qemu-kvm with ceph crash - coredump - qemu

qemu-kvm crash with this:
terminate called after throwing an instance of 'std::system_error'
what(): Resource deadlock avoided 2022-10-10 13:40:53.238+0000:
shutting down, reason=crashed
HOST OS: ubuntu 20.04
/usr/bin/qemu-system-x86_64 --version
QEMU emulator version 4.2.1 (Debian 1:4.2-3ubuntu6.23) Copyright (c)
2003-2019 Fabrice Bellard and the QEMU Project developers
librbd:
librbd1/stable,now 16.2.10-1focal amd64 [installed,automatic]
libvirt-daemon-driver-storage-rbd/focal-updates,focal-security,now
6.0.0-0ubuntu8.16 amd64 [installed,automatic] python3-rbd/stable,now 16.2.10-1focal amd64 [installed,automatic]
qemu-coredump:
Stack trace of thread 1545349:
#0 0x00007fe2ff0e900b __GI_raise (libc.so.6 + 0x4300b)
#1 0x00007fe2ff0c8859 __GI_abort (libc.so.6 + 0x22859)
#2 0x00007fe2fc8fd911 n/a (libstdc++.so.6 + 0x9e911)
#3 0x00007fe2fc90938c n/a (libstdc++.so.6 + 0xaa38c)
#4 0x00007fe2fc908369 n/a (libstdc++.so.6 + 0xa9369)
#5 0x00007fe2fc908d21 __gxx_personality_v0 (libstdc++.so.6 + 0xa9d21)
#6 0x00007fe2ff2cbbef n/a (libgcc_s.so.1 + 0x10bef)
#7 0x00007fe2ff2cc281 _Unwind_RaiseException (libgcc_s.so.1 + 0x11281)
#8 0x00007fe2fc90969c __cxa_throw (libstdc++.so.6 + 0xaa69c)
#9 0x00007fe2fc90073f _ZSt20__throw_system_errori (libstdc++.so.6 + 0xa173f)
#10 0x00007fe2fc936060 _ZNSt6thread4joinEv (libstdc++.so.6 + 0xd7060)
#11 0x00007fe2fcb6be14 n/a (librados.so.2 + 0xc3e14)
#12 0x00007fe2ef932ca1 _ZN4ceph6common11ConfigProxy12set_mon_valsEPNS0_11CephContextERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIc>
#13 0x00007fe2ef91c3c5 n/a (libceph-common.so.2 + 0x63b3c5)
#14 0x00007fe2ef931c75 _ZN5boost4asio6detail14strand_service11do_completeEPvPNS1_19scheduler_operationERKNS_6system10error_codeEm (libceph>
#15 0x00007fe2fcb79ca2 n/a (librados.so.2 + 0xd1ca2)
#16 0x00007fe2fcb80dea n/a (librados.so.2 + 0xd8dea)
#17 0x00007fe2fc935de4 n/a (libstdc++.so.6 + 0xd6de4)
#18 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#19 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
Stack trace of thread 1545341:
#0 0x00007fe2ef8e6b20 _ZN4ceph6buffer7v15_2_03ptr7releaseEv (libceph-common.so.2 + 0x605b20)
#1 0x00007fe2ef8f0a96 _ZN4ceph6buffer7v15_2_04list13iterator_implILb1EE12copy_shallowEjRNS1_3ptrE (libceph-common.so.2 + 0x60fa96)
#2 0x00007fe2ef82b3f6 _ZN4ceph6decodeISt3setINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4lessIS7_ESaIS7_EE11denc_traitsISB_vEE>
#3 0x00007fe2ef82b95d _ZN6MgrMap12ModuleOption6decodeERN4ceph6buffer7v15_2_04list13iterator_implILb1EEE (libceph-common.so.2 + 0x54a95d)
#4 0x00007fe2ef82bf74 _ZN6MgrMap10ModuleInfo6decodeERN4ceph6buffer7v15_2_04list13iterator_implILb1EEE (libceph-common.so.2 + 0x54af74)
...skipping...
