Tutorial - Electron Density crashes constantly (4 times in row)

Case number:845829-2003018
Topic:Crash/Hang
Opened by:PrzemoF
Status:Open
Type:Bug
Opened on:Sunday, October 30, 2016 - 23:41
Last modified:Thursday, November 3, 2016 - 18:16

$ LANG_ALL=C ./Foldit
terminate called recursively
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (zrzut pamięci)
(Zrzut pamięci = Core dump)

Starting program: /home/przemo/Downloads/Foldit/Foldit
Missing separate debuginfos, use: dnf debuginfo-install glibc-2.23.1-10.fc24.x86_64
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
[New Thread 0x7fffe96ae2c0 (LWP 27619)]
[New Thread 0x7fffe84502c0 (LWP 27620)]
[New Thread 0x7fffe3fff2c0 (LWP 27621)]
[New Thread 0x7fffe3bfb2c0 (LWP 27622)]
[New Thread 0x7fffe34e72c0 (LWP 27635)]
[New Thread 0x7fffe25f62c0 (LWP 27636)]
[New Thread 0x7fffe21f22c0 (LWP 27637)]
[New Thread 0x7fffe05cc2c0 (LWP 27638)]
[Thread 0x7fffe96ae2c0 (LWP 27619) exited]
[Thread 0x7fffe25f62c0 (LWP 27636) exited]
[New Thread 0x7fffe25f62c0 (LWP 27641)]
*** Error in `/home/przemo/Downloads/Foldit/Foldit': double free or corruption (fasttop): 0x00007fffe42552d0 ***
======= Backtrace: =========
terminate called after throwing an instance of 'std::bad_alloc'
/lib64/libc.so.6(+0x7566b)[0x7ffff72e966b]
what(): std::bad_alloc
/lib64/libc.so.6(cfree+0x4c)[0x7ffff72f536c]
cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so(_ZN4core7scoring16electron_density15ElectronDensity13dCCdx_fastResEiiRKN7numeric9xyzVectorIdEERKNS_12conformation7ResidueERKNS_4pose4PoseERS5_+0xbd0)[0x7ffff4bb0370]
cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so(_ZNK4core7scoring16electron_density14FastDensEnergy29eval_residue_pair_derivativesERKNS_12conformation7ResidueES6_RKNS0_25ResSingleMinimizationDataES9_RKNS0_23ResPairMinimizationDataERKNS_4pose4PoseERKNS0_10EMapVectorERN7utility7vector1INS0_15DerivVectorPairESaISM_EEESP_+0xc80)[0x7ffff4bbcb00]

