Tired of crashes on Linux

[jawz101]

Ubuntu 20.04

What do I need to provide for someone to fix. I cannot say what guarantees to cause a crash but if I have helices frozen, throw a few rubber bands in the puzzle, and start wiggling I am guaranteed to crash.

[spvincent]

Same here on Ubuntu 20.04. Crashing happens all the time: sample below.

Running Loop Remix script https://fold.it/portal/recipe/104516 on 1966 (scientist-shared as spvCrash)

One oddity in the log.txt file : repeated lines like

core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91

Tail of log.txt

core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 91
** Encountered Crash at SIGSEGV:11
Segmentation Fault
cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(game::application::CrashReporter::exit_callback(std::string const&, int, std::string const&)+0x2a) [0x7f31256287ea]
cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(game::application::signal_handler(int)+0xc8) [0x7f3125628908]
/lib/x86_64-linux-gnu/libc.so.6(+0x46210) [0x7f312af25210]
/lib/x86_64-linux-gnu/libc.so.6(+0x18e7e4) [0x7f312b06d7e4]
/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_M_clone(std::allocator const&, unsigned long)+0x43) [0x7f312b1dd243] /lib/x86_64-linux-gnu/libstdc++.so.6(std::basic_string<char, std::char_traits, std::allocator >::basic_string(std::string const&)+0x5c) [0x7f312b1dd9dc] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(core::pose::Pose const&, core::io::ResidueInformation const&, core::conformation::Residue const&, unsigned long, bool, unsigned long, unsigned long)+0x27b) [0x7f312835f90b] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(core::pose::Pose const&, core::id::AtomID_Map const&, core::io::StructFileRepOptions const&)+0x73d) [0x7f312836100d] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&)+0x398) [0x7f3128361948] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, core::chemical::ResidueTypeSet const&, utility::vector1<unsigned long, std::allocator > const&, core::io::StructFileRepOptions const&)+0x3b) [0x7f312873031b] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&, core::io::StructFileRepOptions const&)+0x54) [0x7f31287304f4] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&)+0x32) [0x7f31287305c2] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::subpose_from_selection(utility::vector1<bool, std::allocator > const&, core::pose::Pose const&, core::id::SequenceMapping const&, core::pose::Pose&, core::id::SequenceMapping&)+0x140) [0x7f3125cd1810] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::appfilter::RoScriptScoreFilter::apply(std::shared_ptr) const+0x321) [0x7f31259ee461] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::Filter::apply_filter(std::shared_ptr, interactive::util::owning_ptr, bool) const+0x285) [0x7f3125cb9185] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::ReferencePoseInfo::score_pose(std::shared_ptr, core::scoring::ScoreFunction&, bool, utility::vector1<bool, std::allocator >, utility::vector1<bool, std::allocator >, bool) const+0x7d1) [0x7f3125cc2381] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::update_game_pose_from_work_pose(bool)+0x249) [0x7f312595eda9] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run()+0x1286) [0x7f3125960b46] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(boost::detail::function::void_function_obj_invoker0<boost::_bi::bind_t<boost::_bi::unspecified, interactive::util::detail::checked_fxn_wrapper<void (interactive::application::shared::ToolActionThreaded::*)()>, boost::_bi::list1<boost::_bi::value<interactive::util::access_ptr > > >, void>::invoke(boost::detail::function::function_buffer&)+0xcf) [0x7f3125c20aff] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::util::Thread::thread_entry_func()+0x2d) [0x7f3125c756dd] cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::util::Thread::pthread_startup_helper(void*)+0x23) [0x7f3125c75cd3] /lib/x86_64-linux-gnu/libpthread.so.0(+0x9609) [0x7f3122bd8609] /lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f312b001293]

