Acid Tweeker "angle range error" crashes -- test case

Case number:845829-1998668
Topic:Crash/Hang
Opened by:LociOiling
Status:Closed
Type:Bug
Opened on:Thursday, November 6, 2014 - 03:02
Last modified:Tuesday, July 31, 2018 - 20:44

Some puzzles crash the Windows client repeatedly during Acid Tweeker and other recipes. One symptom is the message "AtomTree::torsion_angle_dof_id: angle range error" in debug.txt.

On puzzle 1006, a test for this condition has been shared with scientists as "9405.597 angle range error". The simplified recipe ATGrinder 1.0 has been shared as recipe 100190.

To recreate, set wiggle power to high, and load the solution. Start ATGrinder 1.0. Let Wiggle Factor default to 4. Set the start segment to 45 and click OK.

The crash results should look something like this:

version: 1
{
"build_id" : "20141017-7524f3104e-win_x86-devprev"
"crash_id" : "4c3ed21a-1fe3-4ba1-a0ff-af63fff6215b"
"current_actions" : "MacroScriptRunnerAction\,ActionGlobalMinimizeSidechains"
"current_tool" : "Selection Interface"
"file" : "core/kinematics/AtomTree.cc:637"
"machine_id" : "1ffe9484-82e3-4e6d-a2e9-ab43baa5f599"
"macro_id" : "0"
"message" : "AtomTree::torsion_angle_dof_id: angle range error"
"player_id" : "476462"
"puzzle_id" : "1998631"
"puzzle_running_time" : "87"
"running_time" : "36628.6"
"timestamp" : "1415241641"
}
verify: 658d55e87826230e3c80ddfcf72abfa8

(Thu, 11/06/2014 - 03:02  |  8 comments)


Joined: 07/21/2013
Groups: Beta Folders

I reproduced LociOiling's crash using the 11/12/14 release buildid: 20141110-b740d73796-win_x86-devprev
I created two batch files in a c:\FolditLogs directory that gets the Lua script output and Error Log files:

C:\FolditLogs>od default ATGrind_b

C:\FolditLogs>copy C:\Foldit.dev\scriptlog.default.xml C:\FolditLogs\ATGrind_b_output.txt
1 file(s) copied.

C:\FolditLogs>ed ATGrind_b

C:\FolditLogs>copy C:\Foldit.dev\log.txt C:\FolditLogs\ATGrind_b_error_log.txt
1 file(s) copied.

C:\FolditLogs>type od.bat
copy C:\Foldit.dev\scriptlog.%1.xml C:\FolditLogs\%2_output.txt
C:\FolditLogs>type ed.bat
copy C:\Foldit.dev\log.txt C:\FolditLogs\%1_error_log.txt
C:\FolditLogs>

Joined: 07/21/2013
Groups: Beta Folders

These two bugs were created by resetting puzzle 1006, then running ATGrinder at high Wiggle Power and clearing the disable slow filters check box.

This procedure was run four times, but only crashing twice on segment 45. One crash had the message "UNHANDLED EXCEPTION", the other AtomTree::torsion_angle_dof_id: angle range error then the "UNHANDLED EXCEPTION"

LociOiling's picture
User offline. Last seen 18 min 48 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders

At brgreening's suggestion, I googled "AtomTree::torsion_angle_dof_id: angle range error". The results seem to indicate Rosetta is the source of the issue.

For example, I found https://www.rosettacommons.org/content/atomtreetorsionangle-cant-find-dof-match-and-enzdes, where the original poster sees messages like:

core.kinematics.AtomTree: AtomTree::torsion_angle() cant find dof! atomno= 6 rsd= 5 atomno= 9 rsd= 5 atomno= 10 rsd= 5 atomno= 11 rsd= 5

in output from Rosetta tools. The only response suggests "If the torsion isn't found, the function returns zero, which may or may not cause problems for the calling function, depending on what it's expecting."

So perhaps foldit could adjust its expectations? Or at least not crash the client? It seems like this condition is more like a warning than a fatal error. No clue on the architecture of the foldit/Rosetta interface, but maybe simple routine to catch this exception would do the trick?