#3 0x000055fefaaa85a9 n/a (qemu-system-x86_64 + 0x5515a9)
#4 0x000055fefa9160d3 main (qemu-system-x86_64 + 0x3bf0d3)
#5 0x00007fe2ff0ca083 __libc_start_main (libc.so.6 + 0x24083)
#6 0x000055fefa91999e _start (qemu-system-x86_64 + 0x3c299e)
Stack trace of thread 1545357:
#0 0x00007fe2ff2a7376 futex_wait_cancelable (libpthread.so.0 + 0xf376)
#1 0x00007fe2fc92fe30 _ZNSt18condition_variable4waitERSt11unique_lockISt5mutexE (libstdc++.so.6 + 0xd0e30)
#2 0x00007fe2ef64055d _ZN15CommonSafeTimerISt5mutexE12timer_threadEv (libceph-common.so.2 + 0x35f55d)
#3 0x00007fe2ef641601 _ZN21CommonSafeTimerThreadISt5mutexE5entryEv (libceph-common.so.2 + 0x360601)
#4 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#5 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
Stack trace of thread 1545363:
#0 0x00007fe2ff2a7376 futex_wait_cancelable (libpthread.so.0 + 0xf376)
#1 0x000055fefada665f qemu_cond_wait_impl (qemu-system-x86_64 + 0x84f65f)
#2 0x000055fefaca57b1 n/a (qemu-system-x86_64 + 0x74e7b1)
#3 0x000055fefaca6010 n/a (qemu-system-x86_64 + 0x74f010)
#4 0x000055fefada5f33 n/a (qemu-system-x86_64 + 0x84ef33)
#5 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#6 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
Stack trace of thread 1545360:
#0 0x00007fe2ff1b899f __GI___poll (libc.so.6 + 0x11299f)
#1 0x00007fe2ffbff36e n/a (libglib-2.0.so.0 + 0x5236e)
#2 0x00007fe2ffbff6f3 g_main_loop_run (libglib-2.0.so.0 + 0x526f3)
#3 0x000055fefaaa21f1 n/a (qemu-system-x86_64 + 0x54b1f1)
#4 0x000055fefada5f33 n/a (qemu-system-x86_64 + 0x84ef33)
#5 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#6 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
Stack trace of thread 1545340:
#0 0x00007fe2ff2a7376 futex_wait_cancelable (libpthread.so.0 + 0xf376)
#1 0x00007fe2fc92fe30 _ZNSt18condition_variable4waitERSt11unique_lockISt5mutexE (libstdc++.so.6 + 0xd0e30)
#2 0x00007fe2ef8f6a30 _ZN4ceph7logging3Log5entryEv (libceph-common.so.2 + 0x615a30)
#3 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#4 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
Stack trace of thread 1545351:
#0 0x00007fe2ff2a77d1 futex_abstimed_wait_cancelable (libpthread.so.0 + 0xf7d1)
#1 0x00007fe2fcbda7cd n/a (librados.so.2 + 0x1327cd)
#2 0x00007fe2fc935de4 n/a (libstdc++.so.6 + 0xd6de4)
#3 0x00007fe2ff2a0609 start_thread (libpthread.so.0 + 0x8609)
#4 0x00007fe2ff1c5133 __clone (libc.so.6 + 0x11f133)
root#computer01:/data# gdb /usr/bin/qemu-system-x86_64 core.qemu-system-x86.64055.1af0c28ed8944098961b13dbf7d3264d.1545331.1666005737000000000000
gdb:
(gdb) bt
#0 __GI_raise (sig=sig#entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
#1 0x00007fe2ff0c8859 in __GI_abort () at abort.c:79
#2 0x00007fe2fc8fd911 in ?? () from /lib/x86_64-linux-gnu/libstdc++.so.6
#3 0x00007fe2fc90938c in ?? () from /lib/x86_64-linux-gnu/libstdc++.so.6
#4 0x00007fe2fc908369 in ?? () from /lib/x86_64-linux-gnu/libstdc++.so.6
#5 0x00007fe2fc908d21 in __gxx_personality_v0 () from /lib/x86_64-linux-gnu/libstdc++.so.6
#6 0x00007fe2ff2cbbef in ?? () from /lib/x86_64-linux-gnu/libgcc_s.so.1
#7 0x00007fe2ff2cc281 in _Unwind_RaiseException () from /lib/x86_64-linux-gnu/libgcc_s.so.1
#8 0x00007fe2fc90969c in __cxa_throw () from /lib/x86_64-linux-gnu/libstdc++.so.6
#9 0x00007fe2fc90073f in std::__throw_system_error(int) () from /lib/x86_64-linux-gnu/libstdc++.so.6
#10 0x00007fe2fc936060 in std::thread::join() () from /lib/x86_64-linux-gnu/libstdc++.so.6
#11 0x00007fe2fcb6be14 in ?? () from /lib/librados.so.2
#12 0x00007fe2ef932ca1 in ceph::common::ConfigProxy::set_mon_vals(ceph::common::CephContext*, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<void>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&, std::function<bool (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)>) () from /usr/lib/ceph/libceph-common.so.2
#13 0x00007fe2ef91c3c5 in ?? () from /usr/lib/ceph/libceph-common.so.2
#14 0x00007fe2ef931c75 in boost::asio::detail::strand_service::do_complete(void*, boost::asio::detail::scheduler_operation*, boost::system::error_code const&, unsigned long) () from /usr/lib/ceph/libceph-common.so.2
#15 0x00007fe2fcb79ca2 in ?? () from /lib/librados.so.2
#16 0x00007fe2fcb80dea in ?? () from /lib/librados.so.2
#17 0x00007fe2fc935de4 in ?? () from /lib/x86_64-linux-gnu/libstdc++.so.6
#18 0x00007fe2ff2a0609 in start_thread (arg=<optimized out>) at pthread_create.c:477
#19 0x00007fe2ff1c5133 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95
Do you find out the realy reason by the coredump?
