bug in linux version (intro puzzle 5-3)

Started by siriusjbw

Qfast Lv 1

I have the same problem. Console output after crash:

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

jflat06 Staff Lv 1

I am not getting this crash on my local client.

Which distribution are you using?

Does it happen immediately upon opening the puzzle and pressing wiggle? Or are you doing anything else before pressing wiggle?

Nerd1000 Lv 1

I have Ubuntu 16.04. Same issue, crash whenever I use wiggle or shake (It has also happened just from moving the structure with the mouse). Aside from crashing in the electron density puzzle the issue also appears in some of the other tutorial puzzles, such as the ligand constraints one.

charli9 Lv 1

How to reproduce:

  • Start level 5-3 (Electron Density) in Online Mode.
  • Press Wiggle All

— Investigation

Running strace on the program reveals the following actions after pressing Wiggle All:

clone(child_stack=0x7f6871becb70, flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTID, parent_tidptr=0x7f6871bed590, tls=0x7f6871bed2c0, child_tidptr=0x7f6871bed590) = 12894
mmap(NULL, 140086330449920, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = -1 ENOMEM (Cannot allocate memory)
mmap(NULL, 140086330585088, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = -1 ENOMEM (Cannot allocate memory)
mmap(NULL, 134217728, PROT_NONE, MAP_PRIVATE|MAP_ANONYMOUS|MAP_NORESERVE, -1, 0) = 0x7f6844000000
munmap(0x7f6848000000, 67108864)        = 0
mprotect(0x7f6844000000, 135168, PROT_READ|PROT_WRITE) = 0
mmap(NULL, 140086330449920, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = -1 ENOMEM (Cannot allocate memory)

This would suggest that I don't have enough available memory, even though I can guarantee that that is not the case.

The first lines of strace said:

strace: Process 12934 attached
strace: [ Process PID=12934 runs in x32 mode. ]
strace: [ Process PID=12934 runs in 64 bit mode. ]

I'm not sure if this program indeed runs at x32, which could explain the memory issue.

— Digging deeper into the memory issue

Running a loop counting the memory usage of Foldit:

while true; do cat /proc/`pidof Foldit`/status | grep VmSize >> memusage; done

then running uniq memusage gives the following result:

[...]
VmSize:	  882128 kB
VmSize:	  882640 kB
VmSize:	  888888 kB
-- Here I executed Shuffle All --
VmSize:	  954424 kB
VmSize:	 1019960 kB

So it looks like the program crashes after using ~1GB of memory. Before pressing wiggle all, I had 4G of memory free, so that shouldn't be a problem.

Running any of the previous levels gives a maximum memory usage of ~900MB.

If you need any more information, please let me know, so I can help!

corvuscorax Lv 1

I have the same issue with the same tutorial (electron cloud) with Ubuntu 14.04.5 LTS 64bit

various memory corruption errors cause it to crash
** Error in `./Foldit': double free or corruption (fasttop): 0x00007fa99c25b470 **
Aborted (core dumped)

I also got

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

It happens when trying to fix the protein, either by wriggling or by shaking, and once even just by manually dragging the loose sheet near where it belongs.

jeff101 Lv 1

http://fold.it/portal/node/2003635 is also about 5-3 crashing in Linux.

Are there any Linux users who have gotten around this problem?
Have you been able to play any Foldit Electron Density puzzles?
How did you get around these crashes?

Please help!
Thanks,
Jeff