error in loop?

dear ,

When i try to run a loop with substructure match node i find an library c++ runtime error and in log console i found this error :

WARN IndigoSubstructureMatcherNodeModel indigo error while matching: target key='Row4057' query key='values': array: reserve(): no memory


I trie to write all to disk but the error is still present


thanks for your help


I believe this had been identified as a bug in the Indigo nodes a few weeks ago but it was posted that this has been fixed. Do you have the most recent nightly build of Indigo nodes installed.

Also, try changing the memory policy of the Substructure node to "Write to Disc" to see if this error still occurs.



Dear simon,

I used try to disc option and still occour, for the nightly build i have the



Hmmm, sounds like this is a job for the Indigo team!

Dear fab,

Could you provide more information how to reproduce this bug? It would be great if you can attach an example of the workflow that shows the issue.

PS: Simon, thank you for providing help on our nodes!

Best regards,

dear mikhail,


You can use the pains workflow and the error still occours.

I tried to use other node to do the same but sometimes happen and sometimes no , seems to be an memory error of knime!? as an overflow not resolved ...maybe a clean not fixed.

With the indigo node this error is always present.




Hello fab,

Could you try the latest Indigo Nodes version 1.1.2 from the nightly builds repository. We have improved the memory management for the substructure matcher node. If this approach works fine for you then we will do the same for all our nodes.

Best regards,