java makes knime crash when displaying molecules

KNIME Analytics Platform
1

Hello,

Let's say I read a sd file using the SDF reader node. If I want to visualize the content of the file doing right click on the node, then 0 Read molecules, almost every time, Knime crashes...

I say almost, because according to my experience, if I use Knime a few time (minutes, hours, it depends), the problem does not appear.

I tried a new Knime install but the problem is the same.

My current java version is 1.7.0_25 (java -version), but Knime seems to use a previous verison.

I have attached the log file.

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f439c531f09, pid=6236, tid=139929224967936
#
# JRE version: 7.0_07-b10
# Java VM: Java HotSpot(TM) 64-Bit Server VM (23.3-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libQtCore.so.4+0xccf09]  QString::fromLocal8Bit(char const*, int)+0x29
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/nico/hs_err_pid6236.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
 

2

Hi Nico,

What renderer are you using?  It sounds like some 3rd party library may be causing the problem.  Bugs in native java code don't usually crash the VM, but are caught with some sort of exception and error message.  

Regards,

Aaron

3

Hello Aaron,

There are several renderers available:

- Canvas 2D (from Schrodinger)

- Marvin

- MOE molecule 3D (+H)

- MOE molecule 3D (-H)

- Indigo Renderer

- others that display strings (String, Multi-line string...)

 

I can't say which renderer is used when Knime crashes. Is there a way to disable each renderer one by one?

Thank you

4

You can check the default renderer in File > Preferences > KNIME > Chemistry. I would guess that's the render you would use when it crashed unless you change it (right click options you showed)

5

Thank you. Knime only crashes for a specific sd render.

6

I have noticed in Knime 2.8.1, the default renderer is not in File | Preferences | Knime | Chemistry anymore. Where can I find this setting now?

I still have this java error that makes Knime crashes when I try to display molecules with the wrong renderer...

7

All renderers for al data types are now available in the preferences under KNIME -> Preferred Renderers.