Appreciate for your help!

Related

C:\xampp\htdocs\blueberry-test\wp-includes\script-loader.php on line 2407

Fatal error: Uncaught Error: Call to undefined function get_current_screen() in C:\xampp\htdocs\blueberry-test\wp-includes\script-loader.php:2407 Stack trace: #0 C:\xampp\htdocs\blueberry-test\wp-includes\class-wp-hook.php(307): wp_global_styles_render_svg_filters('') #1 C:\xampp\htdocs\blueberry-test\wp-includes\class-wp-hook.php(331): WP_Hook->apply_filters(NULL, Array) #2 C:\xampp\htdocs\blueberry-test\wp-includes\plugin.php(476): WP_Hook->do_action(Array) #3 C:\xampp\htdocs\blueberry-test\wp-includes\general-template.php(3074): do_action('wp_body_open') #4 C:\xampp\htdocs\blueberry-test\wp-content\themes\blueberrys\header-home.php(35): wp_body_open() #5 C:\xampp\htdocs\blueberry-test\wp-includes\template.php(770): require_once('C:\xampp\htdocs...') #6 C:\xampp\htdocs\blueberry-test\wp-includes\template.php(716): load_template('C:\xampp\htdocs...', true, Array) #7 C:\xampp\htdocs\blueberry-test\wp-includes\general-template.php(48): locate_template(Array, true, true, Array) #8 C:\xampp\htdocs\blueberry-test\wp-content\themes\blueberrys\inc\woocommerce\storefront-woocommerce-template-functions.php(9): get_header('home') #9 C:\xampp\htdocs\blueberry-test\wp-content\themes\blueberrys\functions.php(47): require('C:\xampp\htdocs...') #10 C:\xampp\htdocs\blueberry-test\wp-settings.php(566): include('C:\xampp\htdocs...') #11 C:\xampp\htdocs\blueberry-test\wp-config.php(96): require_once('C:\xampp\htdocs...') #12 C:\xampp\htdocs\blueberry-test\wp-load.php(50): require_once('C:\xampp\htdocs...') #13 C:\xampp\htdocs\blueberry-test\wp-admin\admin.php(34): require_once('C:\xampp\htdocs...') #14 C:\xampp\htdocs\blueberry-test\wp-admin\plugins.php(10): require_once('C:\xampp\htdocs...') #15 {main} thrown in C:\xampp\htdocs\blueberry-test\wp-includes\script-loader.php on line 2407
Please at the description and format your code to code.

Version 1.35: Fatal exception of type MWException Error, The code that appears is:

Anyone know what I'm supposed to do?
[cb49891230242084931e4968] /index.php?title=%D7%99%D7%97%D7%99%D7%93%D7%94:%D7%AA%D7%91%D7%A0%D7%99%D7%AA_%D7%9E%D7%99%D7%93%D7%A2&action=submit MWException from line 95 of /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaStandalone/LuaStandaloneInterpreter.php: The lua binary (/home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaStandalone/binaries/lua5_1_5_linux_64_generic/lua) is not executable.
