Happens multiple times per day

I see a lot of this too (sample fragment below on Mac). Long range debugging is always suspect, but the memory used by FoldIt increases substantially when in use: perhaps there is a bad memory leak?

Thread 9 Crashed:
0 libSystem.B.dylib 0x957ad2b5 usleep$NOCANCEL$UNIX2003 + 0
1 libSystem.B.dylib 0x957ce9a8 abort + 105
2 libstdc++.6.dylib 0x95634fda __gnu_cxx::__verbose_terminate_handler() + 433
3 libstdc++.6.dylib 0x9563317a __cxxabiv1::__terminate(void (*)()) + 10
4 libstdc++.6.dylib 0x956331ba __cxxabiv1::__unexpected(void (*)()) + 0
5 libstdc++.6.dylib 0x956332b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
6 libstdc++.6.dylib 0x95633658 operator new(unsigned long) + 101
7

We will try to resolve this as soon as possible (as well as the many other recent feedbacks) but this one is a top priority.

If you notice anything else that can help us fix this (ie it always happens running long scripts or a particular recipe) that would very helpful. Thanks!

Valgrind returns...
Conditional jump or move depends on uninitialised value(s)
at 0x4C7E499: memchr (mc_replace_strmem.c:446)
by 0x6F7E662: std::string::find(char, unsigned int) const (in /usr/lib/libstdc++.so.6.0.13)
by 0x9B9A4C0: bool boost::char_separator >::operator()<__gnu_cxx::__normal_iterator, std::string>(__gnu_cxx::__normal_iterator&, __gnu_cxx::__normal_iterator, std::string&) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x9B95EA1: interactive::util::Dictionary::parse_csv_string_into_dictionaries(std::string const&, utility::vector1, std::allocator > >&) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x97E84CE: game::application::novice::boinc::parse_url_into_dictionaries(std::string const&, bool, utility::vector1, std::allocator > >&, boost::function) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x97DDA4F: game::application::novice::boinc::Updater::get_components(game::application::novice::boinc::Boinc&, std::string const&, std::string const&, std::vector >&, boost::function) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x97DE2E7: game::application::novice::boinc::Updater::fetch_update_info(std::string const&) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x9728784: game::application::novice::UpdateDialog::check(std::string const&) (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x9607115: game::application::novice::NoviceGame::init_self_update() (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x968DED3: game::application::novice::NoviceGame::init() (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x96D1DB8: boost::function0::operator()() const (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)
by 0x9BFE2EC: interactive::application::Thread::thread_entry_func() (in /Foldit/cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so)

more soon in file attachment

Normal run of valgrind produced all these errors...

File is compressed with gzip

thanks thom001,
any clues can help us, including the end of the log.txt file when Foldit crashes.

The log.txt can be found here:

on Windows XP at C:\Documents and Settings\All Users\Application Data\Foldit\
on Windows 7 and Vista at C:\ProgramData\Foldit\
on a Mac, Ctrl-click on the app and choose "Show Package Contents, then go to Contents/Resources
on Linux, it is the Foldit directory

There were no related errors when it crashes. The only errors I see in the log are:
1) "Error: Unknown enum value for Puzzle::Type: ."
2) "Inaccurate G! step= number Deriv= number Finite Diff= number"
3) "core.optimization.LineMinimizer: step= number Deriv= number Finite Diff= number" - Similar to 2 but with prefix
I don't believe any are relevant to the error
The rest of the file appears to be info-level messages
It would also be helpful if the messages were datestamped

One time it ruined my best score such that the server knew the higher score but the local file had no record of it

If you run on a 64-bit Linux system, you should see it fairly quickly. It is too inconsistent to isolate further. Is there any information you can supply to help us debug? I run it under gdb so I have the debugger available at time of crash but need guidance since:
1) Program is not packaged as an RPM (I use Fedora x86_64)
2) Program is 32-bit
3) No debuginfo
Can you provide a 64-bit Linux client? It would allow the problem to be isolated quickly. I haven't seen crashes on Windows

@thom001:
That's right, I run it on 2 systems with Win7 64 bit, and since now no crash occurred.

Error reported appears to be in Dunbrack Rotamer library (see http://dunbrack.fccc.edu/bbdep/ for more information).

get_rsd_library refers to residue?

Data stored in cmp-database-307d41cd20e292f4c5d928df7ed9e08b/minirosetta_database/bbdep02.May.sortlib? The data seems to match the freely available Dunbrack Rotamer library backbone-dependent library as detailed on http://dunbrack.fccc.edu/bbdep/bbdepformat.php

See http://dunbrack.fccc.edu/Software.php for other software.

More specifically, the error appears in the scoring based on the data from the library. The library only supplies data, not code....

