KNIME automatic shutdown

When viewing the data of small moleculers in Product molecules and sliding to the rignt to view more small molecyles,KNIME blinks back and the following error occurs:
*** Error in `/soft/knime_4.0.1//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.202-b08/jre/bin/java’: free(): invalid pointer: 0x00007efa33069820 ***
Thank you!

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Hi & welcome -

Could you provide some more information, like:

  • which version of KNIME (4.0.1 or 4.0.2?)
  • i see you’re on some flavor of Linux, but which?
  • what node are you using when you’re viewing this output?
  • when you say ‘viewing the data’ - what data? a 2d representation? a SMILES string? a calculated property? …

Also, can you attach the workspace’s .metadata/.log and .metadata/knime/knime.log files in a ZIP to your reply?

~The version is 4.0.1
~Opensuse linux
~For example:the RDKit Substructure Filter, RDKit Two Component Reaction, and other nodes which can show the molecule structures in their output.
~There are the SDF, Salt Stripped molecule, or Mol(Rdkit Mol) and so on. When sliding to the rignt to view more small molecyles, KNIME shut down and the following error occurs: *** Error in `/soft/knime_4.0.1//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.202-b08/jre/bin/java’: free(): invalid pointer: 0x00007efa33069820 ***
Okay, I attach the log fileslog.zip (209.4 KB)

Thanks for the follow up and the logs. Where do you see this error message (concerning the invalid pointer)?

Thanks for your reply. I saw these information from the Linux Terminal.
These are the information of the last fer lines in the terminal:

WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-33 AbstractRDKitReactionNodeModel The following product could not be sanitized and will be skipped: c1(N+(=O)[O-])c©c(N+[O-])cc(N)c1
WARN KNIME-Worker-15 Node A product molecule could not be sanitized successfully - Skipping it. [5457 of 11449 products]

(KNIME:4754): Gtk-CRITICAL **: gtk_box_gadget_distribute: assertion ‘size >= 0’ failed in GtkScrollbar

(KNIME:4754): Gtk-CRITICAL **: gtk_box_gadget_distribute: assertion ‘size >= 0’ failed in GtkScrollbar
*** Error in `/soft/knime_4.0.1//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.202-b08/jre/bin/java’: free(): invalid pointer: 0x00007efa33069820 ***

Thanks for the reply - there is no following log information - something that looks vaguely like:

======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f415e1457e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f415e14e37a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f415e15253c]
...

?

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