And debug.txt

version: 1
{
"backtrace" : "cmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(game::application::CrashReporter::exit_callback(std::string const&, int, std::string const&)+0x2a) [0x7f31256287ea]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(game::application::signal_handler(int)+0xc8) [0x7f3125628908]\n/lib/x86_64-linux-gnu/libc.so.6(+0x46210) [0x7f312af25210]\n/lib/x86_64-linux-gnu/libc.so.6(+0x18e7e4) [0x7f312b06d7e4]\n/lib/x86_64-linux-gnu/libstdc++.so.6(std::string::_Rep::_M_clone(std::allocator const&, unsigned long)+0x43) [0x7f312b1dd243]\n/lib/x86_64-linux-gnu/libstdc++.so.6(std::basic_string<char, std::char_traits, std::allocator >::basic_string(std::string const&)+0x5c) [0x7f312b1dd9dc]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(core::pose::Pose const&, core::io::ResidueInformation const&, core::conformation::Residue const&, unsigned long, bool, unsigned long, unsigned long)+0x27b) [0x7f312835f90b]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(core::pose::Pose const&, core::id::AtomID_Map const&, core::io::StructFileRepOptions const&)+0x73d) [0x7f312836100d]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&)+0x398) [0x7f3128361948]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, core::chemical::ResidueTypeSet const&, utility::vector1<unsigned long, std::allocator > const&, core::io::StructFileRepOptions const&)+0x3b) [0x7f312873031b]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&, core::io::StructFileRepOptions const&)+0x54) [0x7f31287304f4]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(core::io::pose_from_pose(core::pose::Pose&, core::pose::Pose const&, utility::vector1<unsigned long, std::allocator > const&)+0x32) [0x7f31287305c2]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::subpose_from_selection(utility::vector1<bool, std::allocator > const&, core::pose::Pose const&, core::id::SequenceMapping const&, core::pose::Pose&, core::id::SequenceMapping&)+0x140) [0x7f3125cd1810]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::appfilter::RoScriptScoreFilter::apply(std::shared_ptr) const+0x321) [0x7f31259ee461]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::Filter::apply_filter(std::shared_ptr, interactive::util::owning_ptr, bool) const+0x285) [0x7f3125cb9185]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::rosetta_util::ReferencePoseInfo::score_pose(std::shared_ptr, core::scoring::ScoreFunction&, bool, utility::vector1<bool, std::allocator >, utility::vector1<bool, std::allocator >, bool) const+0x7d1) [0x7f3125cc2381]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::update_game_pose_from_work_pose(bool)+0x249) [0x7f312595eda9]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::application::actions::cart::PoseLoopThreadActionCart::on_thread_run()+0x1286) [0x7f3125960b46]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(boost::detail::function::void_function_obj_invoker0<boost::_bi::bind_t<boost::_bi::unspecified, interactive::util::detail::checked_fxn_wrapper<void (interactive::application::shared::ToolActionThreaded::*)()>, boost::_bi::list1<boost::_bi::value<interactive::util::access_ptr > > >, void>::invoke(boost::detail::function::function_buffer&)+0xcf) [0x7f3125c20aff]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::util::Thread::thread_entry_func()+0x2d) [0x7f3125c756dd]\ncmp-binary-dcbc32c491668d761cfec401aa6b04e8/game_library.so(interactive::util::Thread::pthread_startup_helper(void*)+0x23) [0x7f3125c75cd3]\n/lib/x86_64-linux-gnu/libpthread.so.0(+0x9609) [0x7f3122bd8609]\n/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f312b001293]\n" "build_id" : "20210223-46aaceaf66-linux_x64" "crash_id" : "31a6fc00-18b3-4a7d-b97b-a4119c6d07bf" "current_actions" : "MacroScriptRunnerAction,ActionRepackDesign" "current_tool" : "Pull Mode" "file" : "SIGSEGV:11" "machine_id" : "d7af9488-4160-4e8e-b945-0484bdb8933c" "macro_id" : "206358" "message" : "Segmentation Fault" "player_id" : "3010" "puzzle_id" : "2011301" "puzzle_running_time" : "5513" "running_time" : "5735.47" "timestamp" : "1615573918" } verify: c19dad5d2a1386955699b58ab04ea7ba

[jawz101]

Extremely tired of crashes on Linux. I can't work in the app for more than 30 seconds sometimes without it crashing on me. What logs can I upload? The logfile in the application folder does not reveal any information on app crashes so I don't know what would be helpful. If any Fold.it developers are out here I would love to help troubleshoot.

[milkshake]

Hi Jawz, I can try to look into this.

1. Could you please use the “share to scientists” feature and type your username in the name or description field .
2. What puzzle and what recipes are you using?
3. Is show hydrogens or any non-cartoon view mode enabled?

Thank you,
Milkshake

[mrhastyrib]

I'm using Linux Mint 19.3. I get the occasion crash (I'm still new, perhaps it will get worse as I move up), but my problem right now is with the Reaction Design puzzle in the Campaign tutorial. Every time that I accept a reaction, it crashes within a few seconds of evaluating the fit. This is on every reaction that I have tried thus far, with both good and bad results. I won't be able to finish the campaign unless I can get past this.

[Sciren]

Hi mrhastyrib,

We were recently made aware of this issue with the Reaction Design campaign puzzle, and are addressing it currently. Please look out for an update soon correcting this. Very sorry for the progression hurtle!