Requests take too much time in Tomcat 8 on peak time

Javanshir :

I have configured tomcat with the following configurations:

<Connector port="8080" protocol="HTTP/1.1"
           connectionTimeout="20000"
           maxThreads="500"
           maxConnections="20000"
           acceptCount="150"
           etc... />

same numbers for AJP connector, maxThreads=500 and acceptCount="150".

It works fine most of the time, but on peak times, when I have much more requests than usual, it takes too long to respond. Sometimes above 15 seconds and in rare cases timeOut. It may look okay, as maxThreads=500 and I have several thousand requests, however, on Server Status I see:

Max threads: 500 Current thread count: 17 Current thread busy: 1 Keep alive sockets count: 1

The max number of currentThreadCount I have seen so far was 27. If there are so many connections, shouldn't tomcat create more threads (up to 500) to respond faster?

So, what am I doing wrong? What am I missing? I have 2 core CPU (max usage during peak hours ~10%) and 2GB of RAM (max usage 60%).

Short info about web app: normally, each user makes at least 2 requests per session: static JSON response and 1 database query. In peak time I have 15-20k active users, but I don't know how many requests per second do I get. However, slow responses start from 5k active users.

I also increased max-active connections on app properties, with no change on performance, my current application.properties:

spring.jpa.hibernate.ddl-auto=update
spring.datasource.driverClassName=com.mysql.jdbc.Driver
spring.datasource.url=jdbc:mysql://localhost:3306/database_name
spring.datasource.username=$username$
spring.datasource.password=$password$
spring.datasource.tomcat.max-active=200
spring.datasource.tomcat.max-wait=10000
spring.datasource.tomcat.max-idle=50
spring.datasource.tomcat.min-idle=10
spring.datasource.tomcat.initial-size=10

UPDATE I changed default JDBC connection pool to Hikari with the following configurations and enabled jta, however, didn't feel any difference on peak times:

spring.jta.enabled=true
spring.datasource.hikari.maximum-pool-size=125
spring.datasource.hikari.minimum-idle=5

I am adding database query below. Results of the query later added into another object and returned as ResponseBody.

@Query("select new ObjectClass(s.id, s.a, s.b, s.c") from TableName s " +
        "where s.x > :param order by id desc")
List<ObjectClass> getObjects(@Param("param") long param);

CPU usage doesn't grow, RAM is almost half-free, if I am having too many requests, shouldn't I have overloaded on the server? Instead, I just get slow response time. Therefore, I think I have a configuration problem which I want to resolve.

-Xms512M -Xmx1024M

The app that hangs on peak time:

Active sessions: 3243 Session count: 475330 Max active sessions: 4685 Rejected session creations: 0 Expired sessions: 472105 Longest session alive time: 7457 s Average session alive time: 9 s Processing time: 3177 ms JSPs loaded: 0 JSPs reloaded: 0

Stack trace:

"Attach Listener" #502 daemon prio=9 os_prio=0 tid=0x00007fde58007800 nid=0x3ff waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Abandoned connection cleanup thread" #69 daemon prio=5 os_prio=0 tid=0x00007fde6c03e800 nid=0xa44 in Object.wait() [0x00007fde471ba000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    - locked <0x00000000c259e618> (a java.lang.ref.ReferenceQueue$Lock)
    at com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:64)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-exec-25" #68 daemon prio=5 os_prio=0 tid=0x00007fde40016000 nid=0x741 waiting on condition [0x00007fde35fe0000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1cc6758> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:85)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-exec-11" #54 daemon prio=5 os_prio=0 tid=0x00007fde38041800 nid=0x733 waiting on condition [0x00007fde36fee000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1cc6758> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:85)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-AsyncTimeout" #52 daemon prio=5 os_prio=0 tid=0x00007fde884e8800 nid=0x732 waiting on condition [0x00007fde370ef000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at org.apache.coyote.AbstractProtocol$AsyncTimeout.run(AbstractProtocol.java:1211)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-Acceptor-0" #51 daemon prio=5 os_prio=0 tid=0x00007fde884e6800 nid=0x731 runnable [0x00007fde371f0000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.ServerSocketChannelImpl.accept0(Native Method)
    at sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:422)
    at sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:250)
    - locked <0x00000000c019d7e8> (a java.lang.Object)
    at org.apache.tomcat.util.net.NioEndpoint$Acceptor.run(NioEndpoint.java:455)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-ClientPoller-1" #50 daemon prio=5 os_prio=0 tid=0x00007fde884e4800 nid=0x730 runnable [0x00007fde372f1000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
    at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
    at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
    at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
    - locked <0x00000000c1da2fa0> (a sun.nio.ch.Util$3)
    - locked <0x00000000c1da2f90> (a java.util.Collections$UnmodifiableSet)
    - locked <0x00000000c1d5b1e0> (a sun.nio.ch.EPollSelectorImpl)
    at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
    at org.apache.tomcat.util.net.NioEndpoint$Poller.run(NioEndpoint.java:787)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-ClientPoller-0" #49 daemon prio=5 os_prio=0 tid=0x00007fde884d6000 nid=0x72f runnable [0x00007fde373f2000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
    at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
    at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
    at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
    - locked <0x00000000c1d510d8> (a sun.nio.ch.Util$3)
    - locked <0x00000000c1d510c8> (a java.util.Collections$UnmodifiableSet)
    - locked <0x00000000c1ce78c0> (a sun.nio.ch.EPollSelectorImpl)
    at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
    at org.apache.tomcat.util.net.NioEndpoint$Poller.run(NioEndpoint.java:787)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-exec-10" #48 daemon prio=5 os_prio=0 tid=0x00007fde884c7000 nid=0x72e waiting on condition [0x00007fde374f3000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1cc6758> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:85)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-exec-2" #40 daemon prio=5 os_prio=0 tid=0x00007fde884b7000 nid=0x726 waiting on condition [0x00007fde37cfb000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1cc6758> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:85)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"ajp-nio-8009-exec-1" #39 daemon prio=5 os_prio=0 tid=0x00007fde884b5000 nid=0x725 waiting on condition [0x00007fde37dfc000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1cc6758> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:85)
    at org.apache.tomcat.util.threads.TaskQueue.poll(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"http-nio-127.0.0.1-8080-AsyncTimeout" #38 daemon prio=5 os_prio=0 tid=0x00007fde884b3000 nid=0x724 waiting on condition [0x00007fde37efd000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at org.apache.coyote.AbstractProtocol$AsyncTimeout.run(AbstractProtocol.java:1211)
    at java.lang.Thread.run(Thread.java:748)

"http-nio-127.0.0.1-8080-Acceptor-0" #37 daemon prio=5 os_prio=0 tid=0x00007fde884b1800 nid=0x723 runnable [0x00007fde37ffe000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.ServerSocketChannelImpl.accept0(Native Method)
    at sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:422)
    at sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:250)
    - locked <0x00000000c01a03b8> (a java.lang.Object)
    at org.apache.tomcat.util.net.NioEndpoint$Acceptor.run(NioEndpoint.java:455)
    at java.lang.Thread.run(Thread.java:748)

"http-nio-127.0.0.1-8080-exec-1" #25 daemon prio=5 os_prio=0 tid=0x00007fde88324000 nid=0x717 waiting on condition [0x00007fde46db8000]
   java.lang.Thread.State: WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c1d9c4e0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
    at org.apache.tomcat.util.threads.TaskQueue.take(TaskQueue.java:103)
    at org.apache.tomcat.util.threads.TaskQueue.take(TaskQueue.java:31)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)

"ContainerBackgroundProcessor[StandardEngine[Catalina]]" #24 daemon prio=5 os_prio=0 tid=0x00007fde88323000 nid=0x716 waiting on condition [0x00007fde476bb000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1355)
    at java.lang.Thread.run(Thread.java:748)

"Abandoned connection cleanup thread" #22 daemon prio=5 os_prio=0 tid=0x00007fde4ca72800 nid=0x6f5 in Object.wait() [0x00007fde45c22000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    - locked <0x00000000c102c4b0> (a java.lang.ref.ReferenceQueue$Lock)
    at com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:64)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

"Tomcat JDBC Pool Cleaner[1595428806:1507838479700]" #21 daemon prio=5 os_prio=0 tid=0x00007fde4ca5b800 nid=0x6f4 in Object.wait() [0x00007fde470b9000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at java.util.TimerThread.mainLoop(Timer.java:552)
    - locked <0x00000000c0f6fe80> (a java.util.TaskQueue)
    at java.util.TimerThread.run(Timer.java:505)

"NioBlockingSelector.BlockPoller-2" #13 daemon prio=5 os_prio=0 tid=0x00007fde8847e000 nid=0x66f runnable [0x00007fde478bd000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
    at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
    at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
    at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
    - locked <0x00000000c019bd40> (a sun.nio.ch.Util$3)
    - locked <0x00000000c019bd30> (a java.util.Collections$UnmodifiableSet)
    - locked <0x00000000c019bbf8> (a sun.nio.ch.EPollSelectorImpl)
    at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
    at org.apache.tomcat.util.net.NioBlockingSelector$BlockPoller.run(NioBlockingSelector.java:339)

