Knime crashes when viewing RDKit output

Hi,

I use the RDKit to Molecule node to convert smiles to RDKit format. I get the following error messages:

WARN Create File Name 1:5:9 Selected directory ‘/tmp/knime_tc_qyb4fml4u1v6’ cannot be accessed!
WARN Create File Name 1:6:9 Selected directory ‘/tmp/knime_tc_sb18yac4qhfr’ cannot be accessed!
WARN Create File Name 1:7:9 Selected directory ‘/tmp/knime_tc_aib9z54vhu7x’ cannot be accessed!
WARN Create File Name 1:8:9 Selected directory ‘/tmp/knime_tc_iqnrmhqju78e’ cannot be accessed!
WARN Create File Name 1:10:9 Selected directory ‘/tmp/knime_tc_2fg5d0slwwgj’ cannot be accessed!
WARN Create File Name 1:11:9 Selected directory ‘/tmp/knime_tc_4hpyaljrv7lg’ cannot be accessed!

Then, when viewing the output, Knime crashes abruptly (the output window appears briefly without showing anything, then Knime just dissappears). Same behaviour when trying to convert an SD file.

Attached the Knime log file.

This is on Ubuntu 16.04 LTS, with Knime 3.5.3, RDKit KNIME integration 3.3.1.v201804190838

Please advice.

Thanks/Evert

knime.log (2.0 MB)

Hi Evert,

I had a look at your log file, but I do not see the connection between the warnings that you see and RDKit. The warnings are generated by the “Create File Name” of KNIME, and they should be rather ERRORs, because you assume at that point that the temporary directory that was created by the node before is there and readable. Apparently it is not, which might be one of the symptoms related to the crash afterwards. I found in the implementation of the CreateFileName node that the following conditions are checked for the directory:

    // first try if file string is an URL (files in drop dir come as URLs)
    final URL url = FileUtil.toURL(file);
    final Path path = FileUtil.resolveToPath(url);

    // Some sanity checks for local files
    if ((path != null) && (!Files.isDirectory(path) || !Files.isReadable(path))) {
        throw new InvalidSettingsException("Selected directory '" + file + "' cannot be accessed!");
    } 

That means, the directory is either not there or it is not readable. What should usually work, seems to be broken for some reason. It could be storage related… file system that KNIME has an issue with, how it is mounted in case it is, … - maybe try to set the temp path for KNIME to something else, just as a test: You can do this in File - Preferences: Then look at the preference page of “KNIME”.

The log reports that the RDKit Node has finished successfully, and since it seems to be the last node within a metanode that state is propagated to your “SETD8 TH vsw” metanode, which is also fully executed now. The table output that brings KNIME to the crash is not RDKit related anymore but is handled fully by KNIME.

I would suggest, for further investigations it would make sense to involve KNIME support.

Kind regards,
Manuel Schwarze

PS: One more thing: When KNIME crashes there is usually some dump file generated with additional very useful information. You would find that file in the current working directory. Please attach it as well.