1364 Segmentation fault

Case number:845829-2003684
Topic:Crash/Hang
Opened by:actiasluna
Status:Open
Type:Bug
Opened on:Wednesday, April 12, 2017 - 02:30
Last modified:Thursday, April 13, 2017 - 22:16

Thread 11.

Reproducible given that this happened on the last variable length monomer. Running DRW at the time. No help in the log.txt or script logs.

Excerpt from mac backtrace

Thread 11 Crashed:
0 game_library.dylib 0x02d84a92 std::__1::enable_if<__is_forward_iterator::value, void>::type std::__1::basic_string, std::__1::allocator >::__init(char*, char*) + 98
1 game_library.dylib 0x02d90a0c std::__1::basic_stringbuf, std::__1::allocator >::str() const + 108
2 game_library.dylib 0x00614cb6 basic::basic_otstream >::basic_tstringbuf >::sync() + 44
3 game_library.dylib 0x02fd9f70 std::__1::basic_ostream >::flush() + 64
4 game_library.dylib 0x00611ae5 basic::Tracer::TracerProxy::t_flush(std::__1::basic_string, std::__1::allocator > const&) + 133
5 game_library.dylib 0x00614cc2 basic::basic_otstream >::basic_tstringbuf >::sync() + 56
6 game_library.dylib 0x02fd9f70 std::__1::basic_ostream >::flush() + 64
7 game_library.dylib 0x00cbf624 core::scoring::dssp::StrandPairing::extend(unsigned long, unsigned long, bool, unsigned long) + 804
8 game_library.dylib 0x00cbcb0a core::scoring::dssp::StrandPairingSet::add_pairing(unsigned long, unsigned long, bool, unsigned long) + 74
9 game_library.dylib 0x00cbc936 core::scoring::dssp::StrandPairingSet::compute(ObjexxFCL::FArray2 const&, float, core::pose::Pose const&) + 404
10 game_library.dylib 0x00cbc9bd core::scoring::dssp::StrandPairingSet::StrandPairingSet(ObjexxFCL::FArray2 const&, float, core::pose::Pose const&) + 81
11 game_library.dylib 0x00cb7f03 core::scoring::dssp::Dssp::compute(core::pose::Pose const&) + 1213
12 game_library.dylib 0x00cb7976 core::scoring::dssp::Dssp::Dssp(core::pose::Pose const&, bool) + 98
13 game_library.dylib 0x00cb882a core::scoring::dssp::Dssp::Dssp(core::pose::Pose const&, bool) + 22
14 game_library.dylib 0x02ae96ea interactive::application::appfilter::LayerScoreFilter::compute_layers(core::pose::Pose const&, interactive::application::appfilter::LayerScoreFilter::LayerData&) const + 56
15 game_library.dylib 0x02ae7d66 interactive::application::appfilter::LayerScoreFilter::apply(interactive::util::access_ptr) const + 88
16 game_library.dylib 0x02d2f89a interactive::util::Filter::apply_filter(interactive::util::access_ptr, interactive::util::owning_ptr, bool) const + 134
17 game_library.dylib 0x02d39924 interactive::util::ReferencePoseInfo::score_pose(interactive::util::access_ptr, core::scoring::ScoreFunction&, bool) const + 4636
18 game_library.dylib 0x02aa373b interactive::application::actions::cart::PoseLoopThreadActionCart::update_game_pose_from_work_pose(bool) + 305
19 game_library.dylib 0x02aa4728 interactive::application::actions::cart::PoseLoopThreadActionCart::minimizer_callback_with_game_update(boost::function > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*) + 482
20 game_library.dylib 0x02aa5a5c boost::_mfi::mf3 > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*>::operator()(interactive::application::actions::cart::PoseLoopThreadActionCart*, boost::function > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*) const + 128
21 game_library.dylib 0x02aa59b3 bool boost::_bi::list4, boost::arg<1>, boost::arg<2>, boost::_bi::value >::operator() > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*>, boost::_bi::rrlist2 > const&)>, utility::vector1 > const*> >(boost::_bi::type, boost::_mfi::mf3 > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*>&, boost::_bi::rrlist2 > const&)>, utility::vector1 > const*>&, long) + 79
22 game_library.dylib 0x02aa5959 boost::detail::function::function_obj_invoker2 > const&)>, utility::vector1 > const*, interactive::application::actions::cart::PoseLoopThreadActionCart::CallbackInfo*>, boost::_bi::list4, boost::arg<1>, boost::arg<2>, boost::_bi::value > >, bool, boost::function > const&)>, utility::vector1 > const*>::invoke(boost::detail::function::function_buffer&, boost::function > const&)>, utility::vector1 > const*) + 45
23 game_library.dylib 0x0134b132 boost::function2 > const&)>, utility::vector1 > const*>::operator()(boost::function > const&)>, utility::vector1 > const*) const + 74
24 game_library.dylib 0x0134afa9 core::optimization::MinimizerHelper::progress(utility::vector1 > const*) + 105
25 game_library.dylib 0x0134af35 core::optimization::MinimizerHelper::keep_going(core::optimization::MinimizerHelper*, utility::vector1 > const*) + 27
26 game_library.dylib 0x01351552 core::optimization::Minimizer::dfpmin_armijo(utility::vector1 >&, double&, core::optimization::ConvergenceTest&, boost::shared_ptr, int) const + 3600
27 game_library.dylib 0x0134ecdf core::optimization::Minimizer::run(utility::vector1 >&) + 2361
28 game_library.dylib 0x013411d4 core::optimization::AtomTreeMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&) + 736
29 game_library.dylib 0x01341a1b core::optimization::AtomTreeMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&, core::optimization::MinimizerHelper&) + 43
30 game_library.dylib 0x02aa43f2 interactive::application::actions::cart::PoseLoopThreadActionCart::run_minimizer_on_work_pose(core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&) + 604
31 game_library.dylib 0x02a916ca interactive::application::actions::cart::ActionCartGlobalWiggle::thread_body_loop_unlocked(core::pose::Pose&) + 114
32 game_library.dylib 0x02aa21e1 interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run() + 4669
33 game_library.dylib 0x02baaf96 boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > >, void>::invoke(boost::detail::function::function_buffer&) + 32
34 game_library.dylib 0x02d3ef43 boost::function0::operator()() const + 35
35 game_library.dylib 0x02d3d763 interactive::util::Thread::operator()() + 45
36 game_library.dylib 0x02d3d925 interactive::util::Thread::thread_entry_func() + 31
37 game_library.dylib 0x02d3d581 interactive::util::Thread::pthread_startup_helper(void*) + 17
38 libsystem_pthread.dylib 0x9f99810b _pthread_body + 184
39 libsystem_pthread.dylib 0x9f998053 _pthread_start + 243
40 libsystem_pthread.dylib 0x9f99790e thread_start + 34

