Crashes on Linux

Started by ieewm

vakobo Lv 1

Unusual crash on 1593:
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

My system is Xubuntu 18.04.01 x64

vakobo Lv 1

Crash after crash (Segmentation fault) on 1601:
terminate called after throwing an instance of 'utility::UtilityExitException'
what():

File: /home/jflat06/foldit/develop/source/src/core/chemical/ResidueTypeSet.cc:124
[ ERROR ] UtilityExitException
ERROR: The residue could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)

vakobo Lv 1

I suppose disulfide bug is not fixed completely yet.
There is console output from some crashes on 1611:

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

2) terminate called after throwing an instance of '__gnu_cxx::recursive_init_error'
what(): std::exception

First one is most common.
Second never happens on my system before.

I agree that situation is much better and crashes don't happen few minutes after script start.
But they still exists.

vakobo Lv 1

Another 1611 crash with logs.
Console output:
terminate called after throwing an instance of 'utility::UtilityExitException'
what():

File: /home/jflat06/foldit/develop/source/src/core/conformation/Conformation.cc:1675
[ ERROR ] UtilityExitException
ERROR: CYS doesnt have connection at SG

vakobo Lv 1

Crash on puzzle change - was working one puzzle (running script) and switch to other. Two cases.
Console output looks like:
double free or corruption (fasttop)
Aborted (core dumped)

vakobo Lv 1

Crash on 1620 (disulfide bridges present)
sh: 1: xclip: not found
Segmentation fault (core dumped)

vakobo Lv 1

Crash on 1624 (disulfide briges present)
Console output:

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

File: /home/jflat06/foldit/develop/source/src/core/chemical/ResidueTypeSet.cc:835
[ ERROR ] UtilityExitException
ERROR: unable to find desired variant residue:
Aborted (core dumped)

vakobo Lv 1

Crash on 1629 (Symmetric Trimer)
Console output:

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

File: /home/jflat06/foldit/develop/source/src/interactive/application/actions/cart/ActionCartPull.cc:258
[ ERROR ] UtilityExitException
ERROR: it == constraint_pulls_.end()

Aborted (core dumped)

vakobo Lv 1

Crash on puzzle change - was working one puzzle 1648 - running many scripts.
After puzzle expiration stop last script, attach STRACE by PID and switch to puzzle 1650b.

Fragment of STRACE log file:

fstat(10, {st_mode=S_IFCHR|0666, st_rdev=makedev(1, 9), …}) = 0
ioctl(10, TCGETS, 0x7fff7b34d330) = -1 EINVAL (Invalid argument)
read(10, "\326\273\310_+\276\335\240FC\264x\177Ml\r:\323\236\340\232R\334\374\237\347g\3717\4\33\20"…, 4096) = 4096
getpid() = 22812
clock_gettime(CLOCK_PROCESS_CPUTIME_ID, {tv_sec=177541, tv_nsec=107958844}) = 0
…
getpid() = 22812
clock_gettime(CLOCK_PROCESS_CPUTIME_ID, {tv_sec=177541, tv_nsec=107975915}) = 0
close(10) = 0
writev(2, [{iov_base="malloc_consolidate(): invalid ch"…, iov_len=40}, {iov_base="\n", iov_len=1}], 2) = 41
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f02dd048000
rt_sigprocmask(SIG_UNBLOCK, [ABRT], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, ~[RTMIN RT_1], [], 8) = 0
getpid() = 22812
gettid() = 22812
tgkill(22812, 22812, SIGABRT) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
— SIGABRT {si_signo=SIGABRT, si_code=SI_TKILL, si_pid=22812, si_uid=1000} —
+++ killed by SIGABRT (core dumped) +++

From log.txt:

downloading: http://fold.it/portal/files/puzzle_pdb/puzzle_post_1782.zip
has key .ocmdline
has key .owts
has key .opdb
has key .opuzzle_setup
has key .ocnstr
has key .ofilters
starting score : 961.593
puzzle loaded

Console output looks like:

malloc_consolidate(): invalid chunk size
Aborted (core dumped)

More frequent in such situation console output is:

double free or corruption (fasttop)
Aborted (core dumped)