Crash moving structures on [DEVPREV] Symmetric Dimer: Buried Hydrogen Bond Networks

Case number:699969-2003770
Topic:General
Opened by:actiasluna
Status:Open
Type:DevPrev Issue
Opened on:Saturday, April 29, 2017 - 17:27
Last modified:Monday, May 8, 2017 - 12:07

2 crashes in a row, had built structures in Blueprint. Banded sheets, froze some structures, and was moving helix when first crash occurred.

Second crash, I turned off view for symmetric chain and got 1 step further, was able to move first helix but upon trying second, crash.

Both Segmentation Faults, thread 11. (this is current and recorded issue for the monomer puzzles that use blueprint and mutate, along with the Thread 10 "double free" and variations on that theme).

Devprev latest update being run, mac OS, the usual.

Mac crashlogs for both attached

AttachmentSize
Crash2SegFault11.txt54.29 KB
Crash1SegFault11.txt55.23 KB
(Sat, 04/29/2017 - 17:27  |  11 comments)


jflat06's picture
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By moving, do you mean the move tool? (purple cross)

I believe there's a known bug with that that will cause it to occasionally crash. I can look into it.

Joined: 03/05/2015
Groups: Gargleblasters

Ok.. . in Selection Interface, I freeze the helix, leaving the loops unfrozen, then click the end segment of the helix to unfreeze it. I select the helix by double clicking, then Ctrl-drag that end seg.. That is my usual way of doing it in the monomers... so no, it isn't the move tool activated.

jflat06's picture
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Ok, so you are using the pull tool?

Joined: 03/05/2015
Groups: Gargleblasters

Actually, just dragging the helix... not ctrl-drag. Whatever that is in SI.

LociOiling's picture
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I think the crash in the attached was similar, but not 100% sure if it was the move tool.

LociOiling's picture
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The crash in this log happened with undo (ctrl+z).

LociOiling's picture
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A couple of more crashes, one on a wiggle, one during an LWS recipe with just 5 minutes left on the puzzle.

The puzzle actually ran normally for about 14 hours with no crashes. I had procmon running, and collected a PML file of just under 600 KB if anyone's interested.

(Not going to try attaching it, as I suspect the spam filters would kick in. As it was, they renamed "log.v4.lws.txt" to "log.v4.lws_.txt", which seems a little odd.)

In procmon, just moments before the crash, there are suddenly tons of these QueryNameInformationFile calls with a BUFFER OVERFLOW result, like this one:

5:55:28.4750762 PM Foldit.exe 7680 QueryNameInformationFile C:\Windows\System32\oleaut32.dll BUFFER OVERFLOW Name: \W

Many of them hit the same dll multiple times, for example gdi32.dll is queried four times in quick succession. They all have "Name: \W", "Name: \F" and similar valuesin the detail field. It's not clear to me whether this is a symptom of anything, but the timing is suspicious.

The Windows event reported the problem occurring in C:\WINDOWS\AppPatch\AcLayers.DLL at 2017-05-04T22:55:29.286067200Z:

Faulting application name: Foldit.exe, version: 0.0.0.0, time stamp: 0x579aa6ee
Faulting module name: AcLayers.DLL, version: 10.0.14393.953, time stamp: 0x58ba5d8a
Exception code: 0xc0000374
Fault offset: 0x00021f87
Faulting process id: 0x1e00
Faulting application start time: 0x01d2c4abad1f33d7
Faulting application path: C:\Foldit\foldit1\Foldit.exe
Faulting module path: C:\WINDOWS\AppPatch\AcLayers.DLL
Report Id: 19b50e40-b6f3-4b90-b41e-a440e248b91a
Faulting package full name:
Faulting package-relative application ID:

LociOiling's picture
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I did a little more digging into the crash above. In procmon, I see a new thread start. The events for the new thread are attached as a csv file. The first thing the new thread does is write "***** STARTING THREAD ActionLocalMinimize" to log.txt. This is the last thing written to log.txt.

