Crashing Linux with RDKit

This seems to have been brought up before 5 years ago by a few people but the issue still remains. @greglandrum

Using RDKit with KNIME on Linux causes a crash of the whole Linux environment inducing a reboot. No errors reported.

I find it always happens when the dataset is large (>1 million rows), and it is with the RDKit One Component and Two Component Reaction nodes.

I have tried running these in loops of 100k rows at a time, and the problem persists.

The Linux has 120Gb of memory, 2Tb of Hard Drive space. KNIME is set to use 80Gb of memory in the knime.ini file.

KNIME never gets blocked with memory with the heap space being stuck or anything like this. The same workflow works perfectly on Mac.

The workflows on Linux always start off well, and then at some point during many loops it suddenly induces the crash.

I have had around 20-30 crashes in the last week, so it easily happens. Unfortunately I cannot share any data.

Example of the table structure is input of 2.3 million rows with 38 columns. All columns are just SMILES, Strings, Numerical Double, Numerical Integer. And 60 SMARTS are fed into the node via Flow Variable and Looped over.

Any advice would be greatly appreciated.

Simon.