Backtrace:
#0 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaStandalone/LuaStandaloneEngine.php(104): Scribunto_LuaStandaloneInterpreter->__construct(Scribunto_LuaStandaloneEngine, array)
#1 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaCommon/LuaEngine.php(120): Scribunto_LuaStandaloneEngine->newInterpreter()
#2 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaStandalone/LuaStandaloneEngine.php(16): Scribunto_LuaEngine->load()
#3 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaCommon/LuaEngine.php(223): Scribunto_LuaStandaloneEngine->load()
#4 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaCommon/LuaModule.php(38): Scribunto_LuaEngine->getInterpreter()
#5 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaCommon/LuaModule.php(25): Scribunto_LuaModule->getInitChunk()
#6 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/common/ScribuntoEngineBase.php(193): Scribunto_LuaModule->validate()
#7 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/common/ScribuntoContent.php(35): ScribuntoEngineBase->validate(string, string)
#8 /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/common/Hooks.php(366): ScribuntoContent->validate(Title)
#9 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/HookContainer/HookContainer.php(320): ScribuntoHooks::validateScript(DerivativeContext, ScribuntoContent, Status, string, User, boolean)
#10 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/HookContainer/HookContainer.php(131): MediaWiki\HookContainer\HookContainer->callLegacyHook(string, array, array, array)
#11 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/HookContainer/HookRunner.php(1529): MediaWiki\HookContainer\HookContainer->run(string, array)
#12 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/EditPage.php(1903): MediaWiki\HookContainer\HookRunner->onEditFilterMergedContent(DerivativeContext, ScribuntoContent, Status, string, User, boolean)
#13 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/EditPage.php(2231): EditPage->runPostMergeFilters(ScribuntoContent, Status, User)
#14 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/EditPage.php(1723): EditPage->internalAttemptSave(NULL, boolean)
#15 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/EditPage.php(680): EditPage->attemptSave(NULL)
#16 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/actions/EditAction.php(71): EditPage->edit()
#17 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/actions/SubmitAction.php(38): EditAction->show()
#18 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/MediaWiki.php(527): SubmitAction->show()
#19 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/MediaWiki.php(313): MediaWiki->performAction(Article, Title)
#20 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/MediaWiki.php(940): MediaWiki->performRequest()
#21 /home/u657493073/domains/tzefunotwiki.com/public_html/includes/MediaWiki.php(543): MediaWiki->main()
#22 /home/u657493073/domains/tzefunotwiki.com/public_html/index.php(53): MediaWiki->run()
#23 /home/u657493073/domains/tzefunotwiki.com/public_html/index.php(46): wfIndexMain()
#24 {main}
תפריט ניווט
Try making the Lua file executable: sudo chmod +x /home/u657493073/domains/tzefunotwiki.com/public_html/extensions/Scribunto/includes/engines/LuaStandalone/binaries/lua5_1_5_linux_64_generic/lua.

Deadlocks in mysql database (Percona Server for mysql 5.7.22-22-1.trusty)

We have a problem with deadlocks in mysql database (Percona Server for mysql 5.7.22-22-1.trusty).
Every 24 hours our mysql stops responding. The process is still running but we can't create new connections.
After analysis of threads we saw that there are cycles in locks.
Do you have any idea what can we do to solve our problem?
Enviroment
Linux version 3.13.0-151-generic (buildd#lgw01-amd64-034) (gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.4) ) #201-Ubuntu SMP Wed May 30 14:22:13 UTC 2018
MemTotal: 528281684 kB
cpu: Intel(R) Xeon(R) CPU E5-2660 v3 # 2.60GHz
jupyther (kvm, qemu)
MemTotal: 154745476 kB
GDB session:
(gdb) thread 1634
[Switching to thread 1634 (Thread 0x7fe9bacdb700 (LWP 124547))]
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
135 ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file or directory.
(gdb) bt
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
#1 0x00007feb62d3767f in _L_lock_1081 () from /lib/x86_64-linux-gnu/libpthread.so.0
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x2cba198) at ../nptl/pthread_mutex_lock.c:134
#3 0x000000000079d77d in Global_THD_manager::do_for_all_thd_copy(Do_THD_Impl*) ()
#4 0x0000000000cedba0 in calc_sum_of_all_status(system_status_var*) ()
#5 0x0000000000ca3fbc in dispatch_command(THD*, COM_DATA const*, enum_server_command) ()
#6 0x0000000000ca5097 in do_command(THD*) ()
#7 0x0000000000d6a9d0 in handle_connection ()
#8 0x0000000000ede1e4 in pfs_spawn_thread ()
#9 0x00007feb62d35184 in start_thread (arg=0x7fe9bacdb700) at pthread_create.c:312
#10 0x00007feb6224203d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
(gdb) up 2
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x2cba198) at ../nptl/pthread_mutex_lock.c:134
134 ../nptl/pthread_mutex_lock.c: No such file or directory.
(gdb) print mutex.__data.__owner
$9 = 142327
(gdb) thread find 142327
Thread 1611 has target id 'Thread 0x7fe9bb762700 (LWP 142327)'
(gdb) thread 1611
[Switching to thread 1611 (Thread 0x7fe9bb762700 (LWP 142327))]
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
135 ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file or directory.