Thread 11 crashed with X86 Thread State (32-bit):
eax: 0x29145000 ebx: 0x71100000 ecx: 0x2927b340 edx: 0x00000000
edi: 0x0995a621 esi: 0x7a9242e1 ebp: 0xb0dadc88 esp: 0xb0dadc70
ss: 0x00000023 efl: 0x00010206 eip: 0x02d84a92 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000023 gs: 0x0000000f
cr2: 0x71100000

Logical CPU: 6
Error Code: 0x00000004
Trap Number: 14

AttachmentSize
1364_SegFault11.txt64.58 KB
(Wed, 04/12/2017 - 02:30  |  3 comments)


actiasluna's picture
User offline. Last seen 2 weeks 3 days ago. Offline
Joined: 03/05/2015
Groups: Gargleblasters
Topic: General » Crash/Hang
Type: Suggestion » Bug

Conditions slightly different but still this crash. (also updated topic to crash/hang, bug)

actiasluna's picture
User offline. Last seen 2 weeks 3 days ago. Offline
Joined: 03/05/2015
Groups: Gargleblasters

Don't know if this will help or not. system log excerpt about the time of the crash.
(conditions that changed: Running out of SSD Applications file instead of Mac HD, not running multiple client folders, running multiple clients with Automator)

Apr 11 22:19:17 Kathleens-iMac com.apple.xpc.launchd[1] (edu.washington.foldit.2172.F770A5A5-9C62-437C-9BE1-C3DBECDF57B7[23273]): Service exited due to signal: Segmentation fault: 11 sent by exc handler[0]
Apr 11 22:19:17 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.ReportCrash[33092]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.ReportCrash
Apr 11 22:19:24 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:19:44 --- last message repeated 2 times ---
Apr 11 22:19:44 Kathleens-iMac syslogd[49]: ASL Sender Statistics
Apr 11 22:19:46 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
Apr 11 22:19:54 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:20:24 --- last message repeated 2 times ---
Apr 11 22:20:24 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:20:54 --- last message repeated 2 times ---
Apr 11 22:20:54 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:21:06 --- last message repeated 1 time ---
Apr 11 22:21:06 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
Apr 11 22:21:14 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:21:16 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.quicklook[33143]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
Apr 11 22:21:24 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:21:25 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb832f1a0, 3, 0)
Apr 11 22:21:25 Kathleens-iMac logd[65]: _volume_contains_cached_data(is /private/var/db/diagnostics/ in /) - YES
Apr 11 22:21:25 Kathleens-iMac logd[65]: 144962432 bytes of purgeable space from log files
Apr 11 22:21:25 Kathleens-iMac logd[65]: _purge_uuidtext only runs at urgency 0 (3)
Apr 11 22:21:25 Kathleens-iMac logd[65]: 0 bytes of purgeable space from uuidtext files
Apr 11 22:21:25 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
Apr 11 22:21:26 Kathleens-iMac logd[65]: metadata page is missing PID information for CVMServer (247)
Apr 11 22:21:26 Kathleens-iMac logd[65]: metadata page is missing main binary UUID info CVMServer (247)
Apr 11 22:21:26 Kathleens-iMac logd[65]: metadata shared cached uuid is null (using logd's shared cache info) CVMServer (247)
Apr 11 22:21:26 Kathleens-iMac LogViewer[22700]: assertion failed: 16D32: libxpc.dylib + 74307 [65E41BB6-EBD5-3D93-B0BE-B190CEE4DD93]: 0x89
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb5d559a0, 3, 0)
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb8009c20, 3, 0)
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb8152540, 3, 0)
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb5f36380, 3, 0)
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb8153260, 3, 0)
Apr 11 22:21:30 Kathleens-iMac logd[65]: _handle_cache_delete_with_urgency(0x7fbfb8230810, 3, 0)
Apr 11 22:21:34 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.nowplayingtouchui): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Apr 11 22:21:42 Kathleens-iMac LogViewer[22700]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked

actiasluna's picture
User offline. Last seen 2 weeks 3 days ago. Offline
Joined: 03/05/2015
Groups: Gargleblasters

Again, today. Not hugely frequent, but consistent.

Mac crashlog attached... log.txt and script log no help on this one.

Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons