crashes on puzzles 1495 and 1498 on linux

Case number:845829-2004905
Topic:Crash/Hang
Opened by:pauldunn
Status:Open
Type:Bug
Opened on:Tuesday, March 20, 2018 - 15:10
Last modified:Monday, December 10, 2018 - 18:03

I have crashes on both 1495 and 1498 puzzles on linux (Ubuntu 16.04). Just need to wiggle. I suspect that it is cysteine related (old bug is back?).

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

shows up in terminal. I don't know how to get more information on linux.

Moving back to windows for now.

(Tue, 03/20/2018 - 15:10  |  5 comments)


rmoretti's picture
User offline. Last seen 1 day 1 hour ago. Offline
Joined: 01/15/2010
Groups: None

The 'std::bad_alloc' error most often occurs when a program runs out of memory.

How much memory do you have on your Linux machine, and do you know how much of it the Foldit program was taking up at the time of the crash?

Joined: 09/20/2010
Groups: Go Science

I have a 16Gb machine and these are small puzzles. I've run another pose from a group's share and run it under a debugger (gdb). I get different output each time I run it. The recipe is just running wiggle, shake, and change CI.

Here's gdb output #1:

[New Thread 0x7fffdc858700 (LWP 5013)]
terminate called after throwing an instance of 'utility::UtilityExitException'
what():

File: /home/jflat06/foldit/develop/source/src/core/chemical/ResidueType.cc:4071
[ ERROR ] UtilityExitException
ERROR: unknown atom_name: '' in residue CYS:disulfide

Thread 178 "Foldit" received signal SIGABRT, Aborted.

Joined: 09/20/2010
Groups: Go Science

Here is a similar crash but with a different atom name:

[New Thread 0x7fffdc9cb700 (LWP 5255)]
terminate called after throwing an instance of 'utility::UtilityExitException'
what():

File: /home/jflat06/foldit/develop/source/src/core/chemical/ResidueType.cc:4071
[ ERROR ] UtilityExitException
ERROR: unknown atom_name: ' SG ' in residue CYS:disulfide

Thread 90 "Foldit" received signal SIGABRT, Aborted.

Joined: 09/24/2012
Groups: Go Science

I used to run up to 7 clients a time on Linux Ubuntu 16.4 (8GB mem, 8 vitual CPUs), but after the new update, it slows down to 2-3 clients max.

The supplementary clients simply crash after some times, hand fold or recipes.

Indeed, I think all of this is related to memory.

After a long recipe run, the RAM goes quickly to max and the client crash.

Needs to restart computer some times in order to reset memory.

Joined: 09/20/2010
Groups: Go Science

Latest foldit (20181204-a8c39fb2f8-linux_x64-devprev) still crashing on puzzles with disulfide bonds.

Posted release notice on fold.it:
Bug Fixes:
* General crash fixes.
* Fix crash with disulfides.

Tested using puzzle 1371 (only puzzle I have on devprev with disulfide bonding scores)

terminate called after throwing an instance of 'utility::UtilityExitException'
what():

File: /home/jflat06/foldit/develop/source/src/core/chemical/ResidueType.cc:4071
[ ERROR ] UtilityExitException
ERROR: unknown atom_name: ' SG ' in residue CYS:disulfide

I'll try again when a newer disulfide puzzle is released.

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