import java.io.IOException;
2
3    /** 
4     * A class that represents a heavy weight resource. 
5     */ 

6    public class Resource
7    {
8        private boolean closed;
9
10       private Exception closedAt;
11
12       public void close() throws IOException{
13           if(closed) {
14               closedAt.printStackTrace();
15               throw new IOException("Resource already closed.");
16           }
17           //resource cleanup 

18           closed=true;
19           closedAt=new Exception("Resource closed here the first time.");
20       }
21       //code snipped for brevity ...

The output would after making the changes would look like …

C:\learn\classes>java ResourceTest
java.lang.Exception: Resource closed here the first time.
        at Resource.close(Resource.java:19)
        at ResourceTest.useResource(ResourceTest.java:32)
        at ResourceTest.run(ResourceTest.java:25)
        at ResourceTest.main(ResourceTest.java:50)
java.io.IOException: Resource already closed.
        at Resource.close(Resource.java:15)
        at ResourceTest.closeResource(ResourceTest.java:41)
        at ResourceTest.run(ResourceTest.java:26)
        at ResourceTest.main(ResourceTest.java:50)

So now from the stack traces we know that a close was called first at line 32 of ResourceTest.java and later at line 41 we called a close on the same resource for the second time.

There are a lot of multi threaded problems [NullPointers] which we were not able to debug with a debugger because the whole application would become too slow to simulate the problem scenario. However, by using Exception objects to track threads which were setting the fields to null, we were able to resolve the issues. A word of caution though … creating exception objects is resource intensive. Creating too many exception objects takes lot of CPU. And if you are holding references to all the objects it requires memory too! 

Thread dump 101

If the stack trace which gives the information on what a thread was doing at that moment can help us in so many ways, just imagine the possibilites if you could find out what every single thread in the Java VM is doing at any given moment! A Full Thread Dump or a thread dump for short gives us exactly that information. Consider the following source

1    public class Test
2    {
3        public Test(char[] chars){
4            System.out.println("New line at "+findNewLine(chars));
5        }
6
7        private int findNewLine(char[] chars)
8        {
9            int i = 0;
10           char aChar;
11           do{
12               aChar = chars[i];
13           }while(aChar!='\n');
14           return i;
15       }
16
17       public static void main(String argv[])
18               throws Exception
19       {
20           new Test("Hello World!\nHowz goin?!">.toCharArray());
21       }
22   }

The method findNewLine is supposed to return the first index of a new line character in a given char array. [Purists please don't mail me with the list of reasons why this approach is not right ... the idea here is not really to write the best way to find a new line character!] Now when you run the program it just won’t print the result. One look at top in unix or the task manager in windows we get to know that VM has taken the CPU for a spin…. 100% CPU consumption for ever! Now wouldn’t you want to know what the VM is doing. Why is it taking all this CPU and not printing the output it is supposed. 

One way to do this would be rerun the program in debug mode. Use the debugger and debug the application. However, many a times you come across such the situation on a live system after running the app for a long duration. Since it is a live system and we hit the issue only after running the application for a long duration we can not leave it in debug mode for ever. The first line of defense under such circumstances is the thread dump.

Run the program from the command prompt and when the CPU peaks take a thread dump. You can get a thread dump by pressing the following at the command prompt: Ctrl+\ for unices or Ctrl+Break for windows machines. If you are running your application as a back ground process in unix, you could execute kill -SIGQUIT <pid> from another command prompt. The above signals the VM to generate a full thread dump. Sun’s VM prints the dump on the error stream while IBM’s JDK generates a new file with the thread dump every time you send the signal. In our case the thread dump would look something like this:

C:\learn\classes>java Test
Full thread dump Java HotSpot(TM) Client VM (1.4.2_04-b05 mixed mode):

"Signal Dispatcher" daemon prio=10 tid=0x0091db28 nid=0x744 waiting on condition [0..0]