I don't believe this is related either but also receive the following:
*** glibc detected *** /Foldit: double free or corruption (!prev): 0x09754a70 ***
======= Backtrace: =========
/lib/libc.so.6[0x93d1a1]
/usr/lib/libstdc++.so.6(_ZdlPv+0x22)[0xd35d52]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1e)[0xd14e1e]
/usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x4e)[0xd1643e]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4core4pose7PDBInfoD0Ev+0xfb)[0x296037b]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4core4pose4Pose5clearEv+0xd1)[0x296a161]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4core4pose4PoseD0Ev+0x40)[0x296dac0]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4game11application6novice5boinc6PuzzleD0Ev+0x158)[0x1cd2288]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNSt8_Rb_treeIjSt4pairIKjN7utility7pointer10owning_ptrIN4game11application6novice5boinc6PuzzleEEEESt10_Select1stISB_ESt4lessIjESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E+0x59)[0x1b142c9]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNSt8_Rb_treeIjSt4pairIKjN7utility7pointer10owning_ptrIN4game11application6novice5boinc6PuzzleEEEESt10_Select1stISB_ESt4lessIjESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E+0x32)[0x1b142a2]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNSt8_Rb_treeIjSt4pairIKjN7utility7pointer10owning_ptrIN4game11application6novice5boinc6PuzzleEEEESt10_Select1stISB_ESt4lessIjESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E+0x32)[0x1b142a2]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNSt8_Rb_treeIjSt4pairIKjN7utility7pointer10owning_ptrIN4game11application6novice5boinc6PuzzleEEEESt10_Select1stISB_ESt4lessIjESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E+0x32)[0x1b142a2]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNSt8_Rb_treeIjSt4pairIKjN7utility7pointer10owning_ptrIN4game11application6novice5boinc6PuzzleEEEESt10_Select1stISB_ESt4lessIjESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E+0x32)[0x1b142a2]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(+0x104099b)[0x1db499b]
/lib/libc.so.6(exit+0xdf)[0x8fc44f]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(+0x1438622)[0x21ac622]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4game11application6novice10NoviceGame11handle_exitEv+0xcf)[0x1b9b58f]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNK5boost9function0IvEclEv+0x79)[0x1bf7db9]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN5boost6detail8function26void_function_obj_invoker0INS_3_bi6bind_tIvPFvN7utility7pointer10access_ptrIN11interactive3gui11ModalDialogEEENS_8functionIFvvEEEENS3_5list2INS3_5valueIPSA_EENSI_ISE_EEEEEEvE6invokeERNS1_15function_bufferE+0x32)[0x201a9d2]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNK5boost9function0IvEclEv+0x79)[0x1bf7db9]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive3gui6Button14generate_clickEv+0x4b)[0x1fbc82b]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive3gui6Button11on_mouse_upERKNS0_7Point2DEi+0x50)[0x1fbc8b0]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive3gui8TopLevel11on_mouse_upERKNS0_7Point2DEi+0xc5)[0x200ff15]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive11application10GUIWrapper25generic_mouse_button_funcEibii+0x1f8)[0x211bae8]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN5boost6detail8function26void_function_obj_invoker0INS_3_bi6bind_tIvNS_4_mfi3mf4IvN11interactive11application10GUIWrapperEibiiEENS3_5list5INS3_5valueIPNS8_11GLUTWrapperEEENSC_IiEENSC_IbEESG_SG_EEEEvE6invokeERNS1_15function_bufferE+0x69)[0x21ae839]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZNK5boost9function0IvEclEv+0x79)[0x1bf7db9]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive11application10GUIWrapper13enqueue_eventEN5boost8functionIFvvEEE+0x26)[0x211d106]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive11application11GLUTWrapper15glut_mouse_funcEiiii+0x1af)[0x21ad2af]
/usr/lib/libglut.so.3(glutMainLoopEvent+0x78e)[0x79507e]
/usr/lib/libglut.so.3(glutMainLoop+0x55)[0x795395]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive11application11GLUTWrapper5startEv+0x7c)[0x21ad8ec]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN11interactive11application16interactive_mainEiPPcN5boost8functionIFPNS0_11ApplicationERKSsEEE+0x61e)[0x212653e]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(_ZN4game11application9game_mainEiPPc+0x17c)[0x1aace6c]
cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so(library_main+0x3d)[0x1aac71d]
/Foldit(_Z16run_library_mainRKSsbS0_RiiPPcRSs+0x7b)[0x804a16b]
/Foldit(main+0x16c)[0x8049a0c]
/lib/libc.so.6(__libc_start_main+0xe6)[0x8e4cc6]
/Foldit[0x8049831]
======= Memory map: ========
00110000-00117000 r-xp 00000000 fd:03 74369 /lib/librt-2.12.so
00117000-00118000 r--p 00006000 fd:03 74369 /lib/librt-2.12.so