The thread reads the .sym file. It deletes (?) an .und file. Over a second goes by, and the thread reads AcLayers.dll. Then all the QueryNameInformationFile calls happen. The BUFFER_OVERFLOWs are just a red herring, each one is matched with a SUCCESS later. No idea why it queries foldit.exe seven times with BUFFER_OVERFLOW, followed by seven times with SUCCESS. Maybe there are seven different attributes wanted. The BUFFER_OVERFLOW part is just to get the buffer size needed, which is then used on the calls that end in SUCCESS.

Shortly after all the queries complete another thread starts a process for WerFault.exe. So presumably all the QueryNameInformationFile calls are just part of Windows error reporting. Perhaps the actual error occurs after the .und file activity, triggering the AcLayers.dll action. I haven't been able to find anything online about what AcLayers.dll does, so the trail has gone cold for the moment.

Joined: 03/05/2015
Groups: Gargleblasters

Reproduced the crash. Folded up and blueprinted the pattern, then froze the helices one at a time. Moved both of them successfully for a little while but finally when snugging up the core the last drag sequence (double-click unfrozen end segment of helix then left click-hold-and-drag) crashed immediately. Logs (mac and Foldit) and script log attached.

Last thing that happened from foldit log:

delta_score: 0
Playing sound: 4
***** STARTING THREAD ActionLocalMinimizePull

Excerpt of mac crashlog:

Thread 10:
0 game_library.dylib 0x02fc41e2 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 0x02fd015c std::__1::basic_stringbuf, std::__1::allocator >::str() const + 108
2 game_library.dylib 0x007dee46 basic::basic_otstream >::basic_tstringbuf >::sync() + 44
3 game_library.dylib 0x0321f3a0 std::__1::basic_ostream >::flush() + 64
4 game_library.dylib 0x00b09e2b core::conformation::symmetry::SymmetricConformation::replace_residue(unsigned long, core::conformation::Residue const&, bool) + 185
5 game_library.dylib 0x00c23c32 core::pose::Pose::replace_residue(unsigned long, core::conformation::Residue const&, bool) + 44
6 game_library.dylib 0x02fa15fb interactive::util::copy_backbone(core::pose::Pose&, core::pose::Pose const&, unsigned long, unsigned long, unsigned long) + 682
7 game_library.dylib 0x02c8165c interactive::application::actions::cart::PoseLoopThreadActionCart::update_centroid_pose(boost::shared_ptr) + 364
8 game_library.dylib 0x02c72a4a interactive::application::actions::cart::ActionCartPull::thread_body_loop_unlocked(core::pose::Pose&) + 290
9 game_library.dylib 0x02c7fa01 interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run() + 4669
10 game_library.dylib 0x02dc0f66 boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > >, void>::invoke(boost::detail::function::function_buffer&) + 32
11 game_library.dylib 0x02f7c103 boost::function0::operator()() const + 35
12 game_library.dylib 0x02f7a923 interactive::util::Thread::operator()() + 45
13 game_library.dylib 0x02f7aae5 interactive::util::Thread::thread_entry_func() + 31
14 game_library.dylib 0x02f7a741 interactive::util::Thread::pthread_startup_helper(void*) + 17
15 libsystem_pthread.dylib 0xa1734073 _pthread_body + 184
16 libsystem_pthread.dylib 0xa1733fbb _pthread_start + 243
17 libsystem_pthread.dylib 0xa1733876 thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x1fbec000 ebx: 0x70b00000 ecx: 0x20c45f30 edx: 0x00000000
edi: 0x0c705221 esi: 0x7c1ab2f1 ebp: 0xbff30a68 esp: 0xbff30a50
ss: 0x00000023 efl: 0x00010202 eip: 0x02fc41e2 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x70b00000

Logical CPU: 2
Error Code: 0x00000004
Trap Number: 14

System log from around the time of the crash: (look at italicized text)

May 6 09:19:17 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 09:26:37 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.quicklook[1223]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
May 6 09:26:47 Kathleens-iMac com.apple.xpc.launchd[1] (edu.washington.foldit.3412[1209]): Service exited due to signal: Segmentation fault: 11 sent by exc handler[0]
May 6 09:26:47 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.ReportCrash[1224]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.ReportCrash

