bug in linux version (intro puzzle 5-3)

Started by siriusjbw

jeff101 Lv 1

On Windows at least, when Foldit crashes, it puts key
info in the files log.txt and debug.txt. These files
are in the same directory as the puzzles, cmp-binary-,
cmp-database-, and cmp-resources-* directories. The
endings to these cmp-* directories depend on when you
installed Foldit. If you can attach your log.txt and
debug.txt files to posts here, it can help determine
what went wrong. Listing the full names for your cmp-*
directories like below is also helpful:

11/2/16 1:16am cmp-binary-73e1721ff27bbcaee4c54d6970b5073d
11/2/16 1:16am cmp-database-771dc52e1548805e069e408cdfc4d236
11/2/16 1:16am cmp-resources-ab3bbc6032c8a9370a11d4d559996aad

log.txt seems to list them too:

binary
local:  '73e1721ff27bbcaee4c54d6970b5073d'
remote: '723ed6cab4ebe4776d6b41b7c6f68bf6'
database
local:  '771dc52e1548805e069e408cdfc4d236'
remote: '13ca17eee5b5fb0b2e0e69fc866b1800'
resources
local:  'ab3bbc6032c8a9370a11d4d559996aad'
remote: '489ec613e4217d895035188c54ae9fb9'

pauldunn Lv 1

Jeff,
I have crashed on all the Density puzzles using linux ( http://fold.it/portal/node/2003463 ). I hadn't gotten any response from UW, so I told inkycatz about it in veteran chat. Still haven't got any reply from UW.
I've had to switch back to Windows to do any Density puzzles.
Paul

jeff101 Lv 1

jflat06, I am curious what distribution of Linux you used above.
Do Tutorial 5-3 and other ED puzzles still not crash on your Linux machine?
What is so special about your system that the crashes don't occur on it?

pauldunn Lv 1

Running 5-3 under gdb (ubuntu 16.04)

Reading symbols from Foldit…(no debugging symbols found)…done.
(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 14123)]
[New Thread 0x7fffe89062c0 (LWP 14124)]
[New Thread 0x7fffe85022c0 (LWP 14125)]
[New Thread 0x7fffe3fff2c0 (LWP 14126)]
[New Thread 0x7fffe3afb2c0 (LWP 14219)]
[New Thread 0x7fffe2bfa2c0 (LWP 14220)]
[New Thread 0x7fffe27f62c0 (LWP 14221)]
[New Thread 0x7fffe23f22c0 (LWP 14222)]
[Thread 0x7fffea15d2c0 (LWP 14123) exited]
[Thread 0x7fffe2bfa2c0 (LWP 14220) exited]
[New Thread 0x7fffe2bfa2c0 (LWP 14224)]
terminate called recursively
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

Thread 1 "Foldit" received signal SIGABRT, Aborted.
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.

pauldunn Lv 1

Running 5-3 under gdb (ubuntu 16.04)

Reading symbols from Foldit…(no debugging symbols found)…done.
(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 14123)]
[New Thread 0x7fffe89062c0 (LWP 14124)]
[New Thread 0x7fffe85022c0 (LWP 14125)]
[New Thread 0x7fffe3fff2c0 (LWP 14126)]
[New Thread 0x7fffe3afb2c0 (LWP 14219)]
[New Thread 0x7fffe2bfa2c0 (LWP 14220)]
[New Thread 0x7fffe27f62c0 (LWP 14221)]
[New Thread 0x7fffe23f22c0 (LWP 14222)]
[Thread 0x7fffea15d2c0 (LWP 14123) exited]
[Thread 0x7fffe2bfa2c0 (LWP 14220) exited]
[New Thread 0x7fffe2bfa2c0 (LWP 14224)]
terminate called recursively
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

Thread 1 "Foldit" received signal SIGABRT, Aborted.
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.

eromana Lv 1 


Hi All

I can also confirm Foldit 5-3
crash on linux mint.
the command line
~/foldit/Foldit $ ./Foldit
loads the ed intro puzzle
which crashes after the first shake

The console output looks like

*** Error in `./Foldit':
double free or corruption
(fasttop): 0x00007fcd782561a0 ***
======= Backtrace: =========
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fcd8c7627e5]
Aborted

According to the log file generated by

~/foldit/Foldit $ sudo strace -o foldit_5_3_log01.txt ./Foldit

On my system the required files /x86_64/libdl.so.2 and others
are instead in my local directories under lib/x86_64-linux-gnu

perhaps compile foldit with

LD_LIBRARY_PATH=…./lib/x86_64-linux-gnu

might help

Best ed

~~~

jeff101 Lv 1

A day couple days ago, isaksson told me he tried
5-3 in Linux and it crashed immediately every time.
He said it gave the following messages:

updating surface…
setting side chain mode to: 1 Show stubs
sending SOPs
core.scoring.electron_density.xray_scattering
[warning] Unknown atom
(many of these rows)
like 300-400 rows

jflat06 Staff Lv 1

Interesting - I am now getting this crash. I was (and still am) on Ubuntu 14.04.

I'm not sure why it wasn't crashing before. A curious note is that it doesn't crash on my development build - it's possible that I had mistakenly tested for the crash on my build instead of the deployed game client.

So I can repro it now. The next trick will be repro'ing it in a development environment so that I can get some useful debug info.