00118000-00119000 rw-p 00007000 fd:03 74369 /lib/librt-2.12.so
00119000-0024d000 r-xp 00000000 fd:03 928664 /usr/lib/libX11.so.6.3.0
0024d000-00251000 rw-p 00133000 fd:03 928664 /usr/lib/libX11.so.6.3.0
00251000-00253000 r-xp 00000000 fd:03 928671 /usr/lib/libXdamage.so.1.1.0
00253000-00254000 rw-p 00001000 fd:03 928671 /usr/lib/libXdamage.so.1.1.0
00254000-0025e000 r-xp 00000000 fd:03 15935 /usr/lib/libdrm.so.2.4.0
0025e000-0025f000 rw-p 0000a000 fd:03 15935 /usr/lib/libdrm.so.2.4.0
0025f000-0027c000 r-xp 00000000 fd:03 99167 /usr/lib/libxcb.so.1.1.0
0027c000-0027d000 rw-p 0001c000 fd:03 99167 /usr/lib/libxcb.so.1.1.0
0027d000-00299000 r-xp 00000000 fd:03 20324 /lib/libselinux.so.1
00299000-0029a000 r--p 0001b000 fd:03 20324 /lib/libselinux.so.1
0029a000-0029b000 rw-p 0001c000 fd:03 20324 /lib/libselinux.so.1
0029b000-002c1000 r-xp 00000000 fd:03 29545 /lib/libexpat.so.1.5.2
002c1000-002c3000 rw-p 00025000 fd:03 29545 /lib/libexpat.so.1.5.2
002c3000-003aa000 r-xp 00000000 fd:03 24705 /lib/libasound.so.2.0.0
003aa000-003ae000 rw-p 000e7000 fd:03 24705 /lib/libasound.so.2.0.0
003ae000-003ba000 r-xp 00000000 fd:03 74345 /lib/libnss_files-2.12.so
003ba000-003bb000 r--p 0000b000 fd:03 74345 /lib/libnss_files-2.12.so
003bb000-003bc000 rw-p 0000c000 fd:03 74345 /lib/libnss_files-2.12.so
003bc000-003be000 r-xp 00000000 fd:03 123749 /lib/libnss_mdns4_minimal.so.2
003be000-003bf000 rw-p 00001000 fd:03 123749 /lib/libnss_mdns4_minimal.so.2
003c1000-003c5000 r-xp 00000000 fd:03 928668 /usr/lib/libXxf86vm.so.1.0.0
003c5000-003c6000 rw-p 00004000 fd:03 928668 /usr/lib/libXxf86vm.so.1.0.0
003c6000-003db000 r-xp 00000000 fd:03 74365 /lib/libresolv-2.12.so
003db000-003dc000 r--p 00014000 fd:03 74365 /lib/libresolv-2.12.so
003dc000-003dd000 rw-p 00015000 fd:03 74365 /lib/libresolv-2.12.so
003dd000-003df000 rw-p 00000000 00:00 0
0040d000-00411000 r-xp 00000000 fd:03 928669 /usr/lib/libXfixes.so.3.1.0
00411000-00412000 rw-p 00003000 fd:03 928669 /usr/lib/libXfixes.so.3.1.0
004ad000-00520000 r-xp 00000000 fd:03 11798 /usr/lib/libGL.so.1.2
00520000-00526000 rw-p 00073000 fd:03 11798 /usr/lib/libGL.so.1.2
005f8000-00608000 r-xp 00000000 fd:03 928666 /usr/lib/libXext.so.6.4.0
00608000-00609000 rw-p 00010000 fd:03 928666 /usr/lib/libXext.so.6.4.0
006ce000-006d0000 r-xp 00000000 fd:03 632645 /usr/lib/libXau.so.6.0.0
006d0000-006d1000 rw-p 00001000 fd:03 632645 /usr/lib/libXau.so.6.0.0
00720000-00721000 r-xp 00000000 00:00 0 [vdso]
0077f000-007b2000 r-xp 00000000 fd:03 59606 /usr/lib/libglut.so.3.9.0
007b2000-007b7000 rw-p 00033000 fd:03 59606 /usr/lib/libglut.so.3.9.0
00838000-008a0000 r-xp 00000000 fd:03 114835 /usr/lib/libGLU.so.1.3.070801
008a0000-008a1000 rw-p 00067000 fd:03 114835 /usr/lib/libGLU.so.1.3.070801
008ac000-008ca000 r-xp 00000000 fd:03 64385 /lib/ld-2.12.so
008ca000-008cb000 r--p 0001d000 fd:03 64385 /lib/ld-2.12.so
008cb000-008cc000 rw-p 0001e000 fd:03 64385 /lib/ld-2.12.so
008ce000-00a53000 r-xp 00000000 fd:03 74157 /lib/libc-2.12.so
00a53000-00a54000 ---p 00185000 fd:03 74157 /lib/libc-2.12.so
00a54000-00a56000 r--p 00185000 fd:03 74157 /lib/libc-2.12.so
00a56000-00a57000 rw-p 00187000 fd:03 74157 /lib/libc-2.12.so
00a57000-00a5a000 rw-p 00000000 00:00 0
00a5c000-00a5f000 r-xp 00000000 fd:03 39271 /lib/libdl-2.12.so
00a5f000-00a60000 r--p 00002000 fd:03 39271 /lib/libdl-2.12.so
00a60000-00a61000 rw-p 00003000 fd:03 39271 /lib/libdl-2.12.so
00a6a000-00a87000 r-xp 00000000 fd:03 29508 /lib/libgcc_s-4.4.4-20100503.so.1
00a87000-00a88000 rw-p 0001d000 fd:03 29508 /lib/libgcc_s-4.4.4-20100503.so.1
00a9a000-00a9f000 r-xp 00000000 fd:03 74330 /lib/libnss_dns-2.12.so
00a9f000-00aa0000 r--p 00004000 fd:03 74330 /lib/libnss_dns-2.12.so
00aa0000-00aa1000 rw-p 00005000 fd:03 74330 /lib/libnss_dns-2.12.so
00aa8000-00ad0000 r-xp 00000000 fd:03 74286 /lib/libm-2.12.so
00ad0000-00ad1000 r--p 00027000 fd:03 74286 /lib/libm-2.12.so
00ad1000-00ad2000 rw-p 00028000 fd:03 74286 /lib/libm-2.12.so
00ba2000-00bb9000 r-xp 00000000 fd:03 66277 /lib/libpthread-2.12.so
00bb9000-00bba000 r--p 00016000 fd:03 66277 /lib/libpthread-2.12.so
00bba000-00bbb000 rw-p 00017000 fd:03 66277 /lib/libpthread-2.12.so
00bbb000-00bbd000 rw-p 00000000 00:00 0
00c03000-00c10000 r-xp 00000000 fd:03 928673 /usr/lib/libXi.so.6.1.0
00c10000-00c11000 rw-p 0000d000 fd:03 928673 /usr/lib/libXi.so.6.1.0
00c89000-00d68000 r-xp 00000000 fd:03 76903 /usr/lib/libstdc++.so.6.0.13
00d68000-00d6c000 r--p 000de000 fd:03 76903 /usr/lib/libstdc++.so.6.0.13
00d6c000-00d6d000 rw-p 000e2000 fd:03 76903 /usr/lib/libstdc++.so.6.0.13
00d6d000-00d74000 rw-p 00000000 00:00 0
00d74000-034ba000 r-xp 00000000 fd:00 6686770 /cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so
034ba000-034da000 rw-p 02746000 fd:00 6686770 /cmp-binary-dc068cd43ceac9da1e521ab3d752a329/game_library.so
Program received signal SIGABRT, Aborted.
0x00720430 in __kernel_vsyscall ()

End of log.txt for segmentation violation:
Error: Unknown enum value for Puzzle::Type: .
trying puzzle 987803
trying puzzle 987825
trying puzzle 987844
trying puzzle 987848
trying puzzle 987857
trying puzzle 987860
SRVR_THRD sending play event log...
delta_score: -16.902
Playing sound: 3

Program terminated with signal 11, Segmentation fault.
#0 0x0023aa6a in ?? ()
info registers
eax 0x12ef7000 317681664
ecx 0x7a567bc 128280508
edx 0xd7e491b0 -672886352
ebx 0x297ff4 2719732
esp 0x4715d68 0x4715d68
ebp 0x4715da8 0x4715da8
esi 0x9ad3e58 162348632
edi 0xcea26008 -828219384
eip 0x23aa6a 0x23aa6a
eflags 0x210202 [ IF RF ID ]
cs 0x23 35
ss 0x2b 43
ds 0x2b 43
es 0x2b 43
fs 0x0 0
gs 0x63 99
info frame
Stack level 0, frame at 0x4715d6c:
eip = 0x23aa6a; saved eip 0x525ff4
called by frame at 0x4715db0
Arglist at 0x4715d64, args:
Locals at 0x4715d64, Previous frame's sp is 0x4715d6c
Saved registers:
eip at 0x4715d68
Without symbols, it's hard to get much more...

Segmentation violation still occurs after update:

Program terminated with signal 11, Segmentation fault.
#0 0x0210b463 in ?? ()

For Beta Prediction puzzle, was running Loop Rebuild when it faulted.

Segmentation violation STILL occurs after NEW update this morning :-(

I'm seeing a memory leak when running the script Sidechain Flipper 1.0. The combined real and virtual memory continually rises and eventually you get a crash when a memory allocation fails (see attached file). Have tried to narrow down the offending call but no luck so far.

Not sure if the file got attached: here's the log from the crashed thread

Thread 9 Crashed:
0 libSystem.B.dylib 0x93e2a2b5 usleep$NOCANCEL$UNIX2003 + 0
1 libSystem.B.dylib 0x93e4b9a8 abort + 105
2 libstdc++.6.dylib 0x92204fda __gnu_cxx::__verbose_terminate_handler() + 433
3 libstdc++.6.dylib 0x9220317a __cxxabiv1::__terminate(void (*)()) + 10
4 libstdc++.6.dylib 0x922031ba __cxxabiv1::__unexpected(void (*)()) + 0
5 libstdc++.6.dylib 0x922032b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
6 libstdc++.6.dylib 0x92203658 operator new(unsigned long) + 101
7 game_library.dylib 0x014579a5 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, core::scoring::AtomNeighbor const&) + 315
8 game_library.dylib 0x01457ad8 std::vector >::push_back(core::scoring::AtomNeighbor const&) + 62
9 game_library.dylib 0x0121ccc5 core::scoring::NeighborList::declare_atoms_neighbors(core::id::AtomID, core::id::AtomID, double, double) const + 263
10 game_library.dylib 0x01347edb void core::scoring::NeighborList::setup(core::pose::Pose const&, core::scoring::ScoreFunction const&, core::scoring::etable::EtableEnergy const&) const + 3587
11 game_library.dylib 0x01348379 core::scoring::etable::BaseEtableEnergy::setup_for_minimizing(core::pose::Pose&, core::scoring::ScoreFunction const&, core::optimization::MinimizerMap const&) const + 559
12 game_library.dylib 0x0122fbc3 core::scoring::ScoreFunction::setup_for_minimizing(core::pose::Pose&, core::optimization::MinimizerMap const&) const + 71
13 game_library.dylib 0x01690159 interactive::core_optimization::AtomTreeMinimizer::run(core::pose::Pose&, core::kinematics::MoveMap const&, core::scoring::ScoreFunction const&, core::optimization::MinimizerOptions const&, boost::function > const&, bool)>) const + 181
14 game_library.dylib 0x0162f602 interactive::application::shared::exp::ActionGlobalMinimize::on_thread_run() + 4606
15 game_library.dylib 0x015eccb9 boost::_bi::bind_t, boost::_bi::list1 > >::operator()() + 43
16 game_library.dylib 0x0183d2e7 boost::function0::operator()() const + 79
17 game_library.dylib 0x015c0539 interactive::application::Thread::thread_entry_func() + 35
18 game_library.dylib 0x015c07d5 interactive::application::Thread::pthread_startup_helper(void*) + 17
19 libSystem.B.dylib 0x93d6fa19 _pthread_start + 345
20 libSystem.B.dylib 0x93d6f89e thread_start + 34

http://gcc.gnu.org/onlinedocs/libstdc++/manual/termination.html#support.termination.verbose

"Verbose Terminate Handler

If you are having difficulty with uncaught exceptions and want a little bit of help debugging the causes of the core dumps, you can make use of a GNU extension, the verbose terminate handler.

#include

int main()
{
std::set_terminate(__gnu_cxx::__verbose_terminate_handler);
...

throw anything;
}

The __verbose_terminate_handler function obtains the name of the current exception, attempts to demangle it, and prints it to stderr. If the exception is derived from exception then the output from what() will be included. "

It also mentions mtrace and mudflap but all these require recompilation. As an alternative to the 64-bit binary, can you provide a debug version with different compilation options?

Also happens under another account and system. SIGSEGV happens most frequently with "Loop Rebuild" or "Overnight Script"

This seems to be exactly what I was talking about in global chat a few days ago. I'm running Foldit on 2 different iMacs, with the same problem.

Both have Foldit crashes with Loop Rebuild, Overnight Script, and with Doom2.

One iMac is OS 10.5, 2.8 Intel Core Duo, the other is OS 10.6, i7.

I keep forgetting to grab the log after a crash, usually eager to reopen. I will discipline myself to do it on next occasion & post here.

anyone have these problems on PCs as well?

thom002, originally you noticed this under 64-bit Linux, right? And now under OSX as well.

Hopefully we'll be able to reproduce this bug using "Loop Rebuild", "Overnight Script", and "Doom2".

auntdeen, any additional info from the log.txt will be very useful!

Thanks everyone, we'll try to solve this problem this week!

Hi beta, yes under 64 bit Linux (Fedora). I believe there are at least 2 separate errors:
1) Throwing the exception
2) Segmentation faults (SIGSEGV)

If we do determine that, I would be happy to open separate feedback as you guys direct. For now, I'm lumping everything together. It appears to be frequent but random (i.e. no reproducible test case).

terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create

Just occurred in CASP Training Puzzle 2: Multiple templates
running tlaloc contract 2.11
tail log.txt
trying puzzle 987885
core.scoring.NeighborList: Minimization stats: 400 score/deriv cals, 103 narrow-from-wide updates, 3 full updates.
delta_score: 116.239
Playing sound: 5
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 64 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 10776 bytes
Autosaved autosave-172510-987724.ir_solution.
Autosaved autosave-best-noscore-172510-987724.ir_solution.
Autosaved autosave-recentbest-noscore-172510-987724.ir_solution.

Failed AFTER yesterday's update...
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create
log.txt is short...
"args passed:"
and that's it

No SIGSEGV's yet...

SIGSEGV

tail log.txt:
"trying puzzle 987913
Autosaved autosave-172510-987913.ir_solution.
Autosaved autosave-best-172510-987913.ir_solution.
Autosaved autosave-recentbest-172510-987913.ir_solution.
Autosaved autosave-creditbest-172510-987913.ir_solution."

Solution saved soon before SIGSEGV - try running "Quake" on it

Over several days, still crashes (both SIGSEGV and exception thrown) but not nearly as frequently.

Reported today on global chat by Datstadin

Select a recipe while wiggling, crash everytime

Here's another one of the situations in which the application crash: if very strongly increase or decrease the scale (zoom in/out camera), then the application crashes with 100% probability.
It seems to overflow a variable.

Some crashes since last update
The last
Recipes Quake running
new interfaces
Puzzle 323
I click on green logo "fold it" on left

Playing sound: 4
core.scoring.NeighborList: Minimization stats: 12 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 7 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 8 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 7 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 7 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 7 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 9 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
delta_score: 0.188766
Playing sound: 4
macro run 987901 33153 195 3297 449 -117.252115 -120.731330 0

UNHANDLED EXCEPTION
1: no symbol (no line)
2: no symbol (no line)
3: no symbol (no line)
4: no symbol (no line)
5: no symbol (no line)
6: no symbol (no line)

Windows XP 5.1 windows media player running on radio
Firefox running

Still crashes after today's update

Latest log.txt...
trying puzzle 987971
WARNING: DFPMIN (Armijo) MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
core.scoring.NeighborList: Minimization stats: 722 score/deriv cals, 149 narrow-from-wide updates, 10 full updates.
Autosaved autosave-174968-898974.ir_solution.
Autosaved autosave-best-174968-898974.ir_solution.
Autosaved autosave-recentbest-174968-898974.ir_solution.
Autosaved autosave-creditbest-174968-898974.ir_solution.
SRVR_THRD sending...
SRVR_THRD starting solution upload...

terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create

New one...
terminate called after throwing an instance of 'game::application::novice::boinc::BoincException'

Last few lines of log.txt

ViewOptionsWidget::refresh()
Printing buddies list

new crash
Segmentation fault (core dumped)

core.scoring.NeighborList: Minimization stats: 12 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 13 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 13 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
core.scoring.NeighborList: Minimization stats: 14 score/deriv cals, 0 narrow-from-wide updates, 0 full updates.
SRVR_THRD error: Couldn't resolve host name: Error contacting server. (/scratch/scooper/rosetta/src/mini-interactive-main/mini/src/game/application/novice/boinc/Boinc.cc:67)
SRVR_THRD sending: x y group_score

Had 2 crashes close together on the Beta Disulfide puzzle:
terminate called recursively
terminate called after throwing an instance of 'std::length_error'
core.pack.pack_rotamers: built 308 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 136724 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 210 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 71496 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 126 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 25380 bytes
delta_score: -1.10465
Playing sound: 4

Within a couple of hours:
Segmentation fault (exit 139)
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 77 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 17468 bytes
delta_score: 1.93903e-06
Playing sound: 4
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 140 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 32296 bytes
delta_score: 3.63798e-12
Playing sound: 4

Do you have any more stack traces (like from the first post)? What happens if you turn off all the view options, like voids, clashes, hydrophobics, etc., does that make it more stable?

after the next crash, i will setup gdb for stack tracing. After the following crash, I will try turning off all view options. Can you supply a debug version of the program?

I had turned off all view options and it still crashed with segmentation violation...
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 213 rotamers at 10 positions.
core.pack.pack_rotamers: IG: 60052 bytes
delta_score: 1.27329e-11
Playing sound: 4

Running under debugger to get stack trace (for Developer Preview)

Gotcha!
terminate called recursively
terminate called after throwing an instance of 'std::length_error'
what():
Program received signal SIGABRT, Aborted.
[Switching to Thread (LWP
)]
0x00a88430 in __kernel_vsyscall ()

stack trace to follow

log.txt...
Playing sound: 4
SRVR_THRD finished solution upload. took 3.83914 seconds.
SRVR_THRD uploading oracle...
Experimental oracle written
core.scoring.NeighborList: Minimization stats: 67 score/deriv cals, 1 narrow-from-wide updates, 0 full updates.
delta_score: 12.1352
Playing sound: 5
SRVR_THRD sending: 174968 898974 group_score

Full stacktrace
Thread 427 (Thread 0xf00bcb70 (LWP 12413)): <- THIS IS THE ACTIVE THREAD
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x008f8d31 in raise () from /lib/libc.so.6
No symbol table info available.
#2 0x008fa60a in abort () from /lib/libc.so.6
No symbol table info available.
#3 0x0041fb23 in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#4 0x0041dac6 in ?? () from /usr/lib/libstdc++.so.6
No symbol table info available.
#5 0x0041db03 in std::terminate() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#6 0x0041dc42 in __cxa_throw () from /usr/lib/libstdc++.so.6
No symbol table info available.
#7 0x003be990 in std::__throw_length_error(char const*) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#8 0x003faf46 in std::basic_string, std::allocator >::_Rep::_S_create(unsigned int, unsigned int, std::allocator const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#9 0x003fc089 in std::basic_string, std::allocator >::_Rep::_M_clone(std::allocator const&, unsigned int) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#10 0x003fc1c7 in std::basic_string, std::allocator >::basic_string(std::basic_string, std::allocator > const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#11 0x02169781 in interactive::application::shared::FixedDofInfo::save_fixed_dofs(core::pose::Pose const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#12 0x01fda1f5 in interactive::application::shared::exp::ActionRepack::on_thread_run() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#13 0x01cc9989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#14 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#15 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#16 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#17 0x02237a21 in boost::detail::function::void_function_obj_invoker0, std::allocator > const&>, boost::_bi::list2, boost::_bi::value, std::allocator > > > >, void>::invoke(boost::detail::function::function_buffer&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#18 0x01cc9989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#19 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#20 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#21 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#22 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 7 (Thread 0x615db70 (LWP 9034)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x009a41d1 in select () from /lib/libc.so.6
No symbol table info available.
#2 0x01d75ba3 in game::util::IRC::run(boost::function) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#3 0x01bf7388 in game::application::novice::NoviceGame::irc_thread_body(std::basic_string, std::allocator > const&, int, std::basic_string, std::allocator > const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x01ca1cf4 in boost::detail::function::void_function_obj_invoker0, std::allocator > const&, int, std::basic_string, std::allocator > const&>, boost::_bi::list4, boost::_bi::value, std::allocator > >, boost::_bi::value, boost::_bi::value, std::allocator > > > >, void>::invoke(boost::detail::function::function_buffer&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01cc9989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#9 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 6 (Thread 0x7806b70 (LWP 9033)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x009a0f26 in poll () from /lib/libc.so.6
No symbol table info available.
#2 0x02fd85bb in Curl_socket_ready () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#3 0x02ff0139 in Curl_perform () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x01d8deae in game::application::novice::boinc::CurlFetcher::exec_curl() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01d8b0a8 in game::application::novice::boinc::Boinc::fetch_string(std::basic_string, std::allocator > const&, bool, std::basic_string, std::allocator >&, utility::pointer::owning_ptr, boost::function) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01ddbf6f in game::application::novice::boinc::send_message(unsigned int, std::basic_string, std::allocator > const&, std::basic_string, std::allocator > const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x01e3fe7b in game::application::novice::send_score_message(unsigned int, unsigned int, std::basic_string, std::allocator > const&, double, double) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x01e40cd1 in game::application::novice::BoincThread::send_boinc() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x01e41680 in game::application::novice::BoincThread::periodically_send_and_check_boinc() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#11 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#12 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#13 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 5 (Thread 0x575cb70 (LWP 9032)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00bac5e4 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libpthread.so.0
No symbol table info available.
#2 0x009bbb84 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libc.so.6
No symbol table info available.
#3 0x02f7d750 in boost::condition_variable::timed_wait(boost::unique_lock&, boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x02f7ca20 in boost::this_thread::sleep(boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x02201967 in interactive::application::Thread::sleep(double) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01c96ec5 in game::application::novice::NoviceGame::autosave_thread_body() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x01cc9989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#11 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 4 (Thread 0x6be8b70 (LWP 8934)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x0099babb in write () from /lib/libc.so.6
No symbol table info available.
#2 0x00938844 in _IO_new_file_write () from /lib/libc.so.6
No symbol table info available.
#3 0x009386f0 in _IO_new_file_xsputn () from /lib/libc.so.6
No symbol table info available.
#4 0x0092e3be in fwrite () from /lib/libc.so.6
No symbol table info available.
#5 0x0041fc83 in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#6 0x0041dac6 in ?? () from /usr/lib/libstdc++.so.6
No symbol table info available.
#7 0x0041db03 in std::terminate() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#8 0x0041dc42 in __cxa_throw () from /usr/lib/libstdc++.so.6
No symbol table info available.
#9 0x003be990 in std::__throw_length_error(char const*) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#10 0x003faf46 in std::basic_string, std::allocator >::_Rep::_S_create(unsigned int, unsigned int, std::allocator const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#11 0x003fc089 in std::basic_string, std::allocator >::_Rep::_M_clone(std::allocator const&, unsigned int) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#12 0x003fc1c7 in std::basic_string, std::allocator >::basic_string(std::basic_string, std::allocator > const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#13 0x02baecb5 in core::scoring::dunbrack::RotamerLibrary::get_rsd_library(core::chemical::ResidueType const&) const ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#14 0x0293cb8a in core::chemical::ResidueType::get_RotamerLibrary() const ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#15 0x02787497 in core::scoring::methods::DunbrackEnergy::residue_energy(core::conformation::Residue const&, core::scoring::EMapVector&) const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#16 0x0289f688 in core::scoring::ScoreFunction::eval_ci_1b(core::conformation::Residue const&, core::scoring::EMapVector&) const ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#17 0x028a20ba in core::scoring::ScoreFunction::eval_onebody_energies(core::pose::Pose&) const ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#18 0x028a1b2c in core::scoring::ScoreFunction::operator()(core::pose::Pose&) const ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#19 0x0205bb5a in interactive::pose_view::HydrophobicComposite::calculate_residues() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#20 0x0205c028 in interactive::pose_view::HydrophobicComposite::HydroThread::operator()() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#21 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#22 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#23 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#24 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 3 (Thread 0x4d5bb70 (LWP 8931)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00bac5e4 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libpthread.so.0
No symbol table info available.
#2 0x009bbb84 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libc.so.6
No symbol table info available.
#3 0x02f7d750 in boost::condition_variable::timed_wait(boost::unique_lock&, boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x02f7ca20 in boost::this_thread::sleep(boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x02201967 in interactive::application::Thread::sleep(double) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x020924d5 in interactive::pose_view::VoidGeom::VoidThread::operator()() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x02201dcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x02f7acec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#10 0x009abdde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 1 (Thread 0xf7fce950 (LWP 8925)):
#0 0x00a88430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x009a41d1 in select () from /lib/libc.so.6
No symbol table info available.
#2 0x00746559 in glutMainLoop () from /usr/lib/libglut.so.3
No symbol table info available.
#3 0x0228c7fc in interactive::application::GLUTWrapper::start() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x0220401e in interactive::application::interactive_main(int, char**, boost::function, std::allocator > const&)>) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01b787ac in game::application::game_main(int, char**) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01b7805d in library_main () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x0804a16b in run_library_main(std::basic_string, std::allocator > const&, bool, std::basic_string, std::allocator > const&, int&, int, char**, std::basic_string, std::allocator >&) ()
No symbol table info available.
#8 0x08049a0c in main ()
No symbol table info available.