Thread 1 "Foldit" received signal SIGABRT, Aborted.
0x00007ffff72a86f5 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: dnf debuginfo-install expat-2.1.1-2.fc24.x86_64 freeglut-3.0.0-3.fc24.x86_64 libICE-1.0.9-5.fc24.x86_64 libX11-1.6.3-3.fc24.x86_64 libXau-1.0.8-6.fc24.x86_64 libXcursor-1.1.14-6.fc24.x86_64 libXdamage-1.1.4-8.fc24.x86_64 libXext-1.3.3-4.fc24.x86_64 libXfixes-5.0.2-2.fc24.x86_64 libXi-1.7.6-2.fc24.x86_64 libXrender-0.9.9-3.fc24.x86_64 libXxf86vm-1.1.4-3.fc24.x86_64 libattr-2.4.47-16.fc24.x86_64 libcap-2.24-9.fc24.x86_64 libdrm-2.4.70-1.fc24.x86_64 libgcc-6.2.1-2.fc24.x86_64 libpciaccess-0.13.4-3.fc24.x86_64 libselinux-2.5-9.fc24.x86_64 libstdc++-6.2.1-2.fc24.x86_64 libxcb-1.11.1-2.fc24.x86_64 libxshmfence-1.2-3.fc24.x86_64 mesa-dri-drivers-12.0.3-1.fc24.x86_64 mesa-libGL-12.0.3-1.fc24.x86_64 mesa-libGLU-9.0.0-10.fc24.x86_64 mesa-libglapi-12.0.3-1.fc24.x86_64 nss-mdns-0.10-17.fc24.x86_64 pcre-8.39-3.fc24.x86_64 systemd-libs-229-13.fc24.x86_64
(gdb) bt
#0 0x00007ffff72a86f5 in raise () from /lib64/libc.so.6
#1 0x00007ffff72aa2fa in abort () from /lib64/libc.so.6
#2 0x00007ffff78de50d in __gnu_cxx::__verbose_terminate_handler() () from /lib64/libstdc++.so.6
#3 0x00007ffff78dc2b6 in ?? () from /lib64/libstdc++.so.6
#4 0x00007ffff78dc301 in std::terminate() () from /lib64/libstdc++.so.6
#5 0x00007ffff78dc519 in __cxa_throw () from /lib64/libstdc++.so.6
#6 0x00007ffff78dcadc in operator new(unsigned long) () from /lib64/libstdc++.so.6
#7 0x00007ffff791ec59 in std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&) () from /lib64/libstdc++.so.6
#8 0x00007ffff791fa7b in std::string::_Rep::_M_clone(std::allocator const&, unsigned long) () from /lib64/libstdc++.so.6
#9 0x00007ffff79201ec in std::basic_string, std::allocator >::basic_string(std::string const&) ()
from /lib64/libstdc++.so.6
#10 0x00007ffff30ac12b in interactive::application::shared::Visor::apply_cpk_to_hydrogens(core::pose::Pose const&, interactive::util::access_ptr) () from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#11 0x00007ffff30ac43d in interactive::application::shared::Visor::update(double) () from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#12 0x00007ffff3090a62 in interactive::application::shared::ToolApplication::update_colors(double) ()
from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#13 0x00007ffff3094b6a in interactive::application::shared::ToolApplication::update(double) ()
from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#14 0x00007ffff2d66c44 in standalone::application::novice::StandaloneApplication::update(double) ()
from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#15 0x00007ffff2b354c1 in game::application::GameApplication::update(double) () from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#16 0x00007ffff2fa4fbe in interactive::guiwrapper::glut::GLUTWrapper::glut_display_func() ()
from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#17 0x00007ffff03df504 in fghRedrawWindow () from /lib64/libglut.so.3
#18 0x00007ffff03df9a8 in fghcbProcessWork () from /lib64/libglut.so.3
#19 0x00007ffff03e0a99 in fgEnumWindows () from /lib64/libglut.so.3
#20 0x00007ffff03dfa87 in glutMainLoopEvent () from /lib64/libglut.so.3
#21 0x00007ffff03dfb25 in glutMainLoop () from /lib64/libglut.so.3
#22 0x00007ffff2f55a4e in interactive::application::interactive_main(utility::vector1 > const&, boost::function, boost::function, bool) () from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#23 0x00007ffff2ad6d3c in game::application::game_main(int, char**, char const*, game::application::ExecutableKindEnum) ()
from cmp-binary-d65e20e5bbea0910b2bbedf52f5eea1b/game_library.so
#24 0x0000000000402864 in run_library_main(std::string const&, bool, std::string const&, int&, int, char**, std::string&) ()
#25 0x000000000040238c in main ()
(gdb)

(Sun, 10/30/2016 - 23:41  |  5 comments)


PrzemoF's picture
User offline. Last seen 3 years 4 weeks ago. Offline
Joined: 10/30/2016
Groups: None

Keeps crashing in the same place Is there a debuginfo file or source code somewhere?
The problem is here:
/home/scooper/foldit/local-interactive-src/openal-soft-1.15.1/OpenAL32/alBuffer.c

P.S. scooper, feel free to contact me directly if you need

Susume's picture
User offline. Last seen 7 hours 37 min ago. Offline
Joined: 10/02/2011

There were a rash of crashes from the OpenAL library a few months ago, some of which were resolved by the developers disabling sound in the game. Looks like you have found another one.

There is a file named log.txt in the foldit directory that may include the application's error message. It may help the developers if you can attach that file to the feedback. It is overwritten each time you start the game, so grab a copy after a crash and before re-starting.

PrzemoF's picture
User offline. Last seen 3 years 4 weeks ago. Offline
Joined: 10/30/2016
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Thanks, file attached.

PrzemoF's picture
User offline. Last seen 3 years 4 weeks ago. Offline
Joined: 10/30/2016
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Is there a way of skipping that tutorial step?

jflat06's picture
User offline. Last seen 17 hours 31 min ago. Offline
Joined: 09/29/2010
Groups: Window Group

Hi,

There is a known issue with Electron Density on linux that we haven't been able to track down.

You should be able to skip this Tutorial puzzle, though - simply select a different puzzle in the Intro Puzzle menu.

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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