May 6 09:27:08 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 09:27:09 --- last message repeated 1 time ---
May 6 09:27:09 Kathleens-iMac com.apple.appkit.xpc.openAndSavePanelService[1245]: assertion failed: 16E195: libxpc.dylib + 74307 [ABC45890-DA23-3A4A-B50B-1384BD4CBBDF]: 0x89
May 6 09:27:31 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 09:27:51 Kathleens-iMac DocumentPopoverViewService[1254]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked
May 6 09:28:42 Kathleens-iMac syslogd[49]: ASL Sender Statistics
May 6 09:28:53 Kathleens-iMac LogViewer[1257]: assertion failed: 16E195: libxpc.dylib + 74307 [ABC45890-DA23-3A4A-B50B-1384BD4CBBDF]: 0x89
May 6 09:29:11 Kathleens-iMac LogViewer[1257]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked

Joined: 03/05/2015
Groups: Gargleblasters

Interesting that the move succeeded. Opening up the crash test thread it had moved the helix and closed the core "gap." Try 2 I'm continuing on as I would normally. Mutating puzzle in position next to symmetric chain. This worked and I ran Local Mutate and Quake Shearing without incident. Then I moved the chain around to try to find H-Bonds and when wiggling the structure it crashed a second time.

Maclog excerpts:>/b>

Crashed Thread: 10

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
abort() called
*** error for object 0x850263e0: pointer being freed was not allocated

...And...down the log text ...>/b>

Thread 10 Crashed:
0 libsystem_kernel.dylib 0xa1650496 __pthread_kill + 10
1 libsystem_pthread.dylib 0xa1736d8b pthread_kill + 90
2 libsystem_c.dylib 0xa15b0a34 abort + 141
3 libsystem_malloc.dylib 0xa16a78e7 free + 529
4 libc++.1.dylib 0xa017e589 std::__1::basic_string, std::__1::allocator >::__grow_by(unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long) + 187
5 libc++.1.dylib 0xa017e233 std::__1::basic_string, std::__1::allocator >::push_back(char) + 57
6 game_library.dylib 0x031d2a0e std::__1::basic_stringbuf, std::__1::allocator >::overflow(int) + 110
7 game_library.dylib 0x02fd0fb6 std::__1::basic_streambuf >::xsputn(char const*, int) + 86
8 libc++.1.dylib 0xa015cd0b std::__1::ostreambuf_iterator > std::__1::__pad_and_output >(std::__1::ostreambuf_iterator >, char const*, char const*, char const*, std::__1::ios_base&, char) + 181
9 libc++.1.dylib 0xa015d013 std::__1::num_put > >::do_put(std::__1::ostreambuf_iterator >, std::__1::ios_base&, char, unsigned long) const + 321
10 game_library.dylib 0x033036b5 std::__1::basic_ostream >::operator<<(unsigned long) + 261
11 game_library.dylib 0x00e3e4c0 core::scoring::dssp::StrandPairing::show_internals(std::__1::basic_ostream >&) const + 292
12 game_library.dylib 0x00e3cd0e core::scoring::dssp::StrandPairing::extend(unsigned long, unsigned long, bool, unsigned long) + 2398
13 game_library.dylib 0x00e39bba core::scoring::dssp::StrandPairingSet::add_pairing(unsigned long, unsigned long, bool, unsigned long) + 74
14 game_library.dylib 0x00e399e6 core::scoring::dssp::StrandPairingSet::compute(ObjexxFCL::FArray2 const&, float, core::pose::Pose const&) + 404
15 game_library.dylib 0x00e39a6d core::scoring::dssp::StrandPairingSet::StrandPairingSet(ObjexxFCL::FArray2 const&, float, core::pose::Pose const&) + 81
16 game_library.dylib 0x00e34fb3 core::scoring::dssp::Dssp::compute(core::pose::Pose const&) + 1213
17 game_library.dylib 0x00e34a26 core::scoring::dssp::Dssp::Dssp(core::pose::Pose const&, bool) + 98
18 game_library.dylib 0x00e358da core::scoring::dssp::Dssp::Dssp(core::pose::Pose const&, bool) + 22
19 game_library.dylib 0x02c94a0a interactive::application::appfilter::LayerScoreFilter::compute_layers(core::pose::Pose const&, interactive::application::appfilter::LayerScoreFilter::LayerData&) const + 56
20 game_library.dylib 0x02c93086 interactive::application::appfilter::LayerScoreFilter::apply(interactive::util::access_ptr) const + 88
21 game_library.dylib 0x02f0f6fa interactive::util::Filter::apply_filter(interactive::util::access_ptr, interactive::util::owning_ptr, bool) const + 134
22 game_library.dylib 0x02f19a90 interactive::util::ReferencePoseInfo::score_pose(interactive::util::access_ptr, core::scoring::ScoreFunction&, bool) const + 4636
23 game_library.dylib 0x02c23f5b interactive::application::actions::cart::PoseLoopThreadActionCart::update_game_pose_from_work_pose(bool) + 305
24 game_library.dylib 0x02c22a4b interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run() + 4743
25 game_library.dylib 0x02d63f66 boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > >, void>::invoke(boost::detail::function::function_buffer&) + 32
26 game_library.dylib 0x02f1f103 boost::function0::operator()() const + 35
27 game_library.dylib 0x02f1d923 interactive::util::Thread::operator()() + 45
28 game_library.dylib 0x02f1dae5 interactive::util::Thread::thread_entry_func() + 31
29 game_library.dylib 0x02f1d741 interactive::util::Thread::pthread_startup_helper(void*) + 17
30 libsystem_pthread.dylib 0xa1734073 _pthread_body + 184
31 libsystem_pthread.dylib 0xa1733fbb _pthread_start + 243
32 libsystem_pthread.dylib 0xa1733876 thread_start + 34