As you can see, it died again in repack -- this time in degrees of freedom

Bonus crash in BETA docking....
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create

Program received signal SIGABRT, Aborted.
[Switching to Thread 0x3f14b70 (LWP
)]
0x00c00430 in __kernel_vsyscall ()
Thread 2330 (Thread 0x3f14b70 (LWP 15272)):
#0 0x00c00430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x008f8d31 in raise () from /lib/libc.so.6
No symbol table info available.
#2 0x008fa60a in abort () from /lib/libc.so.6
No symbol table info available.
#3 0x0023fc37 in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#4 0x0023dac6 in ?? () from /usr/lib/libstdc++.so.6
No symbol table info available.
#5 0x0023db03 in std::terminate() () from /usr/lib/libstdc++.so.6
No symbol table info available.
#6 0x0023dc42 in __cxa_throw () from /usr/lib/libstdc++.so.6
No symbol table info available.
#7 0x001de990 in std::__throw_length_error(char const*) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#8 0x0021af46 in std::basic_string, std::allocator >::_Rep::_S_create(unsigned int, unsigned int, std::allocator const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#9 0x0021c089 in std::basic_string, std::allocator >::_Rep::_M_clone(std::allocator const&, unsigned int) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#10 0x0021c1c7 in std::basic_string, std::allocator >::basic_string(std::basic_string, std::allocator > const&) () from /usr/lib/libstdc++.so.6
No symbol table info available.
#11 0x01f33781 in interactive::application::shared::FixedDofInfo::save_fixed_dofs(core::pose::Pose const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#12 0x01da0379 in interactive::application::shared::exp::ActionGlobalMinimize::on_thread_run() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#13 0x01a93989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#14 0x01fcbdcd in interactive::application::Thread::thread_entry_func() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#15 0x02d44cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#16 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.

Another degree of freedom. Any change of getting a version with symbols to eliminate "No symbol table info available." and narrow this down?

happened during a manual wiggle sidechains

3rd one today in Beta alignment...
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x4cc8b70 (LWP 20372)]