(gdb) bt
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
#1 0x00007feb62d3767f in _L_lock_1081 () from /lib/x86_64-linux-gnu/libpthread.so.0
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x7fe76142fbe8) at ../nptl/pthread_mutex_lock.c:134
#3 0x0000000000cfecac in Fill_process_list::operator()(THD*) ()
#4 0x000000000079d8dd in Global_THD_manager::do_for_all_thd_copy(Do_THD_Impl*) ()
#5 0x0000000000ce61bc in fill_schema_processlist(THD*, TABLE_LIST*, Item*) ()
#6 0x0000000000ce628c in ?? ()
#7 0x0000000000cf914c in get_schema_tables_result(JOIN*, enum_schema_table_state) ()
#8 0x0000000000cdc0ad in JOIN::prepare_result() ()
#9 0x0000000000c6cce0 in JOIN::exec() ()
#10 0x0000000000cdc9fd in handle_query(THD*, LEX*, Query_result*, unsigned long long, unsigned long long) ()
#11 0x000000000075cf43 in ?? ()
#12 0x0000000000c9f8f6 in mysql_execute_command(THD*, bool) ()
#13 0x0000000000ca2afd in mysql_parse(THD*, Parser_state*) ()
#14 0x0000000000ca36bd in dispatch_command(THD*, COM_DATA const*, enum_server_command) ()
#15 0x0000000000ca5097 in do_command(THD*) ()
#16 0x0000000000d6a9d0 in handle_connection ()
#17 0x0000000000ede1e4 in pfs_spawn_thread ()
#18 0x00007feb62d35184 in start_thread (arg=0x7fe9bb762700) at pthread_create.c:312
#19 0x00007feb6224203d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
(gdb) up 2
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x7fe76142fbe8) at ../nptl/pthread_mutex_lock.c:134
134 ../nptl/pthread_mutex_lock.c: No such file or directory.
(gdb) print mutex.__data.__owner
$10 = 109111
(gdb) thread find 109111
Thread 1648 has target id 'Thread 0x7fe9bbb98700 (LWP 109111)'
(gdb) thread 1648
[Switching to thread 1648 (Thread 0x7fe9bbb98700 (LWP 109111))]
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
135 ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file or directory.
(gdb) bt
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
#1 0x00007feb62d37649 in _L_lock_909 () from /lib/x86_64-linux-gnu/libpthread.so.0
#2 0x00007feb62d37470 in __GI___pthread_mutex_lock (mutex=0x1d7ebe8 <mysql_bin_log+8>) at ../nptl/pthread_mutex_lock.c:79
#3 0x0000000000d3021f in PolyLock_lock_log::rdlock() ()
#4 0x0000000000c133b5 in sys_var::value_ptr(THD*, THD*, enum_var_type, st_mysql_lex_string*) ()
#5 0x0000000000ceda2c in get_one_variable_ext(THD*, THD*, st_mysql_show_var const*, enum_var_type, enum_mysql_show_type, system_status_var*, charset_info_st const**, char*, unsigned long*) ()
#6 0x0000000000f08869 in System_variable::init(THD*, st_mysql_show_var const*, enum_var_type) ()
#7 0x0000000000f08e75 in PFS_system_variable_cache::do_materialize_all(THD*) ()
#8 0x0000000000f34b0a in table_session_variables::rnd_init(bool) ()
#9 0x0000000000edca2c in ha_perfschema::rnd_init(bool) ()
#10 0x0000000000807722 in handler::ha_rnd_init(bool) ()
#11 0x0000000000c04f34 in init_read_record(READ_RECORD*, THD*, TABLE*, QEP_TAB*, int, bool, bool) ()
#12 0x0000000000c705be in join_init_read_record(QEP_TAB*) ()
#13 0x0000000000c73f8b in sub_select(JOIN*, QEP_TAB*, bool) ()
#14 0x0000000000c6ce97 in JOIN::exec() ()
#15 0x0000000000c68c14 in TABLE_LIST::materialize_derived(THD*) ()
#16 0x0000000000c6d8bf in join_materialize_derived(QEP_TAB*) ()
#17 0x0000000000c6d3b2 in QEP_TAB::prepare_scan() ()
#18 0x0000000000c73eb0 in sub_select(JOIN*, QEP_TAB*, bool) ()
#19 0x0000000000c6ce97 in JOIN::exec() ()
#20 0x0000000000cdc9fd in handle_query(THD*, LEX*, Query_result*, unsigned long long, unsigned long long) ()
#21 0x000000000075cf43 in ?? ()
#22 0x0000000000c9f8f6 in mysql_execute_command(THD*, bool) ()
#23 0x0000000000ca2afd in mysql_parse(THD*, Parser_state*) ()
#24 0x0000000000ca36bd in dispatch_command(THD*, COM_DATA const*, enum_server_command) ()
#25 0x0000000000ca5097 in do_command(THD*) ()
#26 0x0000000000d6a9d0 in handle_connection ()
#27 0x0000000000ede1e4 in pfs_spawn_thread ()
#28 0x00007feb62d35184 in start_thread (arg=0x7fe9bbb98700) at pthread_create.c:312
#29 0x00007feb6224203d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
(gdb) up 2
#2 0x00007feb62d37470 in __GI___pthread_mutex_lock (mutex=0x1d7ebe8 <mysql_bin_log+8>) at ../nptl/pthread_mutex_lock.c:79
79 ../nptl/pthread_mutex_lock.c: No such file or directory.