"Finalizer" daemon prio=9 tid=0x0091ab78 nid=0x73c in Object.wait() [1816f000..1816fd88]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x10010498> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(Unknown Source)
        - locked <0x10010498> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(Unknown Source)
        at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)

"Reference Handler" daemon prio=10 tid=0x009196f0 nid=0x738 in Object.wait() [1812f000..1812fd88]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x10010388> (a java.lang.ref.Reference$Lock)
        at java.lang.Object.wait(Unknown Source)
        at java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)
        - locked <0x10010388> (a java.lang.ref.Reference$Lock)

"main" prio=5 tid=0x00234998 nid=0x4c8 runnable [6f000..6fc3c]
        at Test.findNewLine(Test.java:13)
        at Test.<init>(Test.java:4)
        at Test.main(Test.java:20)

"VM Thread" prio=5 tid=0x00959370 nid=0x6e8 runnable

"VM Periodic Task Thread" prio=10 tid=0x0023e718 nid=0x74c waiting on condition
"Suspend Checker Thread" prio=10 tid=0x0091cd58 nid=0x740 runnable

The thread dump generated here is on Sun’s JDK 1.4.2. Though the output differs from version to version and from vendor to vendor, the basic structure is the same. The output is somewhat like going over all the threads and doing a Thread.dumpStack in each of them. In this case we can see that, at the time we took the thread dump, there were seven threads:

  1. Signal Dispatcher
  2. Finalizer
  3. Reference Handler
  4. main
  5. VM Thread
  6. VM Periodic Task Thread
  7. Suspend Checker Thread 

Each thread name is followed by whether the thread is a daemon thread or not. Then comes prio the priority of the thread [ex: prio=5]. I am not sure what the tid and nid are. My best guess is that they are the Java thread id and the native thread id. Would love if someone could comment on that. Then what follows the state of the thread. It is either:

  • Runnable [marked as R in some VMs]: This state indicates that the thread
    is either running currently or is ready to run the next time the OS thread
    scheduler schedules it. 
  • Suspended [marked as S in some VMs]: I presume this indicates that the
    thread is not in a runnable state. Can some one please confirm?!
  • Object.wait() [marked as CW in some VMs]: indicates that the thread is
    waiting on an object using Object.wait()
  • waiting for monitor entry [marked as MW in some VMs]: indicates that the
    thread is waiting to enter a synchronized block

What follows the thread description line is a regular stack trace. 

Debugging run away CPU

When we are trying to debug a run away CPU, as in this case, what we need to look at is the set of Runnable threads  in the thread dump. The question to ask is: What was the thread which was consuming CPU doing? At the instant we took the above thread dump, the thread was at line 13 of Test.java. Well … looks like it was checking the condition for the while loop. But eventually it should have returned right?! So we take a few more thread dumps. Each time it shows us the thread is within the while loop. This definitely indicates from the first time you took a dump to the last time you took a dump, the thread never got out of the loop. The problem is narrowed down that loop. Putting the loop under the magnifying glass, we realize that the counter i was never being incremented. 

Well … if you have a single class in your application it is no big deal! But when you have gazillions of classes, narrowing down the problem to a single loop within single class is a big saver! I have found this a useful tool even when I am using a debugger. It helps me choose a good location to set my first break point! 

Debugging performance issues

Its the night before the release and your application is not performing good enough. You really don’t have enough time to run the app through a profiler. Take heart! Like Ramesh says … there are always some low hanging fruits! The way a java profiler works is, it takes snapshots of what the CPU was doing at frequent intervals and generates a statistical report on where most of the CPU time was being spent during the run. If your application is performing so poorly that you could take say 10-12 thread dumps before an operation completes, you would get a rough idea of distribution of CPU time. Some of the easy kills I can think of:

  • Symptom: High CPU consumption and poor response time

    Thread dump profile: Most of the dumps show the same thread in the same method or same class