Joined: 07/21/2013
Groups: Beta Folders

I thought that I had appended the error log previous comment. This section shows bad floating point values for THETA1 and bad xyz coordinates for Atom3 and Atom4. I will attempt again to attach the error log

core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (113)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (113)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (113)
core.kinematics.AtomTree: dof_atom1 atomno= 3 rsd= 37
core.kinematics.AtomTree: atom1 atomno= 1 rsd= 37
core.kinematics.AtomTree: atom2 atomno= 2 rsd= 37
core.kinematics.AtomTree: atom3 atomno= 5 rsd= 37
core.kinematics.AtomTree: atom4 atomno= 6 rsd= 37
core.kinematics.AtomTree: THETA1 -1.#IND
core.kinematics.AtomTree: THETA3 1.94869
core.kinematics.AtomTree: PHI2 0
core.kinematics.AtomTree: Atom1 position 2.771 -3.485 -0.894
core.kinematics.AtomTree: Atom2 position 2.857 -4.608 0.032
core.kinematics.AtomTree: Atom3 position -1.#IO -1.#IO -1.#IO
core.kinematics.AtomTree: Atom4 position -1.#IO -1.#IO 1.#QO

ERROR: AtomTree::torsion_angle_dof_id: angle range error
ERROR:: Exit from: ..\..\..\source\src\core\kinematics\AtomTree.cc line: 637

UNHANDLED EXCEPTION
1: RaiseException +72 bytes (no line)
2: library_main +38290543 bytes (no line)
3: library_main +36362886 bytes (no line)
4: library_main +34856320 bytes (no line)
5: library_main +34734746 bytes (no line)
6: library_main +34800322 bytes (no line)
7: library_main +34800634 bytes (no line)
8: library_main +4372007 bytes (no line)
9: library_main +26908093 bytes (no line)
10: library_main +24837361 bytes (no line)
11: library_main +24800570 bytes (no line)
12: library_main +25667466 bytes (no line)
13: library_main +25678593 bytes (no line)
14: library_main +24787771 bytes (no line)
15: library_main +24786879 bytes (no line)
16: library_main +7040809 bytes (no line)
17: library_main +6456640 bytes (no line)
18: library_main +7037427 bytes (no line)
19: library_main +402177 bytes (no line)
20: library_main +4209525 bytes (no line)
21: library_main +4209979 bytes (no line)
22: BaseThreadInitThunk +14 bytes (no line)
23: RtlInitializeExceptionChain +132 bytes (no line)
24: RtlInitializeExceptionChain +90 bytes (no line)

Doing a search for "AtomTree.cc" shows some information related to Rosetta.

Joined: 07/21/2013
Groups: Beta Folders

ATGrinder was run on an instance of the 1022 puzzle that was created by retiredmichael.
That file was uploaded for Scientists.
ATGrinder was run with high wiggle power. It crashed on segment 94.
The dump of the error log for this 1022 puzzle run is similar to the dump of the error log
for puzzle 1006.

core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (99)
core.kinematics.AtomTree: dof_atom1 atomno= 3 rsd= 10
core.kinematics.AtomTree: atom1 atomno= 1 rsd= 10
core.kinematics.AtomTree: atom2 atomno= 2 rsd= 10
core.kinematics.AtomTree: atom3 atomno= 5 rsd= 10
core.kinematics.AtomTree: atom4 atomno= 6 rsd= 10
core.kinematics.AtomTree: THETA1 -1.#IND
core.kinematics.AtomTree: THETA3 1.93374
core.kinematics.AtomTree: PHI2 0
core.kinematics.AtomTree: Atom1 position 38.402 24.868 -25.746
core.kinematics.AtomTree: Atom2 position 38.169 23.487 -26.156
core.kinematics.AtomTree: Atom3 position -1.#IO -1.#IO -1.#IO
core.kinematics.AtomTree: Atom4 position -1.#IO -1.#IO 1.#QO

ERROR: AtomTree::torsion_angle_dof_id: angle range error
ERROR:: Exit from: ..\..\..\source\src\core\kinematics\AtomTree.cc line: 637

UNHANDLED EXCEPTION
1: RaiseException +72 bytes (no line)
2: library_main +38290543 bytes (no line)
3: library_main +36362886 bytes (no line)
4: library_main +34856320 bytes (no line)
5: library_main +34734746 bytes (no line)
6: library_main +34800322 bytes (no line)
7: library_main +34800634 bytes (no line)
8: library_main +4372007 bytes (no line)
9: library_main +26908093 bytes (no line)
10: library_main +24837361 bytes (no line)
11: library_main +24800570 bytes (no line)
12: library_main +25667466 bytes (no line)
13: library_main +25678593 bytes (no line)
14: library_main +24787771 bytes (no line)
15: library_main +24786879 bytes (no line)
16: library_main +7040809 bytes (no line)
17: library_main +6456640 bytes (no line)
18: library_main +7037427 bytes (no line)
19: library_main +402177 bytes (no line)
20: library_main +4209525 bytes (no line)
21: library_main +4209979 bytes (no line)
22: BaseThreadInitThunk +14 bytes (no line)
23: RtlInitializeExceptionChain +132 bytes (no line)
24: RtlInitializeExceptionChain +90 bytes (no line)

NickyCGS's picture
User offline. Last seen 4 years 22 weeks ago. Offline
Joined: 06/27/2013
Groups: Repro-men

Thanks for the feedback and the uploaded save file Brgreening. I was able to reproduce the issue and have forwarded it on.