Thread 10 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x00000003 ecx: 0xb083c94c edx: 0x00000000
edi: 0xb083e000 esi: 0x00000006 ebp: 0xb083c978 esp: 0xb083c94c
ss: 0x00000023 efl: 0x00000292 eip: 0xa1650496 cs: 0x0000000b
ds: 0x00000023 es: 0x00000023 fs: 0x00000023 gs: 0x0000000f
cr2: 0xa6f19320

Logical CPU: 0
Error Code: 0x00080148
Trap Number: 132

Foldit log excerpt Just before the crash:

Playing sound: 4
***** STARTING THREAD ActionRepack
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=4 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JGS: [master 4] 5:0
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JGSS: [master 1] 2:0
Packer cancelled
delta_score: 0
Playing sound: 4
***** ENDING THREAD ActionRepack
***** STARTING THREAD ActionRepack
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=4 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JGS: [master 4] 5:0
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JGSS: [master 1] 2:0
delta_score: 0
Playing sound: 4
***** ENDING THREAD ActionRepack
***** STARTING THREAD ActionGlobalMinimize

And here's what was going on in system at the time:

May 6 09:48:59 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.quicklook[1276]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
May 6 09:58:50 Kathleens-iMac syslogd[49]: ASL Sender Statistics
May 6 10:03:24 Kathleens-iMac game_dynamic[1269]: game_dynamic(1269,0xb083e000) malloc: *** error for object 0x850263e0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
May 6 10:03:24 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.ReportCrash[1279]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.ReportCrash
May 6 10:04:01 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 10:04:31 --- last message repeated 1 time ---
May 6 10:05:14 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 10:08:53 Kathleens-iMac syslogd[49]: ASL Sender Statistics
May 6 10:09:42 Kathleens-iMac com.apple.xpc.launchd[1] (com.apple.imfoundation.IMRemoteURLConnectionAgent): Unknown key for integer: _DirtyJetsamMemoryLimit
May 6 10:09:43 --- last message repeated 1 time ---
May 6 10:09:43 Kathleens-iMac LogViewer[1306]: assertion failed: 16E195: libxpc.dylib + 74307 [ABC45890-DA23-3A4A-B50B-1384BD4CBBDF]: 0x89

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