Crash on puzzle 1343 with simple wiggle on Linux

Case number:845829-2003463
Topic:Crash/Hang
Opened by:pauldunn
Status:Open
Type:Bug
Opened on:Saturday, February 18, 2017 - 22:59
Last modified:Saturday, April 15, 2017 - 22:04

Crash wiggling protein with a few bands to space.

Ubuntu, foldit version 20170210-55c03a4ae1-linux_x64 (main)

Terminal: terminate called after throwing an instance of 'std::bad_alloc'
terminate called recursively
what(): std::bad_alloc

AttachmentSize
log.txt156.46 KB
(Sat, 02/18/2017 - 22:59  |  5 comments)


pauldunn's picture
User offline. Last seen 1 hour 17 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

Shared with Scientists "crash on wiggle in linux" solution that crashes when wiggled.

pauldunn's picture
User offline. Last seen 1 hour 17 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

Shared with Scientists "crash on wiggle in linux" solution that crashes when wiggled.

Joined: 09/29/2016
Groups: Gargleblasters

Does your solution have Parallel or Anti-Parallel sheet bonds?
(Not to come across patronizing, but since visually it looks backwards in FoldIt...)
Parallel look like: \ /...\ /...\ /
Anti-Parallel looks: ||...||...||

If it's the above, then it could very well be similar to my crash issue as well. Mine occurred initially with 1336, but also was horrible on 1342 and I wasn't even able to play that puzzle it was so bad. The only common element I've been able to draw between both is they had Parallel sheets. 1336 wasn't so bad since only 2 of the 3 sheets bonds were Parallel, but in my 1342 design which was a Beta-Helix, all of them were Parallel which is why I suspect it crashed easily and often.

pauldunn's picture
User offline. Last seen 1 hour 17 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

Third density puzzle (1357) that crashes on Linux just by wiggling the protein and still no response from UW.
Wiggling 1357 from reset causes crash immediately (terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc)

pauldunn's picture
User offline. Last seen 1 hour 17 min ago. Offline
Joined: 09/20/2010
Groups: Go Science

Crash on puzzle 1366b also. Here is a backtrace:

(gdb) run
Starting program: /home/paul/Foldit/Main/Foldit
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffea15d2c0 (LWP 26587)]
[New Thread 0x7fffe8d062c0 (LWP 26588)]
[New Thread 0x7fffe89022c0 (LWP 26589)]
[New Thread 0x7fffe84fe2c0 (LWP 26590)]
[New Thread 0x7fffe3cff2c0 (LWP 26623)]
[New Thread 0x7fffe2dfe2c0 (LWP 26630)]
[New Thread 0x7fffe26a72c0 (LWP 26631)]
[Thread 0x7fffea15d2c0 (LWP 26587) exited]
[New Thread 0x7fffe110b2c0 (LWP 26634)]
terminate called after throwing an instance of 'std::bad_alloc'
terminate called recursively
what(): std::bad_alloc

Thread 9 "Foldit" received signal SIGABRT, Aborted.
[Switching to Thread 0x7fffe110b2c0 (LWP 26634)]
0x00007ffff72a7428 in __GI_raise (sig=sig@entry=6)
at ../sysdeps/unix/sysv/linux/raise.c:54
54 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 0x00007ffff72a7428 in __GI_raise (sig=sig@entry=6)
at ../sysdeps/unix/sysv/linux/raise.c:54
#1 0x00007ffff72a902a in __GI_abort () at abort.c:89
#2 0x00007ffff78e07dd in __gnu_cxx::__verbose_terminate_handler() ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#3 0x00007ffff78de6b6 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#4 0x00007ffff78de701 in std::terminate() ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#5 0x00007ffff78de919 in __cxa_throw ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#6 0x00007ffff78deebc in operator new(unsigned long) ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#7 0x00007ffff791fe39 in std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&) ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#8 0x00007ffff7920c6b in std::string::_Rep::_M_clone(std::allocator const&, unsigned long) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#9 0x00007ffff792136c in std::basic_string, std::allocator >::basic_string(std::string const&) ()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#10 0x00007ffff4ba9cbd in core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(int, int, numeric::xyzVector const&, core::conformation::Residue const&, core::pose::Pose const&, numeric::xyzVector&) ()

Sitemap

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, Microsoft, Adobe, RosettaCommons