crash wiggling and changing clash importance

Case number:845829-2009830
Topic:Crash/Hang
Opened by:pauldunn
Status:Open
Type:DevPrev Issue
Opened on:Sunday, June 14, 2020 - 01:22
Last modified:Sunday, June 14, 2020 - 13:34

Uploaded for Scientists "crash for developers" protein for puzzle 1851.
Crashes when in wiggling in high power and changing the clash importance up and down.

I have these crashes all the time on Revisiting Puzzles with disulfide bonds using linux.

OS: ubuntu 20.04
Foldit: 20200608-18ae728cfb-linux_x64-devprev

From log.txt:

Sending SOPs:

loading solution: puzzle_2009828_time_1592096094.ir_solution
Sending SOPs:

***** STARTING THREAD ActionGlobalMinimize
RT: 1111111111111111111111111111111111111111111111111111111111111111111111
****** Encountered Crash at Uncaught exception: St9bad_alloc:0
std::bad_alloc
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(game::application::CrashReporter::exit_callback(std::string const&, int, std::string const&)+0x2a) [0x7fc390a84f6a]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(game::application::terminate_handler()+0x1a5) [0x7fc390a85395]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa47c) [0x7fc3965a947c]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa4e7) [0x7fc3965a94e7]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa799) [0x7fc3965a9799]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x9e562) [0x7fc39659d562]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&)+0x69) [0x7fc3965ed179]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_M_clone(std::allocator const&, unsigned long)+0x22) [0x7fc3965ee092]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::basic_string, std::allocator >::basic_string(std::string const&)+0x5c) [0x7fc3965ee84c]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::methods::ResidueCartBondedParameters const&, core::scoring::methods::ResidueCartBondedParameters const&, double, double, core::scoring::EMapVector const&, utility::vector1 >&, utility::vector1 >&) const+0x25d) [0x7fc39386aced]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::ResSingleMinimizationData const&, core::scoring::ResSingleMinimizationData const&, core::scoring::ResPairMinimizationData const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&, utility::vector1 >&) const+0x2f7) [0x7fc393883477]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::scoring::eval_atom_derivatives_for_minedge(core::scoring::MinimizationEdge const&, core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::ResSingleMinimizationData const&, core::scoring::ResSingleMinimizationData const&, core::pose::Pose const&, core::scoring::EMapVector const&, utility::vector1 >&, utility::vector1 >&)+0xa3) [0x7fc39362c483]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::atom_tree_get_atompairE_deriv(core::pose::Pose&, core::optimization::MinimizerMap&, core::scoring::ScoreFunction const&)+0x151) [0x7fc3933b6011]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::atom_tree_dfunc(core::pose::Pose&, core::optimization::MinimizerMap&, core::scoring::ScoreFunction const&, utility::vector1 > const&, utility::vector1 >&)+0xc0) [0x7fc3933b62d0]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::AtomTreeMultifunc::dfunc(utility::vector1 > const&, utility::vector1 >&) const+0x28) [0x7fc3933a4748]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::Minimizer::dfpmin_armijo(utility::vector1 >&, double&, core::optimization::ConvergenceTest&, std::shared_ptr, int) const+0x86c) [0x7fc3933af1ac]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::Minimizer::run(utility::vector1 >&)+0x76e) [0x7fc3933b118e]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::AtomTreeMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&)+0x8b8) [0x7fc3933a3b98]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::optimization::AtomTreeMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&, core::optimization::MinimizerHelper&)+0xe) [0x7fc3933a2f8e]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::run_minimizer_on_work_pose(core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, int)+0x42a) [0x7fc390dab8fa]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::ActionCartGlobalWiggle::thread_body_loop_unlocked(core::pose::Pose&)+0x85) [0x7fc39118c8b5]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run()+0x1121) [0x7fc390da8c51]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > > >, void>::invoke(boost::detail::function::function_buffer&)+0xcf) [0x7fc391051ecf]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::thread_entry_func()+0x2d) [0x7fc3910a6c5d]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::pthread_startup_helper(void*)+0x23) [0x7fc3910a7213]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x9609) [0x7fc38e067609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7fc396412103]

(Sun, 06/14/2020 - 01:22  |  3 comments)


Joined: 09/29/2016
Groups: Gargleblasters

Paul,
I've logged your report but was hoping maybe you could help clear up a few questions I had:

-Does this happen on ANY puzzle when using a HWP Bounce Wiggle technique, or ONLY if there's an already-formed Disulfide Bridge? (The Sandbox puzzle allows for HWP to be used, so you could test there)

-Do you happen to have "Show Bondable H" view setting enabled, and Bands on the White Tips of the Cysteine? (This seems to be the most common way to cause it)

-Is the same stack trace in the log every time it crashes when using the bounce wiggle technique, or does it change?

Thanks :)

pauldunn's picture
User offline. Last seen 12 hours 12 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

Thanks for your quick response.

I've had this crash for puzzles with disulfide bridge bonuses at any power wiggle. Other puzzles don't crash this easily but may crash for other reasons. I can do some puzzles that don't hgave disulfide bridge bonuses without experiencing any crashes while wiggling. Usually the puzzles crash deep inside recipes. I've tried to save the puzzle so that it crashes with a minumum of steps. I can't get it to crash with exactly the same steps (specific clash importance followed by wiggle) but it crashes with repeated bounce wiggles.