(gdb) print mutex.__data.__owner
$11 = 63889
(gdb) thread find 63889
Thread 1808 has target id 'Thread 0x7fea780f5700 (LWP 63889)'
(gdb) thread 1808
[Switching to thread 1808 (Thread 0x7fea780f5700 (LWP 63889))]
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
135 ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file or directory.
(gdb) bt
#0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
#1 0x00007feb62d3767f in _L_lock_1081 () from /lib/x86_64-linux-gnu/libpthread.so.0
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x1d37c80 <LOCK_status>) at ../nptl/pthread_mutex_lock.c:134
#3 0x0000000000e5b098 in MYSQL_BIN_LOG::publish_coordinates_for_global_status() const ()
#4 0x0000000000e6147e in MYSQL_BIN_LOG::ordered_commit(THD*, bool, bool) ()
#5 0x0000000000e64902 in MYSQL_BIN_LOG::commit(THD*, bool) ()
#6 0x00000000008005e1 in ha_commit_trans(THD*, bool, bool) ()
#7 0x0000000000d4b7be in trans_commit_stmt(THD*) ()
#8 0x0000000000c9b6ea in mysql_execute_command(THD*, bool) ()
#9 0x0000000000ca2afd in mysql_parse(THD*, Parser_state*) ()
#10 0x0000000000ca36bd in dispatch_command(THD*, COM_DATA const*, enum_server_command) ()
#11 0x0000000000ca5097 in do_command(THD*) ()
#12 0x0000000000d6a9d0 in handle_connection ()
#13 0x0000000000ede1e4 in pfs_spawn_thread ()
#14 0x00007feb62d35184 in start_thread (arg=0x7fea780f5700) at pthread_create.c:312
#15 0x00007feb6224203d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
(gdb) up 2
#2 0x00007feb62d375f8 in __GI___pthread_mutex_lock (mutex=0x1d37c80 <LOCK_status>) at ../nptl/pthread_mutex_lock.c:134
134 ../nptl/pthread_mutex_lock.c: No such file or directory.
(gdb) print mutex.__data.__owner
$12 = 124547
(gdb) thread find 124547
Thread 1634 has target id 'Thread 0x7fe9bacdb700 (LWP 124547)'

SegFault file.c not found (Works on other computers)

I have a really odd problem with Cython.
I've tested my package on Mac OS and Arch Linux without failure.
Now when I test my package on CentOS I get a Segmentation Fault
Here's the gdb trace
Program received signal SIGSEGV, Segmentation fault.
__Pyx_GetItemInt_Fast (o=0x2aaac56d3b90, i=2, boundscheck=0, wraparound=0, is_list=0) at myprog/Snv.c:10678
10678 myprog/Snv.c: No such file or directory.