    Solution: The method/class is the one which is definitely taking a lot of CPU. See if you can optimize these calls. Some of the REALLY easy kills we have had in this category is using a Collection.remove(Object) where the backend collection is a List. Change the backed collection to be a HashSet. A word of caution though: There have been times when the runnable threads are innocent and the GC is the one consuming the CPU.
  • Symptom: Low CPU consumption most of which is kernel time and poor response time

    Thread dump profile: Most thread dumps have the runnable threads performing some IO operations

    Solution: Most likely your application is IO bound. If you are reading a lot of files from the disc, see if you can implement Producer-Consumer pattern. The Producer can perform the IO operations and Consumers do the processing on the data which has been read by the producer. If you notice that most IO operations are from the data base driver, see if you can reduce the number of queries to the database or see if you can cache the results of the query locally.
  • Symptom: Medium/Low CPU consumption in a highly multithreaded application

    Thread dump profile: Most threads in most thread dumps are waiting for a monitor on same object

    Solution: The thread dump profile says it all. See if you can: eliminate the need for synchronization [using ThreadLocal/Session-scopeobjects] or reduce the amount of code being executed within the synchronized block.
  • Symptom: Medium/Low CPU consumption in a highly multithreaded application

    Thread dump profile: Most threads in most thread dumps are waiting for a resource

    Solution: If all the threads are choked for resources, say waiting on the pool to create EJB-bean objects/DB Connection objects, see if you can increase the pool size.

Debugging “hang” problems

A textbook case of deadlock is the easiest to debug with the newer JDKs. At the end of the thread dump you will find something like this:

Found one Java-level deadlock:
=============================
"Thread-1":
  waiting to lock monitor 0x0091a27c (object 0x140fa790, a java.lang.Class),
  which is held by "Thread-0"

"Thread-0":
  waiting to lock monitor 0x0091a25c (object 0x14026800, a java.lang.Class),
  which is held by "Thread-1"

Java stack information for the threads listed above:
===================================================
"Thread-1":
        at Deadlock$2.run(Deadlock.java:48)
        - waiting to lock <0x140fa790> (a java.lang.Class)
        - locked <0x14026800> (a java.lang.Class)
"Thread-0":
        at Deadlock$1.run(Deadlock.java:33)
        - waiting to lock <0x14026800> (a java.lang.Class)
        - locked <0x140fa790> (a java.lang.Class)

Found 1 deadlock.

But many a times we come across hang’s which are not deadlocks. One thing that easily comes to my mind is a resource limit. For example in an EJB container you have set the maximum bean pool size to 1000. Now say two threads have started executing a finder each returning a collection of 1000 odd beans. Assuming a decent CPU time slice distribution it could happen that the first thread iterates over 500 beans and the next thread iterates over the 500 beans. At this moment both the threads need more beans to proceed further. However the container will not create new beans as the bean pool limit has been reached. So both the threads wait for some beans to be release to the pool … which is not going to happen. We have a hung app here…. however it is not a java-level deadlock. It is an artificial deadlock introduced due to resource limitation.

When your app is not responding and your CPU consumption is 0%, take a thread dump. If it does not have a java level dead lock, then take multiple thread dumps. If all of them show that the threads are waiting for resources [EJBs or DBConnections] see if you can increase the pool limit or decrease the number of resources required within a transaction. 

Finally

Thread Dumps and stackTraces are really good tools … they may not replace a debugging/profiling tools but are definitely good starting points and huge time savers. Unfortunately, I think they are undersold. Classes don’t teach you about them, Books don’t talk about them and tools don’t support them. I mean I can run any class from my IDE. I has buttons to Start/Pause and Stop the app from within the IDE. But why can’t I have a button for “Generate full Thread dump”. Every time I need to generate a thread dump, I have to rerun the application from
command line.

Well … maybe things are not so bad after all. What if the IDEs don’t support generation of a thread dump?! Most of them now open up the file and line number if you double click on a line in the exception stack trace obtained on runninga program! And what if the books don’t talk about it? People like Ashman make sure anyone joining the support team gets their dope on thread dump from me! ;)