The crashes don't appear to have anything to do with View options. I usually run with minimum view options set (Score/Hyrdo+CPK, Cartoon, Hide All H, Don't Show (Fast), Dark background, Show constraints, Show Symmetric Chains, Use releative score coloring, Fade GUI)

This puzzle has been strange because I've been able to build my score up on low power without any crashes. Usually I can't get this far and I just abandon working on the puzzle.

The crash traceback below is from a new version of the puzzle (higher score) running a recipe in its bounce wiggle stage. It looks like a different traceback to me.

***** STARTING THREAD ActionGlobalMinimize
RT: 1111111111111111111111111111111111111111111111111111111111111111111111
****** Encountered Crash at Uncaught exception: St9bad_alloc:0
std::bad_alloc
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(game::application::CrashReporter::exit_callback(std::string const&, int, std::string const&)+0x2a) [0x7f3fe6cf9f6a]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(game::application::terminate_handler()+0x1a5) [0x7f3fe6cfa395]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa47c) [0x7f3fec81e47c]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa4e7) [0x7f3fec81e4e7]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa799) [0x7f3fec81e799]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x9e562) [0x7f3fec812562]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&)+0x69) [0x7f3fec862179]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_M_clone(std::allocator const&, unsigned long)+0x22) [0x7f3fec863092]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::basic_string, std::allocator >::basic_string(std::string const&)+0x5c) [0x7f3fec86384c]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::conformation::disulfide_bonds(core::conformation::Conformation const&, utility::vector1, std::allocator > >&)+0xa9) [0x7f3fea344719]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::rosetta_util::ReferencePoseInfo::score_pose(std::shared_ptr, core::scoring::ScoreFunction&, bool) const+0xc83) [0x7f3fe7365e53]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::update_game_pose_from_work_pose(bool)+0x193) [0x7f3fe701c0d3]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::minimizer_pose_updater()+0x212) [0x7f3fe701ca12]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > > >, void>::invoke(boost::detail::function::function_buffer&)+0x6a) [0x7f3fe7023aca]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::thread_entry_func()+0x2d) [0x7f3fe731bc5d]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::pthread_startup_helper(void*)+0x23) [0x7f3fe731c213]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x9609) [0x7f3fe42dc609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f3fec687103]

pauldunn's picture
User offline. Last seen 12 hours 12 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

There is a simpler way to crash the puzzle (see https://fold.it/portal/node/2008612). This procedure may be quicker to debug.

Load shared puzzle
select cysteine segment
bring up Pick Sidechains tool
change rotamer position
crash

log.txt:

***** STARTING THREAD ActionRotamerPicker
RT: 1111111111111111111111111111111111111111111111111111111111111111111111
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull:NtermProteinFull 1
Sending SOPs:

****** Encountered Crash at /home/jflat06/foldit/release/source/src/core/kinematics/tree/Atom_.cc:429
Atom_::dihedral_between_bonded_children: atoms not found!
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(game::application::CrashReporter::exit_callback(std::string const&, int, std::string const&)+0x2a) [0x7f1597e70f6a]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(boost::detail::function::void_function_obj_invoker3, boost::_bi::list4 >, boost::arg<1>, boost::arg<2>, boost::arg<3> > >, void, std::string const&, int, std::string const&>::invoke(boost::detail::function::function_buffer&, std::string const&, int, std::string const&)+0x10f) [0x7f1597e7302f]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(utility::exit(char const*, int, std::string const&, int)+0x8f) [0x7f159b6e82bf]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::kinematics::tree::Atom_::dihedral_between_bonded_children(core::kinematics::tree::Atom const&, core::kinematics::tree::Atom const&) const+0x1ac) [0x7f159b5c009c]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::kinematics::AtomTree::torsion_angle_dof_id(core::id::AtomID const&, core::id::AtomID const&, core::id::AtomID const&, core::id::AtomID const&, double&, bool) const+0x340) [0x7f159b3f28e0]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::kinematics::AtomTree::set_torsion_angle(core::id::AtomID const&, core::id::AtomID const&, core::id::AtomID const&, core::id::AtomID const&, double, bool)+0x3b) [0x7f159b3f433b]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::conformation::Conformation::set_torsion(core::id::TorsionID const&, double)+0x212) [0x7f159b484fa2]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(core::pose::Pose::set_chi(int, unsigned long, double)+0x2b) [0x7f159a8f5a6b]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::ActionCartRotamerPicker::thread_body_loop_unlocked(core::pose::Pose&)+0xc0) [0x7f159818aad0]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run()+0x1121) [0x7f1598194c51]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > > >, void>::invoke(boost::detail::function::function_buffer&)+0xcf) [0x7f159843decf]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::thread_entry_func()+0x2d) [0x7f1598492c5d]
cmp-binary-950ceb9dbed82a1eb458a25fc458592e/game_library.so(interactive::util::Thread::pthread_startup_helper(void*)+0x23) [0x7f1598493213]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x9609) [0x7f1595453609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f159d7fe103]

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