I first thought “it’s me”, but after several versions of Knime (older versions of 3.7.x which I had (not anymore) in parallel to 4.x) on multiple Linux (Ubuntu) distributions (18 and 20, 2 different machines), I found that Rdkit/Knime on Linux is less stable than on Windows (two different machines).
It often crashed “silently”, Knime simply closes down without warning.
This is in combination with missing or faulty structures, either during calculation phase (e.g. Descriptor calculations, but others as well), or, if it did manage to calculate everything, and one wants to open the table view of the node output, it crashes there. The console doesn’t give any error messages during calculations, just crashes (the same data-sets using other chemistry nodes don’t make Knime crash).
On Windows, this doesn’t happen. Error messages appear in console during calculations and Knime doesn’t silently say good-bye.
It’s also independent on memory allocation or data-set size (100 compounds or 1 000 000).
So I am gonna be a bit amateur here and say Rdkit on Linux/Knime isn’t the same as on Windows independent of version number when it comes to handling faulty/missing structures.