"NioBlockingSelector.BlockPoller-1" #12 daemon prio=5 os_prio=0 tid=0x00007fde8846f800 nid=0x66e runnable [0x00007fde479be000]
   java.lang.Thread.State: RUNNABLE
    at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
    at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
    at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
    at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
    - locked <0x00000000c019ec10> (a sun.nio.ch.Util$3)
    - locked <0x00000000c019ec00> (a java.util.Collections$UnmodifiableSet)
    - locked <0x00000000c019ead8> (a sun.nio.ch.EPollSelectorImpl)
    at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
    at org.apache.tomcat.util.net.NioBlockingSelector$BlockPoller.run(NioBlockingSelector.java:339)

"GC Daemon" #11 daemon prio=2 os_prio=0 tid=0x00007fde883f9000 nid=0x66b in Object.wait() [0x00007fde741c6000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <0x00000000c02f16d8> (a sun.misc.GC$LatencyLock)
    at sun.misc.GC$Daemon.run(GC.java:117)
    - locked <0x00000000c02f16d8> (a sun.misc.GC$LatencyLock)

"AsyncFileHandlerWriter-1510467688" #10 daemon prio=5 os_prio=0 tid=0x00007fde88168800 nid=0x63e waiting on condition [0x00007fde7475c000]
   java.lang.Thread.State: TIMED_WAITING (parking)
    at sun.misc.Unsafe.park(Native Method)
    - parking to wait for  <0x00000000c02f16e8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:522)
    at java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:684)
    at org.apache.juli.AsyncFileHandler$LoggerThread.run(AsyncFileHandler.java:160)

"Service Thread" #7 daemon prio=9 os_prio=0 tid=0x00007fde880af000 nid=0x62e runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C1 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007fde880ac000 nid=0x62d waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007fde880a9000 nid=0x62c waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007fde880a7000 nid=0x62b runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007fde88080000 nid=0x625 in Object.wait() [0x00007fde74f33000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    - locked <0x00000000c02f7408> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007fde8807b800 nid=0x622 in Object.wait() [0x00007fde75034000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:502)
    at java.lang.ref.Reference.tryHandlePending(Reference.java:191)
    - locked <0x00000000c02f7490> (a java.lang.ref.Reference$Lock)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153)

"main" #1 prio=5 os_prio=0 tid=0x00007fde8800a800 nid=0x589 runnable [0x00007fde8f6af000]
   java.lang.Thread.State: RUNNABLE
    at java.net.PlainSocketImpl.socketAccept(Native Method)
    at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
    at java.net.ServerSocket.implAccept(ServerSocket.java:545)
    at java.net.ServerSocket.accept(ServerSocket.java:513)
    at org.apache.catalina.core.StandardServer.await(StandardServer.java:466)
    at org.apache.catalina.startup.Catalina.await(Catalina.java:744)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)

"VM Thread" os_prio=0 tid=0x00007fde88073800 nid=0x5fd runnable 

"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007fde8801f800 nid=0x597 runnable 

"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007fde88021000 nid=0x598 runnable 

"VM Periodic Task Thread" os_prio=0 tid=0x00007fde880bd800 nid=0x62f waiting on condition 

JNI global references: 317

Update: While I haven't resolved my problem, @Per Huss's answer pushed me towards the right direction on analysing each thread separately and find the problem. I have to award my bounty now, therefore, I will award it to him. However, I thank everyone who commented here, as all comments helped me to learn something new.

Update 2: It looks like the problem is within apache. On peak times even static pages have slow response time, even the ones from other apps. Including tomcat manager. So, I changed prefork to mpm_worker and currently testing different configurations. I will update this thread with the results, soon.

Javanshir :

I finally solved my problem. In fact, it was apache that didn't allow enough connections. First of all, I changed prefork to mpm worker. Later, I increased the number of MaxRequestWorkers.

<IfModule mpm_worker_module>
    StartServers             2
    MinSpareThreads          50
    MaxSpareThreads          125
    ThreadLimit              64
    ThreadsPerChild          25
    ServerLimit              5000
    MaxRequestWorkers        5000
    MaxConnectionsPerChild   4500

Earlier, I was getting slow response time already with 3000 active users. With the new configuration even 17000 active users didn't increase response time and it was working like in normal times. As expected, CPU usage and RAM increased on peak time and then went back to normal.

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