(gdb) where
#0 __Pyx_GetItemInt_Fast (o=0x2aaac56d3b90, i=2, boundscheck=0, wraparound=0, is_list=0) at myprog/Snv.c:10678
#1 0x00002aaabe7a8b76 in __pyx_f_3sv2_3Snv_tokenize_vcf (__pyx_v_Bam=<optimized out>, __pyx_v_Variant=<optimized out>, __pyx_optional_args=<optimized out>) at myprog/Snv.c:6685
#2 0x00002aaabe7ac6a2 in __pyx_pf_3sv2_3Snv_6c_preprocess_snv (__pyx_self=<optimized out>, __pyx_v_masked=<optimized out>, __pyx_v_Bam=<optimized out>) at myprog/Snv.c:5374
#3 __pyx_pw_3sv2_3Snv_7c_preprocess_snv (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaaab221870, __pyx_kwds=0x2aaab712d690 <__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__>) at myprog/Snv.c:4916
#4 0x00002aaabe7b7ca1 in __Pyx_PyObject_Call (kw=<optimized out>, arg=<optimized out>, func=<optimized out>) at myprog/Snv.c:10555
#5 __pyx_pf_3sv2_3Snv_2preprocess_snv (__pyx_self=<optimized out>, __pyx_v_masked=<optimized out>, __pyx_v_Bam=<optimized out>) at myprog/Snv.c:2994
#6 __pyx_pw_3sv2_3Snv_3preprocess_snv (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaabe4f2f38, __pyx_kwds=0x2aaaaab41240 <PyCFunction_Call>) at myprog/Snv.c:2935
#7 0x00002aaabe579680 in __Pyx_PyObject_Call (kw=0x0, arg=<optimized out>, func=0x2aaabe4f2d40) at myprog/Preprocess.c:9226
#8 __pyx_f_3sv2_10Preprocess_sv2_preprocess (__pyx_v_Bam=0x2aaac56d3dd0, __pyx_v_ofh=0x2aaac56d22d0, __pyx_v_seed=0x619558, __pyx_v_gen=0x2aaaab23b150, __pyx_v_tmp_dir=0x2aaac5ce6bb8) at myprog/Preprocess.c:3527
#9 0x00002aaabe591307 in __pyx_pf_3sv2_10Preprocess_preprocess (__pyx_self=<optimized out>, __pyx_v_tmp_dir=<optimized out>, __pyx_v_gen=<optimized out>, __pyx_v_seed=<optimized out>,
__pyx_v_ofh=<optimized out>, __pyx_v_Bam=<optimized out>) at myprog/Preprocess.c:2837
#10 __pyx_pw_3sv2_10Preprocess_1preprocess (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaac55fc1e0, __pyx_kwds=0x2aaaaae61270 <_Py_NoneStruct>) at myprog/Preprocess.c:2700
#11 0x00002aaaaabab1e5 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffb908) at Python/ceval.c:4352
#12 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2989
#13 0x00002aaaaabac345 in fast_function (nk=<optimized out>, na=<optimized out>, n=<optimized out>, pp_stack=0x7fffffffba78, func=0x2aaac56ccc08) at Python/ceval.c:4437
#14 call_function (oparg=<optimized out>, pp_stack=0x7fffffffba78) at Python/ceval.c:4372
#15 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2989
#16 0x00002aaaaabacc3e in PyEval_EvalCodeEx (co=0x2aaaab222a30, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
at Python/ceval.c:3584
#17 0x00002aaaaabacd52 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#18 0x00002aaaaabcd450 in run_mod (arena=0x617e10, flags=0x7fffffffbd70, locals=0x2aaaaaf1b168, globals=0x2aaaaaf1b168, filename=<optimized out>, mod=0x6aaa70) at Python/pythonrun.c:1376
#19 PyRun_FileExFlags (fp=0x638fc0, filename=<optimized out>, start=<optimized out>, globals=0x2aaaaaf1b168, locals=0x2aaaaaf1b168, closeit=1, flags=0x7fffffffbd70) at Python/pythonrun.c:1362
#20 0x00002aaaaabcd62f in PyRun_SimpleFileExFlags (fp=0x638fc0, filename=0x7fffffffc47f "/home/me/anaconda/bin/myprog", closeit=1, flags=0x7fffffffbd70) at Python/pythonrun.c:948
#21 0x00002aaaaabe2fd4 in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:645
#22 0x00000033b881ed1d in __libc_start_main () from /lib64/libc.so.6
#23 0x0000000000400729 in _start ()
$ head -n 10678 /home/me/myprog_dist/versions/1.4.0/myprog-1.4.0/myprog/Snv.c | tail -n 1
PyThreadState *tstate = __Pyx_PyThreadState_Current;
I'm running python Python 2.7.13 :: Anaconda custom (64-bit)
I have no idea why this SegFault is happening. This package works on Arch Linux and MacOS. So why does it fail with CentOS?

SQLSTATE[HY000]: General error: 2006 MySQL server has gone away - What to do?

Here is what I get and I don't know what to do....
