jvm stuck in SafepointSynchronize::begin()

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yang liu

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Sep 27, 2017, 2:51:43 AM9/27/17
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One of tomcat program hung and failed to response http request. After inspect the output of "jstack -F" and "pstack", I found the jvm stuck in SafepointSynchronize::begin() method. Why could this happen?

More details following.
1. top -H -p output, thread 25184 cpu 100%
  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
25184 root      20   0 14.8g 5.0g  62m R 100.3 32.8  17:50.67 java           <--------------
25170 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:00.01 java
25172 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:01.09 java
25173 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.61 java
25174 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.61 java
25175 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.59 java
25176 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.66 java
25177 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.62 java
25178 root      20   0 14.8g 5.0g  62m S  0.0 32.8   0:02.63 java

2. pstack output, thread 25184 cpu 100%
Thread 797 (Thread 0x7fe47d506700 (LWP 25184)):
#0  0x00007fe4af098d2b in SafepointSynchronize::begin() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so <--------------
#1  0x00007fe4af191fef in VMThread::loop() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#2  0x00007fe4af192470 in VMThread::run() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#3  0x00007fe4af00b988 in java_start(Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#4  0x00000037b52079d1 in start_thread () from /lib64/libpthread.so.0
#5  0x00000037b4ae88fd in clone () from /lib64/libc.so.6

3. jstack -F result
......
Thread 26488: (state = NEW)
Thread 2 (Thread 0x7fe359282700 (LWP 26488)):
#0  0x00000037b4af805e in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x00000037b4a7cc82 in _L_lock_3495 () from /lib64/libc.so.6
#2  0x00000037b4a77903 in arena_get2 () from /lib64/libc.so.6
#3  0x00000037b4a7a794 in malloc () from /lib64/libc.so.6
#4  0x00000037b4611190 in tls_get_addr_tail () from /lib64/ld-linux-x86-64.so.2
#5  0x00000037b4611660 in __tls_get_addr () from /lib64/ld-linux-x86-64.so.2
#6  0x00007fe4adabd762 in Profiler::Handle(int, siginfo*, void*) () from /usr/local/lightweight-java-profiler-master/build-64/liblagent.so
.......
Thread 26362: (state = IN_VM)
Thread 63 (Thread 0x7fe366e5d700 (LWP 26362)):
#0  0x00000037b520b5bc in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
#1  0x00007fe4af005243 in os::PlatformEvent::park() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#2  0x00007fe4aefcc328 in Monitor::ILock(Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#3  0x00007fe4aefcc55f in Monitor::lock_without_safepoint_check() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#4  0x00007fe4af098127 in SafepointSynchronize::block(JavaThread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#5  0x00007fe4aedead0b in JavaCallWrapper::JavaCallWrapper(methodHandle, Handle, JavaValue*, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#6  0x00007fe4aedeb94a in JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#7  0x00007fe4aedea5c8 in JavaCalls::call(JavaValue*, methodHandle, JavaCallArguments*, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#8  0x00007fe4aedea897 in JavaCalls::call_virtual(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#9  0x00007fe4aedea966 in JavaCalls::call_virtual(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Handle, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#10 0x00007fe4af10e249 in SystemDictionary::load_instance_class(Symbol*, Handle, Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so

jstackF.txt
pstack.txt

Alex Bagehot

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Sep 27, 2017, 3:44:32 AM9/27/17
to mechanica...@googlegroups.com
Nitsan reported and fixed a 1/10 occurrence hang here: https://github.com/jvm-profiling-tools/honest-profiler/issues/75
Assuming You're using the lightweight java profiler which doesn't have that fix.
It is allocating memory in a signal handler see #3 and #9 below.

1 Point in time snapshot of thread state doesn't help much understand cpu usage - you need to take several of them or preferably get some perf output (which gives you a large number of unbiased cpu samples to work with).

However, the high/100% cpu of 1 thread associated with the hang happens because the thread initiating the safepoint (here LWP 25184) will spinpause/yield until all the threads have come to safepoint (which can't happen because of the profiler bug) or a safepoint timeout occurs.

thanks,
Alex

pstack.txt :

Thread 2 (Thread 0x7fe359282700 (LWP 26488)):
#0  0x00000037b4af805e in __lll_lock_wait_private () from /lib64/libc.so.6
#1  0x00000037b4a7cc82 in _L_lock_3495 () from /lib64/libc.so.6
#2  0x00000037b4a77903 in arena_get2 () from /lib64/libc.so.6
#3  0x00000037b4a7a794 in malloc () from /lib64/libc.so.6
#4  0x00000037b4611190 in tls_get_addr_tail () from /lib64/ld-linux-x86-64.so.2
#5  0x00000037b4611660 in __tls_get_addr () from /lib64/ld-linux-x86-64.so.2
#6  0x00007fe4adabd762 in Profiler::Handle(int, siginfo*, void*) () from /usr/local/lightweight-java-profiler-master/build-64/liblagent.so
#7  <signal handler called>
#8  0x00000037b4a77916 in arena_get2 () from /lib64/libc.so.6
#9  0x00000037b4a7a794 in malloc () from /lib64/libc.so.6
#10 0x00000037b5208b3f in pthread_getattr_np () from /lib64/libpthread.so.0
#11 0x00007fe4af00f724 in current_stack_region(unsigned char**, unsigned long*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#12 0x00007fe4af00f815 in os::current_stack_base() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#13 0x00007fe4af13e614 in Thread::record_stack_base_and_size() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#14 0x00007fe4af144dd4 in JavaThread::run() () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#15 0x00007fe4af00b988 in java_start(Thread*) () from /usr/java/jdk1.7.0_65/jre/lib/amd64/server/libjvm.so
#16 0x00000037b52079d1 in start_thread () from /lib64/libpthread.so.0
#17 0x00000037b4ae88fd in clone () from /lib64/libc.so.6





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yang liu

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Sep 27, 2017, 7:13:27 AM9/27/17
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Thank's for the reply! 😄

Nitsan Wakart

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Sep 28, 2017, 4:11:18 PM9/28/17
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Thanks Alex!
For future reference to all here:
AFAIK lightweight-java-profiler has never progressed much beyond the proof of concept stage and is not actively maintained. It was forked and developed into honest-profiler, which offers more features, is actively developed and is more stable. On a different foundation and offering further interesting capabilities we also have async-profiler.
If you are using LWP, or thinking about using it, or know someone who uses it, switch to either HP or AP.
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