LociOiling's picture
User offline. Last seen 18 min 48 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders

It's been a while, but Bertro found another test case for this issue on puzzle 1192. It's been uploaded for scientists as "9745.086 bertro solo CRASH (angle range error)".

Using AtGrinder or the Acid Tweeker of your choice, it produces an "angle range error" crash within a few minutes. Interestingly, the error happens with high Wiggle Power, but not with low, medium, or auto.

In AtGrinder, setting the "start segment" slide to 12 produces a quicker crash. Flipping segment 12's sidechain to a different position before starting ATGrinder avoids the crash.

For some reason, debug.txt does not always get updated. Also, log.txt contains "core.kinematics" lines in some cases, but not in others.

Sample debug.txt

version: 1
{
"build_id" : "20151218-b5ec35b633-win_x86-devprev"
"crash_id" : "4cef4df5-943c-4110-8756-3ccca00ef827"
"current_actions" : "MacroScriptRunnerAction\,ActionGlobalMinimizeSidechains"
"current_tool" : "Selection Interface"
"file" : "core/kinematics/AtomTree.cc:637"
"machine_id" : "dc6c2a74-3319-4d35-ac65-e3a4f7cd149e"
"macro_id" : "200275"
"message" : "AtomTree::torsion_angle_dof_id: angle range error"
"player_id" : "476462"
"puzzle_id" : "2002051"
"puzzle_running_time" : "314"
"running_time" : "679031"
"timestamp" : "1455394925"
}

log.txt (excerpt):

core.kinematics.AtomTree: dof_atom1 atomno= 3 rsd= 96
core.kinematics.AtomTree: atom1 atomno= 1 rsd= 96
core.kinematics.AtomTree: atom2 atomno= 2 rsd= 96
core.kinematics.AtomTree: atom3 atomno= 5 rsd= 96
core.kinematics.AtomTree: atom4 atomno= 6 rsd= 96
core.kinematics.AtomTree: THETA1 -1.#IND
core.kinematics.AtomTree: THETA3 1.96315
core.kinematics.AtomTree: PHI2 -1.#IND
core.kinematics.AtomTree: Atom1 position -8.698 -8.296 12.221
core.kinematics.AtomTree: Atom2 position -8.767 -7.424 13.387
core.kinematics.AtomTree: Atom3 position -1.#IO -1.#IO -1.#IO
core.kinematics.AtomTree: Atom4 position -1.#IO -1.#IO -1.#IO

ERROR: AtomTree::torsion_angle_dof_id: angle range error
ERROR:: Exit from: ..\..\..\source\src\core\kinematics\AtomTree.cc line: 637

UNHANDLED EXCEPTION
1: RaiseException +72 bytes (no line)
2: library_main +38598911 bytes (no line)
3: library_main +36670998 bytes (no line)
4: library_main +35099312 bytes (no line)
5: library_main +34977722 bytes (no line)
6: library_main +35043314 bytes (no line)
7: library_main +35043626 bytes (no line)
8: library_main +4440711 bytes (no line)
9: library_main +35036280 bytes (no line)
10: library_main +4636218 bytes (no line)
11: library_main +753322 bytes (no line)
12: library_main +420113 bytes (no line)
13: library_main +4310822 bytes (no line)
14: library_main +7204191 bytes (no line)
15: library_main +7189403 bytes (no line)
16: library_main +7184992 bytes (no line)
17: library_main +7180889 bytes (no line)
18: library_main +7187058 bytes (no line)
19: library_main +25036496 bytes (no line)
20: library_main +25043401 bytes (no line)
21: library_main +25043042 bytes (no line)
22: library_main +25907004 bytes (no line)
23: library_main +25914913 bytes (no line)
24: library_main +25024027 bytes (no line)
25: library_main +25023135 bytes (no line)
26: library_main +7200497 bytes (no line)
27: library_main +6597520 bytes (no line)
28: library_main +7197140 bytes (no line)
29: library_main +420113 bytes (no line)
30: library_main +4265381 bytes (no line)
31: library_main +4265835 bytes (no line)
32: BaseThreadInitThunk +36 bytes (no line)
33: RtlUnicodeStringToInteger +595 bytes (no line)
34: RtlUnicodeStringToInteger +542 bytes (no line)

LociOiling's picture
User offline. Last seen 18 min 48 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Status: Open » Closed

Old issue, haven't seen this in a while, closing.

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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, Amazon, Microsoft, Adobe, RosettaCommons