There has been an error processing your request
SQLSTATE[HY000]: General error: 2006 MySQL server has gone away
Trace:
#0 /home/autobadges/public_html/stangcenter.com/lib/Zend/Db/Statement.php(300): Zend_Db_Statement_Pdo->_execute(Array)
#1 /home/autobadges/public_html/stangcenter.com/lib/Zend/Db/Adapter/Abstract.php(479): Zend_Db_Statement->execute(Array)
#2 /home/autobadges/public_html/stangcenter.com/lib/Zend/Db/Adapter/Pdo/Abstract.php(238): Zend_Db_Adapter_Abstract->query('SELECT `main_ta...', Array)
#3 /home/autobadges/public_html/stangcenter.com/lib/Varien/Db/Adapter/Pdo/Mysql.php(333): Zend_Db_Adapter_Pdo_Abstract->query('SELECT `main_ta...', Array)
#4 /home/autobadges/public_html/stangcenter.com/lib/Zend/Db/Adapter/Abstract.php(734): Varien_Db_Adapter_Pdo_Mysql->query(Object(Varien_Db_Select), Array)
#5 /home/autobadges/public_html/stangcenter.com/lib/Varien/Data/Collection/Db.php(783): Zend_Db_Adapter_Abstract->fetchAll(Object(Varien_Db_Select), Array)
#6 /home/autobadges/public_html/stangcenter.com/lib/Varien/Data/Collection/Db.php(696): Varien_Data_Collection_Db->_fetchAll(Object(Varien_Db_Select))
#7 /home/autobadges/public_html/stangcenter.com/lib/Varien/Data/Collection/Db.php(617): Varien_Data_Collection_Db->getData()
#8 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Adminhtml/Block/Catalog/Product/Edit/Tabs.php(57): Varien_Data_Collection_Db->load()
#9 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Block/Abstract.php(223): Mage_Adminhtml_Block_Catalog_Product_Edit_Tabs->_prepareLayout()
#10 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/Layout.php(430): Mage_Core_Block_Abstract->setLayout(Object(Mage_Core_Model_Layout))
#11 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/Layout.php(446): Mage_Core_Model_Layout->createBlock('adminhtml/catal...', 'product_tabs')
#12 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/Layout.php(238): Mage_Core_Model_Layout->addBlock('adminhtml/catal...', 'product_tabs')
#13 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/Layout.php(204): Mage_Core_Model_Layout->_generateBlock(Object(Mage_Core_Model_Layout_Element), Object(Mage_Core_Model_Layout_Element))
#14 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/Layout.php(209): Mage_Core_Model_Layout->generateBlocks(Object(Mage_Core_Model_Layout_Element))
#15 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Controller/Varien/Action.php(343): Mage_Core_Model_Layout->generateBlocks()
#16 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Controller/Varien/Action.php(270): Mage_Core_Controller_Varien_Action->generateLayoutBlocks()
#17 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Adminhtml/Controller/Action.php(263): Mage_Core_Controller_Varien_Action->loadLayout(Array, true, true)
#18 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Adminhtml/controllers/Catalog/ProductController.php(246): Mage_Adminhtml_Controller_Action->loadLayout(Array)
#19 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Controller/Varien/Action.php(418): Mage_Adminhtml_Catalog_ProductController->editAction()
#20 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Controller/Varien/Router/Standard.php(253): Mage_Core_Controller_Varien_Action->dispatch('edit')
#21 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Controller/Varien/Front.php(176): Mage_Core_Controller_Varien_Router_Standard->match(Object(Mage_Core_Controller_Request_Http))
#22 /home/autobadges/public_html/stangcenter.com/app/code/core/Mage/Core/Model/App.php(340): Mage_Core_Controller_Varien_Front->dispatch()
#23 /home/autobadges/public_html/stangcenter.com/app/Mage.php(627): Mage_Core_Model_App->run(Array)
#24 /home/autobadges/public_html/stangcenter.com/index.php(80): Mage::run('', 'store')
#25 {main}
write your zend query in a try block
and
catch the exception
Zend_Db_Statement_Mysqli_Exception (check which one you are using 'mysql' or 'mysqli' or 'PDO') in the exception catch code just call {model}->getDefaultAdapter()->closeConnection() and then again call the zend query you have got.
this should solve your problem.
NOTE: Below code is just for reference and should not be used as it is (may have error in it).
try
{
$user = {model}->fetchRow(array('user_id = ?' => $senderid));
}
catch(Zend_Db_Statement_Mysqli_Exception $zenddbmysqliexc)
{
if(stristr($zenddbmysqliexc->getMessage(), 'MySQL server has gone away'))
{
{model}->getDefaultAdapter()->closeConnection();
$user = {model}->fetchRow(array('user_id = ?' => $senderid));
}
}