Thread 1307 (Thread 0x4cc8b70 (LWP 20372)):
#0 0x020ced5b in interactive::pose_view::VoidGeom::rapidly_delete_spheres() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#1 0x01cb7f37 in game::application::novice::NoviceGame::pose_edit() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#2 0x01d07989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#3 0x021f8517 in interactive::util::WrappedPose::call_edit_callback() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x02166313 in interactive::application::shared::ToolActionInstantBandIndices::on_instant_run() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x0216527e in interactive::application::shared::ToolActionInstant::do_launch() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x0217095b in interactive::application::shared::ToolApplication::try_launch_action(utility::pointer::owning_ptr) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x02163337 in interactive::application::shared::ToolAction::launch() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x01d98473 in game::application::novice::run_action_and_wait(utility::pointer::owning_ptr) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x01d9a40c in game::application::novice::lua_band_disable(lua_State*) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x03148b1c in luaD_precall () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#11 0x03151756 in luaV_execute () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#12 0x03148fa9 in luaD_call () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#13 0x03146321 in f_call () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#14 0x03148697 in luaD_rawrunprotected () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#15 0x031486fe in luaD_pcall () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#16 0x0314617a in lua_pcall () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#17 0x02276bd7 in interactive::application::shared::lua::LuaScripter::exec_string(std::basic_string, std::allocator > const&, std::basic_string, std::allocator >&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#18 0x02275195 in interactive::application::shared::lua::LuaExec::on_exec(std::basic_string, std::allocator > const&)
() from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#19 0x02275a21 in boost::detail::function::void_function_obj_invoker0, std::allocator > const&>, boost::_bi::list2, boost::_bi::value, std::allocator > > > >, void>::invoke(boost::detail::function::function_buffer&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#20 0x01d07989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#21 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#22 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#23 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#24 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 796 (Thread 0xf0152b70 (LWP 18798)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00bac5e4 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libpthread.so.0
No symbol table info available.
#2 0x001feb84 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libc.so.6
No symbol table info available.
#3 0x02fbb750 in boost::condition_variable::timed_wait(boost::unique_lock&, boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x02fbaa20 in boost::this_thread::sleep(boost::posix_time::ptime const&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x0223f967 in interactive::application::Thread::sleep(double) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01d3d103 in game::application::novice::RMSDPlotDialog::RefreshThread::operator()() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#10 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 7 (Thread 0x7ecdb70 (LWP 15586)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x001e71d1 in select () from /lib/libc.so.6
No symbol table info available.
#2 0x01db3ba3 in game::util::IRC::run(boost::function) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#3 0x01c35388 in game::application::novice::NoviceGame::irc_thread_body(std::basic_string, std::allocator > const&, int, std::basic_string, std::allocator > const&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x01cdfcf4 in boost::detail::function::void_function_obj_invoker0, std::allocator > const&, int, std::basic_string, std::allocator > const&>, boost::_bi::list4, boost::_bi::value, std::allocator > >, boost::_bi::value, boost::_bi::value, std::allocator > > > >, void>::invoke(boost::detail::function::function_buffer&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01d07989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#9 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 6 (Thread 0x74ccb70 (LWP 15576)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x001e3f26 in poll () from /lib/libc.so.6
No symbol table info available.
#2 0x030165bb in Curl_socket_ready () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#3 0x0302e139 in Curl_perform () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x01dcbeae in game::application::novice::boinc::CurlFetcher::exec_curl() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01dc90a8 in game::application::novice::boinc::Boinc::fetch_string(std::basic_string, std::allocator > const&, bool, std::basic_string, std::allocator >&, utility::pointer::owning_ptr, boost::function) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01e2043b in game::application::novice::boinc::parse_url_into_dictionaries(std::basic_string, std::allocator > const&, bool, utility::vector1, std::allocator > >&, boost::function) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x01e2126a in game::application::novice::boinc::refresh_players_for_puzzle(unsigned int, unsigned int, bool) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x01e7b827 in game::application::novice::BoincThread::get_scores_boinc() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x01e7f698 in game::application::novice::BoincThread::periodically_send_and_check_boinc() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#11 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#12 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#13 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 5 (Thread 0x6acbb70 (LWP 15575)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00bac5e4 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libpthread.so.0
No symbol table info available.
#2 0x001feb84 in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/libc.so.6
No symbol table info available.
#3 0x02fbb750 in boost::condition_variable::timed_wait(boost::unique_lock&, boost::posix_time::ptime const&) ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x02fbaa20 in boost::this_thread::sleep(boost::posix_time::ptime const&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x0223f967 in interactive::application::Thread::sleep(double) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01cd4ec5 in game::application::novice::NoviceGame::autosave_thread_body() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x01d07989 in boost::function0::operator()() const () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#11 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 4 (Thread 0x60cab70 (LWP 15570)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00baefa9 in __lll_lock_wait () from /lib/libpthread.so.0
No symbol table info available.
#2 0x00baa33e in _L_lock_751 () from /lib/libpthread.so.0
No symbol table info available.
#3 0x00baa24a in pthread_mutex_lock () from /lib/libpthread.so.0
No symbol table info available.
#4 0x001fecf6 in pthread_mutex_lock () from /lib/libc.so.6
No symbol table info available.
#5 0x02099fe5 in interactive::pose_view::HydrophobicComposite::HydroThread::operator()() ()
from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#9 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 3 (Thread 0x56c9b70 (LWP 15569)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x00baefa9 in __lll_lock_wait () from /lib/libpthread.so.0
No symbol table info available.
#2 0x00baa33e in _L_lock_751 () from /lib/libpthread.so.0
No symbol table info available.
#3 0x00baa24a in pthread_mutex_lock () from /lib/libpthread.so.0
No symbol table info available.
#4 0x001fecf6 in pthread_mutex_lock () from /lib/libc.so.6
No symbol table info available.
#5 0x020ce3f5 in interactive::pose_view::VoidGeom::VoidSphere::VoidSphere(utility::pointer::access_ptr, numeric::xyzVector const&, double const&) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x020ceb95 in interactive::pose_view::VoidGeom::find_phi_discontinuties(double*, bool*, std::vector, std::allocator > >&, numeric::xyzVector const&, numeric::xyzVector const&, unsigned int) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x020d0284 in interactive::pose_view::VoidGeom::calculate_space() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#8 0x020d04b8 in interactive::pose_view::VoidGeom::VoidThread::operator()() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#9 0x0223fdcd in interactive::application::Thread::thread_entry_func() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#10 0x02fb8cec in thread_proxy () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#11 0x00ba8919 in start_thread () from /lib/libpthread.so.0
No symbol table info available.
#12 0x001eedde in clone () from /lib/libc.so.6
No symbol table info available.

Thread 1 (Thread 0xf7fce950 (LWP 15560)):
#0 0x00110430 in __kernel_vsyscall ()
No symbol table info available.
#1 0x001e71d1 in select () from /lib/libc.so.6
No symbol table info available.
#2 0x002b3559 in glutMainLoop () from /usr/lib/libglut.so.3
No symbol table info available.
#3 0x022ca7fc in interactive::application::GLUTWrapper::start() () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#4 0x0224201e in interactive::application::interactive_main(int, char**, boost::function, std::allocator > const&)>) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#5 0x01bb67ac in game::application::game_main(int, char**) () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#6 0x01bb605d in library_main () from cmp-binary-929a7b27a3d23d912137daf4b4864bfa/game_library.so
No symbol table info available.
#7 0x0804a16b in run_library_main(std::basic_string, std::allocator > const&, bool, std::basic_string, std::allocator > const&, int&, int, char**, std::basic_string, std::allocator >&) ()
No symbol table info available.
#8 0x08049a0c in main ()
No symbol table info available.

Either a version with debugging symbols or a 64-bit client would allow more information...

Clearly, there are multiple issues. This one is in rapidly_delete_spheres()

I have these crashes all the time on a 32-bit XP sp 2, looks like those old 'interrupt a wiggle and die' type of things.
My pc also occasionally reboots at random moments. No virus found. Nothing in particular in the logs.

Did the update posted today have any effect?

Nope, SIGSEGV after update

SIGSEGV after today's update

Seth, we have been here before. The issue is most likely caused by a cleanup routine after an *interruption* of a shake, wiggle, rebuild, whatever. It is repeatable, obvious and very annoying. No update has fixed this problem since it was reported. Although the new features that are introduced are welcome and useful, I'd much rather have the ream focus on resolving this crash bug.

If you check the issue that was solved way back when when we had this same problem, maybe that provides a clue as to what is happening now. Good luck !